Re: [R] Neural Network
Dear All; Many thanks for your attention. what I want to know is: How can I predict the Eutrophication by these parameters in the future? These variables are the most important variables that control the Eutro. in lakes. Let me break it to two parts. 1) How can I predict these variables by NN? 2) Is it possible to predict the Eutro. by these variables? Many thanks for your help. Regards, On Thu, 1/22/15, Charles Determan Jr wrote: Subject: Re: [R] Neural Network roject.org> Date: Thursday, January 22, 2015, 4:41 PM Javad, First, please make sure to hit 'reply all' so that these messages go to the R help list so others (many far more skilled than I) may possibly chime in. The problem here is that you appear to have no dependent variable (i.e. no eutrophication variable). Without it, there is no way to a typical 'supervised' analysis. Given that this is likely a regression type problem (I assume eutrophication would be continous) I'm not quite sure 'supervised' is the correct description but it furthers my point that you need a dependent variable for any neuralnet algorithm I am aware of. As such, if you don't have a dependent variable then you will need to look at unsupervised methods such as PCA. Other users may have other suggestions. Regards,Charles On Wed, Jan 21, 2015 at wrote: Dear Charles; Many thanks for your attention. what I want to know is: How can I predict the Eutrophication by these parameters in the future? These variables are the most important variables that control the Eutro. in lakes. Let me break it to two parts. 1) How can I predict these variables by NN? 2) Is it possible to predict the Eutro. by these variables? Many thanks for your help. Regards, On Wed, 1/21/15, Charles Determan Jr wrote: Subject: Re: [R] Neural Network Cc: "r-help@r-project.org" Date: Wednesday, January 21, 2015, 9:10 PM Javad, You question is a little too broad to be answered definitively. Also, this is not a code writing service. You should make a meaningful attempt and we are here to help when you get stuck. 1. If you want to know if you can do neural nets, the answer is yes. The three packages most commonly used (that I know of) are 'neuralnet', 'nnet' and 'RSNNS'. You should look in to these package documentation for how to use them. There are also many examples online if you simply google them. 2. You question is unclear, are you wanting to predict all the variables (e.g. phosphorus, Total N, etc.) or do you have some metric for eutrophication? What exactly is the model supposed to predict? 3. If you want to know if a neuralnet is appropriate, that is more of a statistical question. It depends more on the question you want to answer. Given your temporal data, you may want to look in to mixed effects models (e.g nlme, lme4) as another potential approach. Regards, On Tue, Jan 20, 2015 at 11:35 PM, javad bayat via R-help wrote: Dear all; I am the new user of R. I want to simulation or prediction the Eutrophication of a lake. I have weekly data(almost for two years) for Total phosphorus, Total N, pH, Chlorophyll a, Alkalinity, Silica. Can I predict the Eutrophication by Neural Network in R? How can I simulation the Eutrophication by these parameter? please help me to write the codes. many thanks. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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. -- Dr. Charles Determan, PhD Integrated Biosciences -- Dr. Charles Determan, PhD Integrated Biosciences __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Neural Network
Dear Charles; I think my variables are dependent. For e.g. the concentration of Phosphorus, Nitrogen, Silica and etc. have effect on the present of Chlorophyll a and the concentration of Chlorophyll a can make the Eutrophication in lake along with other algeas. So I think they are dependent variables. Regards. On Thu, 1/22/15, Charles Determan Jr wrote: Subject: Re: [R] Neural Network roject.org> Date: Thursday, January 22, 2015, 4:41 PM Javad, First, please make sure to hit 'reply all' so that these messages go to the R help list so others (many far more skilled than I) may possibly chime in. The problem here is that you appear to have no dependent variable (i.e. no eutrophication variable). Without it, there is no way to a typical 'supervised' analysis. Given that this is likely a regression type problem (I assume eutrophication would be continous) I'm not quite sure 'supervised' is the correct description but it furthers my point that you need a dependent variable for any neuralnet algorithm I am aware of. As such, if you don't have a dependent variable then you will need to look at unsupervised methods such as PCA. Other users may have other suggestions. Regards,Charles On Wed, Jan 21, 2015 at wrote: Dear Charles; Many thanks for your attention. what I want to know is: How can I predict the Eutrophication by these parameters in the future? These variables are the most important variables that control the Eutro. in lakes. Let me break it to two parts. 1) How can I predict these variables by NN? 2) Is it possible to predict the Eutro. by these variables? Many thanks for your help. Regards, On Wed, 1/21/15, Charles Determan Jr wrote: Subject: Re: [R] Neural Network Cc: "r-help@r-project.org" Date: Wednesday, January 21, 2015, 9:10 PM Javad, You question is a little too broad to be answered definitively. Also, this is not a code writing service. You should make a meaningful attempt and we are here to help when you get stuck. 1. If you want to know if you can do neural nets, the answer is yes. The three packages most commonly used (that I know of) are 'neuralnet', 'nnet' and 'RSNNS'. You should look in to these package documentation for how to use them. There are also many examples online if you simply google them. 2. You question is unclear, are you wanting to predict all the variables (e.g. phosphorus, Total N, etc.) or do you have some metric for eutrophication? What exactly is the model supposed to predict? 3. If you want to know if a neuralnet is appropriate, that is more of a statistical question. It depends more on the question you want to answer. Given your temporal data, you may want to look in to mixed effects models (e.g nlme, lme4) as another potential approach. Regards, On Tue, Jan 20, 2015 at 11:35 PM, javad bayat via R-help wrote: Dear all; I am the new user of R. I want to simulation or prediction the Eutrophication of a lake. I have weekly data(almost for two years) for Total phosphorus, Total N, pH, Chlorophyll a, Alkalinity, Silica. Can I predict the Eutrophication by Neural Network in R? How can I simulation the Eutrophication by these parameter? please help me to write the codes. many thanks. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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. -- Dr. Charles Determan, PhD Integrated Biosciences -- Dr. Charles Determan, PhD Integrated Biosciences __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Operations with dates just as Month and Day and not Year
Hi everyone,
I am trying to calculate the number of days between any two dates in a year
regardless of the year. Specifically, image two dates:
MonDay1 <- "01-30" #January 30
MonDay2 <- "12-31" #December 31
I want the difference of those two dates to be
MonDay1- MonDay2=30 days #January is closer to December from the prior year
than to the December in the year when January is.
FYI. this calculation is to count the number of days between any given date to
the peak of the summer, which in the southern hemisphere can be around December.
Unfortunately, I have not been able to make R recognize a date as just Mon-Day.
If I try:
MonDay1<-as.Date("01-30",format="%m-%d")# this automatically assigns the
current year
[1] "2015-01-30"
This following code allows to define just Mon-Day but it is recognized as
character:
format(strptime("07-30", format="%j"), format="%m-%d")
Any help will be greatly appreciated,
Thanks,
Camilo
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Re: [R] correlation between categorical data
Heinz Tuechler wrote > At 07:40 21.06.2009, J Dougherty wrote: > > [...] >>There are other ways of regarding the FET. Since it is precisely >>what it says >>- an exact test - you can argue that you should avoid carrying over any >>conclusions drawn about the small population the test was applied to and >>employing them in a broader context. In so far as the test is concerned, the >>"sample" data and the contingency table it is arrayed in are the entire >>universe. In that sense, the FET can't be "conservative" or "liberal." It >>isn't actually a hypothesis test and should not be thought of as one or used >>in the place of one. >> > >>JDougherty > > Could you give some reference, supporting this, for me, surprising > view? I don't see a necessary connection between an exact test and > the idea that it does not test a hypothesis. > > Thanks, > Heinz > > __ > R-help@ > 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. Fisher's Exact Test is a nonparametric "test." It tests the distribution in the contingency table against the total possible arrangements and gives you the precise likelihood of that many items being arranged in that manner. No more and no less. You could argue about the greater population from which your sample is drawn, but FET makes no assumptions at all about any greater sample universe. Also, since the "population" being used in FET is strictly limited to the members of the contingency table, the results are a subset of a finite group of possible results that are relevant to that specific arrangement of data. You are not "estimating" parameters of a parent population or making any assumptions about the parent distribution. You can designate a "p" value such as 0.05 as a level of significance, but there is no "error" term in the FET result. Fisher stated that the test DOES assume a null hypothesis of independence to a hypergeometric distribution of the cell members. But that creates other issues if you are attempting to use the results in conjunction with assumptions about a broader sample universe than that in the test. For instance you have to carry the assumption of a hypergeometric distribution over in to the land of reality your sample is drawn from and you then have to justify that. -- View this message in context: http://r.789695.n4.nabble.com/correlation-between-categorical-data-tp888975p4702235.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] get latest dates for different people in a dataset
> do.call(rbind, lapply(split(data, data$Name), function(x) x[order(x$CheckInDate),][nrow(x),])) Name CheckInDate Temp John John 2014-04-01 99.0 Mary Mary 2014-03-01 98.1 Sam Sam 2014-04-01 97.5 > Is this what you are looking for? I hope this helps. Chel Hee Lee On 01/23/2015 05:43 PM, Tan, Richard wrote: Hi, Can someone help for a R question? I have a data set like: NameCheckInDate Temp John 1/3/2014 97 Mary 1/3/2014 98.1 Sam 1/4/2014 97.5 John 1/4/2014 99 I'd like to return a dataset that for each Name, get the row that is the latest CheckInDate for that person. For the example above it would be NameCheckInDate Temp John 1/4/2014 99 Mary 1/3/2014 98.1 Sam 1/4/2014 97.5 Thank you for your help! Richard [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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 -- To UNSUBSCRIBE and more, see 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] get latest dates for different people in a dataset
Here is one way. Sort the data.frame, first by Name then break ties with
CheckInDate.
Then choose the rows that are the last in a run of identical Name values.
> txt <- "NameCheckInDate Temp
+ John 1/3/2014 97
+ Mary 1/3/2014 98.1
+ Sam 1/4/2014 97.5
+ John 1/4/2014 99"
> d <- read.table(header=TRUE,
colClasses=c("character","character","numeric"), text=txt)
> d$CheckInDate <- as.Date(d$CheckInDate, as.Date, format="%d/%m/%Y")
> isEndOfRun <- function(x) c(x[-1] != x[-length(x)], TRUE)
> dSorted <- d[order(d$Name, d$CheckInDate), ]
> dLatestVisit <- dSorted[isEndOfRun(dSorted$Name), ]
> dLatestVisit
Name CheckInDate Temp
4 John 2014-04-01 99.0
2 Mary 2014-03-01 98.1
3 Sam 2014-04-01 97.5
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Fri, Jan 23, 2015 at 3:43 PM, Tan, Richard wrote:
> Hi,
>
> Can someone help for a R question?
>
> I have a data set like:
>
> NameCheckInDate Temp
> John 1/3/2014 97
> Mary 1/3/2014 98.1
> Sam 1/4/2014 97.5
> John 1/4/2014 99
>
> I'd like to return a dataset that for each Name, get the row that is the
> latest CheckInDate for that person. For the example above it would be
>
> NameCheckInDate Temp
> John 1/4/2014 99
> Mary 1/3/2014 98.1
> Sam 1/4/2014 97.5
>
>
> Thank you for your help!
>
> Richard
>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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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[R] get latest dates for different people in a dataset
Hi, Can someone help for a R question? I have a data set like: NameCheckInDate Temp John 1/3/2014 97 Mary 1/3/2014 98.1 Sam 1/4/2014 97.5 John 1/4/2014 99 I'd like to return a dataset that for each Name, get the row that is the latest CheckInDate for that person. For the example above it would be NameCheckInDate Temp John 1/4/2014 99 Mary 1/3/2014 98.1 Sam 1/4/2014 97.5 Thank you for your help! Richard [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] plot circles where z values are circles radius
Hi Alireza,
Part of the problem is the scale of your numbers. You probably want
something like this.
plot(x,y,cex=z/min(z)*2)
What happens here is that the default plotting character, which
happens to be a circle, is plotted in a size relative to the ratio of
each z value to the minimum z value. This is because the default value
of cex is 1. I have multiplied the result by 2 to make what is
happening more obvious. If you want to generate circles with specific
diameters, you will have to scale these to the area of the plot in
user units - see par("usr").
Jim
On Sat, Jan 24, 2015 at 8:29 AM, Thomas Adams wrote:
> I think what you should look at are these web sites I found with a Google
> search:
>
> http://flowingdata.com/2010/11/23/how-to-make-bubble-charts/
> http://www.r-bloggers.com/bubble-plots-ggplot2/
> http://cran.r-project.org/web/packages/HSAUR/vignettes/Ch_logistic_regression_glm.pdf
> http://cran.r-project.org/web/packages/mapplots/mapplots.pdf
>
>
> Cheers!
> Tom
>
> On Fri, Jan 23, 2015 at 2:12 PM, Dr. Alireza Zolfaghari <
> ali.zolfagh...@gmail.com> wrote:
>
>> Hi there,
>> I am trying to plot z values using Circle symbol. Each x and y has a value
>> which will be plotted using a circle where circle's radius is corrlated
>> with the value of z.
>>
>> I wrote the code , but unable to change the size of circle no matter what I
>> chose for Scale. Any help please?
>>
>> x=c(84390255386 ,84390255386, 78028317380 ,53594648044,422)
>> y=c(949849442 ,941645043, 840135292, 74, 821632939)
>> z=c(0.005641896, 0.005641896 ,0.005641896, 0.007978846,0.007978846)
>>
>> convertToRadius<-function(x){return(sqrt(x/pi))}
>>
>> scale=0.3
>>
>> xlims =c(min(x),max(x))
>> ylims =c(min(y),max(y))
>> z=convertToRadius(z)*scale
>>
>> symbols(x,y, circles=z, fg='red')
>>
>> thanks
>> Alireza
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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 -- To UNSUBSCRIBE and more, see
> 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] need help with renaming a variable
Hi Pavel,
I probably should have explained that an object name beginning with a
number is not valid. See "An Introduction to R", section 1.8. I think
that the invalid name "2013fixed.data" has somehow been generated. If
you can find where this occurred and change it to "fixed2013.data" the
original error should disappear.
Jim
On Sat, Jan 24, 2015 at 5:51 AM, Pavel Yakovlev wrote:
> Jim, I tried as you suggested but it also did not work. Here's the error:
> rxSetVarInfo(fixed2013.data, outfile)
> Error in rxSetVarInfoXdf(varInfo, file = data) :
> object 'fixed2013.data' not found
>
> On Thu, Jan 22, 2015 at 5:50 PM, Jim Lemon wrote:
>>
>> Hi Pavel,
>> The problem may be with the name "2013fixed.data". I don't know where
>> that came from, but try naming it "fixed2013.data".
>>
>> Jim
>>
>>
>> On Fri, Jan 23, 2015 at 4:53 AM, Pavel Yakovlev
>> wrote:
>> > Hello.
>> >
>> > I am new to R, so my question/problem might be very basic, but I cannot
>> > figure out how to solve it.
>> > So, I would really appreciate your help.
>> >
>> > I would like to rename a variable in a very large file (181GB) called
>> > "2013.xdf" that is saved on my external hard drive.
>> >
>> > I tried running the following code to rename variable # 2 in the file
>> > and
>> > save this change, which produced some errors that I cannot resolve:
>> >
>> >> temp.data <- rxGetVarInfo("E:/2013.xdf")
>> >> temp.data[2] <- "transsactionnumber"
>> >> rxSetVarInfo(2013fixed.data, outfile)
>> > Error: unexpected symbol in "rxSetVarInfo(2013fixed.data"
>> >> rxSetVarInfo(temp.data, outfile)
>> > Error in is.data.frame(file) : object 'outfile' not found
>> >> rxSetVarInfo(outfile)
>> > Error in rxSetVarInfoXdf(varInfo, file = data) :
>> > object 'outfile' not found
>> >
>> >
>> > Please help me figure out how to do it right.
>> >
>> > Gratefully,
>> > --
>> >
>> > Pavel A. Yakovlev, Ph.D.
>> > Associate Professor
>> > 819 Rockwell Hall
>> > Department of Economics and Finance
>> > Duquesne University
>> > 600 Forbes Avenue
>> > Pittsburgh, PA 15282
>> > Work Phone: 412-396-1908
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > __
>> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > 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.
>
>
>
>
> --
>
> Pavel A. Yakovlev, Ph.D.
> Associate Professor
> 819 Rockwell Hall
> Department of Economics and Finance
> Duquesne University
> 600 Forbes Avenue
> Pittsburgh, PA 15282
> Work Phone: 412-396-1908
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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] plot circles where z values are circles radius
I think what you should look at are these web sites I found with a Google
search:
http://flowingdata.com/2010/11/23/how-to-make-bubble-charts/
http://www.r-bloggers.com/bubble-plots-ggplot2/
http://cran.r-project.org/web/packages/HSAUR/vignettes/Ch_logistic_regression_glm.pdf
http://cran.r-project.org/web/packages/mapplots/mapplots.pdf
Cheers!
Tom
On Fri, Jan 23, 2015 at 2:12 PM, Dr. Alireza Zolfaghari <
ali.zolfagh...@gmail.com> wrote:
> Hi there,
> I am trying to plot z values using Circle symbol. Each x and y has a value
> which will be plotted using a circle where circle's radius is corrlated
> with the value of z.
>
> I wrote the code , but unable to change the size of circle no matter what I
> chose for Scale. Any help please?
>
> x=c(84390255386 ,84390255386, 78028317380 ,53594648044,422)
> y=c(949849442 ,941645043, 840135292, 74, 821632939)
> z=c(0.005641896, 0.005641896 ,0.005641896, 0.007978846,0.007978846)
>
> convertToRadius<-function(x){return(sqrt(x/pi))}
>
> scale=0.3
>
> xlims =c(min(x),max(x))
> ylims =c(min(y),max(y))
> z=convertToRadius(z)*scale
>
> symbols(x,y, circles=z, fg='red')
>
> thanks
> Alireza
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot circles where z values are circles radius
Hi,
see the help and especially the argument inches:
Argument inches controls the sizes of the symbols. If TRUE (the default), the
symbols are scaled so that the largest dimension of any symbol is one inch. If
a positive number is given the symbols are scaled to make largest dimension
this size in inches (so TRUE and 1 are equivalent). If inches is FALSE, the
units are taken to be those of the appropriate axes. (For circles, squares and
stars the units of the x axis are used. For boxplots, the lengths of the
whiskers are regarded as dimensions alongside width and height when scaling by
inches, and are otherwise interpreted in the units of the y axis.)
Try
scale=5000
xlims =c(min(x),max(x))
ylims =c(min(y),max(y))
z=convertToRadius(z)*scale
symbols(x,y, circles=z, fg='red', inches=FALSE)
HTH
kd
Feladó: R-help [r-help-boun...@r-project.org] ; meghatalmazó: Dr. Alireza
Zolfaghari [ali.zolfagh...@gmail.com]
Küldve: 2015. január 23. 22:12
To: R-help; r-help-requ...@r-project.org
Tárgy: [R] plot circles where z values are circles radius
Hi there,
I am trying to plot z values using Circle symbol. Each x and y has a value
which will be plotted using a circle where circle's radius is corrlated
with the value of z.
I wrote the code , but unable to change the size of circle no matter what I
chose for Scale. Any help please?
x=c(84390255386 ,84390255386, 78028317380 ,53594648044,422)
y=c(949849442 ,941645043, 840135292, 74, 821632939)
z=c(0.005641896, 0.005641896 ,0.005641896, 0.007978846,0.007978846)
convertToRadius<-function(x){return(sqrt(x/pi))}
scale=0.3
xlims =c(min(x),max(x))
ylims =c(min(y),max(y))
z=convertToRadius(z)*scale
symbols(x,y, circles=z, fg='red')
thanks
Alireza
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
[R] plot circles where z values are circles radius
Hi there,
I am trying to plot z values using Circle symbol. Each x and y has a value
which will be plotted using a circle where circle's radius is corrlated
with the value of z.
I wrote the code , but unable to change the size of circle no matter what I
chose for Scale. Any help please?
x=c(84390255386 ,84390255386, 78028317380 ,53594648044,422)
y=c(949849442 ,941645043, 840135292, 74, 821632939)
z=c(0.005641896, 0.005641896 ,0.005641896, 0.007978846,0.007978846)
convertToRadius<-function(x){return(sqrt(x/pi))}
scale=0.3
xlims =c(min(x),max(x))
ylims =c(min(y),max(y))
z=convertToRadius(z)*scale
symbols(x,y, circles=z, fg='red')
thanks
Alireza
[[alternative HTML version deleted]]
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Re: [R] Testing for significant differences between groups in multiple linear regression
Look no further! The answer is yes.
However, if you are interested in why your query is probably nonsense
and why overall tests of significance are a **really bad idea** in
most scientific contexts (imho, anyway), then I suggest you post to a
statistical list like stats.stackexchange.com .
... oh, and while you're at it, please read the posting guide for this
list (see link below) and, in particular, DO NOT POST IN HTML, which,
as you can see here, often becomes a mess on this **plain text**
mailing list.
Cheers,
Bert
Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374
"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
Clifford Stoll
On Fri, Jan 23, 2015 at 1:46 AM, Janka Vanschoenwinkel
wrote:
> Dear R-colleagues,
>
> I am looking for a way to test whether one regression has significant
> different coefficients and overall results for 10 groups (grouping variable
> is "irr").
>
>
>
> *What I have*
>
> The regression is:
>
> Depend = temp + temp² + perc + perc² + conti è split up for multiple groups
> of irr
>
>
> *Dataset = Alldata (real dataset has over 5 IDs)*
>
> *ID*
>
> *irr *
>
> *(= grouping variable)*
>
> *temp*
>
> *perc*
>
> *conti*
>
> *Depend*
>
> *w*
>
> 1
>
> 1
>
> 10
>
> 34
>
> 26
>
> 8
>
> 23
>
> 2
>
> 1
>
> 11
>
> 36
>
> 27
>
> 6
>
> 58
>
> 3
>
> 1
>
> 26
>
> 57
>
> 45
>
> 3
>
> 76
>
> 4
>
> 2
>
> 23
>
> 68
>
> 24
>
> 2
>
> 4
>
> 5
>
> 2
>
> 6
>
> 26
>
> 8
>
> 1
>
> 323
>
> 6
>
> 2
>
> 3
>
> 17
>
> 56
>
> 6
>
> 45
>
> 7
>
> 3
>
> 17
>
> 39
>
> 17
>
> 5
>
> 57
>
>
>
> I can obtain the different regression coefficients for the different groups
> with the following code (other codes are possible as wel).
>
>
> datairrigation <- split(Alldata, Alldata$irr)
>
> model.per.irrigation <- lapply(datairrigation, function (x) {
>
> lm(Depend~ temp + temp² + perc + perc² + conti,
>
> weights=w, data = x)
>
> })
>
>
> OR I can do it manually by splitting all the data in subsets (and then I
> also receive the R²…)
>
>
>
> *What I don’t have*
>
> However, now I don’t know how to compare those regressions to test whether
> they differ significantly over all the groups.
>
> (Preferably, I would like to test the coefficients individually (temp(group
> 1) = temp(group2)) and the regression as a whole between the groups.)
>
>
>
> *Note*
>
> I know that one way to test differences in significance between groups, is
> to use dummy variables of that group, in the regression. Yet, this is no
> option for my model because it only allows exogenous variables in the
> regression (and irrigation is an endogenous variable because the farmer can
> decide himself if he irrigates or not).
>
>
>
> Thank you very much in advance! I really appreciate your help!
>
>
> Janka
>
>
> P Please consider the environment before printing this e-mail
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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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and provide commented, minimal, self-contained, reproducible code.
[R] Best method of analysis for negatively skewed longitudinal environmental data?
I have a dataset composed of a dependent variable (species percent cover) and a range of abiotic variables (salinity, temperature, pH, water movement etc). It is a longitudinal study, in which species percent cover was measured once a month for five months. The abiotic variables were measured using data-loggers every five minutes for the entire duration of the study. I have organised those data as monthly means in order to compare them with the species percent cover values. I have 13 study sites, at each of which I used three settlement collectors (each of the collectors is composed of three settlement plates). The goal is to determine the extent of influence of the abiotic variables on the species growth. I was initially planning on carrying out partial least square regression, but I have been unable to account for the repeated measures aspect of the study. I have very limited R experience and have been unable to write script to carry out an appropriate analysis with PLS, so have been primarily been using SPSS and JMP. I am now trying to use Linear Mixed Models. The issue here is that the data are heavily negatively skewed, given the large number of zero percent cover points, especially as every single site I worked at started as zero percent cover. There is also a smaller peak on the positive side where there are a reasonable number of 100% values. In SPSS -> Analyze -> Mixed Models -> Linear I use the settlement collectors as the Subject and Months as the Repeated Measure. Then I use % cover as the Dependent Variable, Site as the Fixed Factor and the abiotic variables of interest as covariates. Fixed effects of abiotic variables and a random effect of the intercept and the subjects. I am not sure if this is appropriate given the non-normality of those data. Any suggestions of alternative methods or enhancements of the ones I have mentioned would be greatly appreciated. Thanks! -- View this message in context: http://r.789695.n4.nabble.com/Best-method-of-analysis-for-negatively-skewed-longitudinal-environmental-data-tp4702212.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] sum of grouped elements of vector
Hi Kathryn,
another solution would be to use tapply function. So the code to
create new1 vector would be:
a <- 1:8
fc <- c('g1','g1','g2','g3','g3','g3','g4','g4') # definitions of
groups to sum over
tapply(a,fc,sum)
ivan
On Fri, Jan 23, 2015 at 10:32 AM, Bert Gunter wrote:
> If Jim's answer is not what you want, then I would say it is because
> your question is too vague to be answered. In particular, how do you
> specify the elements of the vector that are to be summed to create the
> new vectors? ?tapply might then be relevant here, but that's just a
> guess.
>
> -- Bert
>
>
>
>
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
> (650) 467-7374
>
> "Data is not information. Information is not knowledge. And knowledge
> is certainly not wisdom."
> Clifford Stoll
>
>
>
>
> On Fri, Jan 23, 2015 at 12:45 AM, Kathryn Lord
> wrote:
>> Dear R users,
>>
>> I have a quick quesiton.
>>
>> Here is a vector "a".
>>
>> a<- c(1,2,3,4,5,6,7,8).
>>
>> (In fact, I have a huge vector.)
>>
>>
>> With "a", I'd like to create new vectors, for example,
>>
>> new1 = (1+2, 3, 4+5+6, 7+8)
>> new2 = (1, 2+3+4+5+6+7, 8)
>> new3 = (1+2+3+4+5+6+7, 8)
>>
>>
>> How could I make the above vectors using R?
>>
>>
>> Any suggestion will be greatly appreciated.
>>
>> Best,
>>
>> Kathryn Lord
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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 -- To UNSUBSCRIBE and more, see
> 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 -- To UNSUBSCRIBE and more, see
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] Testing for significant differences between groups in multiple linear regression
Dear R-colleagues,
I am looking for a way to test whether one regression has significant
different coefficients and overall results for 10 groups (grouping variable
is "irr").
*What I have*
The regression is:
Depend = temp + temp² + perc + perc² + conti è split up for multiple groups
of irr
*Dataset = Alldata (real dataset has over 5 IDs)*
*ID*
*irr *
*(= grouping variable)*
*temp*
*perc*
*conti*
*Depend*
*w*
1
1
10
34
26
8
23
2
1
11
36
27
6
58
3
1
26
57
45
3
76
4
2
23
68
24
2
4
5
2
6
26
8
1
323
6
2
3
17
56
6
45
7
3
17
39
17
5
57
I can obtain the different regression coefficients for the different groups
with the following code (other codes are possible as wel).
datairrigation <- split(Alldata, Alldata$irr)
model.per.irrigation <- lapply(datairrigation, function (x) {
lm(Depend~ temp + temp² + perc + perc² + conti,
weights=w, data = x)
})
OR I can do it manually by splitting all the data in subsets (and then I
also receive the R²…)
*What I don’t have*
However, now I don’t know how to compare those regressions to test whether
they differ significantly over all the groups.
(Preferably, I would like to test the coefficients individually (temp(group
1) = temp(group2)) and the regression as a whole between the groups.)
*Note*
I know that one way to test differences in significance between groups, is
to use dummy variables of that group, in the regression. Yet, this is no
option for my model because it only allows exogenous variables in the
regression (and irrigation is an endogenous variable because the farmer can
decide himself if he irrigates or not).
Thank you very much in advance! I really appreciate your help!
Janka
P Please consider the environment before printing this e-mail
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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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] sum of grouped elements of vector
Here is some examples using functions 'tapply()' as suggested by Bert Gunter in the previous post, 'aggregate()', and 'xtabs()'. Note that 'grp.id' means 'group indicator'. > a <- c(1,2,3,4,5,6,7,8) > new1 <- c(1+2, 3, 4+5+6, 7+8) > new1 [1] 3 3 15 15 > > grp.id <- c(1,1, 2, 3,3,3, 4,4) > tapply(X=a, INDEX=grp.id, FUN=sum) 1 2 3 4 3 3 15 15 > aggregate(x=a, by=list(grp.id), FUN=sum) Group.1 x 1 1 3 2 2 3 3 3 15 4 4 15 > xtabs(formula=a~grp.id) grp.id 1 2 3 4 3 3 15 15 > > I hope this helps. Chel Hee Lee On 1/23/2015 3:32 AM, Bert Gunter wrote: If Jim's answer is not what you want, then I would say it is because your question is too vague to be answered. In particular, how do you specify the elements of the vector that are to be summed to create the new vectors? ?tapply might then be relevant here, but that's just a guess. -- Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." Clifford Stoll On Fri, Jan 23, 2015 at 12:45 AM, Kathryn Lord wrote: Dear R users, I have a quick quesiton. Here is a vector "a". a<- c(1,2,3,4,5,6,7,8). (In fact, I have a huge vector.) With "a", I'd like to create new vectors, for example, new1 = (1+2, 3, 4+5+6, 7+8) new2 = (1, 2+3+4+5+6+7, 8) new3 = (1+2+3+4+5+6+7, 8) How could I make the above vectors using R? Any suggestion will be greatly appreciated. Best, Kathryn Lord [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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 -- To UNSUBSCRIBE and more, see 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 -- To UNSUBSCRIBE and more, see 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] elegant way to remove cases with many different ids
I did not know there was a warning about that! I usually find it easier to use [ in scripts anyway. -- Ivan Calandra, ATER University of Reims Champagne-Ardenne GEGENAA - EA 3795 CREA - 2 esplanade Roland Garros 51100 Reims, France +33(0)3 26 77 36 89 ivan.calan...@univ-reims.fr https://www.researchgate.net/profile/Ivan_Calandra Le 23/01/15 11:59, Göran Broström a écrit : On 2015-01-23 11:09, Ivan Calandra wrote: Hi Alain, I think you're looking for %in% (see ?'%in%' for the help page) id.vector <- c(1,3) ## here you define the values you want to select: x, y, z... subset(df, id %in% id.vector) But note the Warning in >?subset Göran HTH, Ivan -- Ivan Calandra, ATER University of Reims Champagne-Ardenne GEGENAA - EA 3795 CREA - 2 esplanade Roland Garros 51100 Reims, France +33(0)3 26 77 36 89 ivan.calan...@univ-reims.fr https://www.researchgate.net/profile/Ivan_Calandra Le 23/01/15 10:50, D. Alain a écrit : Dear R-List, I have nested data with cases grouped by IDs and I want to remove all cases with specific IDs. something like df<-data.frame(id=c(1,1,1,2,2,2,3,3,3,4,4,4,5,5,5),var=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15)) subset(df,id== 1 | id == 3) Having a very large dataset with many IDs to remove this solution leaves me to write quite a long list of "id == x | id == y | id == z ...". I wonder if there is a more elegant way to do this? I tried with "id = c(x,y,z)" but this did not give the proper result. Any suggestions? Thank you! Best wishes Alain [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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 -- To UNSUBSCRIBE and more, see 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 -- To UNSUBSCRIBE and more, see 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 -- To UNSUBSCRIBE and more, see 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] elegant way to remove cases with many different ids
On 2015-01-23 11:09, Ivan Calandra wrote: Hi Alain, I think you're looking for %in% (see ?'%in%' for the help page) id.vector <- c(1,3) ## here you define the values you want to select: x, y, z... subset(df, id %in% id.vector) But note the Warning in >?subset Göran HTH, Ivan -- Ivan Calandra, ATER University of Reims Champagne-Ardenne GEGENAA - EA 3795 CREA - 2 esplanade Roland Garros 51100 Reims, France +33(0)3 26 77 36 89 ivan.calan...@univ-reims.fr https://www.researchgate.net/profile/Ivan_Calandra Le 23/01/15 10:50, D. Alain a écrit : Dear R-List, I have nested data with cases grouped by IDs and I want to remove all cases with specific IDs. something like df<-data.frame(id=c(1,1,1,2,2,2,3,3,3,4,4,4,5,5,5),var=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15)) subset(df,id== 1 | id == 3) Having a very large dataset with many IDs to remove this solution leaves me to write quite a long list of "id == x | id == y | id == z ...". I wonder if there is a more elegant way to do this? I tried with "id = c(x,y,z)" but this did not give the proper result. Any suggestions? Thank you! Best wishes Alain [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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 -- To UNSUBSCRIBE and more, see 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 -- To UNSUBSCRIBE and more, see 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] elegant way to remove cases with many different ids
Hi Alain, I think you're looking for %in% (see ?'%in%' for the help page) id.vector <- c(1,3) ## here you define the values you want to select: x, y, z... subset(df, id %in% id.vector) HTH, Ivan -- Ivan Calandra, ATER University of Reims Champagne-Ardenne GEGENAA - EA 3795 CREA - 2 esplanade Roland Garros 51100 Reims, France +33(0)3 26 77 36 89 ivan.calan...@univ-reims.fr https://www.researchgate.net/profile/Ivan_Calandra Le 23/01/15 10:50, D. Alain a écrit : Dear R-List, I have nested data with cases grouped by IDs and I want to remove all cases with specific IDs. something like df<-data.frame(id=c(1,1,1,2,2,2,3,3,3,4,4,4,5,5,5),var=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15)) subset(df,id== 1 | id == 3) Having a very large dataset with many IDs to remove this solution leaves me to write quite a long list of "id == x | id == y | id == z ...". I wonder if there is a more elegant way to do this? I tried with "id = c(x,y,z)" but this did not give the proper result. Any suggestions? Thank you! Best wishes Alain [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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 -- To UNSUBSCRIBE and more, see 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] elegant way to remove cases with many different ids
Dear R-List, I have nested data with cases grouped by IDs and I want to remove all cases with specific IDs. something like df<-data.frame(id=c(1,1,1,2,2,2,3,3,3,4,4,4,5,5,5),var=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15)) subset(df,id== 1 | id == 3) Having a very large dataset with many IDs to remove this solution leaves me to write quite a long list of "id == x | id == y | id == z ...". I wonder if there is a more elegant way to do this? I tried with "id = c(x,y,z)" but this did not give the proper result. Any suggestions? Thank you! Best wishes Alain [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] sum of grouped elements of vector
If Jim's answer is not what you want, then I would say it is because your question is too vague to be answered. In particular, how do you specify the elements of the vector that are to be summed to create the new vectors? ?tapply might then be relevant here, but that's just a guess. -- Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." Clifford Stoll On Fri, Jan 23, 2015 at 12:45 AM, Kathryn Lord wrote: > Dear R users, > > I have a quick quesiton. > > Here is a vector "a". > > a<- c(1,2,3,4,5,6,7,8). > > (In fact, I have a huge vector.) > > > With "a", I'd like to create new vectors, for example, > > new1 = (1+2, 3, 4+5+6, 7+8) > new2 = (1, 2+3+4+5+6+7, 8) > new3 = (1+2+3+4+5+6+7, 8) > > > How could I make the above vectors using R? > > > Any suggestion will be greatly appreciated. > > Best, > > Kathryn Lord > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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 -- To UNSUBSCRIBE and more, see 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] sum of grouped elements of vector
Hi Kathryn,
I think this might do the trick:
make_group_sums<-function(x,maxgroups) {
lenx<-length(x)
runlengths<-sample(1:lenx,1)
for(i in 2:(maxgroups-1)) {
lenx<-lenx-runlengths[i-1]
runlengths[i]<-ifelse(lenx,sample(1:lenx,1),0)
}
runlengths[maxgroups]<-length(x)-sum(runlengths)
groups<-rep(1:maxgroups,runlengths)
groupsums<-by(x,groups,sum)
return(as.vector(groupsums))
}
Jim
On Fri, Jan 23, 2015 at 7:45 PM, Kathryn Lord
wrote:
> Dear R users,
>
> I have a quick quesiton.
>
> Here is a vector "a".
>
> a<- c(1,2,3,4,5,6,7,8).
>
> (In fact, I have a huge vector.)
>
>
> With "a", I'd like to create new vectors, for example,
>
> new1 = (1+2, 3, 4+5+6, 7+8)
> new2 = (1, 2+3+4+5+6+7, 8)
> new3 = (1+2+3+4+5+6+7, 8)
>
>
> How could I make the above vectors using R?
>
>
> Any suggestion will be greatly appreciated.
>
> Best,
>
> Kathryn Lord
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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 -- To UNSUBSCRIBE and more, see
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] sum of grouped elements of vector
Dear R users, I have a quick quesiton. Here is a vector "a". a<- c(1,2,3,4,5,6,7,8). (In fact, I have a huge vector.) With "a", I'd like to create new vectors, for example, new1 = (1+2, 3, 4+5+6, 7+8) new2 = (1, 2+3+4+5+6+7, 8) new3 = (1+2+3+4+5+6+7, 8) How could I make the above vectors using R? Any suggestion will be greatly appreciated. Best, Kathryn Lord [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
