Re: [R] Change values in a dateframe-Speed TEST

On 25-07-2013, at 08:35, Arnaud Michel wrote: > But I just noticed that the two solutions are not comparable : > the change concern only Nom and Prenom (solution Berend) and not also Sexe or > Date.de.naissance orother variables (solution Arun) that can changed. But my > question was badly put

Re: [R] Change values in a dateframe-Speed TEST

But I just noticed that the two solutions are not comparable : the change concern only Nom and Prenom (solution Berend) and not also Sexe or Date.de.naissance orother variables (solution Arun) that can changed. But my question was badly put. Michel Le 25/07/2013 08:06, Arnaud Michel a écrit :

Re: [R] Change values in a dateframe-Speed TEST

Hi For a dataframe with name PaysContrat1 and with nrow(PaysContrat1) [1] 52366 the test of system.time is : system.time(droplevels(do.call(rbind,lapply(split(PaysContrat1,PaysContrat1$Matricule), FUN=function(x) {x[,c("Nom","Prénom")] <- x[nrow(x),c("Nom","Prénom"),drop=TRUE];x} user

Re: [R] [R-pkgs] WriteXLS Version 3.0.0 Released

Hello! None can imagine how this package is helpful for me. I might have understood wrong... is it correct that WriteXLS doesn't no more require Perl? It is because I got this on my machine: > WriteXLS("iris", "iriscomments.xlsx", AdjWidth = TRUE, BoldHeaderRow = TRUE) Can't locate Archive/Zi

[R] Paternity data analysis problem

Hi R-helps, I did an experiment with FAs ['High' and 'Zero'(no w-3) quality; n=24 for each group]. Then I did AI to see their sperm competitiveness based on their paternity performance. My data is as below where Fish ID- Blind ID for each fish; Group ID- Dietary group ID; Diet quality - High=1, ze

Re: [R] flexible approach to subsetting data

Hi, It works in small dataset. rt<- structure(list(sim = c(1L, 1L, 1L, 2L, 2L, 2L), txt.y.obs = c(5L, 4L, 3L, 6L, 7L, 9L), cont.y.obs = c(4L, 3L, 9L, 4L, 8L, 6L),     ID = 1:6, obs.txt = c(5L, 2L, 4L, 8L, 4L, 7L), TE = c(5L,     7L, 4L, 3L, 5L, 8L), X1 = c(1L, 1L, 1L, 2L, 2L, 2L), sim.1 = c(4L,

[R] [packages Sensitivity] Fast99 function,why model runs only 1

library(XML) # Load the XML packages library(sensitivity) source("Yield_APSIM.R") yield_sa <- fast99(model = Yield_APSIM, factors=c("grains_per_gram_stem", "potential_grain_filling_rate", "poten

Re: [R] flexible approach to subsetting data

Hi, all: I have a follow-up question. I have 81 variables in my dataset (all of which are repeated). Reshape seems to give me an error whenever more than six variables are used. The error message is this: Error in reshapeLong(data, idvar = idvar, timevar =timevar , varying = varying, : 'varying

Re: [R] Help to improve prediction from supervised mapping using kohonen package

On 24 July 2013 21:32, Ben Harrison wrote: > On 24 July 2013 19:25, ONKELINX, Thierry wrote: >> Try rescaling your data prior to splitting it up into a training and test >> set. Otherwise you end up with two different ways of scaling. > I still cannot understand how I can sensibly revert the sc

Re: [R] x-axis (categorial variable) ordering with xyplot function (lattice package)

On 07/25/2013 12:17 AM, BLASER Arnaud wrote: Dear R mailing list readers, I am facing the following problem; for simplicity imagine I am working on a data frame of, say, 5 columns. The first column is a list of European countries, the other four are an index (continuous variable) of climate ch

Re: [R] Perform task on error

H ow about a custom error handling function? As in, options(error = quote( ...CODE TO SEND EMAIL ... )) On Wed, Jul 24, 2013 at 4:06 PM, brt wrote: > I have a web service that uses an R script to perform the analysis. At the > end of the R script, I use the system function to call an external

Re: [R] x-axis (categorial variable) ordering with xyplot function (lattice package)

forgot to cc to list Hi For an xyplot you have not got the proper coding for the x value which should be numeric. If you want to make a plot of the style of xyplot a numerical index of the country is needed and then use the scales argument to annote the labels with the country. Do you want

Re: [R] .eps files and powerpoint

Hi Marc I sometimes had trouble with postscript and pdf files with lattice and I printed with trellis.device(device = pdf, ...) or trellis.device(device = postscript, ...) I wonder if this is the case here Duncan Duncan Mackay Department of Agronomy and Soil Science University of New Englan

Re: [R] non-conformable arrays

You need to be careful how you index. In the example code, y is a 'zoo series' and y[i] is gives the ith row, as in y[i, ]. This means t(y[i]) %*% y[i] is actually a 2X2 matrix. Also, the code c(S)[c(1,4,2)] picks off the diagonal and lower triangular elements. The example involves two stocks,

Re: [R] How to split two levels several times?

Hello, As for the first question, note that in the case you describe, the resulting list of df's will not be a split of the original, there will be a duplication in the final 4-1 and 1-3. The following is a hack but will do it. lens <- rle(as.character(XXX$electrode))$lengths m <- length(le

[R] SpatialPolygonsDataFrame and unique()

Hello everyone! I'm a newbie in using the RGDAL and sp packages in R and as written in the object I have a problem with a SPDF and unique(): I would have liked to write a simple script to delete in a couple of clicks the duplicated nodes that sometimes pop-up during the digitizing process in QGIS

[R] Perform task on error

I have a web service that uses an R script to perform the analysis. At the end of the R script, I use the system function to call an external (perl) script that sends the user an e-mail telling them that their analysis has finished running, and where they can download the results. However, if the

Re: [R] List Structure and Acces to data

I may not understand, but if you are looking for a way to extract the second item from each list element, you will need to use lapply(): a <- list(LETTERS[1:3], 10:12, LETTERS[26:24], 15:13) b <- list(LETTERS[4:6], 15:17, LETTERS[23:21], 10:8) c <- list(LETTERS[7:9], 20:22, LETTERS[20:18], 5:3) ab

[R] Utility scores from mlogit/clo​git for CBC

Hello Everyone, I am a graduate student working on a CBC study. I want to give participants 3 choices per task with a None option, so I have been looking at doing a multinomial or conditional logit model. My issue is that in my experience, logistic regressions involve dummy coding or having level

Re: [R] List Structure and Acces to data

What you are doing looks like it is probably more complicated than necessary, but since I have no idea what structure you intend to create, it is hard to say. Here is a suggestion: try this: str(my_echant_hist) It will give you a summary of the structure of that object, which should help you u

[R] grid: Grid graphics flickering

I'm designing an interactive plot using the `grid` package in R. As part of the interactivity, I repeatedly delete and re-create various parts of the plot. However, the total number of grid elements (as obtained using the `grid.ls()` command) stays constant; everything I create was previously remov

Re: [R] Query on R plot : Unequispaced label on x-axis

On 24/07/2013 10:06 AM, ritwi...@isical.ac.in wrote: Dear R users, I want to plot a one variable continuous function f(x) vs x, x=[0,1]. Say for example: f(x)= x^2. Now, using the command plot(f~x) I will get a curve where the range of x-axis is [0,1] with all equispaced label. But, I need somet

Re: [R] Levels of a factor

Benchmark is probably a subset from a larger dataframe. R does not automatically remove empty levels but you can do it: set.seed(42) dataset <- data.frame(Benchmark=factor(sample(LETTERS[1:26], 50, replace=TRUE), levels=LETTERS[1:26])) levels(dataset$Benchmark) # [1] "A" "B" "C" "D" "E" "F" "

Re: [R] .eps files and powerpoint

Rich, I don't have direct access to Windows and I don't run a VM on my Mac. I e-mailed two PPTX files created on my Mac (Office 2011) to a colleague who has Office 2010 on his Windows laptop. The first was the file on DropBox that I linked earlier, with the regular plot. The second is this PPT

Re: [R] Levels of a factor

On Jul 24, 2013, at 11:35 AM, David Winsemius wrote: > > On Jul 24, 2013, at 6:25 AM, Borja Rivier wrote: > >> Hi all, >> >> I am having a bit of trouble using the levels() function. >> I have a factor with many elements, and when I use the function levels() to >> extract the list of unique el

Re: [R] subtracting rows for unique

Thank you so much. It worked perfectly:)   Cc: R help Sent: Tuesday, July 23, 2013 1:34 PM Subject: Re: subtracting rows for unique Hi, Try: dat1<- read.table(text=" ID Date x2 x1  x3 56 25-Jun-01 10 2  126 56 29-Oct-01 10 2  140 56 18-Mar-02 1

[R] x-axis (categorial variable) ordering with xyplot function (lattice package)

Dear R mailing list readers, I am facing the following problem; for simplicity imagine I am working on a data frame of, say, 5 columns. The first column is a list of European countries, the other four are an index (continuous variable) of climate change impact under 4 different scenarios. Coun

Re: [R] Levels of a factor

On Jul 24, 2013, at 6:25 AM, Borja Rivier wrote: > Hi all, > > I am having a bit of trouble using the levels() function. > I have a factor with many elements, and when I use the function levels() to > extract the list of unique elements, some of the elements returned are not > actually in the fa

[R] Query on R plot : Unequispaced label on x-axis

Dear R users, I want to plot a one variable continuous function f(x) vs x, x=[0,1]. Say for example: f(x)= x^2. Now, using the command plot(f~x) I will get a curve where the range of x-axis is [0,1] with all equispaced label. But, I need something else, and that is: my curve will be such that 80%

Re: [R] Problems loading siar package

Hello, I had to load a different package separately. Did you try and find the 'hrdcde' package and load it independently? Best, Gary Roemer, Ph.D. Associate Professor Dept. Fish, Wildlife & Conservation Ecology New Mexico State University Las Cruces, NM 88003 Off: 575-646-3394 Fax:575-646-1281

Re: [R] subtracting rows for unique

Hi, Try: dat1<- read.table(text=" ID Date x2 x1  x3 56 25-Jun-01 10 2  126 56 29-Oct-01 10 2  140 56 18-Mar-02 10 2  445 56 6-Jun-03 10 2    224 56 16-Jan-04  10 2    NA 58 10-Jan-02 10.8 1 715 58 26-Dec-03 10.8 1    NA ",sep="",header=TRUE,stringsAsFactors=FALSE)  unlist(with(da

Re: [R] flexible approach to subsetting data

This is all very helpful. Thank you for your comments. I will try the approaches suggested and let you know if I have any problems. Thank you!!! On Tue, Jul 23, 2013 at 5:59 PM, David Winsemius wrote: > > On Jul 23, 2013, at 2:00 PM, David Carlson wrote: > > > Actually the ".0" on the first va

Re: [R] Change values in a dateframe

Hi Michel, You could try: df1New<-droplevels(TEST[with(TEST,ave(seq_along(Matricule),Matricule,FUN=min)),]) row.names(df1New)<-1:nrow(df1New) df2New<-droplevels(TEST[with(TEST,ave(seq_along(Matricule),Matricule,FUN=max)),]) row.names(df2New)<-1:nrow(df2New)  identical(df1New,df1) #[1] TRUE  ident

[R] R help

Dear R experts, I know this is not the appropriate place to post but I already tried eco (has not used ME) and geo (not available unit Aug 5), so please forgive me. I fitted my spatial data to a glm.nb model. I decided to detect and correct for spatial autocorrelation using ME{spdep}. I received

Re: [R] Levels of a factor

Hi,  vec1<- factor(1:5,levels=1:10)  vec1 #[1] 1 2 3 4 5 #Levels: 1 2 3 4 5 6 7 8 9 10 vec2<-droplevels(vec1)  levels(vec2) #[1] "1" "2" "3" "4" "5"  vec2 #[1] 1 2 3 4 5 #Levels: 1 2 3 4 5 A.K. Hi all, I am having a bit of trouble using the levels() function. I have a factor with many element

Re: [R] function 2 convert matrix to long-format?

Hi, It is better to use ?dput(). a1<-array(c(0.1416,0.1049,0.1328,0.12235,0.11890,0.15510,0.14225,0.09295,0.13350,0.16875,0.09900,0.14560),c(3,2,2))  dimnames(a1)<- list(c("T0","T1","T2"),c("B6","B9"),c("minus","plus")) library(plyr) library(reshape2) res<-melt(adply(a1,c(1,2)),id.vars=c("X1","X2")

[R] Levels of a factor

Hi all, I am having a bit of trouble using the levels() function. I have a factor with many elements, and when I use the function levels() to extract the list of unique elements, some of the elements returned are not actually in the factor. For example I would have this: > vector <- dataset$Benc

Re: [R] How to split two levels several times?

Hi Rui the splitting code worked fine. Thanks for your help. Now I realized that the code cannot handle a table with levels that by chance (or systematically) repeatedly appear after each other. For instance this may happen if I need to extract the final two pairs of the table XXX below: electro

Re: [R] .eps files and powerpoint

office 2011 on mac, 2013 on windows. i see the same misbehavior in base and lattice. my standard simple test is plot(1:10) which is base. did you try the windows side yet? Rich Sent from my iPhone On Jul 24, 2013, at 13:22, Marc Schwartz wrote: > Hi Rich, > > That's curious. > > I noted th

Re: [R] Y label doesn't show up on printing files

On Jul 24, 2013, at 4:14 AM, Mohit Dhingra wrote: > Hi David, > > Thanks for your reply! How do I exactly find it out and solve? Also, > the problem is not reproducible every time :-/ One way would be to follow the directions in the link from ?pdf to ?embedFonts and force fonts to be included

Re: [R] .eps files and powerpoint

Hi Rich, That's curious. I noted that you are using barchart() below which is lattice versus base graphics. Is there any difference in the result on Windows if you use barplot() instead? If so, perhaps there is something about lattice graphics in this context. Also, are you using Office 2008

Re: [R] .eps files and powerpoint

Marc, very interesting. Your example works on Windows. This example doesn't work on windows > postscript(file = "file2.eps", height = 4, width = 4, + horizontal = FALSE, onefile = FALSE, paper = "special") > barchart(1:3) > dev.off() Several examples, including the real one I w

Re: [R] .eps files and powerpoint

Hi Rich, Seems to work for me using Powerpoint in MS Office 2011 for Mac. I used the following code: postscript(file = "file.eps", height = 4, width = 4, horizontal = FALSE, onefile = FALSE, paper = "special") plot(rnorm(20)) dev.off() Then I used the insert picture from fi

Re: [R] .eps files and powerpoint

Thanks Marc, the extra arguments to postscript still don't produce something that PowerPoint will accept. With your call, PP still displayed only the icon. PP did not generate its own png file. Since my immediate goal is the projection screen for a PowerPoint presentation, I will go directly to

Re: [R] Fwd: Why does impulse response function of VAR starts at zero and not at one?

It appeared on the mailing list (https://stat.ethz.ch/pipermail/r-help/2013-July/357190.html ... you have to click on the attachment URL). As did this one. (You are not addressing the moderators... you are addressing the whole list.) Your question is not well-formed. Please read the Posting Gui

Re: [R] .eps files and powerpoint

Rich, You are missing some options in the call to postscript() below. It needs to be: postscript(file = "file.eps", width = x, height = y, horizontal = FALSE, onefile = FALSE, paper = "special") The first line needs to have values for 'x' and 'y' for the width and height of the i

Re: [R] .eps files and powerpoint

png("png300.png", res=300, width=2880, height=1440) gives good behavior. Thank you. This will become my standard for export to powerpoint. postscript(file='file.eps', onefile=FALSE) produces eps files that powerpoint rejects, even though ghostview is satisfied. Rich On Wed, Jul 24, 2013 at 2

Re: [R] Change values in a dateframe

Hi Arun, Merci à toi Bien amicalement Michel Le 24/07/2013 15:29, arun a écrit : Hi Michel, You could try: df1New<-droplevels(TEST[with(TEST,ave(seq_along(Matricule),Matricule,FUN=min)),]) row.names(df1New)<-1:nrow(df1New) df2New<-droplevels(TEST[with(TEST,ave(seq_along(Matricule),Matricule,FUN

Re: [R] Adjusting published survival functions

Have you tried the packages 'survival' and 'eha' yet? You can use the survreg() function in the former to compare between different models. Have a look at this tutorial: http://www.openintro.org/stat/surv.php (a copy can also be found here: http://anson.ucdavis.edu/~hiwang/teaching/10fall/R_tut

[R] Fwd: Why does impulse response function of VAR starts at zero and not at one?

Hi there, I sent this e-mail two days ago, but I did not see it pass by the R-help mailinglist and I was wondering if you could post it or is there a que? Thanks in advance. Kind regards, Jose -- Forwarded message -- From: José Verhoeven Date: 2013/7/22 Subject: Why does impul

[R] prediction survival curves for coxph-models; how to extract the right strata per individual

Hello everyone, It somehow seems like a strange question, but I don't find the answer. I think my question is the same stephenb wanted to ask in January, but it seems he didn't get an answer (see http://r.7

Re: [R] Network analysis

Hi Sarah, It would help to know what the data looks like now and to have some idea of what you have already done. Here are a couple of links what suggest how to frame a question for the R-help list And here is an article using network analysis. No idea if the techniques are at all relevant bu

Re: [R] Paternity data analysis problem

Please use dput() to supply data and send in text format not html. Thanks John Kane Kingston ON Canada > -Original Message- > From: mrahmankuf...@gmail.com > Sent: Wed, 24 Jul 2013 19:00:42 +0800 > To: r-help@r-project.org, r-help-requ...@r-project.org, > r-help-ow...@r-project.org > Su

Re: [R] Function, that assigns two vectors to each other

Welcome to R-help it is a bit hard to see exactly what you want without data. Rest of the explanation looks good though it appears you may have sent this in HTML and the list asks for text. It strips out the html and we lose any html format. Can I suggest reading these https://github.com/hadl

[R] Function, that assigns two vectors to each other

Hey guys, In my data setv ("KD") I have 4 columns ("Punkte.AG1","Punkte.AG2","Punkte.AG3","Punkte.WI") I'm interested in. These columns contain the participants' scores of a specific task. I computed the percentiles of the columns using this code: pe<-apply(X=KD[,c("Punkte.AG1","Punkte.AG2","P

[R] Paternity data analysis problem

Dear R-helps, I did an experiment with FAs ['High' and 'Zero'(no w-3) quality; n=24 for each group]. Then I did AI to see their sperm competitiveness based on their paternity performance. My data is as below where Fish ID- Blind ID for each fish; Group ID- Dietary group ID; Diet quality - High=1,

[R] Network analysis

Hi, I am trying to do network analysis for my data-set but facing few difficulties. Would be very grateful if could get some help from anyone. My dataset has 5 columns and 110 rows and I am trying to build link which rows are more likely to be connected to the columns. I want to use Jaccard

Re: [R] [R-pkgs] WriteXLS Version 3.0.0 Released

On Jul 23, 2013, at 5:40 PM, cognizio wrote: > Great summary! It works great without the heavy PERL library. I am running > the YAML package I thought I needed to support WRITEXLS. Do I need it or is > YAML not a dependency? > > Other question is on your last point: 'WRITEXLS COMMENT:' now show

Re: [R] Help to improve prediction from supervised mapping using kohonen package

On 24 July 2013 19:25, ONKELINX, Thierry wrote: > Try rescaling your data prior to splitting it up into a training and test > set. Otherwise you end up with two different ways of scaling. > I was mistaken, there is a visible improvement! I still cannot understand how I can sensibly revert the s

Re: [R] Help to improve prediction from supervised mapping using kohonen package

On 24 July 2013 19:25, ONKELINX, Thierry wrote: > Try rescaling your data prior to splitting it up into a training and test > set. Otherwise you end up with two different ways of scaling. Thanks, good point. I have adjusted the code, however with no visible improvement. Also, I want to be able

Re: [R] Y label doesn't show up on printing files

Hi David, Thanks for your reply! How do I exactly find it out and solve? Also, the problem is not reproducible every time :-/ Thanks & Regards Mohit Dhingra +919611190435 On 22 July 2013 23:55, David Winsemius wrote: > > On Jul 22, 2013, at 3:17 AM, Mohit Dhingra wr

[R] Adjusting published survival functions

Dear, I would like to know how to adjust survival functions in R and after reading lots of posts I don't have it clear. I downloaded the fitdistrplus package but it seems me like it only fits univariately the functions. Being specific , having a survival curve which corresponds to a set of data

Re: [R] function 2 convert matrix to long-format?

RECALL : found the answer: use aggregate instead of tapply thx On 24 July 2013 12:00, Witold E Wolski wrote: > I would like to convert this (output of tapply) > , , minus > >B6 S9 > T0 0.1416 0.12235 > T1 0.1049 0.11890 > T2 0.1328 0.15510 > > , , plus > > B6 S9 > T0 0.

[R] function 2 convert matrix to long-format?

I would like to convert this (output of tapply) , , minus B6 S9 T0 0.1416 0.12235 T1 0.1049 0.11890 T2 0.1328 0.15510 , , plus B6 S9 T0 0.14225 0.16875 T1 0.09295 0.09900 T2 0.13350 0.14560 to long-format : T0 B6 minus 0.1416 T0 S9 minus 0.12235 T0 B6 plus 0.14225 T0 S

Re: [R] Help to improve prediction from supervised mapping using kohonen package

Try rescaling your data prior to splitting it up into a training and test set. Otherwise you end up with two different ways of scaling. ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quali

[R] Help to improve prediction from supervised mapping using kohonen package

I would really like some or any advice on how I can improve (or fix??) the following analysis. I hope I have provided a completely runnable code - it doesn't produce any errors for me. The resulting plot at the end shows a pretty poor correlation (just speaking visually here) to the test set. How

Re: [R] Help with using unpenalised te smooth in negative binomial mgcv gam

Hi Alice, This is a bug in gam.side, which was assuming that any interaction smooth that needed identifiability constraints would be penalized. thanks for reporting it - fixed for next version. In the meantime have you considered using `ti' terms instead of `te'? These provide a more satisfa

Re: [R] Change values in a dateframe

Thank you Berend It is exactly what I wanted. Michel Le 24/07/2013 09:48, Berend Hasselman a écrit : On 24-07-2013, at 08:39, Arnaud Michel wrote: Hello I have the following problem : The dataframe TEST has multiple lines for a same person because : there are differents values of Nom or diffe

Re: [R] Change values in a dateframe

On 24-07-2013, at 08:39, Arnaud Michel wrote: > Hello > > I have the following problem : > The dataframe TEST has multiple lines for a same person because : > there are differents values of Nom or differents values of Prenom > but the values of Matricule or Sexe or Date.de.naissance are the sam