[R] Built-in Code behind SVM
Hi R,
I need to see the inner code behind the function "svm" in the package
e1071. I enter svm in the console and get the below output.
> svm
function (x, ...)
UseMethod("svm")
Is there any way I can look into the code of what svm (support vector
machine) is doing?
Thanks a lot for your help...
Thanks and Regards, Shubha
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Re: [R] how to automatically select certain columns using for loop in dataframe
In fact you can use only
for (each_name in col_names) {
sub.data <- subset( all.data,
select = c( paste("NUM_", each_name, sep = '') ,
paste("NAME_", each_name, sep = '') )
)
sub.data.2<-subset(sub.data, !is.na(sub.data[,2]))
print(sub.data.2)
}
Because:
!is.na( paste("NAME_", each_name, sep = '') )
only test if the result of the paste() is not null, and never will be null.
Maybe you need to improve and way of evaluate if the expression
that paste() result is null or not... but I don't know how do that.
bests..
miltinho
On Thu, Apr 9, 2009 at 11:30 PM, milton ruser wrote:
> Hi Ferry,
>
> It is not so elegant, but you can try
>
> for (each_name in col_names) {
>
>sub.data <- subset( all.data,
>!is.na( paste("NAME_", each_name, sep = '') ),
>select = c( paste("NUM_", each_name, sep = '') ,
> paste("NAME_", each_name, sep = '') )
> )
> sub.data.2<-subset(sub.data, !is.na(sub.data[,2]))
>print(sub.data.2)
>
> }
>
>
> On Thu, Apr 9, 2009 at 6:30 PM, Ferry wrote:
>
>> Hi,
>>
>> I am trying to display / print certain columns in my data frame that share
>> certain condition (for example, part of the column name). I am using for
>> loop, as follow:
>>
>> # below is the sample data structure
>> all.data <- data.frame( NUM_A = 1:5, NAME_A = c("Andy", "Andrew", "Angus",
>> "Alex", "Argo"),
>>NUM_B = 1:5, NAME_B = c(NA, "Barn", "Bolton",
>> "Bravo", NA),
>>NUM_C = 1:5, NAME_C = c("Candy", NA, "Cecil",
>> "Crayon", "Corey"),
>>NUM_D = 1:5, NAME_D = c("David", "Delta", NA, NA,
>> "Dummy") )
>>
>> col_names <- c("A", "B", "C", "D")
>>
>> > all.data
>> NUM_A NAME_A NUM_B NAME_B NUM_C NAME_C NUM_D NAME_D
>> 1 1 Andy 11 Candy 1 David
>> 2 2 Andrew 2 Barn 22 Delta
>> 3 3 Angus 3 Bolton 3 Cecil 3
>> 4 4 Alex 4 Bravo 4 Crayon 4
>> 5 5 Argo 55 Corey 5 Dummy
>> >
>>
>> Then for each col_names, I want to display the columns:
>>
>> for (each_name in col_names) {
>>
>>sub.data <- subset( all.data,
>>!is.na( paste("NAME_", each_name, sep = '') ),
>>select = c( paste("NUM_", each_name, sep = '')
>> ,
>> paste("NAME_", each_name, sep = '') )
>> )
>>print(sub.data)
>> }
>>
>> the "incorrect" result:
>>
>> NUM_A NAME_A
>> 1 1 Andy
>> 2 2 Andrew
>> 3 3 Angus
>> 4 4 Alex
>> 5 5 Argo
>> NUM_B NAME_B
>> 1 1
>> 2 2 Barn
>> 3 3 Bolton
>> 4 4 Bravo
>> 5 5
>> NUM_C NAME_C
>> 1 1 Candy
>> 2 2
>> 3 3 Cecil
>> 4 4 Crayon
>> 5 5 Corey
>> NUM_D NAME_D
>> 1 1 David
>> 2 2 Delta
>> 3 3
>> 4 4
>> 5 5 Dummy
>> >
>>
>> What I want to achieve is that the result should only display the NUM and
>> NAME that is not NA. Here, the NA can be NULL, or zero (or other specific
>> values).
>>
>> the "correct" result:
>>
>> NUM_A NAME_A
>> 1 1 Andy
>> 2 2 Andrew
>> 3 3 Angus
>> 4 4 Alex
>> 5 5 Argo
>> NUM_B NAME_B
>> 2 2 Barn
>> 3 3 Bolton
>> 4 4 Bravo
>> NUM_C NAME_C
>> 1 1 Candy
>> 3 3 Cecil
>> 4 4 Crayon
>> 5 5 Corey
>> NUM_D NAME_D
>> 1 1 David
>> 2 2 Delta
>> 5 5 Dummy
>> >
>>
>> I am guessing that I don't use the correct type on the following statement
>> (within the subset in the loop):
>> !is.na( paste("NAME_", each_name, sep = '') )
>>
>> But then, I might be completely using a wrong approach.
>>
>> Any idea is definitely appreciated.
>>
>> Thank you,
>>
>> Ferry
>>
>>[[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
[[alternative HTML version deleted]]
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Re: [R] how to automatically select certain columns using for loop in dataframe
Hi Ferry,
It is not so elegant, but you can try
for (each_name in col_names) {
sub.data <- subset( all.data,
!is.na( paste("NAME_", each_name, sep = '') ),
select = c( paste("NUM_", each_name, sep = '') ,
paste("NAME_", each_name, sep = '') )
)
sub.data.2<-subset(sub.data, !is.na(sub.data[,2]))
print(sub.data.2)
}
On Thu, Apr 9, 2009 at 6:30 PM, Ferry wrote:
> Hi,
>
> I am trying to display / print certain columns in my data frame that share
> certain condition (for example, part of the column name). I am using for
> loop, as follow:
>
> # below is the sample data structure
> all.data <- data.frame( NUM_A = 1:5, NAME_A = c("Andy", "Andrew", "Angus",
> "Alex", "Argo"),
>NUM_B = 1:5, NAME_B = c(NA, "Barn", "Bolton",
> "Bravo", NA),
>NUM_C = 1:5, NAME_C = c("Candy", NA, "Cecil",
> "Crayon", "Corey"),
>NUM_D = 1:5, NAME_D = c("David", "Delta", NA, NA,
> "Dummy") )
>
> col_names <- c("A", "B", "C", "D")
>
> > all.data
> NUM_A NAME_A NUM_B NAME_B NUM_C NAME_C NUM_D NAME_D
> 1 1 Andy 11 Candy 1 David
> 2 2 Andrew 2 Barn 22 Delta
> 3 3 Angus 3 Bolton 3 Cecil 3
> 4 4 Alex 4 Bravo 4 Crayon 4
> 5 5 Argo 55 Corey 5 Dummy
> >
>
> Then for each col_names, I want to display the columns:
>
> for (each_name in col_names) {
>
>sub.data <- subset( all.data,
>!is.na( paste("NAME_", each_name, sep = '') ),
>select = c( paste("NUM_", each_name, sep = '') ,
> paste("NAME_", each_name, sep = '') )
> )
>print(sub.data)
> }
>
> the "incorrect" result:
>
> NUM_A NAME_A
> 1 1 Andy
> 2 2 Andrew
> 3 3 Angus
> 4 4 Alex
> 5 5 Argo
> NUM_B NAME_B
> 1 1
> 2 2 Barn
> 3 3 Bolton
> 4 4 Bravo
> 5 5
> NUM_C NAME_C
> 1 1 Candy
> 2 2
> 3 3 Cecil
> 4 4 Crayon
> 5 5 Corey
> NUM_D NAME_D
> 1 1 David
> 2 2 Delta
> 3 3
> 4 4
> 5 5 Dummy
> >
>
> What I want to achieve is that the result should only display the NUM and
> NAME that is not NA. Here, the NA can be NULL, or zero (or other specific
> values).
>
> the "correct" result:
>
> NUM_A NAME_A
> 1 1 Andy
> 2 2 Andrew
> 3 3 Angus
> 4 4 Alex
> 5 5 Argo
> NUM_B NAME_B
> 2 2 Barn
> 3 3 Bolton
> 4 4 Bravo
> NUM_C NAME_C
> 1 1 Candy
> 3 3 Cecil
> 4 4 Crayon
> 5 5 Corey
> NUM_D NAME_D
> 1 1 David
> 2 2 Delta
> 5 5 Dummy
> >
>
> I am guessing that I don't use the correct type on the following statement
> (within the subset in the loop):
> !is.na( paste("NAME_", each_name, sep = '') )
>
> But then, I might be completely using a wrong approach.
>
> Any idea is definitely appreciated.
>
> Thank you,
>
> Ferry
>
>[[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
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Re: [R] Subset a data frame for plotting
Jim's points are well taken. I wonder if you might get greater efficiency by examining the opportunities in the lattice or ggplot2 packages that allow specification of grouping variables. It might get tedious creating all those micro-data.frames and might not really be necessary. From the first example on the xyplots help page: library(lattice) Depth <- equal.count(quakes$depth, number=8, overlap=.1) # Depth is used for grouping xyplot(lat ~ long | Depth, data = quakes) update(trellis.last.object(), strip = strip.custom(strip.names = TRUE, strip.levels = TRUE), par.strip.text = list(cex = 0.75), aspect = "iso") -- David Winsemius On Apr 9, 2009, at 9:32 PM, jim holtman wrote: I am not sure what you are trying to assign a value to '200706183<-'; does not look like a valid object name. This should work: x200706183<-subset(AllData, ID == 200706183) Notice the use of the '==' for the logical compare. On Thu, Apr 9, 2009 at 8:58 PM, Paul Warren Simonin wrote: Hello, I have a question regarding how to subset/select parts of a data frame (matrix) in order to plot data associated only with this subset. Specifically I have a large data frame in which one column contains ID values (dates), and other columns contain data I would like to plot (temperature, light, etc.). I would like to break up this large matrix so as to plot data associated with specific ID values (dates) separately. I have learned of several commands that supposedly subset matrices in this manner and have tried the following code with no success: 200706183<-subset(AllData, ID = 200706183) 200706183<-gx.subset(AllData, ID == 200706183) 200706183<-subset(x=AllData, AllData$ID = 200706183) 200706183<-gx.subset(x=AllData, AllData$ID == 200706183) In using this code my plan was to create smaller data frame objects which I could then plot. My first question, though, is whether this is the correct approach. Is there a more efficient way I can create plots conditional on certain criteria such as "code = 200706183" ? If I do need to first create separate smaller data frames, how do I go about doing this? Am I missing something in the above commands? Any other advice is certainly welcome too, as I admit to being a bit new to R. Thank you very much for any answers, tips, suggestions, etc.! Best wishes, Paul Simonin -- Paul W. Simonin Graduate Research Assistant, MS Program Vermont Cooperative Fish and Wildlife Research Unit The Rubenstein School of Environment and Natural Resources University of Vermont 81 Carrigan Dr. Burlington, VT 05405 Ph:802-656-3153 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Subset a data frame for plotting
I am not sure what you are trying to assign a value to '200706183<-'; does not look like a valid object name. This should work: x200706183<-subset(AllData, ID == 200706183) Notice the use of the '==' for the logical compare. On Thu, Apr 9, 2009 at 8:58 PM, Paul Warren Simonin wrote: > Hello, > > I have a question regarding how to subset/select parts of a data frame > (matrix) in order to plot data associated only with this subset. > Specifically I have a large data frame in which one column contains ID > values (dates), and other columns contain data I would like to plot > (temperature, light, etc.). I would like to break up this large matrix so as > to plot data associated with specific ID values (dates) separately. I have > learned of several commands that supposedly subset matrices in this manner > and have tried the following code with no success: > > 200706183<-subset(AllData, ID = 200706183) > 200706183<-gx.subset(AllData, ID == 200706183) > 200706183<-subset(x=AllData, AllData$ID = 200706183) > 200706183<-gx.subset(x=AllData, AllData$ID == 200706183) > > In using this code my plan was to create smaller data frame objects which I > could then plot. My first question, though, is whether this is the correct > approach. Is there a more efficient way I can create plots conditional on > certain criteria such as "code = 200706183" ? > If I do need to first create separate smaller data frames, how do I go > about doing this? Am I missing something in the above commands? > Any other advice is certainly welcome too, as I admit to being a bit new to > R. Thank you very much for any answers, tips, suggestions, etc.! > > Best wishes, > Paul Simonin > > -- > Paul W. Simonin > Graduate Research Assistant, MS Program > Vermont Cooperative Fish and Wildlife Research Unit > The Rubenstein School of Environment and Natural Resources > University of Vermont > 81 Carrigan Dr. > Burlington, VT 05405 > Ph:802-656-3153 > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Subset a data frame for plotting
Hello, I have a question regarding how to subset/select parts of a data frame (matrix) in order to plot data associated only with this subset. Specifically I have a large data frame in which one column contains ID values (dates), and other columns contain data I would like to plot (temperature, light, etc.). I would like to break up this large matrix so as to plot data associated with specific ID values (dates) separately. I have learned of several commands that supposedly subset matrices in this manner and have tried the following code with no success: 200706183<-subset(AllData, ID = 200706183) 200706183<-gx.subset(AllData, ID == 200706183) 200706183<-subset(x=AllData, AllData$ID = 200706183) 200706183<-gx.subset(x=AllData, AllData$ID == 200706183) In using this code my plan was to create smaller data frame objects which I could then plot. My first question, though, is whether this is the correct approach. Is there a more efficient way I can create plots conditional on certain criteria such as "code = 200706183" ? If I do need to first create separate smaller data frames, how do I go about doing this? Am I missing something in the above commands? Any other advice is certainly welcome too, as I admit to being a bit new to R. Thank you very much for any answers, tips, suggestions, etc.! Best wishes, Paul Simonin -- Paul W. Simonin Graduate Research Assistant, MS Program Vermont Cooperative Fish and Wildlife Research Unit The Rubenstein School of Environment and Natural Resources University of Vermont 81 Carrigan Dr. Burlington, VT 05405 Ph:802-656-3153 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Random Cluster Generation Question
Try: > clust <- rMatClust(10, 0.05, 50) > plot(clust) > Y <- rThomas(10, 0.05, 50) > plot(Y) On Apr 9, 2009, at 7:28 PM, Jason L. Simms wrote: Hello, Thanks for your note. I recognize that the points per cluster is random, and also that it is possible to set the mean number of points per cluster through the function. What I was hoping was that I could specify a maximum number of points overall across all clusters, but conceptually I don't know how that could even be implemented. I ended up adjusting the parameters of the function until I produced right around 2,000 points in a 10x10 box, and then I just multiplied everything by 100. Not sure whether it's perfect, but I suspect that it will work for my needs currently. I'll look into the rThomas() function, too. I am much more of an applied stats person, so the subtle (or even not-so-subtle) differences and advantages/disadvantages between a Thomas Process and a Matern Process are unclear to me at the moment. Jason On Thu, Apr 9, 2009 at 7:06 PM, David Winsemius > wrote: On Apr 9, 2009, at 5:01 PM, Jason L. Simms wrote: Hello, I am fairly new to R, but I am not new to programming at all. I want to generate random clusters in a 1,000x1,000 box such that I end up with a total of about 2,000 points. Once done, I need to export the X,Y coordinates of the points. I have looked around, and it seems that the spatstat package has what I need. The rMatClust() function can generate random clusters, but I have run into some problems. First, I can't seem to specify that I want x number of points. The number of points per cluster IS random. So, right now it appears that if I want around 2,000 total points that I must play around with the parameters of the function (e.g., mean number of points per cluster, cluster radius, etc.) until I end up with roughly 2,000 points. More problematic, however, is that specifying a 1,000x1,000 box is too much to handle. I have been running the following function for over 24 hours straight on a decent computer and it has not stopped yet: clust <- rMatClust(1, 50, 5, win=owin(c(0,1000),c(0,1000))) It might well be due to the 1000 x 1000 dimensions but it is because of your parameters. It took a significant amount of time to yield 4-10 points on a 1 x 1 window. Whereas this particular invocation much more quickly produced 2707 points with a mean of 100 points per uniform cluster within a 1 x 1 square: Y <- rMatClust(20, 0.05, 100) If you wanted the x and y dimensions to be in the range of 0-1000, couldn't you just multiply the x and y values inside Y by 1000. Y$x <- 1000*Y$x Y$y <- 1000*Y$y plot(Y) # cannot see any points, probably because the plot.kkpm method is using # internal ranges inside that Y object. So you might loose the ability to use # other functions in that package plot(Y$x, Y$y) # as expected and took seconds at most. I would think that the most important task would be deciding on the function that controls the intensity process of the "offspring points". The points in this simple example clearly violate my notions of randomness because of the sharp edges at the cluster boundaries. So, you may want to examine rThomas(...) in the same package. There is, of course, a SIG spatial stats mailing list full of people better qualified than I on such questions. Clearly, I need to rethink my strategy. Could I generate the points in a 10x10 box with a radius of .5 and then multiply out the resulting point coordinates by 100? Is there another package that might meet my needs better than spatstat for easy cluster generation? Any suggestions are appreciated. -- Jason L. Simms, M.A. USF Graduate Multidisciplinary Scholar David Winsemius, MD Heritage Laboratories West Hartford, CT -- Jason L. Simms, M.A. USF Graduate Multidisciplinary Scholar Co-President, Graduate Assistants United Ph.D. / M.P.H. Student Departments of Anthropology and Environmental and Occupational Health University of South Florida David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Los Angeles area R users group's first meeting
We would like to invite you to the Los Angeles area R user group's first meeting. This group is aimed to bring together practitioners (from industry and academia alike) in order to exchange knowledge and experience in solving data analysis/statistical problems by using R. More information about the group at: http://www.meetup.com/LAarea-R-usergroup/ Meeting: Four case studies of using R The goal of this first meeting is to bring together people of a wide range of interests related to R and to open a forum for discussions and further interaction. Agenda: - Introduction - Using R in research (Jan de Leeuw, UCLA) - Using R in applications related to credit card transactions (Szilard Pafka, Epoch) - Using R in teaching (Rob Gould, UCLA) - Using R in consulting (Brigid Brett-Esborn, UCLA) - Q&A, general discussions - Discussions/networking We plan 15 minutes for each speaker and for the general discussions. Then participants are encouraged to initiate discussions with each other (the place is reserved until 9pm). Bottled water and cookies will be available free of charge. Please RSVP on meetup.com (http://www.meetup.com/LAarea-R-usergroup/) as places are limited. Those who are unfamiliar with R but would like to get basic hands-on knowledge (installation, working with data, plotting etc.) are welcome to attend the “Basic R” course (free) of the UCLA Statistical Consulting Center, 5-7pm (right before the meetup) in the same room. Please email to su...@stat.ucla.edu as places are limited. You can also download the notes, or attend the course at another time at your convenience (see http://scc.stat.ucla.edu/mini-courses/ ). Our speakers: - Jan de Leeuw is Distinguished Professor and Chair at UCLA Department of Statistics. He is also Editor in Chief of the Journal of Statistical Software (the primary journal for publishing work related to R) and the Journal of Multivariate Analysis. - Szilard Pafka, PhD is Chief Scientist at Epoch, a credit card transactions processor. He uses R for various data analysis, statistical modeling and visualization projects. Previously, he worked on a variety of research problems ranging from physics to financial prices. - Rob Gould received his PhD from UC San Diego in 1994 and has been at UCLA since. He is director of the UCLA Center for Statistics Education, Associate Director of Professional Development of the Consortium of the Advancement of Undergraduate Statistics Education, and former chair of the ASA Advisory Committee on Teacher Enhancement. - Brigid Brett-Esborn is a PhD student in the Department of Statistics at UCLA. She also works as a consultant with the Department's Statistical Consulting Center and the Statistical Computing group within UCLA's Academic Technology Services department. She has contributed to the Journal of Statistical Software. Time and venue: May 7, 2009, Thursday, 7-9pm UCLA Boelter Hall Room 9413 (this room is next to the Statistical Consulting Center, Boelter Hall 9434) The only way to access the venue is from the southeast corner of Boelter Hall (southeast elevator/southeast stairwell). Directions here: http://scc.stat.ucla.edu/contact-us/map/ To find Boelter Hall on campus: http://maps.ucla.edu/campus/ Information on how to get to UCLA: http://www.ucla.edu/map/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] CFA in R/sem package
Sure, something like that. Store each model as an element of a list,
and then use something like
for(i in 1:4){
indices<-combn(1:4, i)
for (j in 1:length(indices[1,])){
new.model<-combine.models(model.pieces[ indices[,j] ] )
#code for analysis
}
}
Or, if this doesn't fit your problem exactly, some similar approach.
On Apr 9, 2009, at 4:23 PM, Iuri Gavronski wrote:
Jarret,
I've donwloaded the zip file and installed, but maybe have lost some
pre-req check. I have manually installed sna.
Anyway, which would be the approach you suggest? Making (using my
example) 4 different models, one for each construct, then use
combine.models and add.to.models to create the 12 models to be
compared?
Best,
Iuri.
On Thu, Apr 9, 2009 at 8:13 PM, Jarrett Byrnes
wrote:
install.packages("sem-additions",repos="http://R-Forge.R-
project.org")
Sorry, it's sem-additions on r-forge. Not sem.additions, which is
what I
had originally called it. But they won't take . in the name of a
package.
On Apr 9, 2009, at 4:07 PM, Iuri Gavronski wrote:
Jarret,
Look:
install.packages("sem.additions", repos="http://R-Forge.R-project.org
")
Warning message:
package ‘sem.additions’ is not available
Best,
Iuri.
On Thu, Apr 9, 2009 at 3:10 PM, Jarrett Byrnes
wrote:
Ivan,
I recently put together the sem.additions package over at R forge
in part
for just such a multiple model problem. THere are a variety of
methods
that
make it easy to add/delete links that could be automated with a
for loop
and
something from the combn package, I think.
http://r-forge.r-project.org/projects/sem-additions/
-Jarrett
On Apr 9, 2009, at 6:39 AM, Iuri Gavronski wrote:
Hi,
I am not sure if R-help is the right forum for my question. If
not,
please let me know.
I have to do some discriminant validity tests with some
constructs. I
am using the method of doing a CFA constraining the correlation
of a
pair of the constructs to 1 and comparing the chi-square of this
constrained model to the unconstrained model. If the chi-square
difference is not significant, then I cannot reject the null
hypothesis that the two constructs are equal.
Well, if you are going to test, say, 4 constructs (A, B, C, and
D),
you will have to have 2*C(4,2) = 12 models to test, 5
constructs, 20
models, and so forth. A tedious and error prone process...
So far, I have been using AMOS for that shake, given that 1) my
university has the license, 2) my other colleagues use it, and
3) I
know it ;)
I would like to know if any of you use R, namely the sem
package, for
that application and if you can share your thoughts/experiences on
using it. I don't thing I would have problems "porting" my
models to
R/sem, but I would like to know if there is an optimized process
of
doing that tests, without manually coding all the dozens of
models.
Best,
Iuri.
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Re: [R] Random Cluster Generation Question
Hello, Thanks for your note. I recognize that the points per cluster is random, and also that it is possible to set the mean number of points per cluster through the function. What I was hoping was that I could specify a maximum number of points overall across all clusters, but conceptually I don't know how that could even be implemented. I ended up adjusting the parameters of the function until I produced right around 2,000 points in a 10x10 box, and then I just multiplied everything by 100. Not sure whether it's perfect, but I suspect that it will work for my needs currently. I'll look into the rThomas() function, too. I am much more of an applied stats person, so the subtle (or even not-so-subtle) differences and advantages/disadvantages between a Thomas Process and a Matern Process are unclear to me at the moment. Jason On Thu, Apr 9, 2009 at 7:06 PM, David Winsemius wrote: > > On Apr 9, 2009, at 5:01 PM, Jason L. Simms wrote: > >> Hello, >> >> I am fairly new to R, but I am not new to programming at all. I want >> to generate random clusters in a 1,000x1,000 box such that I end up >> with a total of about 2,000 points. Once done, I need to export the >> X,Y coordinates of the points. >> >> I have looked around, and it seems that the spatstat package has what >> I need. The rMatClust() function can generate random clusters, but I >> have run into some problems. >> >> First, I can't seem to specify that I want x number of points. > > The number of points per cluster IS random. > >> So, right now it appears that if I want around 2,000 total points that I >> must play around with the parameters of the function (e.g., mean >> number of points per cluster, cluster radius, etc.) until I end up >> with roughly 2,000 points. >> >> More problematic, however, is that specifying a 1,000x1,000 box is too >> much to handle. I have been running the following function for over >> 24 hours straight on a decent computer and it has not stopped yet: >> >> clust <- rMatClust(1, 50, 5, win=owin(c(0,1000),c(0,1000))) > > It might well be due to the 1000 x 1000 dimensions but it is because of your > parameters. It took a significant amount of time to yield 4-10 points on a 1 > x 1 window. Whereas this particular invocation much more quickly produced > 2707 points with a mean of 100 points per uniform cluster within a 1 x 1 > square: > > Y <- rMatClust(20, 0.05, 100) > > If you wanted the x and y dimensions to be in the range of 0-1000, couldn't > you just multiply the x and y values inside Y by 1000. > Y$x <- 1000*Y$x > Y$y <- 1000*Y$y > plot(Y) # cannot see any points, probably because the plot.kkpm method is > using > # internal ranges inside that Y object. So you might loose the ability to > use > # other functions in that package > plot(Y$x, Y$y) # as expected and took seconds at most. > > I would think that the most important task would be deciding on the function > that controls the intensity process of the "offspring points". The points in > this simple example clearly violate my notions of randomness because of the > sharp edges at the cluster boundaries. So, you may want to examine > rThomas(...) in the same package. > > There is, of course, a SIG spatial stats mailing list full of people better > qualified than I on such questions. >> >> Clearly, I need to rethink my strategy. Could I generate the points >> in a 10x10 box with a radius of .5 and then multiply out the resulting >> point coordinates by 100? Is there another package that might meet my >> needs better than spatstat for easy cluster generation? >> >> Any suggestions are appreciated. >> -- >> Jason L. Simms, M.A. >> USF Graduate Multidisciplinary Scholar > > David Winsemius, MD > Heritage Laboratories > West Hartford, CT > > -- Jason L. Simms, M.A. USF Graduate Multidisciplinary Scholar Co-President, Graduate Assistants United Ph.D. / M.P.H. Student Departments of Anthropology and Environmental and Occupational Health University of South Florida __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] CFA in R/sem package
Jarret,
I've donwloaded the zip file and installed, but maybe have lost some
pre-req check. I have manually installed sna.
Anyway, which would be the approach you suggest? Making (using my
example) 4 different models, one for each construct, then use
combine.models and add.to.models to create the 12 models to be
compared?
Best,
Iuri.
On Thu, Apr 9, 2009 at 8:13 PM, Jarrett Byrnes wrote:
> install.packages("sem-additions",repos="http://R-Forge.R-project.org";)
>
> Sorry, it's sem-additions on r-forge. Not sem.additions, which is what I
> had originally called it. But they won't take . in the name of a package.
>
> On Apr 9, 2009, at 4:07 PM, Iuri Gavronski wrote:
>
>> Jarret,
>>
>> Look:
>>>
>>> install.packages("sem.additions", repos="http://R-Forge.R-project.org";)
>>
>> Warning message:
>> package ‘sem.additions’ is not available
>>>
>>
>> Best,
>>
>> Iuri.
>>
>> On Thu, Apr 9, 2009 at 3:10 PM, Jarrett Byrnes
>> wrote:
>>>
>>> Ivan,
>>>
>>> I recently put together the sem.additions package over at R forge in part
>>> for just such a multiple model problem. THere are a variety of methods
>>> that
>>> make it easy to add/delete links that could be automated with a for loop
>>> and
>>> something from the combn package, I think.
>>>
>>> http://r-forge.r-project.org/projects/sem-additions/
>>>
>>> -Jarrett
>>>
>>> On Apr 9, 2009, at 6:39 AM, Iuri Gavronski wrote:
>>>
Hi,
I am not sure if R-help is the right forum for my question. If not,
please let me know.
I have to do some discriminant validity tests with some constructs. I
am using the method of doing a CFA constraining the correlation of a
pair of the constructs to 1 and comparing the chi-square of this
constrained model to the unconstrained model. If the chi-square
difference is not significant, then I cannot reject the null
hypothesis that the two constructs are equal.
Well, if you are going to test, say, 4 constructs (A, B, C, and D),
you will have to have 2*C(4,2) = 12 models to test, 5 constructs, 20
models, and so forth. A tedious and error prone process...
So far, I have been using AMOS for that shake, given that 1) my
university has the license, 2) my other colleagues use it, and 3) I
know it ;)
I would like to know if any of you use R, namely the sem package, for
that application and if you can share your thoughts/experiences on
using it. I don't thing I would have problems "porting" my models to
R/sem, but I would like to know if there is an optimized process of
doing that tests, without manually coding all the dozens of models.
Best,
Iuri.
__
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PLEASE do read the posting guide
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>>>
>>> __
>>> R-help@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
__
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Re: [R] puzzling lm.fit errors
On 09-Apr-09 22:53:51, Brendan Morse wrote: > Hi everyone, I am running a monte carlo and am getting an error that I > haven't the slightest clue where to begin figuring it out. The error > is as follows: > > Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) >: >0 (non-NA) cases > In addition: Warning message: > In ltm.fit(X, betas, constraint, formula, con) : >Hessian matrix at convergence is not positive definite; unstable > solution. > > The puzzling aspect though is that it successfully runs a number of > complete iterations before this occurs. I am not sure what or where > this is going on. > > Any suggestions? > > Thanks very much (in advance) > - Brendan This is the sort of thing that can happen is the covariates in your linear model lead to a model matrix which singular (or nearly so). In other words, at least one of your covariate vectors is a linear combination of the others (or nearly so). The facts that (a) you are doing a Monte Carlo simulationm and (b) you get a number of satisfactory runs and then it fails, suggest that you are randomly creating covariate (independent-variable) values as well as dependent-variable values. If that is so, then the structure of your model may be such that it is relatively likely for such singularity to arise. While not particularly likely for continuous covariates, near-singularity can nevertheless happen. It can be much more likely if you are generating random levels of factors, since only a finite number of combinations are possible, and sooner or later you will definitely hit exact collinarity. And if you are using a fairly large number of covariates, and not a large number of cases, then it can become really likely! I'm only guessing, of course, and you can either agree with, or deny, the above suggestions. Either way, it would help in clarifying the problem to know the details of how your Monte Carlo simulation is supposed to work. Ted. E-Mail: (Ted Harding) Fax-to-email: +44 (0)870 094 0861 Date: 10-Apr-09 Time: 00:23:04 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] CFA in R/sem package
install.packages("sem-additions",repos="http://R-Forge.R-project.org";)
Sorry, it's sem-additions on r-forge. Not sem.additions, which is
what I had originally called it. But they won't take . in the name of
a package.
On Apr 9, 2009, at 4:07 PM, Iuri Gavronski wrote:
Jarret,
Look:
install.packages("sem.additions", repos="http://R-Forge.R-
project.org")
Warning message:
package ‘sem.additions’ is not available
Best,
Iuri.
On Thu, Apr 9, 2009 at 3:10 PM, Jarrett Byrnes
wrote:
Ivan,
I recently put together the sem.additions package over at R forge
in part
for just such a multiple model problem. THere are a variety of
methods that
make it easy to add/delete links that could be automated with a for
loop and
something from the combn package, I think.
http://r-forge.r-project.org/projects/sem-additions/
-Jarrett
On Apr 9, 2009, at 6:39 AM, Iuri Gavronski wrote:
Hi,
I am not sure if R-help is the right forum for my question. If not,
please let me know.
I have to do some discriminant validity tests with some
constructs. I
am using the method of doing a CFA constraining the correlation of a
pair of the constructs to 1 and comparing the chi-square of this
constrained model to the unconstrained model. If the chi-square
difference is not significant, then I cannot reject the null
hypothesis that the two constructs are equal.
Well, if you are going to test, say, 4 constructs (A, B, C, and D),
you will have to have 2*C(4,2) = 12 models to test, 5 constructs, 20
models, and so forth. A tedious and error prone process...
So far, I have been using AMOS for that shake, given that 1) my
university has the license, 2) my other colleagues use it, and 3) I
know it ;)
I would like to know if any of you use R, namely the sem package,
for
that application and if you can share your thoughts/experiences on
using it. I don't thing I would have problems "porting" my models to
R/sem, but I would like to know if there is an optimized process of
doing that tests, without manually coding all the dozens of models.
Best,
Iuri.
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] CFA in R/sem package
Jarret,
Look:
> install.packages("sem.additions", repos="http://R-Forge.R-project.org";)
Warning message:
package ‘sem.additions’ is not available
>
Best,
Iuri.
On Thu, Apr 9, 2009 at 3:10 PM, Jarrett Byrnes wrote:
> Ivan,
>
> I recently put together the sem.additions package over at R forge in part
> for just such a multiple model problem. THere are a variety of methods that
> make it easy to add/delete links that could be automated with a for loop and
> something from the combn package, I think.
>
> http://r-forge.r-project.org/projects/sem-additions/
>
> -Jarrett
>
> On Apr 9, 2009, at 6:39 AM, Iuri Gavronski wrote:
>
>> Hi,
>>
>> I am not sure if R-help is the right forum for my question. If not,
>> please let me know.
>>
>> I have to do some discriminant validity tests with some constructs. I
>> am using the method of doing a CFA constraining the correlation of a
>> pair of the constructs to 1 and comparing the chi-square of this
>> constrained model to the unconstrained model. If the chi-square
>> difference is not significant, then I cannot reject the null
>> hypothesis that the two constructs are equal.
>>
>> Well, if you are going to test, say, 4 constructs (A, B, C, and D),
>> you will have to have 2*C(4,2) = 12 models to test, 5 constructs, 20
>> models, and so forth. A tedious and error prone process...
>>
>> So far, I have been using AMOS for that shake, given that 1) my
>> university has the license, 2) my other colleagues use it, and 3) I
>> know it ;)
>>
>> I would like to know if any of you use R, namely the sem package, for
>> that application and if you can share your thoughts/experiences on
>> using it. I don't thing I would have problems "porting" my models to
>> R/sem, but I would like to know if there is an optimized process of
>> doing that tests, without manually coding all the dozens of models.
>>
>> Best,
>>
>> Iuri.
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Random Cluster Generation Question
On Apr 9, 2009, at 5:01 PM, Jason L. Simms wrote: Hello, I am fairly new to R, but I am not new to programming at all. I want to generate random clusters in a 1,000x1,000 box such that I end up with a total of about 2,000 points. Once done, I need to export the X,Y coordinates of the points. I have looked around, and it seems that the spatstat package has what I need. The rMatClust() function can generate random clusters, but I have run into some problems. First, I can't seem to specify that I want x number of points. The number of points per cluster IS random. So, right now it appears that if I want around 2,000 total points that I must play around with the parameters of the function (e.g., mean number of points per cluster, cluster radius, etc.) until I end up with roughly 2,000 points. More problematic, however, is that specifying a 1,000x1,000 box is too much to handle. I have been running the following function for over 24 hours straight on a decent computer and it has not stopped yet: clust <- rMatClust(1, 50, 5, win=owin(c(0,1000),c(0,1000))) It might well be due to the 1000 x 1000 dimensions but it is because of your parameters. It took a significant amount of time to yield 4-10 points on a 1 x 1 window. Whereas this particular invocation much more quickly produced 2707 points with a mean of 100 points per uniform cluster within a 1 x 1 square: Y <- rMatClust(20, 0.05, 100) If you wanted the x and y dimensions to be in the range of 0-1000, couldn't you just multiply the x and y values inside Y by 1000. Y$x <- 1000*Y$x Y$y <- 1000*Y$y plot(Y) # cannot see any points, probably because the plot.kkpm method is using # internal ranges inside that Y object. So you might loose the ability to use # other functions in that package plot(Y$x, Y$y) # as expected and took seconds at most. I would think that the most important task would be deciding on the function that controls the intensity process of the "offspring points". The points in this simple example clearly violate my notions of randomness because of the sharp edges at the cluster boundaries. So, you may want to examine rThomas(...) in the same package. There is, of course, a SIG spatial stats mailing list full of people better qualified than I on such questions. Clearly, I need to rethink my strategy. Could I generate the points in a 10x10 box with a radius of .5 and then multiply out the resulting point coordinates by 100? Is there another package that might meet my needs better than spatstat for easy cluster generation? Any suggestions are appreciated. -- Jason L. Simms, M.A. USF Graduate Multidisciplinary Scholar David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] puzzling lm.fit errors
Hi everyone, I am running a monte carlo and am getting an error that I haven't the slightest clue where to begin figuring it out. The error is as follows: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 0 (non-NA) cases In addition: Warning message: In ltm.fit(X, betas, constraint, formula, con) : Hessian matrix at convergence is not positive definite; unstable solution. The puzzling aspect though is that it successfully runs a number of complete iterations before this occurs. I am not sure what or where this is going on. Any suggestions? Thanks very much (in advance) - Brendan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] arima on defined lags
Gerard M. Keogh wrote: Dear all, The standard call to ARIMA in the base package such as arima(y,c(5,0,0),include.mean=FALSE) gives a full 5th order lag polynomial model with for example coeffs Coefficients: ar1ar2 ar3 ar4 ar5 0.4715 0.067 -0.1772 0.0256 -0.2550 s.e. 0.1421 0.158 0.1569 0.1602 0.1469 Is it possible (I doubt it but am just checking) to define a more parsimonous lag1 and lag 5 model with coeff ar1 and ar5? Or do I need one of the other TS packages? You can specify the "fixed" argument (with transform.pars=FALSE): > arima(x, c(5, 0, 0), fixed=c(NA, 0, 0, 0, NA), include.mean=FALSE, transform.pars=FALSE) Call: arima(x = x, order = c(5, 0, 0), include.mean = FALSE, transform.pars = FALSE, fixed = c(NA, 0, 0, 0, NA)) Coefficients: ar1 ar2 ar3 ar4 ar5 -0.0483000 0.1355 s.e. 0.1010000 0.1031 -- Gad Abraham Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabra...@csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Cross-platforms solution to export R graphs
Le jeudi 09 avril 2009 à 15:04 +0200, Philippe Grosjean a écrit : > Hello Rusers, > > I have worked on a R Wiki page for solutions in exporting R graphs, > especially, the often-asked questions: > - How can I export R graphs in vectorized format (EMF) for inclusion in > MS Word or OpenOffice outside of Windows? > - What is the best solution(s) for post-editing/annotating R graphs. > > The page is at: > http://wiki.r-project.org/rwiki/doku.php?id=tips:graphics-misc:export. > > I would be happy to receive your comments and suggestions to improve > this document. Well, if you insist ... The PDF import plugin in OpenOffice is still beta, and some report deem it difficult to install correctly an/or flaky. Having checked that both MSWord (>=2000) and OpenOffice (>=2.4) import and display correctly (i. e. vectorially, including fonts) EPS files, I switched to this format, most notably for use with the marvellous Max Kuhn's odfWeave package, which is a *must* for us working in state/administrative/corporate salt mines, where \LaTeX is deemed obscene and plain \TeX causes seizures ... The point is that this format doesn't need any intermediary step, thus allowing for automatisation. Be aware, however, that the embedded EPS images are not editable in-place by OpenOffice nor, as far as I know, by MS Word. But my point was to *avoid* post-production as much as humanly possible (I tend to be inhumanly lazy...). HTH, Emmanuel Charpentier > All the best, > > PhG __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to automatically select certain columns using for loop in dataframe
Hi,
I am trying to display / print certain columns in my data frame that share
certain condition (for example, part of the column name). I am using for
loop, as follow:
# below is the sample data structure
all.data <- data.frame( NUM_A = 1:5, NAME_A = c("Andy", "Andrew", "Angus",
"Alex", "Argo"),
NUM_B = 1:5, NAME_B = c(NA, "Barn", "Bolton",
"Bravo", NA),
NUM_C = 1:5, NAME_C = c("Candy", NA, "Cecil",
"Crayon", "Corey"),
NUM_D = 1:5, NAME_D = c("David", "Delta", NA, NA,
"Dummy") )
col_names <- c("A", "B", "C", "D")
> all.data
NUM_A NAME_A NUM_B NAME_B NUM_C NAME_C NUM_D NAME_D
1 1 Andy 11 Candy 1 David
2 2 Andrew 2 Barn 22 Delta
3 3 Angus 3 Bolton 3 Cecil 3
4 4 Alex 4 Bravo 4 Crayon 4
5 5 Argo 55 Corey 5 Dummy
>
Then for each col_names, I want to display the columns:
for (each_name in col_names) {
sub.data <- subset( all.data,
!is.na( paste("NAME_", each_name, sep = '') ),
select = c( paste("NUM_", each_name, sep = '') ,
paste("NAME_", each_name, sep = '') )
)
print(sub.data)
}
the "incorrect" result:
NUM_A NAME_A
1 1 Andy
2 2 Andrew
3 3 Angus
4 4 Alex
5 5 Argo
NUM_B NAME_B
1 1
2 2 Barn
3 3 Bolton
4 4 Bravo
5 5
NUM_C NAME_C
1 1 Candy
2 2
3 3 Cecil
4 4 Crayon
5 5 Corey
NUM_D NAME_D
1 1 David
2 2 Delta
3 3
4 4
5 5 Dummy
>
What I want to achieve is that the result should only display the NUM and
NAME that is not NA. Here, the NA can be NULL, or zero (or other specific
values).
the "correct" result:
NUM_A NAME_A
1 1 Andy
2 2 Andrew
3 3 Angus
4 4 Alex
5 5 Argo
NUM_B NAME_B
2 2 Barn
3 3 Bolton
4 4 Bravo
NUM_C NAME_C
1 1 Candy
3 3 Cecil
4 4 Crayon
5 5 Corey
NUM_D NAME_D
1 1 David
2 2 Delta
5 5 Dummy
>
I am guessing that I don't use the correct type on the following statement
(within the subset in the loop):
!is.na( paste("NAME_", each_name, sep = '') )
But then, I might be completely using a wrong approach.
Any idea is definitely appreciated.
Thank you,
Ferry
[[alternative HTML version deleted]]
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Re: [R] Convert bits to numbers in base 10
Yes, such a concise and elegant solution! Thanks a lot! Gang On Thu, Apr 9, 2009 at 5:51 PM, Marc Schwartz wrote: > I suspect that Gang was looking for something along the lines of: > >> sum(2 ^ (which(as.logical(rev(nn))) - 1)) > [1] 74 > > You might also want to look at the digitsBase() function in Martin's sfsmisc > package on CRAN. > > HTH, > > Marc Schwartz > > On Apr 9, 2009, at 4:34 PM, Jorge Ivan Velez wrote: > >> Dear Gang, >> Try this: >> >> nn <- c(1, 0, 0, 1, 0, 1,0) >> paste(nn,sep="",collapse="") >> >> See ?paste for more information. >> >> HTH, >> >> Jorge >> >> >> On Thu, Apr 9, 2009 at 5:23 PM, Gang Chen wrote: >> >>> I have some bits stored like the following variable nn >>> >>> (nn <- c(1, 0, 0, 1, 0, 1,0)) >>> [1] 1 0 0 1 0 1 0 >>> >>> not in the format of >>> >>> 1001010 >>> >>> and I need to convert them to numbers in base 10. What's an easy way to >>> do >>> it? >>> >>> TIA, >>> Gang > > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Convert bits to numbers in base 10
Alternatively (nn <- c(1, 0, 0, 1, 0, 1,0)) [1] 1 0 0 1 0 1 0 sum(2^(0:(length(nn)-1))*nn) but of course it depends if your bits are stored big-endian or little-endian so you might want sum(2^((length(nn)-1):0)*nn) I like Marc's approach better (certainly more elegant). If you have the big vs little endian issue you can just remove the rev from Marc's code below. Michael Conklin -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Marc Schwartz Sent: Thursday, April 09, 2009 4:51 PM To: Jorge Ivan Velez Cc: R-help; Gang Chen Subject: Re: [R] Convert bits to numbers in base 10 I suspect that Gang was looking for something along the lines of: > sum(2 ^ (which(as.logical(rev(nn))) - 1)) [1] 74 You might also want to look at the digitsBase() function in Martin's sfsmisc package on CRAN. HTH, Marc Schwartz On Apr 9, 2009, at 4:34 PM, Jorge Ivan Velez wrote: > Dear Gang, > Try this: > > nn <- c(1, 0, 0, 1, 0, 1,0) > paste(nn,sep="",collapse="") > > See ?paste for more information. > > HTH, > > Jorge > > > On Thu, Apr 9, 2009 at 5:23 PM, Gang Chen wrote: > >> I have some bits stored like the following variable nn >> >> (nn <- c(1, 0, 0, 1, 0, 1,0)) >> [1] 1 0 0 1 0 1 0 >> >> not in the format of >> >> 1001010 >> >> and I need to convert them to numbers in base 10. What's an easy >> way to do >> it? >> >> TIA, >> Gang __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Convert bits to numbers in base 10
I suspect that Gang was looking for something along the lines of: > sum(2 ^ (which(as.logical(rev(nn))) - 1)) [1] 74 You might also want to look at the digitsBase() function in Martin's sfsmisc package on CRAN. HTH, Marc Schwartz On Apr 9, 2009, at 4:34 PM, Jorge Ivan Velez wrote: Dear Gang, Try this: nn <- c(1, 0, 0, 1, 0, 1,0) paste(nn,sep="",collapse="") See ?paste for more information. HTH, Jorge On Thu, Apr 9, 2009 at 5:23 PM, Gang Chen wrote: I have some bits stored like the following variable nn (nn <- c(1, 0, 0, 1, 0, 1,0)) [1] 1 0 0 1 0 1 0 not in the format of 1001010 and I need to convert them to numbers in base 10. What's an easy way to do it? TIA, Gang __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Convert bits to numbers in base 10
Dear Gang, Try this: nn <- c(1, 0, 0, 1, 0, 1,0) paste(nn,sep="",collapse="") See ?paste for more information. HTH, Jorge On Thu, Apr 9, 2009 at 5:23 PM, Gang Chen wrote: > I have some bits stored like the following variable nn > > (nn <- c(1, 0, 0, 1, 0, 1,0)) > [1] 1 0 0 1 0 1 0 > > not in the format of > > 1001010 > > and I need to convert them to numbers in base 10. What's an easy way to do > it? > > TIA, > Gang > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Convert bits to numbers in base 10
I have some bits stored like the following variable nn (nn <- c(1, 0, 0, 1, 0, 1,0)) [1] 1 0 0 1 0 1 0 not in the format of 1001010 and I need to convert them to numbers in base 10. What's an easy way to do it? TIA, Gang __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Random Cluster Generation Question
Hello, I am fairly new to R, but I am not new to programming at all. I want to generate random clusters in a 1,000x1,000 box such that I end up with a total of about 2,000 points. Once done, I need to export the X,Y coordinates of the points. I have looked around, and it seems that the spatstat package has what I need. The rMatClust() function can generate random clusters, but I have run into some problems. First, I can't seem to specify that I want x number of points. So, right now it appears that if I want around 2,000 total points that I must play around with the parameters of the function (e.g., mean number of points per cluster, cluster radius, etc.) until I end up with roughly 2,000 points. More problematic, however, is that specifying a 1,000x1,000 box is too much to handle. I have been running the following function for over 24 hours straight on a decent computer and it has not stopped yet: clust <- rMatClust(1, 50, 5, win=owin(c(0,1000),c(0,1000))) Clearly, I need to rethink my strategy. Could I generate the points in a 10x10 box with a radius of .5 and then multiply out the resulting point coordinates by 100? Is there another package that might meet my needs better than spatstat for easy cluster generation? Any suggestions are appreciated. All the best, Jason Simms -- Jason L. Simms, M.A. USF Graduate Multidisciplinary Scholar Co-President, Graduate Assistants United Ph.D. / M.P.H. Student Departments of Anthropology and Environmental and Occupational Health University of South Florida __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in saveLog(currentLogFileName
On Apr 9, 2009, at 2:17 PM, Prew, Paul wrote: David, thank you for your helpful reply. a) The sessionInfo goof is actually kind of enlightening. I'm assuming that the purpose of adding the "()" symbols is to tell R that sessionInfo is a function to be invoked, and leaving "()" empty says to use default arguments? Yes. Exactly. b) In the R GUI, I end my session by using the menu File > Exit. A dialog appears, asking, "Save workspace image?", and I choose Yes. In fact, I just did it and got a message, never seen this one before "Console not found. Error in structure(.External"dotTclObjv:,objv, PACKAGE - "tcltk"), class = "tclObj"):[tcl]invalid command name ". 6.1". I am not an expert in the Windows GUI, but as a former user of it, I would wonder if my installation of tcltk had gotten corrupted and would try to reinstall. Caveat: That advice could be worth what you paid for it. Closed that message, another similar message was behind it, but now the command name was "17.1" c) yes, agreed --- John Fox has been helpful to me a couple of times. I like the R Commander (it automatically adds those pesky details like () that elude me), but I can't go the CRAN to get packages from it, so I end up back at the GUI to install a package. John has told me that moving back and forth between the GUI and Commander is not how Commander was intended to be used. Perhaps this practice has led to some of the present confusions. Let's say I save a script or history or similar file that I would like to recall at a later time, If I save the file using RCommander, should I only open the file using R Commander? Ditto for R GUI? Regardless of which platform I'm saving the files with, they seem to have some of the same extensions, ".R", ".r", ".Rdata", etc. I doubt that would be necessary, assuming the scripts do not have function calls that depend on R Commander being around. Files with .r extensions are just text files by another name. I could not find a saveLog function with R-search restricted to functions but did find it as an argument to RCmdr. IIRC, RCmdr uses Tck/Tl extensively. -- David Thanks, Paul Paul Prew | Statistician 651-795-5942 | fax 651-204-7504 Ecolab Research Center | Mail Stop ESC-F4412-A 655 Lone Oak Drive | Eagan, MN 55121-1560 -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: Thursday, April 09, 2009 12:17 PM To: Prew, Paul Cc: r-help@r-project.org Subject: Re: [R] Error in saveLog(currentLogFileName This is just two suggestions and a guess. a) When you desire the information from sessionInfo ,you need to type : sessionInfo() # not sessionInfo ... results come from function calls and all you got was the sessionInfo code produced by the implicit print function to which you gave the argument sessionInfo. b) Tell us exactly the methods you used to save "my script", "my workspace", "etc"? c) As a guess, you had the Zelig package loaded under R-Commander yesterday but not today. The right person to ask this question of might be one of those package maintainers. (John Fox is very good about supporting R-Commander.) David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] numbers not behaving as expected
On Thu, 9 Apr 2009 steve_fried...@nps.gov wrote: My apologies for sending a binary file. I was following advice from someone (from this list) who insisted I send data via dput. I guess that is frown upon. dput() creates a text file, not a binary file. The problem is probably that your email software did not identify the file as text. -thomas Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] running a .r script and saving the output to a file
On Apr 9, 2009, at 2:21 PM, Gagan Pabla wrote:
I first I saved the following commands in a whatever.r file.
data<-read.csv(file="whatever.csv", head=TRUE, sep=",")
#this is where you put the first sink:
sink("comm.docx") # but it is not going to be in .docx format, but
in text format.
summary(data$SQFT)
hist(data$STAMP)
hist(data$STAMP, col='blue')
hist(data$SHIP, col='blue')
# to get back output to the console, you close the "sunken" output file.
sink()
None of this will get you histograms, however. Sink does not deal with
those. For that you need Sweave or odfWeave.
--
David Winsemius
then I clicked File Menu-> source and chose whatever.r, it runs the
commands and produces the histograms and stuff.
then I did
sink("comm.docx")
sink()
It creates an empty file "comm.docx". Now my problem is that I want
to run
the commands in whatever.r file( this part is working ) and then
save the
output(has graphs hists etc) in a file.
How do I do that ? Your help will be greatly appreciated!!
Gagan
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and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] numbers not behaving as expected
On Thu, Apr 9, 2009 at 2:05 PM, wrote: > WetMonths <- Cell.ave[Cell.ave$month >= "5" and Cell.ave$month <= "11",] > Error: unexpected symbol in "WetMonths <- Cell.ave[Cell.ave$month >= "5" > and" Cell.ave$month <= "11",] a) you are comparing with the *string* "5", not the *number* 5 (as I mentioned before) b) you are now writing "and" rather than "&" The following works fine for me: WetMonths <- Cell.ave[Cell.ave$month >= 5 & Cell.ave$month <= 11,] Better? -s __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] running a .r script and saving the output to a file
I first I saved the following commands in a whatever.r file.
data<-read.csv(file="whatever.csv", head=TRUE, sep=",")
summary(data$SQFT)
hist(data$STAMP)
hist(data$STAMP, col='blue')
hist(data$SHIP, col='blue')
then I clicked File Menu-> source and chose whatever.r, it runs the
commands and produces the histograms and stuff.
then I did
sink("comm.docx")
sink()
It creates an empty file "comm.docx". Now my problem is that I want to run
the commands in whatever.r file( this part is working ) and then save the
output(has graphs hists etc) in a file.
How do I do that ? Your help will be greatly appreciated!!
Gagan
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in saveLog(currentLogFileName
David, thank you for your helpful reply.
a) The sessionInfo goof is actually kind of enlightening. I'm assuming that
the purpose of adding the "()" symbols is to tell R that sessionInfo is a
function to be invoked, and leaving "()" empty says to use default arguments?
b) In the R GUI, I end my session by using the menu File > Exit. A dialog
appears, asking, "Save workspace image?", and I choose Yes.
In fact, I just did it and got a message, never seen this one before
"Console not found. Error in structure(.External"dotTclObjv:,objv, PACKAGE
- "tcltk"), class = "tclObj"):[tcl]invalid command name ".6.1".
Closed that message, another similar message was behind it, but now the command
name was "17.1"
c) yes, agreed --- John Fox has been helpful to me a couple of times. I like
the R Commander (it automatically adds those pesky details like () that elude
me), but I can't go the CRAN to get packages from it, so I end up back at the
GUI to install a package. John has told me that moving back and forth between
the GUI and Commander is not how Commander was intended to be used. Perhaps
this practice has led to some of the present confusions.
Let's say I save a script or history or similar file that I would like to
recall at a later time,
If I save the file using RCommander, should I only open the file using R
Commander? Ditto for R GUI? Regardless of which platform I'm saving the files
with, they seem to have some of the same extensions, ".R", ".r", ".Rdata", etc.
Thanks,
Paul
Paul Prew | Statistician
651-795-5942 | fax 651-204-7504
Ecolab Research Center | Mail Stop ESC-F4412-A
655 Lone Oak Drive | Eagan, MN 55121-1560
-Original Message-
From: David Winsemius [mailto:dwinsem...@comcast.net]
Sent: Thursday, April 09, 2009 12:17 PM
To: Prew, Paul
Cc: r-help@r-project.org
Subject: Re: [R] Error in saveLog(currentLogFileName
This is just two suggestions and a guess.
a) When you desire the information from sessionInfo ,you need to type :
sessionInfo() # not sessionInfo
... results come from function calls and all you got was the
sessionInfo code produced by the implicit print function to which you
gave the argument sessionInfo.
b) Tell us exactly the methods you used to save "my script", "my
workspace", "etc"?
c) As a guess, you had the Zelig package loaded under R-Commander
yesterday but not today. The right person to ask this question of
might be one of those package maintainers. (John Fox is very good
about supporting R-Commander.)
On Apr 9, 2009, at 12:18 PM, Prew, Paul wrote:
> Hello, very basic question from a user who is baffled by the
> workings of computers in general
>
> When logging off R, a dialog box asked if I wanted to save my log,
> I chose yes. Then I noticed that the following message appeared in
> the Command Window
>
> Error in saveLog(currentLogFileName) :
> unused argument(s) ("C:/Documents and Settings/prewpj/My Documents/
> Data/Analyses/Healthcare/Hand Care Panel Test_KMolinaro/
> soapfeel_ZeligMixedLogit.R")
>
> My attempts to find the parameters that saveLog requires haven’t
> been successful, so I’m wondering if someone on this list could
> advise me. Yesterday, I saved several files: my script, my
> workspace, etc. to the above filepath, but today they are not
> there. A Windows search of my C:drive using the names of the files
> came up empty. They didn’t show up when I listed the objects from
> the default R directory, either --- ls() command didn’t list
> yesterday’s files.
>
> Further, the sessionInfo output is like nothing I’ve seen before.
> Typically, it starts out with
> “R version 2.8.1 (2008-12-22)
> i386-pc-mingw32
> …
>
> Thank you, Paul
>
>> ?saveLog
> No documentation for 'saveLog' in specified packages and libraries:
> you could try '??saveLog'
>> ??saveLog
> No help files found with alias or concept or title matching 'saveLog'
> using fuzzy matching.
>> help.search(saveLog)
> Error in help.search(saveLog) : object "saveLog" not found
>> help.search("saveLog")
> No help files found with alias or concept or title matching
> 'saveLog' using fuzzy matching.
>
>> sessionInfo
> function (package = NULL)
> {
>z <- list()
>z$R.version <- R.Version()
>z$locale <- Sys.getlocale()
>if (is.null(package)) {
>package <- grep("^package:", search(), value = TRUE)
>keep <- sapply(package, function(x) x == "package:base" ||
>!is.null(attr(as.environment(x), "path")))
>package <- sub("^package:", "", package[keep])
>}
>pkgDesc <- lapply(package, packageDescription)
>if (length(package) == 0)
>stop("no valid packages were specified")
>basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) &&
>x$Priority == "base")
>z$basePkgs <- package[basePkgs]
>if (any(!basePkgs)) {
>z$otherPkgs <- pkgDesc[!basePkgs]
>names(z$otherPkgs) <- package[!basePkgs]
>}
>loadedOnly
Re: [R] CFA in R/sem package
Ivan, I recently put together the sem.additions package over at R forge in part for just such a multiple model problem. THere are a variety of methods that make it easy to add/delete links that could be automated with a for loop and something from the combn package, I think. http://r-forge.r-project.org/projects/sem-additions/ -Jarrett On Apr 9, 2009, at 6:39 AM, Iuri Gavronski wrote: Hi, I am not sure if R-help is the right forum for my question. If not, please let me know. I have to do some discriminant validity tests with some constructs. I am using the method of doing a CFA constraining the correlation of a pair of the constructs to 1 and comparing the chi-square of this constrained model to the unconstrained model. If the chi-square difference is not significant, then I cannot reject the null hypothesis that the two constructs are equal. Well, if you are going to test, say, 4 constructs (A, B, C, and D), you will have to have 2*C(4,2) = 12 models to test, 5 constructs, 20 models, and so forth. A tedious and error prone process... So far, I have been using AMOS for that shake, given that 1) my university has the license, 2) my other colleagues use it, and 3) I know it ;) I would like to know if any of you use R, namely the sem package, for that application and if you can share your thoughts/experiences on using it. I don't thing I would have problems "porting" my models to R/sem, but I would like to know if there is an optimized process of doing that tests, without manually coding all the dozens of models. Best, Iuri. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] numbers not behaving as expected
My apologies for sending a binary file. I was following advice from someone (from this list) who insisted I send data via dput. I guess that is frown upon. Anyway. here is a Cellave.txt file. Stavros, here is the output following your suggestion. WetMonths <- Cell.ave[Cell.ave$month >= "5" and Cell.ave$month <= "11",] Error: unexpected symbol in "WetMonths <- Cell.ave[Cell.ave$month >= "5" and" Cell.ave$month <= "11",] I think the problem lies in leading characters for months with values 1, 10, 11, and 12. These get very confused. (See attached file: Cellave.txt) Steve Friedman Ph. D. Spatial Statistical Analyst Everglades and Dry Tortugas National Park 950 N Krome Ave (3rd Floor) Homestead, Florida 33034 steve_fried...@nps.gov Office (305) 224 - 4282 Fax (305) 224 - 4147 Stavros Macrakis To Sent by: steve_fried...@nps.gov macra...@gmail.co cc m r-help@r-project.org Subject Re: [R] numbers not behaving as 04/09/2009 01:51 expected PM AST On Thu, Apr 9, 2009 at 1:39 PM, wrote: > I have a data.frame Cell.ave (attached and created via dput(Cell.ave, > "Cell.ave") I'm afraid your attachment didn't make it into the r-help mail. Mailing list policy forbids binary attachments other than PS and PDF, but should be forwarding plaintext attachments, I think. Perhaps it requires that the extension be ".txt" or something...? Anyway... the problem seems diagnosable just from your code: > WetSeasonMonths <- Cell.ave[Cell.ave$month >= "5" & Cell.ave$month <= > "11",] There is no *string* which is >= "5" and <= "11". Why aren't you comparing numerically? -s __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] request: maximum depth reached problem
Muhammad Azam wrote:
Dear R community
Hope all of you are fine. I have a question regarding the an error message. Actually, I
am trying to generate classification trees using "tree" package. It works well
but for some datasets e.g., wine, yeast, boston housing etc. it gives an error message.
Error in tree(V14 ~ ., data = training.data, method = c("recursive.partitioning"), :
maximum depth reached
The structure of getting output is given below:
iris.tr = tree(Species ~., data=training.data, method=c("recursive.partitioning"), split
= c("gini"), control=tree.control(nobs = 150, minsize = 5, mincut = 2))
Any suggestion will be appreciated to handle the above problem. Thanks and
Please do not cross-post and only post to the correct mailing list.
I'd suggest to use package rpart (as the tree maintainer suggests) or
other tree generating packages.
Uwe Ligges
best regards
Muhammad Azam
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Re: [R] R interpreter not recognized
Dear Maria, this is quite probably my faul, in some way. The UCS software has been abandoned a bit recently, as I'm planning to rewrite it into a pure R package. On the other hand, I still use the software occasionally, so it should work with recent R versions. I am trying to install a program based on R, but I am receiving the following error message: r...@darkstar:/home/maria/UCS# perl System/Install.perl Error: Can't run the R interpreter (/usr/local/bin/R). Please make sure that R is installed and specify the fully qualified filename of the R interpreter with -R if necessary (see "doc/ install.txt"). This either means that your R installation is damaged and Install.perl can't run the command "R --version"; or that it has problems parsing the output of this command, so it thinks there's something wrong with R. What do you get if you type /usr/local/bin/R --version in a shell window? Which version of UCS are you trying to install? The message printed by "R --version" was changed some time ago (in early 2006, or so), so the Install.perl script stopped working at that time. You need to download UCS-0.5-prerelease, which works for me (version 0.4 will not). If you still can't get it to work, please contact me off-list so we can figure out the problem. Cheers, Stefan [ stefan.ev...@uos.de | http://purl.org/stefan.evert ] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] numbers not behaving as expected
steve_fried...@nps.gov wrote: If someone can explain this odd behavior I'd appreciate it. I have a data.frame Cell.ave (attached and created via dput(Cell.ave, "Cell.ave") which contains three columns of parameters year, month and AveRain. I need to subset the data.frame by months such that DrySeaonMonths are 1,2,3,4, 11, and 12 or Jan - April, November and December and WetSeasonMonths are 5:10 or May-October. I'm using the following code: DrySeasonMonths <- Cell.ave[Cell.ave$month < "5" & Cell.ave$month != "10",] table(DrySeasonMonth$month) 12 34 11 12 36 36 36 36 36 36 # this is expected since the data is for 36 years WetSeasonMonths <- Cell.ave[Cell.ave$month >= "5" & Cell.ave$month <= "11",] WetSeasonMonths [1] yearmonth AveRain <0 rows> (or 0-length row.names) There is an obvious problem with how the values for month are being stored. I've tried converting them to factors, which complines that the subsetting routine is not appropriate for factors. And I've tried as.numeric which also does not return an working dataframe. all suggestions to solve this are appreciated. Thanks Steve (See attached file: Cell.ave) In fact no longer attached (removed by mailing list), but it is sufficient if you just tell us the result of str(Cell.ave$month) instead. Uwe Ligges sessionInfo() R version 2.8.1 (2008-12-22) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base Steve Friedman Ph. D. Spatial Statistical Analyst Everglades and Dry Tortugas National Park 950 N Krome Ave (3rd Floor) Homestead, Florida 33034 steve_fried...@nps.gov Office (305) 224 - 4282 Fax (305) 224 - 4147 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] numbers not behaving as expected
On Thu, Apr 9, 2009 at 1:39 PM, wrote: > I have a data.frame Cell.ave (attached and created via dput(Cell.ave, > "Cell.ave") I'm afraid your attachment didn't make it into the r-help mail. Mailing list policy forbids binary attachments other than PS and PDF, but should be forwarding plaintext attachments, I think. Perhaps it requires that the extension be ".txt" or something...? Anyway... the problem seems diagnosable just from your code: > WetSeasonMonths <- Cell.ave[Cell.ave$month >= "5" & Cell.ave$month <= > "11",] There is no *string* which is >= "5" and <= "11". Why aren't you comparing numerically? -s __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] numbers not behaving as expected
If someone can explain this odd behavior I'd appreciate it. I have a data.frame Cell.ave (attached and created via dput(Cell.ave, "Cell.ave") which contains three columns of parameters year, month and AveRain. I need to subset the data.frame by months such that DrySeaonMonths are 1,2,3,4, 11, and 12 or Jan - April, November and December and WetSeasonMonths are 5:10 or May-October. I'm using the following code: > DrySeasonMonths <- Cell.ave[Cell.ave$month < "5" & Cell.ave$month != "10",] > table(DrySeasonMonth$month) 12 34 11 12 36 36 36 36 36 36 # this is expected since the data is for 36 years WetSeasonMonths <- Cell.ave[Cell.ave$month >= "5" & Cell.ave$month <= "11",] WetSeasonMonths [1] yearmonth AveRain <0 rows> (or 0-length row.names) > There is an obvious problem with how the values for month are being stored. I've tried converting them to factors, which complines that the subsetting routine is not appropriate for factors. And I've tried as.numeric which also does not return an working dataframe. all suggestions to solve this are appreciated. Thanks Steve (See attached file: Cell.ave) sessionInfo() R version 2.8.1 (2008-12-22) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base Steve Friedman Ph. D. Spatial Statistical Analyst Everglades and Dry Tortugas National Park 950 N Krome Ave (3rd Floor) Homestead, Florida 33034 steve_fried...@nps.gov Office (305) 224 - 4282 Fax (305) 224 - 4147__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] running a .r script and saving the output to a file
If you just entered sink(), it would turn *off* sink-ing. You need to tell R where to write the output that would otherwise go to the console. (Or if you did something like that then you need to tell us exactly what you did try.) ?sink # e.g. sink(file="... /test.txt") with correct path substituted for ... ?source And perhaps read up on submitting batch jobs from the Windows command line. See Appendix B of: http://cran.r-project.org/doc/manuals/R-intro.pdf -- David Winsemius On Apr 9, 2009, at 12:46 PM, Gagan Pabla wrote: Hello, I want to run the following commands as a script(.r or .bat) and save the output in an external file through Windows OS. data<-read.csv(file="wgatever.csv", head=TRUE, sep=",") summary(data$SQFT) hist(data$STAMP) hist(data$STAMP, col='blue') hist(data$SHIP, col='blue') How could I do that? I have a great problem using the sink() function because it produces empty file. Please help! Gagan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in saveLog(currentLogFileName
This is just two suggestions and a guess.
a) When you desire the information from sessionInfo ,you need to type :
sessionInfo() # not sessionInfo
... results come from function calls and all you got was the
sessionInfo code produced by the implicit print function to which you
gave the argument sessionInfo.
b) Tell us exactly the methods you used to save "my script", "my
workspace", "etc"?
c) As a guess, you had the Zelig package loaded under R-Commander
yesterday but not today. The right person to ask this question of
might be one of those package maintainers. (John Fox is very good
about supporting R-Commander.)
On Apr 9, 2009, at 12:18 PM, Prew, Paul wrote:
Hello, very basic question from a user who is baffled by the
workings of computers in general
When logging off R, a dialog box asked if I wanted to save my log,
I chose yes. Then I noticed that the following message appeared in
the Command Window
Error in saveLog(currentLogFileName) :
unused argument(s) ("C:/Documents and Settings/prewpj/My Documents/
Data/Analyses/Healthcare/Hand Care Panel Test_KMolinaro/
soapfeel_ZeligMixedLogit.R")
My attempts to find the parameters that saveLog requires haven’t
been successful, so I’m wondering if someone on this list could
advise me. Yesterday, I saved several files: my script, my
workspace, etc. to the above filepath, but today they are not
there. A Windows search of my C:drive using the names of the files
came up empty. They didn’t show up when I listed the objects from
the default R directory, either --- ls() command didn’t list
yesterday’s files.
Further, the sessionInfo output is like nothing I’ve seen before.
Typically, it starts out with
“R version 2.8.1 (2008-12-22)
i386-pc-mingw32
…
Thank you, Paul
?saveLog
No documentation for 'saveLog' in specified packages and libraries:
you could try '??saveLog'
??saveLog
No help files found with alias or concept or title matching 'saveLog'
using fuzzy matching.
help.search(saveLog)
Error in help.search(saveLog) : object "saveLog" not found
help.search("saveLog")
No help files found with alias or concept or title matching
'saveLog' using fuzzy matching.
sessionInfo
function (package = NULL)
{
z <- list()
z$R.version <- R.Version()
z$locale <- Sys.getlocale()
if (is.null(package)) {
package <- grep("^package:", search(), value = TRUE)
keep <- sapply(package, function(x) x == "package:base" ||
!is.null(attr(as.environment(x), "path")))
package <- sub("^package:", "", package[keep])
}
pkgDesc <- lapply(package, packageDescription)
if (length(package) == 0)
stop("no valid packages were specified")
basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) &&
x$Priority == "base")
z$basePkgs <- package[basePkgs]
if (any(!basePkgs)) {
z$otherPkgs <- pkgDesc[!basePkgs]
names(z$otherPkgs) <- package[!basePkgs]
}
loadedOnly <- loadedNamespaces()
loadedOnly <- loadedOnly[!(loadedOnly %in% package)]
if (length(loadedOnly)) {
names(loadedOnly) <- loadedOnly
pkgDesc <- c(pkgDesc, lapply(loadedOnly, packageDescription))
z$loadedOnly <- pkgDesc[loadedOnly]
}
class(z) <- "sessionInfo"
z
}
Paul Prew ▪ Statistician
651-795-5942 ▪ fax 651-204-7504
Ecolab Research Center ▪ Mail Stop ESC-F4412-A
655 Lone Oak Drive ▪ Eagan, MN 55121-1560
CONFIDENTIALITY NOTICE:
This e-mail communication and any attachments may contain
proprietary and privileged information for the use of the designated
recipients named above.
Any unauthorized review, use, disclosure or distribution is
prohibited.
If you are not the intended recipient, please contact the sender by
reply e-mail and destroy all copies of the original message.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] running a .r script and saving the output to a file
Hello, I want to run the following commands as a script(.r or .bat) and save the output in an external file through Windows OS. data<-read.csv(file="wgatever.csv", head=TRUE, sep=",") summary(data$SQFT) hist(data$STAMP) hist(data$STAMP, col='blue') hist(data$SHIP, col='blue') How could I do that? I have a great problem using the sink() function because it produces empty file. Please help! Gagan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error in saveLog(currentLogFileName
Hello, very basic question from a user who is baffled by the workings of
computers in general
When logging off R, a dialog box asked if I wanted to save my log, I chose
yes. Then I noticed that the following message appeared in the Command Window
Error in saveLog(currentLogFileName) :
unused argument(s) ("C:/Documents and Settings/prewpj/My
Documents/Data/Analyses/Healthcare/Hand Care Panel
Test_KMolinaro/soapfeel_ZeligMixedLogit.R")
My attempts to find the parameters that saveLog requires havenât been
successful, so Iâm wondering if someone on this list could advise me.
Yesterday, I saved several files: my script, my workspace, etc. to the above
filepath, but today they are not there. A Windows search of my C:drive using
the names of the files came up empty. They didnât show up when I listed the
objects from the default R directory, either --- ls() command didnât list
yesterdayâs files.
Further, the sessionInfo output is like nothing Iâve seen before. Typically,
it starts out with
âR version 2.8.1 (2008-12-22)
i386-pc-mingw32
â¦
Thank you, Paul
> ?saveLog
No documentation for 'saveLog' in specified packages and libraries:
you could try '??saveLog'
> ??saveLog
No help files found with alias or concept or title matching 'saveLog'
using fuzzy matching.
> help.search(saveLog)
Error in help.search(saveLog) : object "saveLog" not found
> help.search("saveLog")
No help files found with alias or concept or title matching 'saveLog' using
fuzzy matching.
> sessionInfo
function (package = NULL)
{
z <- list()
z$R.version <- R.Version()
z$locale <- Sys.getlocale()
if (is.null(package)) {
package <- grep("^package:", search(), value = TRUE)
keep <- sapply(package, function(x) x == "package:base" ||
!is.null(attr(as.environment(x), "path")))
package <- sub("^package:", "", package[keep])
}
pkgDesc <- lapply(package, packageDescription)
if (length(package) == 0)
stop("no valid packages were specified")
basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) &&
x$Priority == "base")
z$basePkgs <- package[basePkgs]
if (any(!basePkgs)) {
z$otherPkgs <- pkgDesc[!basePkgs]
names(z$otherPkgs) <- package[!basePkgs]
}
loadedOnly <- loadedNamespaces()
loadedOnly <- loadedOnly[!(loadedOnly %in% package)]
if (length(loadedOnly)) {
names(loadedOnly) <- loadedOnly
pkgDesc <- c(pkgDesc, lapply(loadedOnly, packageDescription))
z$loadedOnly <- pkgDesc[loadedOnly]
}
class(z) <- "sessionInfo"
z
}
Paul Prew ⪠Statistician
651-795-5942 ⪠fax 651-204-7504
Ecolab Research Center ⪠Mail Stop ESC-F4412-A
655 Lone Oak Drive ⪠Eagan, MN 55121-1560
CONFIDENTIALITY NOTICE:
This e-mail communication and any attachments may contain proprietary and
privileged information for the use of the designated recipients named above.
Any unauthorized review, use, disclosure or distribution is prohibited.
If you are not the intended recipient, please contact the sender by reply
e-mail and destroy all copies of the original message.
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] xmlEventParse returning trimmed content?
Hi Johannes
I would "guess" that the trimming of the text occurs because
you do not specify trim = FALSE in the call to xmlEventParse().
If you specify this, you might well get the results you expect.
If not, can you post the actual file you are reading so we can
reproduce your results.
D.
Johannes Graumann wrote:
Hello,
I wrote the function below and have the problem, that the "text" bit returns
only a trimmed version (686 chars as far as I can see) of the content under
the "fetchPeaks" condition.
Any hunches why that might be?
Thanks for pointer, Joh
xmlEventParse(fileName,
list(
startElement=function(name, attrs){
if(name == "scan"){
if(.GlobalEnv$ms2Scan == TRUE & .GlobalEnv$scanDone == TRUE){
cat(.GlobalEnv$scanNum,"\n")
MakeSpektrumEntry()
}
.GlobalEnv$scanDone <- FALSE
.GlobalEnv$fetchPrecMz <- FALSE
.GlobalEnv$fetchPeaks <- FALSE
.GlobalEnv$ms2Scan <- FALSE
if(attrs[["msLevel"]] == "2"){
.GlobalEnv$ms2Scan <- TRUE
.GlobalEnv$scanNum <- as.integer(attrs[["num"]])
}
} else if(name == "precursorMz" & .GlobalEnv$ms2Scan == TRUE){
.GlobalEnv$fetchPrecMz <- TRUE
} else if(name == "peaks" & .GlobalEnv$ms2Scan == TRUE){
.GlobalEnv$fetchPeaks <- TRUE
}
},
text=function(text){
if(.GlobalEnv$fetchPrecMz == TRUE){
.GlobalEnv$precursorMz <- as.numeric(text)
.GlobalEnv$fetchPrecMz <- FALSE
}
if(.GlobalEnv$fetchPeaks == TRUE){
.GlobalEnv$peaks <- text
.GlobalEnv$fetchPeaks <- FALSE
.GlobalEnv$scanDone <- TRUE
}
}
)
)
sessionInfo()
R version 2.9.0 beta (2009-04-03 r48277)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=en_US.UTF-8;LC_ADDRESS=en_US.UTF-8;LC_TELEPHONE=en_US.UTF-8;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=en_US.UTF-8
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] caMassClass_1.6 MASS_7.2-46 digest_0.3.1caTools_1.9
[5] bitops_1.0-4.1 rpart_3.1-43nnet_7.2-46 e1071_1.5-19
[9] class_7.2-46PROcess_1.19.1 Icens_1.15.2survival_2.35-4
[13] RCurl_0.94-1XML_2.3-0 rkward_0.5.0
loaded via a namespace (and not attached):
[1] tools_2.9.0
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] .Call()
HI Wudd Wudd -- not really answering your question, but it might pay
to refactor some of your R code first. For instance
for(j in 2:nrow(ranklist)){
phit <- sum(rep(1/Ns, sum(ranklist[1:j,2]==1)))
pmiss <- sum(rep(1/(N-Ns), sum(ranklist[1:j,2]==0)))
if((phit-pmiss)>score[i]) score[i] <- phit - pmiss
}
might be replaced (you'd better check, I'm not sure I have your logic
correct) by
phit <- (cumsum(ranklist[,2]==1) / Ns)[-1]
pmiss <- (cumsum(ranklist[,2]==0) / (N - Ns))[-1]
pmax <- max(phit - pmiss)
if (pmax > score[i]) score[i] <- pmax
These should be much faster than your loop. Your earlier 'apply' might
also be replaced by rowMeans, etc. I think, and once simplified to
that level further higher-level reorganizations might be possible.
Hope that helps
Martin
wudd wudd writes:
> Hi guys,
> I want to transfer the following code from R into .Call compatible form. How
> can i do that?
>
> Thanks!!!
>
> INT sim;
> for(i in 1:sim){
> if(i>2) genemat <- genemat[,sample(1:ncol(genemat))]
> ranklist[,1] <- apply(genemat, 1, function(x){
> (mean(x[cols]) -
> mean(x[-cols]))/sd(x)})
> ranklist <- ranklist[order(ranklist[,1]),]
> if(ranklist[1,2]==1) score[i] <- 1/Ns
> if(ranklist[1,2]==0) score[i] <- -(1/(N-Ns))
> for(j in 2:nrow(ranklist)){
> phit <- sum(rep(1/Ns, sum(ranklist[1:j,2]==1)))
> pmiss <- sum(rep(1/(N-Ns), sum(ranklist[1:j,2]==0)))
> if((phit-pmiss)>score[i]) score[i] <- phit - pmiss
> }
> }
>
> I tried a little bit, but not enough knowledge in C.
> #include
> #include
> #include
> #include
> SEXP ESscore(SEXP Rgeneset, SEXP Rgenemat, SEXP Rranklist, SEXP sim)
> {
> int nc = ncols(Rgenemat);
> double *geneset = NUMERIC_DATA(Rgeneset);
> double *genemat = NUMERIC_DATA(Rgenemat);
>
> SEXP Rscore;
> PROTECT(Rscore=NEW_NUMERIC(sim));
> double *score = NUMERIC_DATA(Rscore);
>
> for(i=1; i<=sim; i++){
> if(i>2) {genemat <- genemat[,sample(1:nc)];}
> for(k=1; k
> }
>
> }
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Cross-platforms solution to export R graphs
Thank you Philippe. That is very helpful. Philippe Grosjean wrote: > > Hello Rusers, > > I have worked on a R Wiki page for solutions in exporting R graphs, > especially, the often-asked questions: > - How can I export R graphs in vectorized format (EMF) for inclusion in > MS Word or OpenOffice outside of Windows? > - What is the best solution(s) for post-editing/annotating R graphs. > > The page is at: > http://wiki.r-project.org/rwiki/doku.php?id=tips:graphics-misc:export. > > I would be happy to receive your comments and suggestions to improve > this document. > All the best, > > PhG > -- > ..<°}))>< > ) ) ) ) ) > ( ( ( ( (Prof. Philippe Grosjean > ) ) ) ) ) > ( ( ( ( (Numerical Ecology of Aquatic Systems > ) ) ) ) ) Mons-Hainaut University, Belgium > ( ( ( ( ( > .. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- View this message in context: http://www.nabble.com/Cross-platforms-solution-to-export-R-graphs-tp22970668p22973759.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] re siduals
Hi All, I am trying to fit a linear regression between the tool speed and the tool type ( type A, Type B , Type C) where the response is the tool speed and the regressor is the tool type. I introduced two dummy variables X1 and X2 as follows X1 X2 Tool A 0 0 Tool B 0 1 Tool C 10 Model<-Lm (y~X1+X2) My question is on the residual plot, it looks like three cluster because I have three tool types. Is such a plot is ok with the constant variance assumption and normality (below is a link for the plot)?I have never seen such a plot of the residuals http://www.nabble.com/file/p22972254/question.JPG question.JPG -- View this message in context: http://www.nabble.com/residuals-tp22972254p22972254.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Genstat into R - Randomisation test
At 04:43 AM 4/9/2009, Tom Backer Johnsen wrote: Peter Dalgaard wrote: > Mike Lawrence wrote: >> Looks like that code implements a non-exhaustive variant of the >> randomization test, sometimes called a permutation test. > > Isn't it the other way around? (Permutation tests can be exhaustive by looking at all permutations, if a randomization test did that, then it wouldn't be random.) Eugene Edgington wrote an early book (1980) on this subject called "Randomization tests", published by Dekker. As far as I remember, he differentiates between "Systematic permutation" tests where one looks at all possible permutations. This is of course prohibitive for anything beyond trivially small samples. For larger samples he uses what he calls "Random permutations", where a random sample of the possible permutations is used. Tom Peter Dalgaard wrote: Mike Lawrence wrote: Looks like that code implements a non-exhaustive variant of the randomization test, sometimes called a permutation test. Isn't it the other way around? (Permutation tests can be exhaustive by looking at all permutations, if a randomization test did that, then it wouldn't be random.) Edginton and Onghena make a similar distinction in their book, but I think such a distinction is without merit. Do we distinguish between "exact" definite integrals and "approximate" ones obtained by numerical integration, of which Monte Carlo sampling is just one class of algorithms? Don't we just say: "The integral was evaluated numerically by the [whatever] method to an accuracy of [whatever], and the value was found to be [whatever]." Ditto for optimization problems. A randomization test has one correct answer based upon theory. We are simply trying to calculate that answer's value when it is difficult to do so. Any approximate method that is used must be performed such that the error of approximation is trivial with respect to the contemplated use. Doing Monte Carlo sampling to find an approximate answer to a randomization test, or to an optimization problem, or to a bootstrap distribution should be carried out with enough realizations to make sure the residual error is trivial. As Monte Carlo sampling is a "random" sampling-based approximate method. The name does create confusion in terminology for "randomization" tests for bootstrapping. Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: r...@lcfltd.com Least Cost Formulations, Ltd.URL: http://lcfltd.com/ 824 Timberlake Drive Tel: 757-467-0954 Virginia Beach, VA 23464-3239Fax: 757-467-2947 "Vere scire est per causas scire" __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Convert data frame containing time stamps to time series
What is zoo? I cannot find anything about zoo int he documentation.
I did try as.ts() see below.
Thank you,
Alex van der Spek
> have you tried using zoo and then using the function as.ts()
>
> On Wed, Apr 8, 2009 at 11:56 AM, wrote:
>> Converting dates is getting stranger still. I am coercing a data frame
>> into a ts as follows:
>>
>>
>> tst1<-as.POSIXct("1/21/09 5:01",format="%m/%d/%y %H:%M")
>> tst2<-as.POSIXct("1/28/09 3:40",format="%m/%d/%y %H:%M")
>> tsdat<-as.ts(dat,start=tst1,end=tst2,frequency=1)
>>
>> This generates a ts object. But strangely enough the first column of
>> that
>> matrix starts at the numeric value of 841 counts up to 1139 and then
>> starts at 1 again, only to count up from there. The restart at 1 occurs
>> at
>> the first day "1/21/09" at 10:00:00.
>>
>> What is so special about that time? This phenomenon happens several
>> times
>> in the long file. But the restart count is always a different number.
>> This creates a ramp with some bumps.
>>
>> Can anybody explain this?
>> Thanks in advance,
>> Alex van der Spek
>>
>>
>>> I read records using scan:
>>>
>>> dat<-data.frame(scan(file="KDA.csv",what=list(t="%m/%d/%y
>>> %H:%M",f=0,p=0,d=0,o=0,s=0,a=0,l=0,c=0),skip=2,sep=",",nmax=np,flush=TRUE,na.strings=c("I/OTimeout","ArcOff-line")))
>>>
>>> which results in:
>>>
dat[1:5,]
>>>        t   f   p  d  o  s   a  l c
>>> 1 1/21/09 5:01 16151 Â 8.2 76 30 282 1060 53 7
>>> 2 1/21/09 5:02 16256 Â 8.3 76 23 282 1059 54 7
>>> 3 1/21/09 5:03 16150 Â 8.4 76 26 282 1059 55 7
>>> 4 1/21/09 5:04 16150 Â 9.0 76 25 282 1051 57 6
>>> 5 1/21/09 5:05 15543 10.4 76 Â 7 282 1024 58 6
>>>
>>> I have been unable to find a way to convert this into a time series. I
>>> did
>>> read the manuals and came across a way to coerce a data frame to a ts
>>> object: as.ts()
>>>
>>> Trouble is I do not know how to keep the timestamps in column t in the
>>> data frame above. The t column is not strings. If I do:
>>>
>>> plot.ts(dat)
>>>
>>> I can see how the first graphics panel is indeed numbers not text. So I
>>> think scan converted the text correctly per the format string I put in.
>>>
>>> Much more difficult still. The datafiles I have contain invalid data,
>>> missing values and other none relevant information. I filter this out
>>> using subset which works brilliantly. However, how can I filter using
>>> subset and convert to a time series afterwards. Since after subsetting
>>> there will be 'holes' i.e. missing records. Can a ts object deal with
>>> missing records? If so, how? Just point me to a document. I can and
>>> will
>>> put in the work to figure it out myself.
>>>
>>> Thank you!
>>> Alex van der Spek
>>>
>>> __
>>> R-help@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
> --
> Stephen Sefick
>
> Let's not spend our time and resources thinking about things that are
> so little or so large that all they really do for us is puff us up and
> make us feel like gods. We are mammals, and have not exhausted the
> annoying little problems of being mammals.
>
> -K. Mullis
>
>
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Re: [R] HELP to cbind several data.frame with a LOOP
I would use 'lapply' to create a list of the matrices:
result <- lapply(c(10,20,30,40,50), function(.num){
do.call(cbind, lapply(c('Tableanalysis_firenze',
'Tableanalysis_siena', 'Tableanalysis_lucca'), function(.file){
read.table(sprintf("%s_%d.txt", .file, .num), header=TRUE)
}))
})
On Thu, Apr 9, 2009 at 10:49 AM, Alessandro
wrote:
> Dear R users,
>
>
>
> thank for help. SORRY I am seeing in google a maillist but I didn't find a
> solution for my problem
>
>
>
> I have several txt file (with the same number of column and HEADER) to merge
> together, this is an example:
>
>
>
> Tableanalysis_firenze_10.txt
>
> Tableanalysis_firenze_20.txt
>
> Tableanalysis_firenze_30.txt
>
> Tableanalysis_firenze_40.txt
>
> Tableanalysis_firenze_50.txt
>
> Tableanalysis_siena_10.txt
>
> Tableanalysis_siena_20.txt
>
> Tableanalysis_siena_30.txt
>
> Tableanalysis_siena_40.txt
>
> Tableanalysis_siena_50.txt
>
> Tableanalysis_lucca_10.txt
>
> Tableanalysis_lucca_20.txt
>
> Tableanalysis_lucca_30.txt
>
> Tableanalysis_lucca_40.txt
>
> Tableanalysis_lucca_50.txt
>
>
>
> I wish to combine a new txt file like this
>
>
>
> Tableanalysis_10 <- cbind(Tableanalysis_firenze_10, Tableanalysis_siena_10,
> Tableanalysis_lucca_10)
>
> Tableanalysis_20 <- cbind(Tableanalysis_firenze_20, Tableanalysis_siena_20,
> Tableanalysis_lucca_20)
>
> Tableanalysis_30 <- cbind(Tableanalysis_firenze_30, Tableanalysis_siena_30,
> Tableanalysis_lucca_30)
>
> Tableanalysis_40 <- cbind(Tableanalysis_firenze_40, Tableanalysis_siena_40,
> Tableanalysis_lucca_40)
>
> Tableanalysis_50 <- cbind(Tableanalysis_firenze_50, Tableanalysis_siena_50,
> Tableanalysis_lucca_50)
>
>
>
> Thanks
>
>
>
> Ale
>
>
>
>
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
__
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Re: [R] problems with integrate ... arguments
On 09/04/2009 10:19 AM, Ravi Varadhan wrote:
Richard,
Your function f() is already vectorized, and it works well (see below). Therefore, you don't need to create f2().
He did say that this was a simplified example.
The problem appears to be in Vectorize, which uses match.call() to get
the args from the call to your f function. match.call() can make
substitutions for ... args, but only seems to do so for one level up,
and the dots are being passed through two levels here: ... as an arg to
integrate, which creates a local function ff, and passes ... through it.
Not sure yet where to fix this...
Duncan Murdoch
f = function(x, const) 2^x + const
testval = 2
integrate(f, 0.5, 1, const=testval)
1.845111 with absolute error < 2.0e-14
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Richard Morey
Date: Thursday, April 9, 2009 8:10 am
Subject: [R] problems with integrate ... arguments
To: r-help@r-project.org
Hi everyone,
I saw this problem dealt with here:
but no one answered that request that I can tell. I'm having the same
problem. I'm having problems passing arguments to functions that I'd
like to integrate. I could swear this worked in the past, but I can't
get it to work now. I'm running R on Windows.
Here's my toy code to reproduce the problem:
R.Version()$version.string
# [1] "R version 2.8.1 (2008-12-22)"
f=function(x,const)
2^x+const
f2=Vectorize(f,c("x"))
testval=2
f2(1:5,testval)
# [1] 4 6 10 18 34
# The vectorized function seems to work right.
integrate(f2,.5,1,c=2)
# Works. Returns
# 1.845111 with absolute error < 2.0e-14
integrate(f=f2,.5,1,const=testval)
# Doesn't work. Returns
# Error in eval(expr, envir, enclos) :
# ..1 used in an incorrect context, no ... to look in
I understand that I don't have to Vectorize this function for it to
work, but the more complicated functions I'm using require Vectorization.
Why can't I pass the argument "const" as a variable, instead of a value?
I don't understand this error.
Thanks in advance,
Richard Morey
--
Richard D. Morey
Assistant Professor
Psychometrics and Statistics
Rijksuniversiteit Groningen / University of Groningen
__
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and provide commented, minimal, self-contained, reproducible code.
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__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] HELP to cbind several data.frame with a LOOP
Dear R users, thank for help. SORRY I am seeing in google a maillist but I didn't find a solution for my problem I have several txt file (with the same number of column and HEADER) to merge together, this is an example: Tableanalysis_firenze_10.txt Tableanalysis_firenze_20.txt Tableanalysis_firenze_30.txt Tableanalysis_firenze_40.txt Tableanalysis_firenze_50.txt Tableanalysis_siena_10.txt Tableanalysis_siena_20.txt Tableanalysis_siena_30.txt Tableanalysis_siena_40.txt Tableanalysis_siena_50.txt Tableanalysis_lucca_10.txt Tableanalysis_lucca_20.txt Tableanalysis_lucca_30.txt Tableanalysis_lucca_40.txt Tableanalysis_lucca_50.txt I wish to combine a new txt file like this Tableanalysis_10 <- cbind(Tableanalysis_firenze_10, Tableanalysis_siena_10, Tableanalysis_lucca_10) Tableanalysis_20 <- cbind(Tableanalysis_firenze_20, Tableanalysis_siena_20, Tableanalysis_lucca_20) Tableanalysis_30 <- cbind(Tableanalysis_firenze_30, Tableanalysis_siena_30, Tableanalysis_lucca_30) Tableanalysis_40 <- cbind(Tableanalysis_firenze_40, Tableanalysis_siena_40, Tableanalysis_lucca_40) Tableanalysis_50 <- cbind(Tableanalysis_firenze_50, Tableanalysis_siena_50, Tableanalysis_lucca_50) Thanks Ale [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] request: maximum depth reached problem
Dear R community
Hope all of you are fine. I have a question regarding the an error message.
Actually, I am trying to generate classification trees using "tree" package. It
works well but for some datasets e.g., wine, yeast, boston housing etc. it
gives an error message.
Error in tree(V14 ~ ., data = training.data, method =
c("recursive.partitioning"), :
maximum depth reached
The structure of getting output is given below:
iris.tr = tree(Species ~., data=training.data,
method=c("recursive.partitioning"), split = c("gini"),
control=tree.control(nobs = 150, minsize = 5, mincut = 2))
Any suggestion will be appreciated to handle the above problem. Thanks and
best regards
Muhammad Azam
[[alternative HTML version deleted]]
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Re: [R] problems with integrate ... arguments
Richard,
I didn't read the last part of your email that you "do" want to Vectorize your
function. Sorry about that.
Here is a solution using "sapply" to vectorize your function.
f <- function(x, const) 2^x + const
f2 <- function(x, ...) sapply(x, function(x) f(x, ...) )
> integrate(f2, 0.5, 1, const=testval)
1.845111 with absolute error < 2.0e-14
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Richard Morey
Date: Thursday, April 9, 2009 8:10 am
Subject: [R] problems with integrate ... arguments
To: r-help@r-project.org
> Hi everyone,
>
> I saw this problem dealt with here:
>
>
> but no one answered that request that I can tell. I'm having the same
> problem. I'm having problems passing arguments to functions that I'd
> like to integrate. I could swear this worked in the past, but I can't
> get it to work now. I'm running R on Windows.
>
> Here's my toy code to reproduce the problem:
>
>
> R.Version()$version.string
> # [1] "R version 2.8.1 (2008-12-22)"
>
> f=function(x,const)
> 2^x+const
>
> f2=Vectorize(f,c("x"))
>
> testval=2
>
> f2(1:5,testval)
> # [1] 4 6 10 18 34
> # The vectorized function seems to work right.
>
> integrate(f2,.5,1,c=2)
> # Works. Returns
> # 1.845111 with absolute error < 2.0e-14
>
> integrate(f=f2,.5,1,const=testval)
> # Doesn't work. Returns
> # Error in eval(expr, envir, enclos) :
> # ..1 used in an incorrect context, no ... to look in
>
> I understand that I don't have to Vectorize this function for it to
> work, but the more complicated functions I'm using require Vectorization.
>
> Why can't I pass the argument "const" as a variable, instead of a value?
>I don't understand this error.
>
> Thanks in advance,
> Richard Morey
>
> --
> Richard D. Morey
> Assistant Professor
> Psychometrics and Statistics
> Rijksuniversiteit Groningen / University of Groningen
>
> __
> R-help@r-project.org mailing list
>
> PLEASE do read the posting guide
> and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Anova interaction not tested
Gabe:
Don't be silly. lme is not appropriate here --you have only one stratum!.
Use lm and you'll see what's going on. It also looks like you should do some
reading up on linear models. V&R's MASS or Peter Dalgaard's INTRO to
Statistics with R might be places to start.
Incidentallyy, Version 2.8.1 of R gives for the output of aov:
aov(speed~brand*material)
Call:
aov(formula = speed ~ brand * material)
Terms:
brand material Residuals
Sum of Squares 49.86190 13.50167 21.00500
Deg. of Freedom22 2
Residual standard error: 3.240756
4 out of 9 effects not estimable
Estimated effects may be unbalanced
Warning messages:
1: In model.matrix.default(mt, mf, contrasts) :
variable 'brand' converted to a factor
2: In model.matrix.default(mt, mf, contrasts) :
variable 'material' converted to a factor
Seems like this should pretty much tell you what's going on -- if you
understand linear models. (and if you don't, why not, since you're using
them?)
Cheers,
Bert
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Gabriel Murray
Sent: Wednesday, April 08, 2009 4:08 PM
To: Patrick Connolly
Cc: r-help@r-project.org
Subject: Re: [R] Anova interaction not tested
Playing around with this some more, it looks like it may purely be due to
the way that R handles unbalanced data. I will investigate lme for this.
Best,
Gabe
On Wed, Apr 8, 2009 at 3:24 PM, Gabriel Murray wrote:
> Here is some toy data to give an example. Imagine someone is test-riding
> several bicycles to decide which to buy, and measures their average speed
> during each test-ride. They want to assess the main effects and
interaction
> of brand and material on speed.
>
> SpeedSizeBrandMaterial
> 20 smallgiantsteel
> 25.1 mediumgiantsteel
> 25.2 medium trekaluminum
> 26 smallcannondalecarbon
> 19.9 largegiantaluminum
> 21 mediumtrekcarbon
> 30 mediumcannondalecarbon
>
> This is the output I get:
>
> > fit = aov(Speed~Brand*Material, data=myData)
> > summary(fit)
> Df Sum Sq Mean Sq F value Pr(>F)
> Brand2 49.862 24.931 2.3738 0.2964
> Material 2 13.502 6.751 0.6428 0.6087
> Residuals2 21.005 10.503
>
>
> I suppose I am missing something very obvious here as to why the
> interaction is not reported, but I don't see what it is.
> Cheers,
>
> Gabe
>
>
>
> On Wed, Apr 8, 2009 at 1:34 PM, Patrick Connolly <
> p_conno...@slingshot.co.nz> wrote:
>
>> On Wed, 08-Apr-2009 at 12:59PM -0700, Gabriel Murray wrote:
>>
>> |> I've noticed with certain datasets that when I try to do an anova and
>> test
>> |> for main effects and interaction for two explanatory variables,
>> sometimes
>> |> the main effect results are given but not the interaction results. For
>> |> example,
>> |>
>> |> ex1 = aov(Score ~ var1*var2, data=myData)
>> |> summary(ex1)
>>
>> Could it be that there are no degrees of freedom left?
>>
>> That's about my best guess without enough information.
>>
>>
>> |> __
>> |> R-help@r-project.org mailing list
>> |> https://stat.ethz.ch/mailman/listinfo/r-help
>> |> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> |> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>> Nothing you sent is reproducible.
>>
>>
>> --
>> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
>>___Patrick Connolly
>> {~._.~} Great minds discuss ideas
>> _( Y )_ Average minds discuss events
>> (:_~*~_:) Small minds discuss people
>> (_)-(_) . Eleanor Roosevelt
>>
>> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
>>
>
>
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Re: [R] better way of recoding factors in data frame?
Thank you for your help! --- On Thu, 4/9/09, Thomas Lumley wrote: > From: Thomas Lumley > Subject: Re: [R] better way of recoding factors in data frame? > To: mohinder_da...@yahoo.com > Cc: r-help@r-project.org > Date: Thursday, April 9, 2009, 2:10 PM > On Thu, 9 Apr 2009 mohinder_da...@yahoo.com > wrote: > > > > > Hi all, > > > > I apologize in advance for the length of this post, > but I wanted to make sure > > I was clear. > > Good strategy. > > > >I tried this: > > > >> myFrame2$newSex <- ifelse(myFrame2$newSex ==1 > || myFrame2$newSex == 2, myFrame2$newSex, 0) > > > > First, you need |, not ||, because || returns just a single > value. > > This still won't quite work, because the condition will be > NA when newSex is NA (if you don't know a number then you > don't know whether it is equal to 1 or 2). > > So, > myFrame2$newSex <- ifelse(myFrame2$newSex %in% c(1,2), > myFrame2$newSex, 0) > > or, slightly shorter > myFrame2$newSex <- with(myFrame2, ifelse(newSex %in% > c(1,2), newSex, 0) > > -thomas > > Thomas Lumley > Assoc. Professor, Biostatistics > tlum...@u.washington.edu > University of Washington, Seattle > > > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problems with integrate ... arguments
Richard,
Your function f() is already vectorized, and it works well (see below).
Therefore, you don't need to create f2().
f = function(x, const) 2^x + const
testval = 2
> integrate(f, 0.5, 1, const=testval)
1.845111 with absolute error < 2.0e-14
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Richard Morey
Date: Thursday, April 9, 2009 8:10 am
Subject: [R] problems with integrate ... arguments
To: r-help@r-project.org
> Hi everyone,
>
> I saw this problem dealt with here:
>
>
> but no one answered that request that I can tell. I'm having the same
> problem. I'm having problems passing arguments to functions that I'd
> like to integrate. I could swear this worked in the past, but I can't
> get it to work now. I'm running R on Windows.
>
> Here's my toy code to reproduce the problem:
>
>
> R.Version()$version.string
> # [1] "R version 2.8.1 (2008-12-22)"
>
> f=function(x,const)
> 2^x+const
>
> f2=Vectorize(f,c("x"))
>
> testval=2
>
> f2(1:5,testval)
> # [1] 4 6 10 18 34
> # The vectorized function seems to work right.
>
> integrate(f2,.5,1,c=2)
> # Works. Returns
> # 1.845111 with absolute error < 2.0e-14
>
> integrate(f=f2,.5,1,const=testval)
> # Doesn't work. Returns
> # Error in eval(expr, envir, enclos) :
> # ..1 used in an incorrect context, no ... to look in
>
> I understand that I don't have to Vectorize this function for it to
> work, but the more complicated functions I'm using require Vectorization.
>
> Why can't I pass the argument "const" as a variable, instead of a value?
>I don't understand this error.
>
> Thanks in advance,
> Richard Morey
>
> --
> Richard D. Morey
> Assistant Professor
> Psychometrics and Statistics
> Rijksuniversiteit Groningen / University of Groningen
>
> __
> R-help@r-project.org mailing list
>
> PLEASE do read the posting guide
> and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] xmlEventParse returning trimmed content?
Hello,
I wrote the function below and have the problem, that the "text" bit returns
only a trimmed version (686 chars as far as I can see) of the content under
the "fetchPeaks" condition.
Any hunches why that might be?
Thanks for pointer, Joh
xmlEventParse(fileName,
list(
startElement=function(name, attrs){
if(name == "scan"){
if(.GlobalEnv$ms2Scan == TRUE & .GlobalEnv$scanDone == TRUE){
cat(.GlobalEnv$scanNum,"\n")
MakeSpektrumEntry()
}
.GlobalEnv$scanDone <- FALSE
.GlobalEnv$fetchPrecMz <- FALSE
.GlobalEnv$fetchPeaks <- FALSE
.GlobalEnv$ms2Scan <- FALSE
if(attrs[["msLevel"]] == "2"){
.GlobalEnv$ms2Scan <- TRUE
.GlobalEnv$scanNum <- as.integer(attrs[["num"]])
}
} else if(name == "precursorMz" & .GlobalEnv$ms2Scan == TRUE){
.GlobalEnv$fetchPrecMz <- TRUE
} else if(name == "peaks" & .GlobalEnv$ms2Scan == TRUE){
.GlobalEnv$fetchPeaks <- TRUE
}
},
text=function(text){
if(.GlobalEnv$fetchPrecMz == TRUE){
.GlobalEnv$precursorMz <- as.numeric(text)
.GlobalEnv$fetchPrecMz <- FALSE
}
if(.GlobalEnv$fetchPeaks == TRUE){
.GlobalEnv$peaks <- text
.GlobalEnv$fetchPeaks <- FALSE
.GlobalEnv$scanDone <- TRUE
}
}
)
)
> sessionInfo()
R version 2.9.0 beta (2009-04-03 r48277)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=en_US.UTF-8;LC_ADDRESS=en_US.UTF-8;LC_TELEPHONE=en_US.UTF-8;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=en_US.UTF-8
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] caMassClass_1.6 MASS_7.2-46 digest_0.3.1caTools_1.9
[5] bitops_1.0-4.1 rpart_3.1-43nnet_7.2-46 e1071_1.5-19
[9] class_7.2-46PROcess_1.19.1 Icens_1.15.2survival_2.35-4
[13] RCurl_0.94-1XML_2.3-0 rkward_0.5.0
loaded via a namespace (and not attached):
[1] tools_2.9.0
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Re: [R] Biexponential Fit
Using algorithm="plinear" as shown by example below makes sum-of-exponentials fitting problems better conditioned. A1 <- 1 A2 <- 2 k1 <- -.5 k2 <- -2 x <- seq(1,10,length=200) y <- A1*exp(k1*x) + A2*exp(k2*x) + .001*rnorm(200) aa <- nls(y~cbind(exp(k1*x), exp(k2*x)), algorithm="plinear", start=list(k1=-.1, k2=-6), data=list(y=y, x=x), trace=TRUE) On Thu, 9 Apr 2009, Peter Dalgaard wrote: > Jonas Weickert wrote: > > Hi, > > > > I want to do a biexponential Fit, i.e. > > > > y ~ A1*exp(k1*x) + A2*exp(k2*x) > > > > Is this possible? I tried nls() but it stopped with several (different) > > errors. I'm using y and x as simple vectors and the formula for nls() > > exactly as mentioned above. > > Yes, it is possible, with some reservations. There is even a > self-starting model for it (SSbiexp), at least if k1,k2 are negative. > > The reservations are that you need good data and good starting values > for the fit. The model is theoretically unidentifiable because you can > switch 1 and 2 and get the same model, which becomes an issue if you > start too fra from the optimum. Worse, if k1 and k2 are similar, the > whole system becomes ill-conditioned. There's a rule of thumb requiring > a factor of 5 or more between k1 and k2, for pharmacokinetic applications. > > > Thanks a lot! > > > > Jonas > > > > __ > > R-help@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > -- > O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B >c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K > (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 > ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] failed when merging two dataframes, why
I would suggest use the same column names for the common columns. Say, use
"codetot" for both df1 and df2. Then you don't even have to specify by.x or
by.y, merge will do it automatically.
merge(df1,df2, all=TRUE).
Otherwise you have to
merge(df1,df2,by.x=c('popcode','codetot'),by.y=c('popcode','codetoto'),all=TRUE)
They both produce
popcode codetot p3need areasec
1 BCPy01-01 BCPy01-01-1 100 0.5089434
2 BCPy01-01 BCPy01-01-2 100 0.6246381
3 BCPy01-01 BCPy01-01-3 100 0.4370059
4 BCPy01-02 BCPy01-02-1 92.5926 0.9253052
5 BCPy01-02 BCPy01-02-1 92.5926 0.6011810
6 BCPy01-02 BCPy01-02-1 100 0.9253052
7 BCPy01-02 BCPy01-02-1 100 0.6011810
8 BCPy01-02 BCPy01-02-2 92.5926 0.6710850
9 BCPy01-02 BCPy01-02-2 92.5926 0.7145839
10 BCPy01-02 BCPy01-02-2 100 0.6710850
11 BCPy01-02 BCPy01-02-2 100 0.7145839
12 BCPy01-02 BCPy01-02-3 92.5926 0.9515256
13 BCPy01-02 BCPy01-02-3 92.5926 0.6555006
14 BCPy01-02 BCPy01-02-3 100 0.9515256
15 BCPy01-02 BCPy01-02-3 100 0.6555006
16 BCPy01-03 BCPy01-03-1 100 0.8683875
On Thu, Apr 9, 2009 at 6:19 AM, Mao Jianfeng wrote:
> Hi, R-listers,
>
> Failed, when I tried to merge df1 and df2 by "codetot" in df1 and
> "codetoto"
> in df2. I want to know the reason and how to merge them together. Data
> frames and codes I have used were listed as followed. Thanks a lot in
> advance.
>
> df1:
> popcode codetot p3need
> BCPy01-01 BCPy01-01-1 100.
> BCPy01-01 BCPy01-01-2 100.
> BCPy01-01 BCPy01-01-3 100.
> BCPy01-02 BCPy01-02-1 92.5926
> BCPy01-02 BCPy01-02-1 100.
> BCPy01-02 BCPy01-02-2 92.5926
> BCPy01-02 BCPy01-02-2 100.
> BCPy01-02 BCPy01-02-3 92.5926
> BCPy01-02 BCPy01-02-3 100.
> BCPy01-03 BCPy01-03-1 100.
>
> df2:
> popcodecodetoto areasec
> BCPy01-01 BCPy01-01-1 0.5089434
> BCPy01-01 BCPy01-01-2 0.6246381
> BCPy01-01 BCPy01-01-3 0.4370059
> BCPy01-02 BCPy01-02-1 0.9253052
> BCPy01-02 BCPy01-02-1 0.6011810
> BCPy01-02 BCPy01-02-2 0.6710850
> BCPy01-02 BCPy01-02-2 0.7145839
> BCPy01-02 BCPy01-02-3 0.9515256
> BCPy01-02 BCPy01-02-3 0.6555006
> BCPy01-03 BCPy01-03-1 0.8683875
>
> code:
> new1<-merge(df1,df2,by=c("popcode","popcode"),all=T) # It is processed
> well.
> But, it is not what I want.
> new2<-merge(df1,df2,by=c("codetot","codetoto"),all=T) # this one failed. I
> exactly want to do that.
>
> Mao J-F
> IBCAS, AC
>
>[[alternative HTML version deleted]]
>
> __
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> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Jun Shen PhD
PK/PD Scientist
BioPharma Services
Millipore Corporation
15 Research Park Dr.
St Charles, MO 63304
Direct: 636-720-1589
[[alternative HTML version deleted]]
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Re: [R] Maple and R
I forgot. You can get the Bessel functions from Robin Hankin's GSL package. R. K. S. Hankin 2006. Introducing gsl, a wrapper for the Gnu Scientific Library. Rnews 6(4):24-26 Joseph F. Lucke Senior Statistician Research Institute on Addictions University at Buffalo State University of New York 1021 Main Street Buffalo, NY 14203-1016 Office: 716-887-6807 Fax: 716-887-2510 http://www.ria.buffalo.edu/profiles/lucke.html Roslina Zakaria Sent by: r-help-boun...@r-project.org 04/07/2009 02:29 AM To r-help@r-project.org cc Subject [R] Maple and R Hi R-users, Can Maple function be exported to R? I have a jacobian matrix (4X4) from maple in algebraic form which involve modified Bessel function of the first kind. I just wonder whether we can use algebraic form into R before the value of the parameters can be estimated. Thank you so much for your attention and help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] better way of recoding factors in data frame?
On Thu, 9 Apr 2009 mohinder_da...@yahoo.com wrote: Hi all, I apologize in advance for the length of this post, but I wanted to make sure I was clear. Good strategy. I tried this: myFrame2$newSex <- ifelse(myFrame2$newSex ==1 || myFrame2$newSex == 2, myFrame2$newSex, 0) First, you need |, not ||, because || returns just a single value. This still won't quite work, because the condition will be NA when newSex is NA (if you don't know a number then you don't know whether it is equal to 1 or 2). So, myFrame2$newSex <- ifelse(myFrame2$newSex %in% c(1,2), myFrame2$newSex, 0) or, slightly shorter myFrame2$newSex <- with(myFrame2, ifelse(newSex %in% c(1,2), newSex, 0) -thomas Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] better way of recoding factors in data frame?
Hi all,
I apologize in advance for the length of this post, but I wanted to make sure I
was clear.
I am trying to merge two dataframes that share a number of rows (but some are
unique to each data frame). Each row represents a subject in a study. The
problem is that sex is coded differently in the two, including the way missing
values are represented.
Here is an example of the merged dataframe:
> myFrame2
SubjCode SubjSex Sex
1 sub1 M
2 sub2 F
3 sub3 M Male
4 sub4 M
5 sub5 F
6 sub6 F Female
7 sub7
8 sub8
9 sub9 Not Recorded
10 sub10 Not Recorded
I then apply the following:
> myFrame2$SubjSex <- factor(myFrame2$SubjSex, levels = c('M','F'))
> myFrame2$SubjSex <- factor(myFrame2$SubjSex, labels = c('Male','Female'))
> myFrame2 <- transform(myFrame2, newSex = ifelse(is.na(SubjSex), Sex, SubjSex))
...and get this:
> myFrame2
SubjCode SubjSex Sex newSex
1 sub1 Male 1
2 sub2 Female 2
3 sub3 Male Male 1
4 sub4 Male 1
5 sub5 Female 2
6 sub6 Female Female 2
7 sub7 NA
8 sub8 NA
9 sub9 Not Recorded 3
10 sub10 Not Recorded 3
I need that last column to have just 1 (Male), 2 (Female) or 0 (Missing), and
the only way I've come up with seems very kludgy:
> myFrame2$newSex[is.na(myFrame2$newSex)] <- 0
> myFrame2$newSex <- ifelse(myFrame2$newSex == 3, 0, myFrame2$newSex)
That gives me the right values for "newSex", but I'd like to positively select
for the values I want to keep, rather than negatively selecting the ones to
change - I tried this:
> myFrame2$newSex <- ifelse(myFrame2$newSex ==1 || myFrame2$newSex == 2,
> myFrame2$newSex, 0)
But I just get 1 for every row in newSex. Does anyone know of a way to do this
by positively selecting the values 1 and 2?
Thanks,
Mohinder
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Re: [R] Maple and R
You can export the Maple code to C or Fortran. I actually found it easier to export it to Fortran and then use a text editor to change Fortran's assignment ='s to R's <-. After additional tweaks for R, you can convert the script into an R function. Joseph F. Lucke Senior Statistician Research Institute on Addictions University at Buffalo State University of New York 1021 Main Street Buffalo, NY 14203-1016 Office: 716-887-6807 Fax: 716-887-2510 http://www.ria.buffalo.edu/profiles/lucke.html Roslina Zakaria Sent by: r-help-boun...@r-project.org 04/07/2009 02:29 AM To r-help@r-project.org cc Subject [R] Maple and R Hi R-users, Can Maple function be exported to R? I have a jacobian matrix (4X4) from maple in algebraic form which involve modified Bessel function of the first kind. I just wonder whether we can use algebraic form into R before the value of the parameters can be estimated. Thank you so much for your attention and help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] CFA in R/sem package
Hi, I am not sure if R-help is the right forum for my question. If not, please let me know. I have to do some discriminant validity tests with some constructs. I am using the method of doing a CFA constraining the correlation of a pair of the constructs to 1 and comparing the chi-square of this constrained model to the unconstrained model. If the chi-square difference is not significant, then I cannot reject the null hypothesis that the two constructs are equal. Well, if you are going to test, say, 4 constructs (A, B, C, and D), you will have to have 2*C(4,2) = 12 models to test, 5 constructs, 20 models, and so forth. A tedious and error prone process... So far, I have been using AMOS for that shake, given that 1) my university has the license, 2) my other colleagues use it, and 3) I know it ;) I would like to know if any of you use R, namely the sem package, for that application and if you can share your thoughts/experiences on using it. I don't thing I would have problems "porting" my models to R/sem, but I would like to know if there is an optimized process of doing that tests, without manually coding all the dozens of models. Best, Iuri. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] seemingly unrelated regression
livia wrote: > > Hello, > > I am working on the model of seemingly unrelated regression. I came across > with the error message: > > Log determinant of residual covariance: NA > Warning messages: > NAs generated in: log(x) > > I have three linear models which contain 21 explanatory variables and > there are about 300 data points. > > Could anyone please give some idea what is wrong with the model? > We can't possibly help without knowing what functions and packages you are trying to use (the results of sessionInfo() would be useful), and most likely we can't help without a reproducible example ... Ben Bolker -- View this message in context: http://www.nabble.com/seemingly-unrelated-regression-tp22970572p22971060.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R segfaulting with glmnet on some data, not other
Thanks, Gad. Lisa's professor knows the glmnet authors, so we will forward this request directly to them. Take care! Dan From: Gad Abraham Cc: r-help@r-project.org; lp...@bu.edu Sent: Tuesday, April 7, 2009 10:26:26 PM Subject: Re: [R] R segfaulting with glmnet on some data, not other Kamalic Dan wrote: > Hello R-help list, > > > I have a piece of code written by a grad student here at BU which will > segfault when using one data set, but complete just fine using another. Both > sets are just text files full of real numbers. > > It seems like a bug within R. It could be a bug within her data, but > again, her data is just a bunch of floats, so her data could be > triggering a bug within R. I have tried this with two different rpm packages > of R for Linux (R-2.8.0-1.rh5 and R-2.8.1-1.rh5) as well as a fresh build > that I just did of the prerelease R-beta_2009-04-02_r48271.tar.gz > I have also tried installing the absolute newest versions of > glmnet_1.1-3.tar.gz and Matrix_0.999375-23.tar.gz. In all cases, the exact > same error occurs. > [[elided Yahoo spam]] >From your traceback it seems it's not a bug in R itself, but in the package >glmnet. It's probably best to chase it up with the package authors since glmnet is not a base R package. -- Gad Abraham MEng Student, Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabra...@csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] seemingly unrelated regression
Hello, I am working on the model of seemingly unrelated regression. I came across with the error message: Log determinant of residual covariance: NA Warning messages: NAs generated in: log(x) I have three linear models which contain 21 explanatory variables and there are about 300 data points. Could anyone please give some idea what is wrong with the model? -- View this message in context: http://www.nabble.com/seemingly-unrelated-regression-tp22970572p22970572.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Cross-platforms solution to export R graphs
Hello Rusers, I have worked on a R Wiki page for solutions in exporting R graphs, especially, the often-asked questions: - How can I export R graphs in vectorized format (EMF) for inclusion in MS Word or OpenOffice outside of Windows? - What is the best solution(s) for post-editing/annotating R graphs. The page is at: http://wiki.r-project.org/rwiki/doku.php?id=tips:graphics-misc:export. I would be happy to receive your comments and suggestions to improve this document. All the best, PhG -- ..<°}))>< ) ) ) ) ) ( ( ( ( (Prof. Philippe Grosjean ) ) ) ) ) ( ( ( ( (Numerical Ecology of Aquatic Systems ) ) ) ) ) Mons-Hainaut University, Belgium ( ( ( ( ( .. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with biOps loading
Hi Bob, > I have tried several times to load biOps package after reading the posts in > this archive regarding the necessity of placing these two libs in the PATH > (libjpeg62.dll and libtiff3.dll). I have tried locating the libs in several > directories that should have worked, but I still get the following message. > -- > Error in inDL(x, as.logical(local), as.logical(now), ...) : > unable to load shared library 'C:/Program > Files/R/R-2.8.1/library/biOps/libs/biOps.dll': > LoadLibrary failure: The specified module could not be found. > > Error: package/namespace load failed for 'biOps' > - > I am using R version 2.8.1 (2008-12-22) with Win-XP and Jaguar GUI > > Can anyone give me a hint about where to place the libs and how to get the > biOps package to work. It looks like the package could solve several of my > image processing problems. It sounds like the required libraries are not correctly installed. In a windows setup it is a kind of complex step to get it to work. We have the idea to improve the installation step. I have a zip file (that you can download here: http://rapidshare.com/files/219274717/libs.zip.html) with the needed dll's that you should decompress in the libs directoryof the biOps package (something similar to C:/R-2.8.1/library/biOps/libs/). Tell me if it helps. I hope you get it to work and solve you needs. Any problem or question, just let me know. Best regards, Matías. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] data.fram zero's
well, you can first create a matrix and then turn into a data frame, e.g., mat <- matrix(0, 5, 10) as.data.frame(mat) I hope it helps. Best, Dimitris Duijvesteijn, Naomi wrote: Hi all, A simple question which I don’t seem to be able to solve: I want to make a data.frame of 360 rows and 94228 column with only zero’s without having to type all these zero’s ;-) What is the easiest method? Thanks, Naomi Disclaimer: De informatie opgenomen in dit bericht (en bijlagen) kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde(n). Indien u dit bericht ten onrechte ontvangt, wordt u geacht de inhoud niet te gebruiken, de afzender direct te informeren en het bericht te vernietigen. Aan dit bericht kunnen geen rechten of plichten worden ontleend. Disclaimer: The information contained in this message may be confidential and is intended to be exclusively for the addressee. Should you receive this message unintentionally, you are expected not to use the contents herein, to notify the sender immediately and to destroy the message. No rights can be derived from this message. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave problem, with multicolumn tables from R to LaTeX
hi Ista,
i did load xtable() before because i was comparing if using it was any
different, but still i got the same problem.
I hope somebody can give us a solution or some tips soon!
thanks
c
---
Christian Salas E-mail:christian.sa...@yale.edu
PhD candidate http://environment.yale.edu/salas
School of Forestry and Environmental Studies
Yale University Tel: +1-(203)-432 5126
360 Prospect St Fax:+1-(203)-432 3809
New Haven, CT 06511-2189Office: Room 35, Marsh Hall
USA
Yale Biometrics Lab http://environment.yale.edu/biometrics
---
Ista Zahn wrote:
Hi Christian,
I've been having this problem as well. There are bug reports about
this (one of them mine):
http://biostat.mc.vanderbilt.edu/trac/Hmisc/ticket/25
http://biostat.mc.vanderbilt.edu/trac/Hmisc/ticket/28
so hopefully the developers are aware of the problem and will address
it in the next release.
By the way: what do you need the xtable library for? I see that you
loaded it, but never call any of the functions in your example code.
All the best,
Ista
From: Christian Salas
To: r-help@r-project.org
Date: Wed, 08 Apr 2009 12:05:34 -0400
Subject: [R] Sweave problem, with multicolumn tables from R to LaTeX
Hi there,
I have been using the example provided bellow for a while, and It was
working without any problem. Nevertheless, just since 2-3 days is not
working, probably because I did update.packages(). I have tried to
re-install the older versions of the packages Hmisc() and xtable(),
but still does not work. Can you run this example, and tell me if you
got the same problems?
I use linux-ubuntu, and R 2.8.1
Here is my .Rnw file
%%%
\documentclass{article}
\usepackage[margin=1in]{geometry}
\usepackage{Sweave}
\SweaveOpts{echo=TRUE}
\title{Why is not working this? a table from R having multi columns
names}
\author{Myself}
\date{\today}
\begin{document}
\maketitle
<>=
#Calling some packages
library(Hmisc)
library(xtable)
#version of the packages
packageDescription('Hmisc')$Version #version of Hmisc
packageDescription('xtable')$Version #version of xtable
#version and features of my PC and R
R.version$platform
R.version$version.string
@
\section{The table ready to be exported}
An R table as an example.
<<>>=
tab.coef.allmodels <-
structure(c(246.8809, 153.6952, 43.6259, 1823.686, -4.0138, -53.8741,
-13.9552, -699.7154, 0, -3.0084, -0.5188, -41.7249, 4.0898,
2.0342, 0.2798, 25.636, 235.5128, 160.0244, 30.0147, 1523.0723,
3.7601, -53.9238, -3.9789, -597.1446, 0, -3.2745, -0.0025, -28.7418,
4.4203, 2.1606, 0.0124, 17.9259), .Dim = c(4L, 8L), .Dimnames = list(
c("NHA", "GHA", "Hdom", "VHA"), c("Intercept", "stand2",
"band3", "band7", "Intercept", "stand2", "band3", "band7"
)))
tab.coef.allmodels
@
\section{Producing the \LaTeX\ table}
\subsection{Showing a simple output table, but not being
the aimed one}
The following syntax produce Table \ref{tab:coefAllmod1}, which is not
what I want.
<>=
l <- latex(tab.coef.allmodels, file="tab.coefAllmod1.tex",
rowlabel="Model for",
first.hline.double=FALSE,
rowlabel.just="l",
caption="MLR and LME parameter estimates by stand variables",
caption.loc="top", label="tab:coefAllmod1",where="!h")
@
\input{tab.coefAllmod1}
\subsection{What I want, but not getting it right}
The following syntax produce Table \ref{tab:coefAllmod2}, which
contains all the information that i want, but is not giving me
the correct format.
<>=
l <- latex(tab.coef.allmodels, file="tab.coefAllmod2.tex",
rowlabel="Model for",
first.hline.double=FALSE,
rowlabel.just="l",
cgroup=c("MLR","LME"),
n.cgroup=c(4,4),
caption="MLR and LME parameter estimates by stand variables",
caption.loc="top", label="tab:coefAllmod2",where="!h")
@
\input{tab.coefAllmod2}
I have been using this
syntax for a while, and was working without any problem.
Nevertheless, just since 2-3 days is not working, probably
because I did {\tt update.packages()}.
I have tried to re-install the older versions of the packages
{\tt Hmisc()} and {\tt xtable()}, but still does not work.
\vspace{1in}
{\Large {\bf What Am I missing here?}}
\end{document}
%%%
The the main .tex file, tables, the ouput pdf, and the .Rnw files are
in the following url, if you want to check them
http://environment.yale.edu/salas/questions/shortTable/multcolTable_short.tex
http://environment.yale.edu/salas/questions/shortTable/tab.coefAllmod1.tex
http://environment.yale.edu/salas/questions/shortTable/tab.coefAllmod2.tex
http://environment.yale.edu/salas/questions/shortTable/multcolTable_short.pdf
http://environment.yale.edu/salas/questions/shortTable/multcolTable_short.Rnw
thanks in advance for your help
__
R-help@r-project.org m
Re: [R] reading an image and adding a legend
Simon Pickett bto.org> writes:
> But my code returns an error
>
> x<-read.pnm("C:/Documents and Settings/simonp/My Documents/Simon BTO/RELU/GIS
data/ten km areas in analysis.bmp")
> Error in pm.readmagicnumber(con) : Not a PNM format file
Error message seems quite clear: bmp a non-supported format. Some year ago,
the wisdom was to convert your images using imagemagick
http://finzi.psych.upenn.edu/R/Rhelp02/archive/23131.html
But read.jpeg should work (another variant in rimage), if that's good enough
for your graphics
Dieter
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] data.fram zero's
Hi all, A simple question which I donât seem to be able to solve: I want to make a data.frame of 360 rows and 94228 column with only zeroâs without having to type all these zeroâs ;-) What is the easiest method? Thanks, Naomi Disclaimer: De informatie opgenomen in dit bericht (en bijlagen) kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde(n). Indien u dit bericht ten onrechte ontvangt, wordt u geacht de inhoud niet te gebruiken, de afzender direct te informeren en het bericht te vernietigen. Aan dit bericht kunnen geen rechten of plichten worden ontleend. Disclaimer: The information contained in this message may be confidential and is intended to be exclusively for the addressee. Should you receive this message unintentionally, you are expected not to use the contents herein, to notify the sender immediately and to destroy the message. No rights can be derived from this message. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sweave problem, with multicolumn tables from R to LaTeX
Hi Christian,
I've been having this problem as well. There are bug reports about
this (one of them mine):
http://biostat.mc.vanderbilt.edu/trac/Hmisc/ticket/25
http://biostat.mc.vanderbilt.edu/trac/Hmisc/ticket/28
so hopefully the developers are aware of the problem and will address
it in the next release.
By the way: what do you need the xtable library for? I see that you
loaded it, but never call any of the functions in your example code.
All the best,
Ista
From: Christian Salas
To: r-help@r-project.org
Date: Wed, 08 Apr 2009 12:05:34 -0400
Subject: [R] Sweave problem, with multicolumn tables from R to LaTeX
Hi there,
I have been using the example provided bellow for a while, and It was
working without any problem. Nevertheless, just since 2-3 days is not
working, probably because I did update.packages(). I have tried to
re-install the older versions of the packages Hmisc() and xtable(),
but still does not work. Can you run this example, and tell me if you
got the same problems?
I use linux-ubuntu, and R 2.8.1
Here is my .Rnw file
%%%
\documentclass{article}
\usepackage[margin=1in]{geometry}
\usepackage{Sweave}
\SweaveOpts{echo=TRUE}
\title{Why is not working this? a table from R having multi columns
names}
\author{Myself}
\date{\today}
\begin{document}
\maketitle
<>=
#Calling some packages
library(Hmisc)
library(xtable)
#version of the packages
packageDescription('Hmisc')$Version #version of Hmisc
packageDescription('xtable')$Version #version of xtable
#version and features of my PC and R
R.version$platform
R.version$version.string
@
\section{The table ready to be exported}
An R table as an example.
<<>>=
tab.coef.allmodels <-
structure(c(246.8809, 153.6952, 43.6259, 1823.686, -4.0138, -53.8741,
-13.9552, -699.7154, 0, -3.0084, -0.5188, -41.7249, 4.0898,
2.0342, 0.2798, 25.636, 235.5128, 160.0244, 30.0147, 1523.0723,
3.7601, -53.9238, -3.9789, -597.1446, 0, -3.2745, -0.0025, -28.7418,
4.4203, 2.1606, 0.0124, 17.9259), .Dim = c(4L, 8L), .Dimnames = list(
c("NHA", "GHA", "Hdom", "VHA"), c("Intercept", "stand2",
"band3", "band7", "Intercept", "stand2", "band3", "band7"
)))
tab.coef.allmodels
@
\section{Producing the \LaTeX\ table}
\subsection{Showing a simple output table, but not being
the aimed one}
The following syntax produce Table \ref{tab:coefAllmod1}, which is not
what I want.
<>=
l <- latex(tab.coef.allmodels, file="tab.coefAllmod1.tex",
rowlabel="Model for",
first.hline.double=FALSE,
rowlabel.just="l",
caption="MLR and LME parameter estimates by stand variables",
caption.loc="top", label="tab:coefAllmod1",where="!h")
@
\input{tab.coefAllmod1}
\subsection{What I want, but not getting it right}
The following syntax produce Table \ref{tab:coefAllmod2}, which
contains all the information that i want, but is not giving me
the correct format.
<>=
l <- latex(tab.coef.allmodels, file="tab.coefAllmod2.tex",
rowlabel="Model for",
first.hline.double=FALSE,
rowlabel.just="l",
cgroup=c("MLR","LME"),
n.cgroup=c(4,4),
caption="MLR and LME parameter estimates by stand variables",
caption.loc="top", label="tab:coefAllmod2",where="!h")
@
\input{tab.coefAllmod2}
I have been using this
syntax for a while, and was working without any problem.
Nevertheless, just since 2-3 days is not working, probably
because I did {\tt update.packages()}.
I have tried to re-install the older versions of the packages
{\tt Hmisc()} and {\tt xtable()}, but still does not work.
\vspace{1in}
{\Large {\bf What Am I missing here?}}
\end{document}
%%%
The the main .tex file, tables, the ouput pdf, and the .Rnw files are
in the following url, if you want to check them
http://environment.yale.edu/salas/questions/shortTable/multcolTable_short.tex
http://environment.yale.edu/salas/questions/shortTable/tab.coefAllmod1.tex
http://environment.yale.edu/salas/questions/shortTable/tab.coefAllmod2.tex
http://environment.yale.edu/salas/questions/shortTable/multcolTable_short.pdf
http://environment.yale.edu/salas/questions/shortTable/multcolTable_short.Rnw
thanks in advance for your help
--
---
Christian Salas E-mail:christian.sa...@yale.edu
PhD candidate http://environment.yale.edu/salas
School of Forestry and Environmental Studies
Yale University Tel: +1-(203)-432 5126
360 Prospect St Fax:+1-(203)-432 3809
New Haven, CT 06511-2189Office: Room 35, Marsh Hall
USA
Yale Biometrics Lab http://environment.yale.edu/biometrics
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] problems with integrate ... arguments
On 09/04/2009 8:07 AM, Richard Morey wrote:
Hi everyone,
I saw this problem dealt with here:
http://markmail.org/search/list:r-project?q=integrate#query:list%3Ar-project%20integrate+page:1+mid:qczmyzr676pgmaaw+state:results
but no one answered that request that I can tell. I'm having the same
problem. I'm having problems passing arguments to functions that I'd
like to integrate. I could swear this worked in the past, but I can't
get it to work now. I'm running R on Windows.
Here's my toy code to reproduce the problem:
R.Version()$version.string
# [1] "R version 2.8.1 (2008-12-22)"
f=function(x,const)
2^x+const
f2=Vectorize(f,c("x"))
testval=2
f2(1:5,testval)
# [1] 4 6 10 18 34
# The vectorized function seems to work right.
integrate(f2,.5,1,c=2)
# Works. Returns
# 1.845111 with absolute error < 2.0e-14
integrate(f=f2,.5,1,const=testval)
# Doesn't work. Returns
# Error in eval(expr, envir, enclos) :
# ..1 used in an incorrect context, no ... to look in
I understand that I don't have to Vectorize this function for it to
work, but the more complicated functions I'm using require Vectorization.
Why can't I pass the argument "const" as a variable, instead of a value?
I don't understand this error.
I'm not sure what's happening exactly; both Vectorize and integrate do
tricky things with evaluation frames, and it looks as though they are
not interacting well.
As a workaround, I'd suggest using a single argument function f instead:
> makef <- function(const) {
+ return(function(x) 2^x + const)
+ }
makef(testval) will capture the value of testval, so we don't need to
pass it, and then things work:
> f <- makef(testval)
> f2 <- Vectorize(f)
> integrate(f=f2, 0.5, 1)
1.845111 with absolute error < 2.0e-14
Duncan Murdoch
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] R interpreter not recognized
Hi Paul, I am using Slackware 12.0.0. Maria On Thu, Apr 9, 2009 at 2:35 PM, Paul Smith wrote: > On Thu, Apr 9, 2009 at 9:01 AM, Maria I. Tchalakova > wrote: >> I am trying to install a program based on R, but I am receiving the >> following error message: >> r...@darkstar:/home/maria/UCS# perl System/Install.perl >> Error: Can't run the R interpreter (/usr/local/bin/R). >> Please make sure that R is installed and specify the fully qualified >> filename of the R interpreter with -R if necessary (see "doc/install.txt"). >> >> I do have installed R, and I can see it (it is working also fine when I use >> it): >>> which R >>> /usr/local/bin/R >> I have specified the location of the R interpreter with -R (or -rh) >> /usr/local/bin/R" when running the program, but it still doesn't work. >> I have also used -R /usr/local/lib/R/bin/R or -rh >> /usr/local/lib/R/bin/R. >> I have also added the locations to my search path. >> >> It seems that the problem comes from my environment, but I cannot >> figure out what's wrong. Do you have any clues why the interpreter >> cannot be found? > > Maria: what is the Linux distribution that you are using? > > Paul > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Find a zero of a composition of functions
Good morning to all,
I should find the zero of a specific function,
func(x,f.
me,c,t)=x+f.me*c-t
where 'c' and 't' are constants and 'f.me' is an other
function of 'x'.
Actually, I am interested in considering 'f.me' as an
expression().
Namely,
uniroot.me<-function(f.me,c,t){
func<-function(x,
f.me,c,t) x+eval(f.me)*c-t
uniroot(func,c(0,1),f.me=f.me,c=c,t=t)$root
}
uniroot.me(expression(x*(1-x)),c=1,t=1)
For instance, let me suppose
that 'f.me=expression(x^a*(1-x))'. How should I do in order to introduce the
new constant 'a' in function 'uniroot.me'?
Thank you very much,
Enrico
Foscolo
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Re: [R] Biexponential Fit
Thank you! Now it's working. Peter Dalgaard schrieb: Jonas Weickert wrote: Hi, I want to do a biexponential Fit, i.e. y ~ A1*exp(k1*x) + A2*exp(k2*x) Is this possible? I tried nls() but it stopped with several (different) errors. I'm using y and x as simple vectors and the formula for nls() exactly as mentioned above. Yes, it is possible, with some reservations. There is even a self-starting model for it (SSbiexp), at least if k1,k2 are negative. The reservations are that you need good data and good starting values for the fit. The model is theoretically unidentifiable because you can switch 1 and 2 and get the same model, which becomes an issue if you start too fra from the optimum. Worse, if k1 and k2 are similar, the whole system becomes ill-conditioned. There's a rule of thumb requiring a factor of 5 or more between k1 and k2, for pharmacokinetic applications. Thanks a lot! Jonas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Template Engine Package for R?
Jason Rupert wrote: Related to the posting below, by any chance is there a "Template Engine" package for R? Indeed there is. It's called brew: http://cran.r-project.org/web/packages/brew/index.html Jeff http://en.wikipedia.org/wiki/Template_processor This may make this type of editing much easier? Maybe... Thanks again. --- On Wed, 4/8/09, Jason Rupert wrote: From: Jason Rupert Subject: Re: [R] R File I/O Capability - Writing output to specific lines of existing file To: "jim holtman" Cc: R-help@r-project.org Date: Wednesday, April 8, 2009, 11:26 PM Darn. I was afraid of this. Always kind of weak when it comes to file I/O approaches, so I guess I will have to stretch and try to put something together. Yeah. The input flat text file is about 600 lines long. I will be replacing about 200. I already have the template for those 200 lines. I guess I will just need to read down to line 400 and replace until line 600. Thanks again for all the insights regarding this. --- On Wed, 4/8/09, jim holtman wrote: From: jim holtman Subject: Re: [R] R File I/O Capability - Writing output to specific lines of existing file To: jasonkrup...@yahoo.com Cc: R-help@r-project.org Date: Wednesday, April 8, 2009, 8:02 PM You can always read in the initialization file, make the updates to it and then write it back out. If it is a text file, it would be very hard to write into the middle of it since there is no structure to the file. You can read it in as a table (read.table) or just as lines (readLines) and the make any changes you want. You can use regular expressions if you want to put something in the middle of one of the lines you have read in. On Wed, Apr 8, 2009 at 10:13 AM, Jason Rupert wrote: Currently I am using the R "write"command to output results to a *.txt file and then copying those results into an initialization file. In an attempt to continue to automate the process I would like to have R write to the location in the existing initialization file, instead of me copying the data over. By any chance are there any R commands to help? Primarily, I will be using Windows, and the initialization file is a simple flat file, i.e. not XML or binary. I looked at: (a) http://www.stat.ucl.ac.be/ISdidactique/Rhelp/library/R.io/html/00Index.html (b) http://search.r-project.org/cgi-bin/namazu.cgi?query=File+I%2FO&max=100&result=normal&sort=score&idxname=functions&idxname=Rhelp08 But, this did not appear to provide the functionality to edit an existing file by adding information to the middle of the file. Thank you again for any help and insight. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- http://biostat.mc.vanderbilt.edu/JeffreyHorner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R interpreter not recognized
On Thu, Apr 9, 2009 at 9:01 AM, Maria I. Tchalakova wrote: > I am trying to install a program based on R, but I am receiving the > following error message: > r...@darkstar:/home/maria/UCS# perl System/Install.perl > Error: Can't run the R interpreter (/usr/local/bin/R). > Please make sure that R is installed and specify the fully qualified > filename of the R interpreter with -R if necessary (see "doc/install.txt"). > > I do have installed R, and I can see it (it is working also fine when I use > it): >> which R >> /usr/local/bin/R > I have specified the location of the R interpreter with -R (or -rh) > /usr/local/bin/R" when running the program, but it still doesn't work. > I have also used -R /usr/local/lib/R/bin/R or -rh > /usr/local/lib/R/bin/R. > I have also added the locations to my search path. > > It seems that the problem comes from my environment, but I cannot > figure out what's wrong. Do you have any clues why the interpreter > cannot be found? Maria: what is the Linux distribution that you are using? Paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] reading an image and adding a legend
Hi all,
I would like to
1. Read in an arcmap image into R (I can export pretty much any type of image
jpeg, bitmap etc from arcmap)
2. Use R to create a nice colour legend in the plot
First of all, Is this possible?
So far I'm stuck on point 1. I have tried read.pnm() from pixmap and
read.jpeg() from rgl.
the pnm example provided works fine
x <- read.pnm(system.file("pictures/logo.ppm", package="pixmap")[1])
plot(x)
#draws an R logo, nice :-)
But my code returns an error
x<-read.pnm("C:/Documents and Settings/simonp/My Documents/Simon BTO/RELU/GIS
data/ten km areas in analysis.bmp")
Error in pm.readmagicnumber(con) : Not a PNM format file
I have tried changing the dpi when I export the image but still no cigar.
I have dredged the help forum for related files and read the help files. My Os
is windows XP and i'm running 2.8.1.
I feel I'm missing something obvious!
Thanks
Dr. Simon Pickett
Research Ecologist
Land Use Department
Terrestrial Unit
British Trust for Ornithology
The Nunnery
Thetford
Norfolk
IP242PU
01842750050
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Biexponential Fit
Jonas Weickert wrote: Hi, I want to do a biexponential Fit, i.e. y ~ A1*exp(k1*x) + A2*exp(k2*x) Is this possible? I tried nls() but it stopped with several (different) errors. I'm using y and x as simple vectors and the formula for nls() exactly as mentioned above. Yes, it is possible, with some reservations. There is even a self-starting model for it (SSbiexp), at least if k1,k2 are negative. The reservations are that you need good data and good starting values for the fit. The model is theoretically unidentifiable because you can switch 1 and 2 and get the same model, which becomes an issue if you start too fra from the optimum. Worse, if k1 and k2 are similar, the whole system becomes ill-conditioned. There's a rule of thumb requiring a factor of 5 or more between k1 and k2, for pharmacokinetic applications. Thanks a lot! Jonas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Template Engine Package for R?
On Thu, Apr 9, 2009 at 12:42 PM, Jason Rupert wrote: > > Related to the posting below, by any chance is there a "Template Engine" > package for R? > > http://en.wikipedia.org/wiki/Template_processor > > This may make this type of editing much easier? Maybe... Have you tried the 'brew' package? It lets you embed tagged R expressions inside text files: http://ftp.heanet.ie/mirrors/cran.r-project.org/web/packages/brew/index.html (or a mirror near you) Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] problems with integrate ... arguments
Hi everyone,
I saw this problem dealt with here:
http://markmail.org/search/list:r-project?q=integrate#query:list%3Ar-project%20integrate+page:1+mid:qczmyzr676pgmaaw+state:results
but no one answered that request that I can tell. I'm having the same
problem. I'm having problems passing arguments to functions that I'd
like to integrate. I could swear this worked in the past, but I can't
get it to work now. I'm running R on Windows.
Here's my toy code to reproduce the problem:
R.Version()$version.string
# [1] "R version 2.8.1 (2008-12-22)"
f=function(x,const)
2^x+const
f2=Vectorize(f,c("x"))
testval=2
f2(1:5,testval)
# [1] 4 6 10 18 34
# The vectorized function seems to work right.
integrate(f2,.5,1,c=2)
# Works. Returns
# 1.845111 with absolute error < 2.0e-14
integrate(f=f2,.5,1,const=testval)
# Doesn't work. Returns
# Error in eval(expr, envir, enclos) :
# ..1 used in an incorrect context, no ... to look in
I understand that I don't have to Vectorize this function for it to
work, but the more complicated functions I'm using require Vectorization.
Why can't I pass the argument "const" as a variable, instead of a value?
I don't understand this error.
Thanks in advance,
Richard Morey
--
Richard D. Morey
Assistant Professor
Psychometrics and Statistics
Rijksuniversiteit Groningen / University of Groningen
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Re: [R] R File I/O Capability - Writing output to specific lines of existing file
With only 600 lines, it is relatively easy to read it in and replace
some lines. For example (untested) is you wanted to replace lines
150:250 with your data, you would do
input <- readLines('filename')
input <- c(input[1:149], newData, input[251:length(input)])
writeLines(input, file='filename')
That does not seem too hard.
On Thu, Apr 9, 2009 at 12:26 AM, Jason Rupert wrote:
>
> Darn.
>
> I was afraid of this. Always kind of weak when it comes to file I/O
> approaches, so I guess I will have to stretch and try to put something
> together.
>
> Yeah. The input flat text file is about 600 lines long. I will be replacing
> about 200. I already have the template for those 200 lines. I guess I will
> just need to read down to line 400 and replace until line 600.
>
> Thanks again for all the insights regarding this.
>
>
>
> --- On Wed, 4/8/09, jim holtman wrote:
>
>> From: jim holtman
>> Subject: Re: [R] R File I/O Capability - Writing output to specific lines of
>> existing file
>> To: jasonkrup...@yahoo.com
>> Cc: R-help@r-project.org
>> Date: Wednesday, April 8, 2009, 8:02 PM
>> You can always read in the initialization file, make the
>> updates to it
>> and then write it back out. If it is a text file, it would
>> be very
>> hard to write into the middle of it since there is no
>> structure to the
>> file. You can read it in as a table (read.table) or just
>> as lines
>> (readLines) and the make any changes you want. You can use
>> regular
>> expressions if you want to put something in the middle of
>> one of the
>> lines you have read in.
>>
>> On Wed, Apr 8, 2009 at 10:13 AM, Jason Rupert
>> wrote:
>> >
>> > Currently I am using the R "write" command
>> to output results to a *.txt file and then copying those
>> results into an initialization file. In an attempt to
>> continue to automate the process I would like to have R
>> write to the location in the existing initialization file,
>> instead of me copying the data over.
>> >
>> > By any chance are there any R commands to help?
>> >
>> > Primarily, I will be using Windows, and the
>> initialization file is a simple flat file, i.e. not XML or
>> binary.
>> >
>> > I looked at:
>> > (a)
>> http://www.stat.ucl.ac.be/ISdidactique/Rhelp/library/R.io/html/00Index.html
>> >
>> > (b)
>> http://search.r-project.org/cgi-bin/namazu.cgi?query=File+I%2FO&max=100&result=normal&sort=score&idxname=functions&idxname=Rhelp08
>> >
>> > But, this did not appear to provide the functionality
>> to edit an existing file by adding information to the middle
>> of the file.
>> >
>> > Thank you again for any help and insight.
>> >
>> > __
>> > R-help@r-project.org mailing list
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained,
>> reproducible code.
>> >
>>
>>
>>
>> --
>> Jim Holtman
>> Cincinnati, OH
>> +1 513 646 9390
>>
>> What is the problem that you are trying to solve?
>
>
>
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Template Engine Package for R?
Related to the posting below, by any chance is there a "Template Engine" package for R? http://en.wikipedia.org/wiki/Template_processor This may make this type of editing much easier? Maybe... Thanks again. --- On Wed, 4/8/09, Jason Rupert wrote: > From: Jason Rupert > Subject: Re: [R] R File I/O Capability - Writing output to specific lines of > existing file > To: "jim holtman" > Cc: R-help@r-project.org > Date: Wednesday, April 8, 2009, 11:26 PM > Darn. > > I was afraid of this. Always kind of weak when it comes to > file I/O approaches, so I guess I will have to stretch and > try to put something together. > > Yeah. The input flat text file is about 600 lines long. I > will be replacing about 200. I already have the template > for those 200 lines. I guess I will just need to read down > to line 400 and replace until line 600. > > Thanks again for all the insights regarding this. > > > > --- On Wed, 4/8/09, jim holtman > wrote: > > > From: jim holtman > > Subject: Re: [R] R File I/O Capability - Writing > output to specific lines of existing file > > To: jasonkrup...@yahoo.com > > Cc: R-help@r-project.org > > Date: Wednesday, April 8, 2009, 8:02 PM > > You can always read in the initialization file, make the > > updates to it and then write it back out. If it is a text > > file, it would be very hard to write into the middle of > > it since there is no structure to the file. You can read > > it in as a table (read.table) or just as lines > > (readLines) and the make any changes you want. You can use > > regular expressions if you want to put something in the > > middle of one of the lines you have read in. > > > > On Wed, Apr 8, 2009 at 10:13 AM, Jason Rupert > > wrote: > > > > > Currently I am using the R "write"command > > to output results to a *.txt file and then copying those > > results into an initialization file. In an attempt to > > continue to automate the process I would like to have R > > write to the location in the existing initialization file, > > instead of me copying the data over. > > By any chance are there any R commands to help? > > Primarily, I will be using Windows, and the > > initialization file is a simple flat file, i.e. not XML or > > binary. > > > > I looked at: > > (a) > http://www.stat.ucl.ac.be/ISdidactique/Rhelp/library/R.io/html/00Index.html > > (b) > > http://search.r-project.org/cgi-bin/namazu.cgi?query=File+I%2FO&max=100&result=normal&sort=score&idxname=functions&idxname=Rhelp08 > > > > But, this did not appear to provide the functionality > > to edit an existing file by adding information to the middle > > of the file. > > > > Thank you again for any help and insight. > > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] failed when merging two dataframes, why
try this:
> merge(df1, df2, by.x='codetot',by.y='codetoto', all=TRUE)
codetot popcode.x p3need popcode.y areasec
1 BCPy01-01-1 BCPy01-01 100. BCPy01-01 0.5089434
2 BCPy01-01-2 BCPy01-01 100. BCPy01-01 0.6246381
3 BCPy01-01-3 BCPy01-01 100. BCPy01-01 0.4370059
4 BCPy01-02-1 BCPy01-02 92.5926 BCPy01-02 0.9253052
5 BCPy01-02-1 BCPy01-02 92.5926 BCPy01-02 0.6011810
6 BCPy01-02-1 BCPy01-02 100. BCPy01-02 0.9253052
7 BCPy01-02-1 BCPy01-02 100. BCPy01-02 0.6011810
8 BCPy01-02-2 BCPy01-02 92.5926 BCPy01-02 0.6710850
9 BCPy01-02-2 BCPy01-02 92.5926 BCPy01-02 0.7145839
10 BCPy01-02-2 BCPy01-02 100. BCPy01-02 0.6710850
11 BCPy01-02-2 BCPy01-02 100. BCPy01-02 0.7145839
12 BCPy01-02-3 BCPy01-02 92.5926 BCPy01-02 0.9515256
13 BCPy01-02-3 BCPy01-02 92.5926 BCPy01-02 0.6555006
14 BCPy01-02-3 BCPy01-02 100. BCPy01-02 0.9515256
15 BCPy01-02-3 BCPy01-02 100. BCPy01-02 0.6555006
16 BCPy01-03-1 BCPy01-03 100. BCPy01-03 0.8683875
>
On Thu, Apr 9, 2009 at 7:19 AM, Mao Jianfeng wrote:
> Hi, R-listers,
>
> Failed, when I tried to merge df1 and df2 by "codetot" in df1 and "codetoto"
> in df2. I want to know the reason and how to merge them together. Data
> frames and codes I have used were listed as followed. Thanks a lot in
> advance.
>
> df1:
> popcode codetot p3need
> BCPy01-01 BCPy01-01-1 100.
> BCPy01-01 BCPy01-01-2 100.
> BCPy01-01 BCPy01-01-3 100.
> BCPy01-02 BCPy01-02-1 92.5926
> BCPy01-02 BCPy01-02-1 100.
> BCPy01-02 BCPy01-02-2 92.5926
> BCPy01-02 BCPy01-02-2 100.
> BCPy01-02 BCPy01-02-3 92.5926
> BCPy01-02 BCPy01-02-3 100.
> BCPy01-03 BCPy01-03-1 100.
>
> df2:
> popcode codetoto areasec
> BCPy01-01 BCPy01-01-1 0.5089434
> BCPy01-01 BCPy01-01-2 0.6246381
> BCPy01-01 BCPy01-01-3 0.4370059
> BCPy01-02 BCPy01-02-1 0.9253052
> BCPy01-02 BCPy01-02-1 0.6011810
> BCPy01-02 BCPy01-02-2 0.6710850
> BCPy01-02 BCPy01-02-2 0.7145839
> BCPy01-02 BCPy01-02-3 0.9515256
> BCPy01-02 BCPy01-02-3 0.6555006
> BCPy01-03 BCPy01-03-1 0.8683875
>
> code:
> new1<-merge(df1,df2,by=c("popcode","popcode"),all=T) # It is processed well.
> But, it is not what I want.
> new2<-merge(df1,df2,by=c("codetot","codetoto"),all=T) # this one failed. I
> exactly want to do that.
>
> Mao J-F
> IBCAS, AC
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
__
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Re: [R] Does R support [:punct:] in regexps?
On 09/04/2009 7:10 AM, Daniel Brewer wrote:
Hello does R support [:punct:] in regular expressions? I am trying to
strip all regular expressions for a vector of strings.
It does, but remember that the [] chars are part of the character class;
you need extra [] brackets around the whole thing, and you don't want
the slash delimiters:
> x <- c("yoda-yoda","billy!")
> gsub("[[:punct:]]","",x)
[1] "yodayoda" "billy"
Duncan Murdoch
x <- c("yoda-yoda","billy!")
gsub("/[:punct:]/","",x)
[1] "yoda-yoda" "billy!"
Thanks
Dan
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] change default output size when using Sweave
Hi,
I had a similar problem, and I took the direction of squeezing the
output into a minipage, e.g.:
...
@
\begin{minipage}[c]{0.6\textwidth}
<>=
plot(...)
abline(...)
@
\end{minipage}
...
HTH,
Gabriele Franzini
ICT Applications Manager
Nerviano Medical Sciences SRL
Nerviano Italy
-Original Message-
From: Mark Heckmann [mailto:mark.heckm...@gmx.de]
Sent: 08 April 2009 10:31
To: 'Duncan Murdoch'
Cc: r-help@r-project.org
Subject: Re: [R] change default output size when using Sweave
Dear Duncan,
Thanks for the reply. This works, but unfortunately I need a different
solution.
My script is supposed to run completely automated and the graphics I
produce vary in size each time I run the script. But I want the graphics
to be fitted to my .pdf output without specifying the height argument
manually each time.
That is why I do not want a fixed height as a code chunk argument.
Actually I do not know if it is possible to have a variable placed in a
code chunk header. I tried the following which does not work:
<<>>=
size <- 3
@
<>=
pushViewport(viewport(height = unit(80, "mm")))
grid.rect()
grid.text("I want this viewport to be the whole output size")
popViewport()
@
So still I face the problem to have Sweave generate a .pdf graphic that
is just as big I want it to be.
In the Sweave Docu paragraph A.9 I discovered something I use as a
workaround. I produce the .pdf output manually (where I can control the
size) and add each graphic to LaTex manually as well.
<>=
for (i in 1){
file=paste("myfile", i, ".pdf", sep="")
pdf(file=file, paper="special", width=6, height=3)
pushViewport(viewport(height = unit(5, "inches")))
grid.rect()
grid.text("I want this viewport to be the whole output size")
popViewport()dev.off()
cat("\\includegraphics{", file, "}\n\n", sep="") } @
I use parenthesis around the code as it prints out something I do not
want if no parenthesis are used (I use Windows).
I am not too happy with the solution. I would prefer a more
straightforward approach to define the size of the output graphic. I
wonder if there are some Sweave settings that can be modified.
In the Sweave manual (A.11) I found the following to customize the par
settings for each figure:
options(SweaveHooks=list(fig=function() par(bg="red", fg="blue")))
I wonder if something similar could be done changing the size of the
default output device (pdf or eps) for each figure like
>pdf.options(height=2) or similar (it seems that this does not work)?
I suppose this type of graphic customization is quite a common issue
when producing automated customized output/reports using R and Sweave
but I haven't found anything concerning this topic yet.
So I would be really glad if someone knows a solution.
TIA, Mark
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[R] failed when merging two dataframes, why
Hi, R-listers,
Failed, when I tried to merge df1 and df2 by "codetot" in df1 and "codetoto"
in df2. I want to know the reason and how to merge them together. Data
frames and codes I have used were listed as followed. Thanks a lot in
advance.
df1:
popcode codetot p3need
BCPy01-01 BCPy01-01-1 100.
BCPy01-01 BCPy01-01-2 100.
BCPy01-01 BCPy01-01-3 100.
BCPy01-02 BCPy01-02-1 92.5926
BCPy01-02 BCPy01-02-1 100.
BCPy01-02 BCPy01-02-2 92.5926
BCPy01-02 BCPy01-02-2 100.
BCPy01-02 BCPy01-02-3 92.5926
BCPy01-02 BCPy01-02-3 100.
BCPy01-03 BCPy01-03-1 100.
df2:
popcodecodetoto areasec
BCPy01-01 BCPy01-01-1 0.5089434
BCPy01-01 BCPy01-01-2 0.6246381
BCPy01-01 BCPy01-01-3 0.4370059
BCPy01-02 BCPy01-02-1 0.9253052
BCPy01-02 BCPy01-02-1 0.6011810
BCPy01-02 BCPy01-02-2 0.6710850
BCPy01-02 BCPy01-02-2 0.7145839
BCPy01-02 BCPy01-02-3 0.9515256
BCPy01-02 BCPy01-02-3 0.6555006
BCPy01-03 BCPy01-03-1 0.8683875
code:
new1<-merge(df1,df2,by=c("popcode","popcode"),all=T) # It is processed well.
But, it is not what I want.
new2<-merge(df1,df2,by=c("codetot","codetoto"),all=T) # this one failed. I
exactly want to do that.
Mao J-F
IBCAS, AC
[[alternative HTML version deleted]]
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[R] Multiple Hexbinplots in 2 columns with a Single Categorical Variable
Dear Ladies and Gentlemen, I have a fairly large database (N=13,000) and a single main categorical discriminator between the groups. I want to look at the time course of a number of continuous biochemical variables over chronologic age. Therefore I believe I need to prepare hexbinplots in two columns with simple regression lines in them (with useOuterStrips (in library(latticeExtra) if possible) and also single hexbinplots with two regression lines (panel.lmlines) corresponding to the two groups to facilitate data comparison. Tick marks and labels should be off in most panels, and the scale in each row will be different. I have some code written for the NHANES dataset in library(hexbin) which almost does this job, but leaves blank paper up the middle of the two columns of panels. I have been exploring lattice for this which almost gets me there but not quite. The code I have written is as follows. I would be ever so grateful for any advice anyone may be able to offer. With best wishes, Stuart Reece, Australia. useOuterStrips(hexbinplot(Transferin ~ Age | factor(Race) + factor(Sex), data = NHANES, type = "r", aspect = 1, scales = list(x = list(relation = "free", rot = 0, at=list(TRUE, TRUE, NULL, NULL)), y = list(relation = "free", rot = 0, at=list(TRUE, NULL, TRUE, NULL))), par.settings = list(layout.heights = list(axis.panel = rep(c(1, 0),c(1, 1, par.strip.text = list(cex = 1))) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Does R support [:punct:] in regexps?
Hello does R support [:punct:] in regular expressions? I am trying to
strip all regular expressions for a vector of strings.
> x <- c("yoda-yoda","billy!")
> gsub("/[:punct:]/","",x)
[1] "yoda-yoda" "billy!"
Thanks
Dan
--
**
Daniel Brewer, Ph.D.
Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.bre...@icr.ac.uk
**
The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company
Limited by Guarantee, Registered in England under Company No. 534147 with its
Registered Office at 123 Old Brompton Road, London SW7 3RP.
This e-mail message is confidential and for use by the a...{{dropped:2}}
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[R] arima on defined lags
Dear all, The standard call to ARIMA in the base package such as arima(y,c(5,0,0),include.mean=FALSE) gives a full 5th order lag polynomial model with for example coeffs Coefficients: ar1ar2 ar3 ar4 ar5 0.4715 0.067 -0.1772 0.0256 -0.2550 s.e. 0.1421 0.158 0.1569 0.1602 0.1469 Is it possible (I doubt it but am just checking) to define a more parsimonous lag1 and lag 5 model with coeff ar1 and ar5? Or do I need one of the other TS packages? thanks Gerard ** The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. It is the policy of the Department of Justice, Equality and Law Reform and the Agencies and Offices using its IT services to disallow the sending of offensive material. Should you consider that the material contained in this message is offensive you should contact the sender immediately and also mailminder[at]justice.ie. Is le haghaidh an duine nó an eintitis ar a bhfuil sí dírithe, agus le haghaidh an duine nó an eintitis sin amháin, a bheartaítear an fhaisnéis a tarchuireadh agus féadfaidh sé go bhfuil ábhar faoi rún agus/nó faoi phribhléid inti. Toirmisctear aon athbhreithniú, atarchur nó leathadh a dhéanamh ar an bhfaisnéis seo, aon úsáid eile a bhaint aisti nó aon ghníomh a dhéanamh ar a hiontaoibh, ag daoine nó ag eintitis seachas an faighteoir beartaithe. Má fuair tú é seo trí dhearmad, téigh i dteagmháil leis an seoltóir, le do thoil, agus scrios an t-ábhar as aon ríomhaire. Is é beartas na Roinne Dlí agus Cirt, Comhionannais agus Athchóirithe Dlí, agus na nOifígí agus na nGníomhaireachtaí a úsáideann seirbhísí TF na Roinne, seoladh ábhair cholúil a dhícheadú. Más rud é go measann tú gur ábhar colúil atá san ábhar atá sa teachtaireacht seo is ceart duit dul i dteagmháil leis an seoltóir láithreach agus le mailminder[ag]justice.ie chomh maith. *** __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Biexponential Fit
Hi, I want to do a biexponential Fit, i.e. y ~ A1*exp(k1*x) + A2*exp(k2*x) Is this possible? I tried nls() but it stopped with several (different) errors. I'm using y and x as simple vectors and the formula for nls() exactly as mentioned above. Thanks a lot! Jonas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] combine words and dataframe
Ravi S. Shankar ambaresearch.com> writes:
> I am trying to get an output like this
> Hi
> Hello
> 1 a b
# The easy way: good for logging of results, but commands print too,
# depending how you run it
df = data.frame(a=rep("a",3),b=rep("b",3))
sink(file="a.txt")
cat("Hello\n")
print(df)
sink()
# a bit better
cat("Hello\n",file="b.txt")
write.table(df,file="b.txt",append=TRUE,col.names=FALSE,
row.names=FALSE,quote=FALSE)
Dieter
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[R] problem with creating a netcdf file under script sh
Hi everyone,
I try to make a netcdf file which disposes a difference between 2 variables of
2netcdf files same dimension
When I programmed under R, everything is ok but when I put the code under EOF
of a sh script, an error occurs:
"Error, passed variable has a dim that is NOT of class dim.ncdf!". My programme
is:
x1<-open.ncdf("file1.nc")
x2<-open.ncdf("file2.nc")
y1<-get.var.ncdf(x1,"a")
y2<-get.var.ncdf(x2,"a")
y<- y1-y2
t<-var.def.ncdf("t",units="c",dim=x1$dim,-1)
nc<-create.ncdf("test.nc",vars=t)
put.var.ncdf(nc,t,y)
close.ncdf(nc)
Thanks in advance,
T.A
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Genstat into R - Randomisation test
Peter Dalgaard wrote: > Mike Lawrence wrote: >> Looks like that code implements a non-exhaustive variant of the >> randomization test, sometimes called a permutation test. > > Isn't it the other way around? (Permutation tests can be exhaustive by looking at all permutations, if a randomization test did that, then it wouldn't be random.) Eugene Edgington wrote an early book (1980) on this subject called "Randomization tests", published by Dekker. As far as I remember, he differentiates between "Systematic permutation" tests where one looks at all possible permutations. This is of course prohibitive for anything beyond trivially small samples. For larger samples he uses what he calls "Random permutations", where a random sample of the possible permutations is used. Tom Peter Dalgaard wrote: Mike Lawrence wrote: Looks like that code implements a non-exhaustive variant of the randomization test, sometimes called a permutation test. Isn't it the other way around? (Permutation tests can be exhaustive by looking at all permutations, if a randomization test did that, then it wouldn't be random.) -- ++ | Tom Backer Johnsen, Psychometrics Unit, Faculty of Psychology | | University of Bergen, Christies gt. 12, N-5015 Bergen, NORWAY | | Tel : +47-5558-9185Fax : +47-5558-9879 | | Email : bac...@psych.uib.noURL : http://www.galton.uib.no/ | ++ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Invoking bond_prices function of termstrc package
Hi,
I'm trying to invoke the function bond_prices from termstrc package.
Here is the code snippet:
library(termstrc)
data(eurobonds)
b <- matrix(rep(c(0,0,0, 1),1),nrow=1,byrow=TRUE)
group<-c("GERMANY")
colnames(b) <- c("beta0","beta1","beta2","tau1")
germaturities<-create_maturities_matrix(eurobonds$GERMANY)
bp<-bond_prices(method =
"Nelson/Siegel",b,germaturities,eurobonds$GERMANY$CASHFLOWS$CF)
bp
Running this, I get the following warning message:
In cf * discount_factors :
longer object length is not a multiple of shorter object length
Also the values I get (bp) seems not correct (way too high). I'm not sure if
I need to change b.
I'm on Windows XP and using R-2.7.2 + *termstrc* 1.1.
Any help will be appreciated.
Regards,
Visit us at http://www.2pirad.com
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Re: [R] Constrined dependent optimization.
Kevin, sorry I don't understand this sentence: "It has been suggested that I do a cluster analysis. Wouldn't this bet mepart way there?" Let your products be numbered 1, ..., n, and let p(i) be the location where product i is stored (assigned to) in the warehouse. Then p is a permutation of the set 1, ..., n and the task is an "assignment" problem. A sale v is simply a subset of 1, ..., n and the contribution to the target function could, for example, be f_v(p) = max( p(v) ) - min( p(v) ) for each sale v, or whatever your evaluation criterion is. The total function to minimize will then be Sum( f_v) for all historical sales v. Because it is based on a distance, the whole task is called a "quadratic" assignment problem (and is certainly not linear). In the literature you will find algorithms and tools mentioned to solve such a task, and n = 20,000 is not that much nowadays. But the difference between n = 100 and n = 20,000 is huge for tools not specialized to the task. For the TSP, imagine two groups of cities very far apart. Then under some mild restrictions it would not be reasonable to go back and forth between these groups several times, and therefore the problem could be split into two independent subproblems. So the question of clustering belongs to the data preparation part. Whether such really different classes of sales exist in your data, only you can decide. In my experience, most of the time such preprocessing is not worth doing and will not speed up the optimization procedure considerably. Regards, Hans Werner rkevinburton wrote: > > > It has been suggested that I do a cluster analysis. Wouldn't this bet > mepart way there? > > Thank you for your response I am looking up the book now. > > Kevin > > "Hans W. Borchers" wrote: >> >> Just in case you are still interested in theoretical aspects: >> >> In combinatorial optimization, the problem you describe is known as the >> Quadratic (Sum) Assignment Problem (QAP or QSAP) and is well known to >> arise in facility and warehouse layouts. The task itself is considered >> hard, comparable to the Traveling Salesman Problem (TSP). >> >> I would clearly advise to turn to some specialized commercial software >> for solving it, otherwise you will very likely get stuck in suboptimal >> solutions miles away from the true optimum. And for a real commercial >> situation this may be disastrous. >> >> Regards, Hans Werner >> >> P.S.: See for instance Cela: The Quadratic Assignment Problem. Theory >> and Algorithms, Springer, 2000. (Partly available at books.google.com) >> > > -- View this message in context: http://www.nabble.com/Constrined-dependent-optimization.-tp22772520p22966416.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] .Call()
Hi guys,
I want to transfer the following code from R into .Call compatible form. How
can i do that?
Thanks!!!
INT sim;
for(i in 1:sim){
if(i>2) genemat <- genemat[,sample(1:ncol(genemat))]
ranklist[,1] <- apply(genemat, 1, function(x){
(mean(x[cols]) -
mean(x[-cols]))/sd(x)})
ranklist <- ranklist[order(ranklist[,1]),]
if(ranklist[1,2]==1) score[i] <- 1/Ns
if(ranklist[1,2]==0) score[i] <- -(1/(N-Ns))
for(j in 2:nrow(ranklist)){
phit <- sum(rep(1/Ns, sum(ranklist[1:j,2]==1)))
pmiss <- sum(rep(1/(N-Ns), sum(ranklist[1:j,2]==0)))
if((phit-pmiss)>score[i]) score[i] <- phit - pmiss
}
}
I tried a little bit, but not enough knowledge in C.
#include
#include
#include
#include
SEXP ESscore(SEXP Rgeneset, SEXP Rgenemat, SEXP Rranklist, SEXP sim)
{
int nc = ncols(Rgenemat);
double *geneset = NUMERIC_DATA(Rgeneset);
double *genemat = NUMERIC_DATA(Rgenemat);
SEXP Rscore;
PROTECT(Rscore=NEW_NUMERIC(sim));
double *score = NUMERIC_DATA(Rscore);
for(i=1; i<=sim; i++){
if(i>2) {genemat <- genemat[,sample(1:nc)];}
for(k=1; khttps://stat.ethz.ch/mailman/listinfo/r-help
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