On Mon, 10 Sep 2012, Filipa J. wrote:
Dear R users,
I want to apply zero inflated models with continuous and categorical
variables and I used pscl package from R and the zeroinf() function. My
question are the follow:
a) The value of fitted.values is mu or (1-p)*mu? where p is the
probabil
Hi Team,
I am not sure how to run some r queries in continuos time interval for say in
each 30 minutes.
Will be very grateful if some one can give me some heads up in good direction.
Unfortunately I dont have any query written or data which I can share and I
know most of the respected people wi
I don't understand at all what the problem is, but a workaround
is simply not to specify the "pdf" argument in "name=value" form
but rather in positional form. I.e. just make it the first argument
to .Fortran(). As in:
tmp <- .Fortran("pdf", )
Works for me! :-)
cheers,
Rolf
I want to change it because I don't want to compare in this instance between
conditions, but I simply want to see the contrast t-statistic between
patient and control at every level of condition (1, 2, and 3).
>From there I'd like to be able to plot the t-statistic for the contrast
between patient
McCall, Ken (CMG-Dayton coxinc.com> writes:
> I'm trying to run a linear mixed effects analysis on fairly large
> datasets with lmer (from the lme4 package) on a 32-bit Windows
> machine running XP with 3 GB of RAM. It's not working. (details
> below)
> I've researched the ff and bigmemory pack
Hi all
I've been getting some emails from the R package maintainers that I need
to update some code in a CRAN packge that uses FORTRAN, to comply with
(not so recent) changes. I've been a little busy...
I'm having trouble adjusting my code. I hope someone can help.
The package was working fine
On Sep 10, 2012, at 5:14 PM, semperparatus wrote:
> Your problem seems to be exactly the problem I've been having for the past
> week. So glad to find this thread.
> However, when I follow the syntax you used to get around the issue, I still
> didn't get the output to work in the way yours did.
Your problem seems to be exactly the problem I've been having for the past
week. So glad to find this thread.
However, when I follow the syntax you used to get around the issue, I still
didn't get the output to work in the way yours did. I don't believe my
factors are truly nested however (nor yo
To exclude the color key use
plotBiomRatio2 <- segplot(
reorder(factor(Species), ratioBiomass) ~ (-SEratio ) + SEratio,
data = dfInOutBiom2,
col = "black",
level = NULL,
#-- this changed
colorkey = FALSE,
#-- end
draw.bands = FALSE,
c
Is it somehow possible to use the the predict method of the raster package
with a prediction model obtained using caret's train()?
/
predict(rasterStack, carettrain, filename="...", progress='text',
format="BSQ",
datatype='INT1U', type='response', overwrite=TRUE) /
Thank you
--
View t
Hello R List,
I'm trying to run a linear mixed effects analysis on fairly large datasets with
lmer (from the lme4 package) on a 32-bit Windows machine running XP with 3 GB
of RAM. It's not working. (details below)
I've researched the ff and bigmemory packages, but it appears they won't handle
A permissions problem in the current working directory?
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
On 9/10/12 1:29 PM, "Christian Hoffmann" wrote:
>Hi,
>
>What could the cause of
>
> > history()
>Error in savehistory(file)
Either way, there is a par() parameter to control the axis and label title
position.
Look at the entry for 'mgp' in ?par
-Don
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
On 9/10/12 2:17 PM, "David Winsemius" wrote:
>
>On S
On Mon, 10 Sep 2012, Bert Gunter wrote:
In addition, try this:
x <- rep(1:10,2); y <- runif(20);f<-factor(rep(paste("This
is\nLevel",1:2),e=10))
xyplot(y~x|f,
par.strip.text=list(lineheight=.8,lines=3))
Bert,
Thanks very much. If the docs are less than clear to you, they will
certainly be
Dear R helpers,
I am trying to test for linkage disequilibrium (LD) in R between all pairs
of loci. Importantly, my loci are microsatellites and have up to 30
alleles per locus. Do you know of any R packages that can either (1)
calculate measures of LD directly or (2) test for the presence of L
Hi,
I just got started analyzing data for a charter school, and am trying to
open Riverside Publishing's file of ITBS scores. I just assume that
someone, somewhere has opened this file before, and I was wondering if this
person had the code right now. There are over 100 variables, all of
different
On Sep 10, 2012, at 8:24 AM, Nicolai Schneider wrote:
> Hello,
>
> I´m really sorry to bother you with this problem but it took me a whole day
> searching for a solution.
>
> I want the y axis labels positioned closer to the y axis, by default they are
> partly outside the window.
>
>
> Exa
On Sep 10, 2012, at 1:48 PM, Bert Gunter wrote:
> In addition, try this:
>
> x <- rep(1:10,2); y <- runif(20);f<-factor(rep(paste("This
> is\nLevel",1:2),e=10))
> xyplot(y~x|f,
> par.strip.text=list(lineheight=.8,lines=3))
Bert;
I had imagined that the factor level character strings could b
Thanks, David. I am working on a biology-related project where I have a
matrix of gene-to-gene interactions,
( interactions * distances ) and depending on the basic R functions, I do
get vary different results ...
Bogdan
On Mon, Sep 10, 2012 at 1:52 PM, David Winsemius wrote:
>
> On Sep 10, 201
On Sep 10, 2012, at 1:43 PM, Bogdan Tanasa wrote:
> Dear all,
>
> please do you have any recommendation about a more advanced function in R
> for lowess/loess regression ?
> the basics lowess() or loess() do not perform as well as I would expect.
> thanks very much,
>
You should probably look
In addition, try this:
x <- rep(1:10,2); y <- runif(20);f<-factor(rep(paste("This
is\nLevel",1:2),e=10))
xyplot(y~x|f,
par.strip.text=list(lineheight=.8,lines=3))
I find the documentation here confusing and incomplete:
"par.strip.text" is listed as a parameter both in ?xyplot and
?strip.custom.
Dear all,
please do you have any recommendation about a more advanced function in R
for lowess/loess regression ?
the basics lowess() or loess() do not perform as well as I would expect.
thanks very much,
Bogdan
[[alternative HTML version deleted]]
__
Thanks!!
That did the trick!!
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__
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https://stat.
Dear R users,
I want to apply zero inflated models with continuous and categorical
variables and I used pscl package from R and the zeroinf() function. My
question are the follow:
a) The value of fitted.values is mu or (1-p)*mu? where p is the probability
of zero came form a zero point mass
b)
Thank you for the help and fast response. I'm going to look into getting
some time on the unix machines.
On Sep 10, 2012 10:28 AM, "Prof Brian Ripley [via R]" <
ml-node+s789695n4642670...@n4.nabble.com> wrote:
On 10/09/2012 16:13, chrisk wrote:
> I having issues with my memory size in R for Win
Hello,
Please use dput(dfA) to post your data examples. The following is it's
output. All one has to do is to copy and paste to an R session to get
the data example.
dfA <-
structure(list(Site = c(929L, 929L, 930L, 930L, 931L, 932L),
State = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = "VA",
On Mon, 10 Sep 2012, David Winsemius wrote:
The text that appears in the "panel header" is called the "strip". I
didn't see it in the help page for bwplot. You need to look at:
David,
That explains why I did not find it in the book's index.
?strip.custom.
And since you have the Lattice b
On Sep 10, 2012, at 11:35 AM, Rich Shepard wrote:
> A conditioning factor for bwplot() is the stream name. There are 17
> streams so each panel is comparatively small and the names in the panel
> header are truncated at both ends. I would like to wrap the names on two
> lines for each panel but
Hi,
What could the cause of
> history()
Error in savehistory(file) : no history available to save
> savehistory(file="myhist")
Error in savehistory(file) : no history available to save
> save.image()
be?.
Cheers
Christian
--
Christian W. Hoffmann,
CH - 8915 Hausen am Albis, Switzerland
Rigibl
Hello,
Try the following.
#-- this is new
colfun <- colorRampPalette(c("black", "white"))
cols <- colfun(nrow(dfInOutBiom2))
#-- end
plotBiomRatio2 <- segplot(
reorder(factor(Species), ratioBiomass) ~ (-SEratio ) + SEratio,
data = dfInOutBiom2,
#-- thi
A conditioning factor for bwplot() is the stream name. There are 17
streams so each panel is comparatively small and the names in the panel
header are truncated at both ends. I would like to wrap the names on two
lines for each panel but do not see if this can be done when I look at the
online d
On Mon, Sep 10, 2012 at 11:23:42AM -0700, kborgmann wrote:
> Hi,
> I am trying to identify duplicate values in a column in a date frame. The
> duplicated function identifies the duplicate rows in the data frame but it
> only does this for the second record, not both records. Is there a way to
> ma
try this:
dfA$dups<-duplicated(dfA$Value) | duplicated(dfA$Value, fromLast = TRUE)
On Mon, Sep 10, 2012 at 2:23 PM, kborgmann wrote:
> Hi,
> I am trying to identify duplicate values in a column in a date frame. The
> duplicated function identifies the duplicate rows in the data frame but it
> o
Hi,
I am trying to identify duplicate values in a column in a date frame. The
duplicated function identifies the duplicate rows in the data frame but it
only does this for the second record, not both records. Is there a way to
mark both rows in the data frame as TRUE?
dfA$dups<-duplicated(dfA$Val
HI,
Sorry, there was a mistake. I forgot to add some code.
Try this:
dat1<-read.table(text="
a b c d
x 3 6 7 6
y 7 8 6 5
z 5 4 7 8
",sep="",header=TRUE)
new1<-sapply(combn(dat1[,1:4],2),`[`,1:3)
colnames(new1)<-sapply(combn(colnames(dat1),2),`[`,1)
new2<-as.matrix(new1)
dim(new2)<-c(3,
On Sep 10, 2012, at 11:03 AM, David Winsemius wrote:
>
> On Sep 10, 2012, at 7:00 AM, priya wrote:
>
>> Hi ,
>> I am new to R .
>
> How new? Is this still in a file? ... or has it been imported to an R object.
> If it really still is in a file, then Bert's suggestion of first reading
> "Int
On Sep 10, 2012, at 7:00 AM, priya wrote:
> Hi ,
> I am new to R .
How new? Is this still in a file? ... or has it been imported to an R object.
If it really still is in a file, then Bert's suggestion of first reading
"Intro to R" rather than posting to R help is on point. If it is an R objec
On Sep 10, 2012, at 9:14 AM, Hermann Norpois wrote:
> Hello,
>
> I have a list with gene names, fold changes (=expression level) and
> chromosomes.
>
> Names fold change chromosome
> hz 1.5 2
>
>
> If I plot fold change versus chromosome (or vice versa):
>
> plot (ch
The answer to your question probably lies in your data. If you follow the
instructions at the footer of every email on this list and provide an example
that we can run (reproducible), we will be able to do more than guess.
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reprod
You will have to **show** what you did; it isn't sufficient to
**describe** what you did.
The problem could be that somewhere in your program there is something
that only works in an interactive session.
The problem could be that your "command-line" attempt is using a different
working directory
On 10/09/2012 16:13, chrisk wrote:
I having issues with my memory size in R for Windows. I have implemented the
3gb switch for Windows 7 32 bit with 8gb of memory, only 4gb is available
for use due to 32 bit limitations. 512Mb is taken by the shared video card,
the memory limit is 2559mb yet I
On 10-09-2012, at 17:10, berg1546 wrote:
> Thank you for your suggestion - my only question is what is the 'par'
> variable?
>
>
par is the argument of the function f.
So when you do
a <- c(2,3)
f(a)
then in the body of the function par will be equal to c(2,3).
I strongly advise you to re
1. Be forewarned: There may be special approaches built into specific
packages that are better than "generalist" approaches like the one I
suggest here.
2. The general approach to this sort of thing is with ?outer, if I
understand you correctly.
3. Have you read an Introduction to R (ships with e
Hi to all
I hope you can help me.
# I'm trying to plot the following ratio data with standard error bars
(horizontal).
ratioBiomass <- c(1.327, 0.865, 1.900, 0.992, 1.469, 1.381, 1.230,1.269,
2.411, 1.288, 1.861, 0.714, 1.341, 1.362, 1.065, 2.374)
SEratio <- c(19.28, 5.04, 0.01, 0.01, 0.90,
I having issues with my memory size in R for Windows. I have implemented the
3gb switch for Windows 7 32 bit with 8gb of memory, only 4gb is available
for use due to 32 bit limitations. 512Mb is taken by the shared video card,
the memory limit is 2559mb yet I cannot use more than 1.5 gb of memory
Hello,
I have a list with gene names, fold changes (=expression level) and
chromosomes.
Names fold change chromosome
hz 1.5 2
If I plot fold change versus chromosome (or vice versa):
plot (ch, fc)
I see only the chromosomes with numbers but not those with letter (x an
Hello, I have a question regarding the predict command for ARIMA models. Why do
I not have to give any input except the number of steps for the forecast? Which
input value is used (in my case for y(t))? Will the last parameter of the
estimate vector be used (in my example 6)? x <- c(1,2,3
Thank you for your suggestion - my only question is what is the 'par'
variable?
--
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Howdy,
Last week I got some great help on why I was getting an error code when trying
to run this model, thanks everyone! I was able to get the code up and running
beautifully for several data sets. Now I am getting different errors with this
new data set. I can't figure out why, I have more
Thanks for this. A few things
First, yes, my lmer syntax was indeed bad - I was writing this as an example of
what my data & code look like. Apologies. So, 1|studyID indeed. Also
1/variance.
I've also been wondering - I often have more than 2 drugs - so, T1, T2, T3,
etc. It depends on wh
Hi ,
I am new to R . I am facing difficulty how to make pairwise comparisions.
For example. I have a file which looks like below
a b c d
x 3 6 7 6
y 7 8 6 5
z 5 4 7 8
Here I need to look for the each pairwise comparisions (ab,ac,ad,bc,bd,cd
for each row)
For instance ,looking at first row, f
Dear all,
As David mentioned, I used his R-code to try to see the dimension behind the
'LO2' variable. These are the results:
> lapply (subsets, function (x) {table(x$LO2)})
[[1]]
nee geen atrofie ja atrofie aanweizg
173 0
[[2]]
nee geen atrofie ja atro
HI Sridhar,
You may not need to order the dataset by the "X" to do the merge.
It's already ordered.
Combinedat1<-merge(testMaster1,test2Sorted1,by="X")
new1<-merge(testMaster,test2Sorted,by="X")
identical(Combinedat1,new1)
#[1] TRUE
A.K.
- Original Message -
From: Sridhar Iyer
To:
Hello,
I´m really sorry to bother you with this problem but it took me a whole day
searching for a solution.
I want the y axis labels positioned closer to the y axis, by default they are
partly outside the window.
Example:
x <- as.zoo(EuStockMarkets)
par(las=1)
plot.zoo(x, type="l", main="
Jonas Stein jonasstein.de> writes:
>
> Hi,
>
> i would like to plot a few hundred .csv files.
> Each file contains one curve with x,y values to plot.
>
> I have been searching for "gnu r read many files qplot"
> and similar words. I found for loops that use assign to generate
> one variable
HI Sridhar,
Try this:
#I saved the file as .csv.
testMaster<-read.csv("test1Master.csv")
test2Sorted<-read.csv("test2Sorted.csv")
testMaster1<-testMaster[order(testMaster[,1]),]
test2Sorted1<-test2Sorted[order(test2Sorted[,1]),]
Combinedat<-as.matrix(merge(testMaster1,test2Sorted1,by="X"))
row
HI,
You can also use ?merge()
Same example data from Milan:
A <- matrix(runif(4*10), 10)
rownames(A) <- LETTERS[1:10]
B <- matrix(runif(10), 10)
rownames(B) <- sample(LETTERS[1:10])
#Either, use
C<-as.matrix(merge(A,B[order(rownames(B)),],by="row.names"))
#or C<-as.matrix(merge(A,B[order(rownames
Hi Rolf,
I suggested that in matrix, duplicate row names are possible.
set.seed(1)
dat1<-data.frame(a=sample(1:50,5,replace=TRUE),b=rnorm(5,15))
dat2<-as.matrix(dat1)
row.names(dat2)<-rep("a",5)
A.K.
- Original Message -
From: Rolf Turner
To: Fred
Cc: r-help@r-project.org
Sent:
Hi everyone,
Here is a summary of what I am trying to do. Please take a look and let me
know how can i complete this below mentioned objective using R for a large
dataset.
**
- *Objective:*
- To calculate the number of points that fall inside each cell of a
given raster
- *Input
On 10/09/2012 11:49, Duncan Murdoch wrote:
On 12-09-10 3:28 AM, Christian Hoffmann wrote:
Sorry to bother everyone. What has changed in Sweave since 2009?
Sweave("Crs.Rnw")
Error: c("'Crs.HdrFct.Rnw'", "'Crs.Rnw'") is not ASCII and does not
declare an encoding
No error in 2009 with the same fi
On 12-09-10 3:28 AM, Christian Hoffmann wrote:
Sorry to bother everyone. What has changed in Sweave since 2009?
Sweave("Crs.Rnw")
Error: c("'Crs.HdrFct.Rnw'", "'Crs.Rnw'") is not ASCII and does not
declare an encoding
No error in 2009 with the same files.
heers
Christian
vignettes are now
Hello,
Something like this?
step <- myLength %/% 500
ix500 <- seq(1, myLength, by = step)
curSubset <- currentSet[ix500]
plot(seq(from = 1, to = myMax, length.out = 500), curSubset, ...etc...
Hope this helps,
Rui Barradas
Em 10-09-2012 09:14, Alaios escreveu:
> Dear all,
> I am including in
> > Dear all,
> > I am including in a plot 6 different lines (?lines) with 6
> different line types.
> > The problem is that I have so dense information that the
> line types are not visible any more.
Perhaps plot a lowess or loess curve to show trend instead of a point to point
line?
S Elliso
On 09/10/2012 06:14 PM, Alaios wrote:
Dear all,
I am including in a plot 6 different lines (?lines) with 6 different line types.
The problem is that I have so dense information that the line types are not
visible any more.
In the code below
myLength<-length(currentSet)
plot(seq(from=1,to=myMa
As usual, Michael was faster than I in responding. Let me add a few thoughts of
my own. See comments below in text.
Best,
Wolfgang
--
Wolfgang Viechtbauer, Ph.D., Statistician
Department of Psychiatry and Psychology
School for Mental Health and Neuroscience
Faculty of Health, Medicin
Hi
> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
> project.org] On Behalf Of Fred
> Sent: Sunday, September 09, 2012 7:45 PM
> To: r-help@r-project.org
> Subject: Re: [R] how to save a heatmap.2 in png /jpeg /tiff
>
> Hey Jeff, sorry for the "it just
Hi,
i would like to plot a few hundred .csv files.
Each file contains one curve with x,y values to plot.
I have been searching for "gnu r read many files qplot"
and similar words. I found for loops that use assign to generate
one variable containing a dataframe.
When i uesed the classic "plot
Thanks everyone for your comments and help.
Actually, I found my mistake (probably stupid for y'all). I was drawing
first the heatmap and then putting the
>png("heatmap.2.png").
What you have to do is :
>a<- read.csv (" .csv)
>a_matrix <- data.matrix (a)
>row.names(a_matrix) <-a$Name # In my
Dear all,
I am including in a plot 6 different lines (?lines) with 6 different line types.
The problem is that I have so dense information that the line types are not
visible any more.
In the code below
myLength<-length(currentSet)
plot(seq(from=1,to=myMax,length.out=myLength),currentSet,
typ
Sorry to bother everyone. What has changed in Sweave since 2009?
Sweave("Crs.Rnw")
Error: c("'Crs.HdrFct.Rnw'", "'Crs.Rnw'") is not ASCII and does not
declare an encoding
No error in 2009 with the same files.
heers
Christian
--
Christian W. Hoffmann,
CH - 8915 Hausen am Albis, Switzerland
R
Le dimanche 09 septembre 2012 à 19:29 -0500, Sridhar Iyer a écrit :
> Hi,
>
> I have two matrices. (same size, same number of rows,
> same names for the rows - one has data in sorted
> order, another one master data in unsorted order. I need to
> combine both).
>
> Rows names of Matrix A
> P, Q
On 10-09-2012, at 01:22, berg1546 wrote:
> Hi,
>
> I am trying to find a simple way to numerically solve a system of two
> equations equal to zero with two unknowns (x_loc and y_loc). Here is a mock
> data set and below it, the equations I need to solve.
>
> theta<-c(180,135,90)/(2*pi)
> x<-c(0
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