Re: [R] ginv / LAPACK-SVD causes R to segfault on a large matrix.
Thanks for trying it out, David. Unfortunately it isn't reproducible with a machine with 64 Gb of RAM or more. Yours, Cyrus On Mon, Jan 14, 2013 at 8:25 PM, David Winsemius dwinsem...@comcast.netwrote: On Jan 14, 2013, at 9:07 AM, Cyrus Shaoul wrote: No, Mehmet, I haven't tried that yet. I was hoping to find out if there was some other option. I have no experience using LAPACK directly. I have looked into RcppEigen and RcppArmadillo, but have not tested them yet. If there are no other options, I guess I will go down that path. I tried it on a 64 bit R with 32GB of RAM. It exhausted those resources and started paging out into virtual memory. No error, but I killed the process. -- David. Thanks a lot, Cyrus On Mon, Jan 14, 2013 at 4:17 PM, Suzen, Mehmet msu...@gmail.com wrote: On 14 January 2013 15:08, Cyrus Shaoul cyrus.sha...@uni-tuebingen.de wrote: La.svd Dear Cyrus, Have you tried running La.svd ; LAPACK only version (without R) via C/C++ or Fortran code? After all it can be a LAPACK issue and R-team has no control on that. David Winsemius Alameda, CA, USA -- Cyrus Shaoul, PhD http://www.sfs.uni-tuebingen.de/~cshaoul/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to open grib file in R?
On Mon, Jan 14, 2013 at 6:26 PM, Jonsson amen.alya...@bordeaux.inra.fr wrote: I have just contacted the sources and I am told that he checked min/max lat/lon for the file and it was right. He is using Linux while I am using Windows, would that be problematic? gdalinfo on a Linux box says it has the same problem: $ gdalinfo Vol_025_H14_2010060700.grib Warning: Inside GRIB2Inventory, Message # 5 ERROR: Ran out of file reading SECT0 There were 76 trailing bytes in the file. Driver: GRIB/GRIdded Binary (.grb) Files: Vol_025_H14_2010060700.grib Size is 1440, 721 Coordinate System is: GEOGCS[Coordinate System imported from GRIB file, DATUM[unknown, SPHEROID[Sphere,6367470,0]], PRIMEM[Greenwich,0], UNIT[degree,0.0174532925199433]] Origin = (-0.125,90.125) Pixel Size = (0.250,-0.250) Corner Coordinates: Upper Left ( -0.125, 90.125) ( 0d 7'30.00W, 90d 7'30.00N) Lower Left ( -0.125, -90.125) ( 0d 7'30.00W, 90d 7'30.00S) Upper Right ( 359.875, 90.125) (359d52'30.00E, 90d 7'30.00N) Lower Right ( 359.875, -90.125) (359d52'30.00E, 90d 7'30.00S) Center ( 179.875, 0.000) (179d52'30.00E, 0d 0' 0.01N) Now go ask your source why they are using 721 pixels from N to S... I don't have anything else that can read grib files, so I can't say any more, and as a binary file format its hard to tell if gdalinfo is correct or not, but its usually pretty good. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] information
Hi, I have a graph where my y axis are scaled in the interval of 500 ,i want to make them i the interval of 2,so pls can u help me out. karan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] function coverage
On 14/01/2013 22:25, Hadley Wickham wrote: I think codetools could do this reasonably well with the walkCode function, but I've never done it so I don't have sample code, and walkCode is mostly an internal function. There are a couple of approaches here: http://stackoverflow.com/questions/14276728/ Hadley I've used foodweb in mvbutils for that kind of thing. HTH KJ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] information
On 01/15/2013 04:06 PM, Karan Anand wrote: Hi, I have a graph where my y axis are scaled in the interval of 500 ,i want to make them i the interval of 2,so pls can u help me out. Hi karan, This appears to be a nonsensical request, as you seem to be asking for the number of tick marks on the Y axis to be multiplied by 250 times. R typically puts five or six tick marks on an axis by default, and 1250 to 1500 tick marks would produce a solid line if you could manage to do it. Perhaps if you could give a bit more information about what you want to achieve we could be more helpful. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Need some help on Text manipulation.
Hi, If you only need aa to be replaced by a, bb by b and so on, try the following: Dat$att - as.factor(substr(Dat$att,1,1)) HTH, Pascal Le 15/01/2013 18:48, Christofer Bogaso a écrit : Dear all, Let say I have following data-frame: Dat - structure(list(dat = c(-0.387795842956327, -0.23270882099043, -0.89528973290562, 0.95857175595512, 1.61680582493783, -1.17738110289352, 0.210601060411423, -0.827369747447338, -0.36896112964414, 0.440288648776096, 1.28018410608809, -0.897113649961341, 0.342216546981718, -1.17288066266219, -1.57994101992621, -0.913655547602414, -2.54753726314408, -0.617703410989815, -0.443272763891558, 0.359181170918489), att = structure(c(2L, 2L, 2L, 4L, 2L, 2L, 1L, 3L, 1L, 4L, 1L, 2L, 2L, 2L, 2L, 4L, 2L, 2L, 4L, 2L), .Label = c(aa, bb, cc, dd), class = factor)), .Names = c(dat, att), row.names = c(NA, -20L), class = data.frame); Dat Now I want to replace the 2nd column with: Replace - letters[1:20] The rule is as follows: Consider the 1st element of the 2nd colume: 'bb'. Now I need to see which element of 'Replace' is contained in 'bb'? Obviously, this will be 'b'. Therefore I need to replace bb with b. And so on for all elements of 2nd column. This is obviously an straightforward example. However I have some more complex problem of replacing like that. I want to get the idea how to achieve that programmatically. Can somebody help me? Thanks and regards, __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Removing an attached object
Dear All, I am a bit confused, I attached my data frame using 'attach(DATA)' Then I removed it using 'rm(DATA)' But for some reason it is still at position 2 at the search path search() [1] .GlobalEnvDATA package:foreign [4] package:stats package:graphics package:grDevices [7] package:datasets package:rcom package:rscproxy [10] package:utils package:methods RExcelEnv [13] Autoloads package:base Also when I enter the names of factors in this dataframe, such as 'AGE', I get a list of data values. This is weird, why does it not disappear from the search path? Thanks Pancho Mulongeni Research Assistant PharmAccess Foundation 1 Fouché Street Windhoek West Windhoek Namibia Tel: +264 61 419 000 Fax: +264 61 419 001/2 Mob: +264 81 4456 286 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Removing an attached object
Hi, Please read the following: http://stackoverflow.com/questions/3536036/rmlist-ls-doesnt-completely-clear-the-workspace HTH, Pascal Le 15/01/2013 19:55, Pancho Mulongeni a écrit : Dear All, I am a bit confused, I attached my data frame using 'attach(DATA)' Then I removed it using 'rm(DATA)' But for some reason it is still at position 2 at the search path search() [1] .GlobalEnvDATA package:foreign [4] package:stats package:graphics package:grDevices [7] package:datasets package:rcom package:rscproxy [10] package:utils package:methods RExcelEnv [13] Autoloads package:base Also when I enter the names of factors in this dataframe, such as 'AGE', I get a list of data values. This is weird, why does it not disappear from the search path? Thanks Pancho Mulongeni Research Assistant PharmAccess Foundation 1 Fouché Street Windhoek West Windhoek Namibia Tel: +264 61 419 000 Fax: +264 61 419 001/2 Mob: +264 81 4456 286 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Removing an attached object
Thanks, that makes it clear -Original Message- From: Pascal Oettli [mailto:kri...@ymail.com] Sent: Tuesday, January 15, 2013 1:07 PM To: Pancho Mulongeni Cc: R help Subject: Re: [R] Removing an attached object Hi, Please read the following: http://stackoverflow.com/questions/3536036/rmlist-ls-doesnt-completely-clear-the-workspace HTH, Pascal Le 15/01/2013 19:55, Pancho Mulongeni a écrit : Dear All, I am a bit confused, I attached my data frame using 'attach(DATA)' Then I removed it using 'rm(DATA)' But for some reason it is still at position 2 at the search path search() [1] .GlobalEnvDATA package:foreign [4] package:stats package:graphics package:grDevices [7] package:datasets package:rcom package:rscproxy [10] package:utils package:methods RExcelEnv [13] Autoloads package:base Also when I enter the names of factors in this dataframe, such as 'AGE', I get a list of data values. This is weird, why does it not disappear from the search path? Thanks Pancho Mulongeni Research Assistant PharmAccess Foundation 1 Fouché Street Windhoek West Windhoek Namibia Tel: +264 61 419 000 Fax: +264 61 419 001/2 Mob: +264 81 4456 286 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] random effects model
Hi AK Got an error message with library(ggplot2) ggplot(BP.stack1,aes(x=factor(HiBP),fill=Obese))+geom_bar(position=fill)Error in rename(x, .base_to_ggplot, warn_missing = FALSE) : could not find function revalue ggplot(BP.stack1,aes(x=factor(HiBP),fill=Overweight))+geom_bar(position=fill)Error in rename(x, .base_to_ggplot, warn_missing = FALSE) : could not find function revalue I got the dot plot, thanks for that. I have attached some plots, not sure how to interpret, they had unusual patterns.Is it because of missing data? I tried removing the missing data too. They still appeared the same. Do I need to transform the data? Thanks in advance. On Tue, Jan 15, 2013 at 8:54 AM, arun smartpink...@yahoo.com wrote: HI, BP_2b-read.csv(BP_2b.csv,sep=\t) BP_2bNM-na.omit(BP_2b) BP.stack3 - reshape(BP_2bNM,idvar=CODEA,timevar=time,sep=,varying=list(c(Obese14,Obese21),c(Overweight14,Overweight21),c(hibp14,hibp21)),v.names=c(Obese,Overweight,HiBP),times=factor(c(1,2)),direction=long) library(car) BP.stack3$Obese- recode(BP.stack3$Obese,1='Obese';0='Not Obese') BP.stack3$Overweight- recode(BP.stack3$Overweight,1='Overweight';0='Not Overweight') library(ggplot2) ggplot(BP.stack3,aes(x=factor(HiBP),fill=Obese))+geom_bar(position=fill) ggplot(BP.stack3,aes(x=factor(HiBP),fill=Overweight))+geom_bar(position=fill) You could try lmer() from lme4. library(lme4) fm1-lmer(HiBP~time+(1|CODEA), family=binomial,data=BP.stack3) #check codes, not sure print(dotplot(ranef(fm1,post=TRUE), scales = list(x = list(relation = free)))[[1]]) qmt1- qqmath(ranef(fm1, postVar=TRUE)) print(qmt1[[1]]) A.K. From: Usha Gurunathan usha.nat...@gmail.com To: arun smartpink...@yahoo.com Cc: R help r-help@r-project.org Sent: Monday, January 14, 2013 6:32 AM Subject: Re: [R] random effects model Hi AK I have been trying to create some plots. All being categorical variables, I am not getting any luck with plots. The few ones that have worked are below: barchart(~table(HiBP)|Obese,data=BP.sub3) ## BP.sub3 is the stacked data without missing values barchart(~table(HiBP)|Overweight,data=BP.sub3) plot(jitter(hibp14,factor=2)~jitter(Obese14,factor=2),col=gray,cex=0.7, data=Copy.of.BP_2) ## Copy.of.BP_2 is the original wide format ## not producing any good plots with mixed models as well. summary(lme.3 - lme(HiBP~time, data=BP.sub3,random=~1|CODEA, na.action=na.omit)) anova(lme.3) head(ranef(lme.3)) print(plot(ranef(lme.3))) ## Thanks for any help. On Mon, Jan 14, 2013 at 4:33 AM, arun smartpink...@yahoo.com wrote: HI, I think I mentioned to you before that when you reshape the columns excluding the response variable, response variable gets repeated (in this case hibp14 or hibp21) and creates the error I run your code, there are obvious problems in the code so I didn't reach up to BP.gee BP_2b-read.csv(BP_2b.csv,sep=\t) BP.stack3 - reshape(BP_2b,idvar=CODEA,timevar=time,sep=_,varying=list(c(Obese14,Obese21),c(Overweight14,Overweight21)),v.names=c(Obese,Overweight),times=factor(c(1,2)),direction=long) BP.stack3 - transform(BP.stack3,CODEA=factor(CODEA),Sex=factor(Sex,labels=c(Male,Female)),MaternalAge=factor(MaternalAge,labels=c(39years or less,40-49 years,50 years or older)),Education=factor(Education,labels=c(Primary/special,Started secondary,Completed grade10, Completed grade12, College,University)),Birthplace=factor(Birthplace,labels=c(Australia,Other English-speaking,Other))) BP.stack3$Sex - factor(BP.stack3$Sex,levels=levels(BP.stack3$Sex)[c(2,1)]) BP.sub3a - subset(BP.stack3,subset=!(is.na(Sex)| is.na(Education)| is.na(Birthplace)|is.na(Education)|is.na(hibp14)| is.na(hibp21))) nrow(BP.sub3a) #[1] 3364 BP.sub5a - BP.sub3a[order(BP.sub3a$CODEA),] # your code was BP.sub5a - BP.sub3a[order(BP.sub5a$CODEA),] ^ was not defined before #Next line BPsub3$Categ[BPsub6$Overweight==1BPsub3$time==1BPsub3$Obese==0]- Overweight14 #It should be BP.sub3 and what is BPsub6, it was not defined previously. #Error in BPsub3$Categ[BPsub6$Overweight == 1 BPsub3$time == 1 BPsub3$Obese == : #object 'BPsub3' not found A.K. From: Usha Gurunathan usha.nat...@gmail.com To: arun smartpink...@yahoo.com Sent: Sunday, January 13, 2013 1:51 AM Subject: Re: [R] random effects model HI AK Thanks a lot for explaining that. 1. With the chi sq. ( in order to find out if the diffce is significant between groups) do I have create a separate excel file and make a dataframe.How do I go about it? I have resent a mail to Jun Yan at a difft email ad( first add.didn't work, mail not delivered). 2. With my previous query ( reg. Obese/Overweight/ Normal at age 14 Vs change of blood pressure status at 21), even though I had compromised without the age-specific regression, but I am still keen to explore why the
Re: [R] Tukey HSD plot with lines indicating (non-)significance
Karl, Thank you for this interesting challenge. It turns out to be reasonably straightforward. This code does it for the first example in ?MMC. ## This example is based on the example in ?HH:::MMC library(HH) ## pairwise comparisons data(catalystm) ## A. individual plots ## base graphics box plot boxplot(concent ~ catalyst, data=catalystm, xlab=catalyst, ylab=concentration, las=1) ## aov catalystm1.aov - aov(concent ~ catalyst, data=catalystm) summary(catalystm1.aov) ## MMC plot old.omd - par(omd=c(0,.95,0,1)) catalystm.mmc - mmc(catalystm1.aov, linfct = mcp(catalyst = Tukey)) catalystm.mmc plot(catalystm.mmc, ry=c(50,58), x.offset=1.8) ## tiebreaker plot plotMatchMMC(catalystm.mmc$mca, xlabel.print=FALSE) ## B. coordinate scales of all three plots by adjusting par values and ##the frame sizes def.par - par(no.readonly = TRUE) # save default, for resetting... ## allocate figure 1 the right 2/3 and top 2/3 of the plotting region ## allocate figure 2 the right 2/3 and bottom 1/3 of the plotting region ## allocate figure 3 the left 1/3 and top 2/3 of the plotting region frame() layout(matrix(c(3,1, 0,2), 2, 2, byrow = TRUE), widths=c(1,2), heights=c(2,1)) ## show the regions that have been allocated to each plot layout.show(3) omd.old - par(omd=c(0,.95,0,1)) plot(catalystm.mmc, ry=c(50,59), x.offset=1.8) usr.mmc - par()$usr mar.old - par(mar=c(5,4,0,2)+.1) plotMatchMMC(catalystm.mmc$mca, xlabel.print=FALSE) par(mar.old) boxplot(concent ~ catalyst, data=catalystm, xlab=catalyst, ylab=concentration, las=1, ylim=usr.mmc[3:4], yaxs=i) ## If you have a set of plots that don't fit comfortably into the ## space illustrated here, then you will need to increase the plotting ## device window from the default 7in x 7in because the cex is ## hardwired into the plot.mmc.multicomp function. On Mon, Jan 14, 2013 at 6:37 PM, Richard M. Heiberger r...@temple.eduwrote: When the group means are close together, the labels will overlap. This overlap is actually informative, indicating that the groups are close. For this common case, we provide the tiebreaker function matchMMC which is also documented and illustrated on the ?MMC page. I have never tried to put the data on the same scale. It should be easy. Let me try, and then post an example. Rich On Mon, Jan 14, 2013 at 3:53 PM, Karl Ove Hufthammer k...@huftis.orgwrote: må. den 14. 01. 2013 klokka 13.58 (-0500) skreiv Richard M. Heiberger: Please look at the MMC (Mean-mean Multiple Comparisons) plot in the HH package. It displays both the means and the differences. install.packages(HH) ## if you don't already have it. library(HH) ?MMC Thanks for the suggestion. Thats a very interesting and clever way of displaying both means and differences. Its not what I was looking for, though, as it doesnt display the actual data. For the record, heres the syntax for using MMC on the dataset mentioned in my original posting: l.mmc=mmc(l, linfct = mcp(trt = Tukey)) plot(l.mmc) (It looks best on data where the group means arent very close; otherwise the labels might overlap.) -- Karl Ove Hufthammer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tukey HSD plot with lines indicating (non-)significance
Den 2013-01-14 19:58 skreiv Richard M. Heiberger:
Please look at the MMC (Mean-mean Multiple Comparisons) plot in the
HH package.
It displays both the means and the differences.
install.packages(HH) ## if you don't already have it.
library(HH)
?MMC
I have now coded a very quick-and-dirty solution for my line graph.
Example follows. I use the results of the 'cld' function in multcomp
to calculcate which groups are significantly different from each other.
Important note: The LetterMatrix object contains the needed
data, but the rows are not in the same order as the original levels,
and unfortunately the row names do *not* match the level names
(spaces seems to be stripped -- I don't know why). That's the reason
I remove the spaces in the example below.
Note: The levels should preferably be ordered by the group means,
but the function works (modulo any bugs) even if they're not.
Dotted lines are then used to indicate significant differences.
Important note: There are bound to be bugs. Do check the results
before using the resulting graph.
# Calculate non-significance lines for Tukey HSD
tukeyHSDLines=function(l, removeEndLines=TRUE,
removeSingleGroups=FALSE) {
# Calculate Tukey HSD values
library(multcomp)
l.glht=glht(l, linfct = mcp(trt = Tukey))
# Calculcate a compact letter display (CLD)
l.cld=cld(l.glht)
lmat=l.cld$mcletters$LetterMatrix[levels(d$trt),]
# Calculate the non-significance lines that should be
# drawn, based on the CLD data
calc.lines=function(x) {
r=rle(x)
lend=cumsum(r$lengths)# Line end index
lstart=c(1,lend[-length(lend)]+1) # Line start index
d2=data.frame(lstart=lstart-.4, lend=lend+.4, nodraw=!r$values)
if( removeEndLines ) {
if(d2$nodraw[1]) d2=d2[-1,] # Remove 'leading'
dotted lines
if(d2$nodraw[nrow(d2)]) d2=d2[-nrow(d2),] # Remove 'trailing'
dotted lines
}
d2
}
linlist=apply(lmat, 2, calc.lines)
lindat=do.call(rbind, linlist)
lindat$y=rep(seq_along(linlist), times=sapply(linlist, nrow))
if (removeSingleGroups) {
lindat=subset(lindat, !(y %in% which(tabulate(lindat$y)==1)))
lindat$y=as.numeric(factor(lindat$y))
}
lindat
}
# Example:
library(DAAG)
d=rice # The dataset to use
levels(d$trt)=gsub( , , levels(d$trt)) # Remove spaces from level
names
# d$trt=reorder(d$trt, -d$ShootDryMass)# Graph looks better with
reordered factor
l=aov(ShootDryMass ~ trt, data=d) # Fit a one-way ANOVA
lindat=tukeyHSDLines(l)
lindat$y=150-lindat$y*3
library(ggplot2)
ggplot(d, aes(x=trt, y=ShootDryMass)) + geom_boxplot(outlier.colour=NA)
+
geom_jitter(col=red, size=3, position=position_jitter(width=.1)) +
geom_segment(aes(x=lstart, xend=lend, y=y, yend=y, linetype=nodraw),
lindat)
--
Karl Ove Hufthammer
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tukey HSD plot with lines indicating (non-)significance
Karl,
I will look at your function later and comment on it.
RIght now, I am replying to your comment The levels should preferably be
ordered by the group means,
One of the features of the tabular printout from the mmc function, and of
both
the MMC plot and the plotMatchMMC plot, is that the levels are ordered by
the group means.
Rich
On Tue, Jan 15, 2013 at 6:46 AM, Karl Ove Hufthammer k...@huftis.orgwrote:
Den 2013-01-14 19:58 skreiv Richard M. Heiberger:
Please look at the MMC (Mean-mean Multiple Comparisons) plot in the HH
package.
It displays both the means and the differences.
install.packages(HH) ## if you don't already have it.
library(HH)
?MMC
I have now coded a very quick-and-dirty solution for my line graph.
Example follows. I use the results of the 'cld' function in multcomp
to calculcate which groups are significantly different from each other.
Important note: The LetterMatrix object contains the needed
data, but the rows are not in the same order as the original levels,
and unfortunately the row names do *not* match the level names
(spaces seems to be stripped -- I don't know why). That's the reason
I remove the spaces in the example below.
Note: The levels should preferably be ordered by the group means,
but the function works (modulo any bugs) even if they're not.
Dotted lines are then used to indicate significant differences.
Important note: There are bound to be bugs. Do check the results
before using the resulting graph.
# Calculate non-significance lines for Tukey HSD
tukeyHSDLines=function(l, removeEndLines=TRUE, removeSingleGroups=FALSE) {
# Calculate Tukey HSD values
library(multcomp)
l.glht=glht(l, linfct = mcp(trt = Tukey))
# Calculcate a compact letter display (CLD)
l.cld=cld(l.glht)
lmat=l.cld$mcletters$**LetterMatrix[levels(d$trt),]
# Calculate the non-significance lines that should be
# drawn, based on the CLD data
calc.lines=function(x) {
r=rle(x)
lend=cumsum(r$lengths)# Line end index
lstart=c(1,lend[-length(lend)]**+1) # Line start index
d2=data.frame(lstart=lstart-.**4, lend=lend+.4, nodraw=!r$values)
if( removeEndLines ) {
if(d2$nodraw[1]) d2=d2[-1,] # Remove 'leading' dotted
lines
if(d2$nodraw[nrow(d2)]) d2=d2[-nrow(d2),] # Remove 'trailing' dotted
lines
}
d2
}
linlist=apply(lmat, 2, calc.lines)
lindat=do.call(rbind, linlist)
lindat$y=rep(seq_along(**linlist), times=sapply(linlist, nrow))
if (removeSingleGroups) {
lindat=subset(lindat, !(y %in% which(tabulate(lindat$y)==1)))
lindat$y=as.numeric(factor(**lindat$y))
}
lindat
}
# Example:
library(DAAG)
d=rice # The dataset to use
levels(d$trt)=gsub( , , levels(d$trt)) # Remove spaces from level names
# d$trt=reorder(d$trt, -d$ShootDryMass)# Graph looks better with
reordered factor
l=aov(ShootDryMass ~ trt, data=d) # Fit a one-way ANOVA
lindat=tukeyHSDLines(l)
lindat$y=150-lindat$y*3
library(ggplot2)
ggplot(d, aes(x=trt, y=ShootDryMass)) + geom_boxplot(outlier.colour=**NA)
+
geom_jitter(col=red, size=3, position=position_jitter(**width=.1)) +
geom_segment(aes(x=lstart, xend=lend, y=y, yend=y, linetype=nodraw),
lindat)
--
Karl Ove Hufthammer
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[R] Need help: R for repetitive tasks
Dear R users, First of all I would like to thank all of you who replayed to my previous questions and problems. Thank you a lot for being great and helpful community. I highly appreciate your suggestions and ideas even if I do not respond after my question! But it means that your help was exactly what I needed. Thank you again! Now the following question I need help: Suppose I do have a file.txt in the working directory. This file contains the names of other files in the same directory: First.txt Second.txt Third.txt etc... Files First.txt, Second.txt...are data files. What I need R to do, is to read this file.txt line by line, open files which names are listed ( First.txt, Second.txt...) and process it: lets say make a FirstPlot.bmp, FirstSummary.txt and save it to working directory, then automatically open Second.txt, do the same, Third.txt etc. until the end of the names in file.txt. This would help me with the following task: I do measurements each day, and I need to process my data: draw some plots, make some analysis. When I have 30 days of measurements each 1 second, there are huge amount of numbers I am dealing with. If you could suggest some automation via R, it would be perfect. Thank you in advance. Cheers. -- Simonas Kecorius **Lithuania [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rbbg for 2.15.2
Tolga, The Rbbg binary for 2.15 works for the .0, .1, and .2 minor versions. The issue here is probably a change to the install.packages function that was introduced in R 2.15.2. You can get around this by first calling R options(install.packages.check.source = no) and then following with the Rbbg installation. Hope that helps, John On Mon, Jan 14, 2013 at 5:18 PM, Tolga Uzuner to...@coubros.com wrote: Dear R Users, Anyone know of a version of Rbbg compiled for R 2.15.2 . The current version does not appear to work with 2.15.2 install.packages(Rbbg, repos = http://r.findata.org;) Installing package(s) into C:/Users/t_uzu_000/Documents/** R/win-library/2.15 (as lib is unspecified) Warning: unable to access index for repository http://r.findata.org/src/** contrib http://r.findata.org/src/contrib Warning message: package Rbbg is not available (for R version 2.15.2) Thanks in advance, Tolga __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Need help: R for repetitive tasks
list.files() to get all the files in the directory (use the pattern argument to be more specific). Then loop over the file names, reading in the data one at a time, do the desired processing, and then use the file name to make the graphics file name as well. Cheers, MW On Tue, Jan 15, 2013 at 12:30 PM, Simonas Kecorius simolas2...@gmail.com wrote: Dear R users, First of all I would like to thank all of you who replayed to my previous questions and problems. Thank you a lot for being great and helpful community. I highly appreciate your suggestions and ideas even if I do not respond after my question! But it means that your help was exactly what I needed. Thank you again! Now the following question I need help: Suppose I do have a file.txt in the working directory. This file contains the names of other files in the same directory: First.txt Second.txt Third.txt etc... Files First.txt, Second.txt...are data files. What I need R to do, is to read this file.txt line by line, open files which names are listed ( First.txt, Second.txt...) and process it: lets say make a FirstPlot.bmp, FirstSummary.txt and save it to working directory, then automatically open Second.txt, do the same, Third.txt etc. until the end of the names in file.txt. This would help me with the following task: I do measurements each day, and I need to process my data: draw some plots, make some analysis. When I have 30 days of measurements each 1 second, there are huge amount of numbers I am dealing with. If you could suggest some automation via R, it would be perfect. Thank you in advance. Cheers. -- Simonas Kecorius **Lithuania [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] paper - download - pubmed
Hi, I actually need to download pdfs through R code. The thing which I want to do is that, search for a paper in pubmed, which is possible by using GetPubMed function in the package NCBI2R’. GetPubMed(searchterm, file = , download = TRUE , showurl = FALSE, xldiv = ;, hyper = HYPERLINK, MaxRet = 3, sme = FALSE, smt = FALSE, quiet = TRUE, batchsize=500,descHead=FALSE) With this function I can not download the pdfs for all hits, although if I go to the pubmed, I can download it. So, the problem is not that, for each paper I have to download the pdfs (which are available if I go to the pubmed and search directly there) and the corresponding supplementary files. Could anybody please help me how I can solve this? Thanks, Nooshin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Function failure in tm
HI all: I have a customized source reader for the package tm (that Milan Bouchet-Vallat has been instrumental in producing). I can get it to produce a corpus of class: VCorpus Corpus list class(mycorp[1]) returns VCorpus Corpus list and class(mycorp[[1]] returns PlainTextDocument TextDocument character But now that I've got a corpsu, none of the transformation functions work at all. They all return the following error (with the respective function name) Error in UseMethod(stripWhitespace, x) : no applicable method for 'stripWhitespace' applied to an object of class NULL I haven't seen this error reported anywhere in the R-list archives. Does anyone have any suggestions? Yours, Simon Kiss P.S. The results of sessionInfo() are R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RWekajars_3.7.7-2 rJava_0.9-3 RWeka_0.4-13 Snowball_0.0-8 [5] tm.plugin.factiva_1.1 tm_0.5-8.1 loaded via a namespace (and not attached): [1] grid_2.15.0 slam_0.1-26 tools_2.15.0 XML_3.9-4 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rbbg for 2.15.2
Many thanks, I got this to work. On 15/01/2013 12:57, John Laing wrote: Tolga, The Rbbg binary for 2.15 works for the .0, .1, and .2 minor versions. The issue here is probably a change to the install.packages function that was introduced in R 2.15.2. You can get around this by first calling R options(install.packages.check.source = no) and then following with the Rbbg installation. Hope that helps, John On Mon, Jan 14, 2013 at 5:18 PM, Tolga Uzuner to...@coubros.com mailto:to...@coubros.com wrote: Dear R Users, Anyone know of a version of Rbbg compiled for R 2.15.2 . The current version does not appear to work with 2.15.2 install.packages(Rbbg, repos = http://r.findata.org;) Installing package(s) into C:/Users/t_uzu_000/Documents/R/win-library/2.15 (as lib is unspecified) Warning: unable to access index for repository http://r.findata.org/src/contrib Warning message: package Rbbg is not available (for R version 2.15.2) Thanks in advance, Tolga __ R-help@r-project.org mailto:R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Code to fetch summary info from vector
Hi all, Thanks in advance for any help. I have a vector b: b=c(1,1,1,2,3,4,3,2,1,1,1,1,1,2,3,4,5,4,3.5,3,2,1,1,1) Imagine b is river flow throughout time. I would like some code that will generate the following information: number of individual 'periods' where b1 (= 2 in this case) period 1 length = 5, max = 4 period 2 length = 8, max = 5 I can't figure anything useful out. Thanks, Ben Gillespie Research Postgraduate School of Geography University of Leeds Leeds LS2 9JT http://www.geog.leeds.ac.uk/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Code to fetch summary info from vector
I don't know if I understand what you want. What are the periods? I suspect this is a time series. What have you tried that didn't work? kind regards, Stephen On 01/15/2013 10:16 AM, Benjamin Gillespie wrote: Hi all, Thanks in advance for any help. I have a vector b: b=c(1,1,1,2,3,4,3,2,1,1,1,1,1,2,3,4,5,4,3.5,3,2,1,1,1) Imagine b is river flow throughout time. I would like some code that will generate the following information: number of individual 'periods' where b1 (= 2 in this case) period 1 length = 5, max = 4 period 2 length = 8, max = 5 I can't figure anything useful out. Thanks, Ben Gillespie Research Postgraduate School of Geography University of Leeds Leeds LS2 9JT http://www.geog.leeds.ac.uk/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick ** Auburn University Biological Sciences 331 Funchess Hall Auburn, Alabama 36849 ** sas0...@auburn.edu http://www.auburn.edu/~sas0025 ** Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis A big computer, a complex algorithm and a long time does not equal science. -Robert Gentleman __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Code to fetch summary info from vector
Hi Ben I'm not sure whether I understood correctly, but is it something like this? sum(ifelse(b==2,1,0)) [1] 4 sum(ifelse(b==3,1,0)) [1] 4 sum(ifelse(b=2,1,0)) [1] 13 sum(ifelse(b2,1,0)) [1] 9 Etc... José José Iparraguirre Chief Economist Age UK -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Benjamin Gillespie Sent: 15 January 2013 16:16 To: r-help@r-project.org Subject: [R] Code to fetch summary info from vector Hi all, Thanks in advance for any help. I have a vector b: b=c(1,1,1,2,3,4,3,2,1,1,1,1,1,2,3,4,5,4,3.5,3,2,1,1,1) Imagine b is river flow throughout time. I would like some code that will generate the following information: number of individual 'periods' where b1 (= 2 in this case) period 1 length = 5, max = 4 period 2 length = 8, max = 5 I can't figure anything useful out. Thanks, Ben Gillespie Research Postgraduate School of Geography University of Leeds Leeds LS2 9JT http://www.geog.leeds.ac.uk/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Wrap Up and Run 10k is back! Also, new for 2013 – 2km intergenerational walks at selected venues. So recruit a buddy, dust off the trainers and beat the winter blues by signing up now: http://www.ageuk.org.uk/10k Milton Keynes | Oxford | Sheffield | Crystal Palace | Exeter | Harewood House, Leeds | Tatton Park, Cheshire | Southampton | Coventry Age UK Improving later life http://www.ageuk.org.uk --- Age UK is a registered charity and company limited by guarantee, (registered charity number 1128267, registered company number 6825798). Registered office: Tavis House, 1-6 Tavistock Square, London WC1H 9NA. For the purposes of promoting Age UK Insurance, Age UK is an Appointed Representative of Age UK Enterprises Limited, Age UK is an Introducer Appointed Representative of JLT Benefit Solutions Limited and Simplyhealth Access for the purposes of introducing potential annuity and health cash plans customers respectively. Age UK Enterprises Limited, JLT Benefit Solutions Limited and Simplyhealth Access are all authorised and regulated by the Financial Services Authority. -- This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you receive a message in error, please advise the sender and delete immediately. Except where this email is sent in the usual course of our business, any opinions expressed in this email are those of the author and do not necessarily reflect the opinions of Age UK or its subsidiaries and associated companies. Age UK monitors all e-mail transmissions passing through its network and may block or modify mails which are deemed to be unsuitable. Age Concern England (charity number 261794) and Help the Aged (charity number 272786) and their trading and other associated companies merged on 1st April 2009. Together they have formed the Age UK Group, dedicated to improving the lives of people in later life. The three national Age Concerns in Scotland, Northern Ireland and Wales have also merged with Help the Aged in these nations to form three registered charities: Age Scotland, Age NI, Age Cymru. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Code to fetch summary info from vector
I don't completely understand the question, but if you are looking for the lengths of the runs of values greater than 1 then rle() would help: b - c(1,1,1,2,3,4,3,2,1,1,1,1,1,2,3,4,5,4,3.5,3,2,1,1,1) r - rle(b1) r Run Length Encoding lengths: int [1:5] 3 5 5 8 3 values : logi [1:5] FALSE TRUE FALSE TRUE FALSE r$lengths[r$values] [1] 5 8 To get the maximum of each run of values greater than one, something like the following may do (there are more elegant ways, but I don't want to spend the time on it until I know what the question is): runNumber - cumsum( c(b[1]1, (b[-1]1) (b[-length(b)]=1)) ) runNumber[b=1] - NA tapply(b, runNumber, max) 1 2 4 5 Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Benjamin Gillespie Sent: Tuesday, January 15, 2013 8:16 AM To: r-help@r-project.org Subject: [R] Code to fetch summary info from vector Hi all, Thanks in advance for any help. I have a vector b: b=c(1,1,1,2,3,4,3,2,1,1,1,1,1,2,3,4,5,4,3.5,3,2,1,1,1) Imagine b is river flow throughout time. I would like some code that will generate the following information: number of individual 'periods' where b1 (= 2 in this case) period 1 length = 5, max = 4 period 2 length = 8, max = 5 I can't figure anything useful out. Thanks, Ben Gillespie Research Postgraduate School of Geography University of Leeds Leeds LS2 9JT http://www.geog.leeds.ac.uk/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Code to fetch summary info from vector
Maybe rle can help a little here rle(b1) Run Length Encoding lengths: int [1:5] 3 5 5 8 3 values : logi [1:5] FALSE TRUE FALSE TRUE FALSE r-rle(b1) r$lengths[r$values] [1] 5 8 # started for the maximum but need to go home now, sorry. Will continue tomorrow if noone else finishes it. groups - rep(1:length(r$lengths),r$lengths) On 15.01.2013, at 17:16, Benjamin Gillespie wrote: Hi all, Thanks in advance for any help. I have a vector b: b=c(1,1,1,2,3,4,3,2,1,1,1,1,1,2,3,4,5,4,3.5,3,2,1,1,1) Imagine b is river flow throughout time. I would like some code that will generate the following information: number of individual 'periods' where b1 (= 2 in this case) period 1 length = 5, max = 4 period 2 length = 8, max = 5 I can't figure anything useful out. Thanks, Ben Gillespie Research Postgraduate School of Geography University of Leeds Leeds LS2 9JT http://www.geog.leeds.ac.uk/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Hist with Dates
Hello R-Helpers, I would like to generate the frequencies of dates (data.RData). str(data) Date[1:43748], format: 2001-01-01 2001-01-01 2001-01-01 2001-01-01 ... test - hist(data,days,freq=T) test$counts [1] 27 17 12 15 6 4 5 13 5 13 15 9 7 10 11 21 10 10 9 11 15 7 10 14 but the count is wrong, because i have only 9 times 01/01/2001 etc. data[1:30] [1] 2001-01-01 2001-01-01 2001-01-01 2001-01-01 2001-01-01 [6] 2001-01-01 2001-01-01 2001-01-01 2001-01-01 2001-01-02 [11] 2001-01-02 2001-01-02 2001-01-02 2001-01-02 2001-01-02 [16] 2001-01-02 2001-01-02 2001-01-02 2001-01-02 2001-01-02 [21] 2001-01-03 2001-01-03 2001-01-03 2001-01-03 2001-01-03 [26] 2001-01-03 2001-01-03 2001-01-03 2001-01-03 2001-01-03 Now, when i give R the breaks. br - seq(as.Date(31.12.2000,format=%d.%m.%Y),as.Date(01.01.2012,format=%d.%m.%Y),by=1) test2- hist(data,br,freq=T) test2$counts[1:10] [1] 12 15 17 12 15 6 4 5 13 5 In this case, neither get the right counts but limiting i get the correct counts: test3- hist(data[1:50],br[1:6],freq=T) test3$counts [1] 9 11 13 9 8 I hope someone can help me with this problem. Thank you very much!! Best regards, Dominic __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] temporal and spatial correlation structures in GAMM
Dear R_help list members!  Iâm studding forest carnivores and I have data on resting site selection and use!  Iâm trying to model the probability that a forest carnivore might have in be located in a tree hollow (1) (the main resting site selected) rather than elsewhere (0) (other resting site types, dens, nests, etc.). The model should be related with several variables such as for instance:  SHRUB_CV â shrub cover; D_RIPARIAN â distance to riparian habitats FOREST_PP â forest habitat (tree availability) proportion in each sampling unit (1 km buffer around each resting site) D_RIP_KM â distance to the nearest riparian habitat.. Day â day of the year⦠ My data consist of a daily resting site monitoring of 21 animals (during the time that each radio-collar battery allowed) ranging from 40-380 daysâ¦The study was conducted in the 2010-12 period⦠So, in the final I got a data base with more than 3300 observation events (an event is an animal present in a resting site each day). Several resting sites were used more than once by the same individual, but some times the same resting site were used by two or more animals (few times I had two animals in the same day and in the same resting)â¦leading to, that for some covariates, the values are the same across animals when they⦠Also, in most of the days I had more than one resting site event because during most of the study I followed more than one animal at the same time⦠Because I was not interest if there is an animal effect on tree hollow probability use, I used animal as random effect in the models. In addition, we assume that an individual from the forest carnivore population will behave more or less the same way concerning tree hollow use. This lead me to the mixed-effects modelling techniques. Additionally, because I get truly non-linear relationship between some of the covariates (e.g. SHRUB_CV) with the response variable it leads me to the gamm option⦠I start the model building procedure by finding firstly the best fixed structure and after the best random effect structure and finally the best model.  I my case my first attempt final model was obtained by:  Model - gamm4(TREE_01 ~ s(Day) + T_MAX + SHRUB_CV + D_AV5RS_KM + D_RIP_KM + FOREST_PP, random = ~ (1 | fAnimal), method = REML, control = lmc, family = binomial, data = RSTEMP_01_X2) summary(Model$gam)  Family: binomial Link function: logit Formula: TREE_01 ~ s(Day) + T_MAX + SHRUB_CV + D_AV5RS_KM + D_RIP_KM +    FOREST_PP Parametric coefficients:                               Estimate   Std. Error    z value    Pr(|z|)   (Intercept)             5.83792    0.91031   6.413   1.43e-10 *** T_MAX               -0.06309   0.02161  -2.919   0.003509 ** SHRUB_CV        -7.72088   0.46859  -16.477  2e-16 *** D_AV5RS_KM    1.94569    0.53025    3.669    0.000243 *** D_RIP_KM          4.65035     0.60978     7.626    2.42e-14 *** FOREST_PP         2.09453    0.58465     3.583    0.000340 *** Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1 Approximate significance of smooth terms:                edf     Ref.df Chi.sq p-value  s(Day)   5.332  5.332   18.57   0.00316 ** Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1 R-sq.(adj) = 0.541    glmer.ML score = 1117.3 Scale est. = 1        n = 3358  I used the âgamm4â package because it performs better than the âmgcvâ for binomial response variables⦠However, now I have to check for temporal correlations structures since my monitoring programs was in a daily basis it seems, at least, biologically that I would have temporal correlation between days, i.e. the resting site that an animal use in one day is correlated with the one used in the day after⦠I used the formula âacfâ from the ânlmeâ package, I got the temporal autocorrelation plot, and I confirmed that I have correlation, especially in the first 5 days⦠The problems arrived after this, when I try to add some correlation structures in the model I got the following error:  Error in Initialize.corARMA(X[[2L]], ...) : covariate must have unique values within groups for corARMA objects for instance⦠ How can I solve this problem, it is because I have the same value for some covariates across the same animal and between animals? If it is? How can I manage that, because my data should allowed for this because it is normal under this ecological data that a animal during their life time use several times the same resting site and some times they are shared between males and females and females and juveniles/sub-adults. Should I have to create a grouping variable that can disentangle the partsâ¦? Should I
[R] How to get F values for a Generalized Linear Model?
Dear All, I have fitted generalized linear models with the glm() function from the package lme4. The statistical values it returns are the z-value and the p-value. Now I am searching for a way to get the F-values for my models to use for reporting - as to my knowledge reporting z-values is not very useful and the F-values together with the p-values would be desired for the report. I tried the commands summary(model) , anova(model) noranova.glm(model), but couldnt get the F-values that way. Is the command stat.anova(table, test = F, scale, df.scale, n) the right choice? If yes, for this I need the 'residual mean square' to use as scale. But how to extract the 'residual mean square' out of my glm in R? I am very thankful for your comments and advice! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Histogram plot spacing
Dear all, I'd like to remove the space between the x-axis and the 0 of the y-axis in the hist function. I saw the previous post https://stat.ethz.ch/pipermail/r-help/2012-September/324177.html suggesting adding the x-axis at position 0 (or the lowest value of y) after making the histogram. Unfortunately, it doesn't work in my case as I want to use it with a histogram with a ylim starting above 0, so that the x-axis ends up superposing the histogram bars. Any suggestion? For info, I've been using: hist(univariateCV$varcomp, ylim=c(10300,11100), xlim=c(-0.002,0.40), breaks=seq(0,1,0.004), axes=FALSE, main=, ylab=, xlab=,col='blue', xaxt=n) axis(1, at=seq(0,0.40,0.05), labels=seq(0,0.40,0.05), pos=10300) which gives the x axis superposed with the histogram bars. Many thanks Julie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Need some help on Text manipulation.
HI,
In this case, all the elements in Dat$att are found in Replace.
Dat1-within(Dat,{att-as.character(att)})
vec1-unlist(lapply(strsplit(Dat1$att,),unique))
vec1
#[1] b b b d b b a c a d a b b b b d b b
d
#[20] b
Dat1[5:7,2]-c(uu,tt,vv)
vec1-unlist(lapply(strsplit(Dat1$att,),unique))
Dat1$att-ifelse(vec1%in%Replace,vec1,Dat1$att)
Dat1$att
# [1] b b b d uu t vv c a d a b b b b
#[16] d b b d b
A.K.
- Original Message -
From: Christofer Bogaso bogaso.christo...@gmail.com
To: r-help r-help@r-project.org
Cc:
Sent: Tuesday, January 15, 2013 4:48 AM
Subject: [R] Need some help on Text manipulation.
Dear all,
Let say I have following data-frame:
Dat - structure(list(dat = c(-0.387795842956327, -0.23270882099043,
-0.89528973290562, 0.95857175595512, 1.61680582493783, -1.17738110289352,
0.210601060411423, -0.827369747447338, -0.36896112964414, 0.440288648776096,
1.28018410608809, -0.897113649961341, 0.342216546981718, -1.17288066266219,
-1.57994101992621, -0.913655547602414, -2.54753726314408, -0.617703410989815,
-0.443272763891558, 0.359181170918489), att = structure(c(2L,
2L, 2L, 4L, 2L, 2L, 1L, 3L, 1L, 4L, 1L, 2L, 2L, 2L, 2L, 4L, 2L,
2L, 4L, 2L), .Label = c(aa, bb, cc, dd), class = factor)),
.Names = c(dat,
att), row.names = c(NA, -20L), class = data.frame); Dat
Now I want to replace the 2nd column with:
Replace - letters[1:20]
The rule is as follows:
Consider the 1st element of the 2nd colume: 'bb'. Now I need to see
which element of 'Replace' is contained in 'bb'? Obviously, this will
be 'b'. Therefore I need to replace bb with b. And so on for all
elements of 2nd column.
This is obviously an straightforward example. However I have some more
complex problem of replacing like that. I want to get the idea how to
achieve that programmatically.
Can somebody help me?
Thanks and regards,
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] random effects model
Hi, Check these links: http://comments.gmane.org/gmane.comp.lang.r.ggplot2/6527 https://groups.google.com/forum/#!msg/ggplot2/nfVjxL0DXnY/5zf50zCeZuMJ A.K. From: Usha Gurunathan usha.nat...@gmail.com To: arun smartpink...@yahoo.com Cc: R help r-help@r-project.org Sent: Tuesday, January 15, 2013 6:31 AM Subject: Re: [R] random effects model Hi AK Got an error message with library(ggplot2) ggplot(BP.stack1,aes(x=factor(HiBP),fill=Obese))+geom_bar(position=fill) Error in rename(x, .base_to_ggplot, warn_missing = FALSE) : could not find function revalue ggplot(BP.stack1,aes(x=factor(HiBP),fill=Overweight))+geom_bar(position=fill) Error in rename(x, .base_to_ggplot, warn_missing = FALSE) : could not find function revalue I got the dot plot, thanks for that. I have attached some plots, not sure how to interpret, they had unusual patterns.Is it because of missing data? I tried removing the missing data too. They still appeared the same. Do I need to transform the data? Thanks in advance. On Tue, Jan 15, 2013 at 8:54 AM, arun smartpink...@yahoo.com wrote: HI, BP_2b-read.csv(BP_2b.csv,sep=\t) BP_2bNM-na.omit(BP_2b) BP.stack3 - reshape(BP_2bNM,idvar=CODEA,timevar=time,sep=,varying=list(c(Obese14,Obese21),c(Overweight14,Overweight21),c(hibp14,hibp21)),v.names=c(Obese,Overweight,HiBP),times=factor(c(1,2)),direction=long) library(car) BP.stack3$Obese- recode(BP.stack3$Obese,1='Obese';0='Not Obese') BP.stack3$Overweight- recode(BP.stack3$Overweight,1='Overweight';0='Not Overweight') library(ggplot2) ggplot(BP.stack3,aes(x=factor(HiBP),fill=Obese))+geom_bar(position=fill) ggplot(BP.stack3,aes(x=factor(HiBP),fill=Overweight))+geom_bar(position=fill) You could try lmer() from lme4. library(lme4) fm1-lmer(HiBP~time+(1|CODEA), family=binomial,data=BP.stack3) #check codes, not sure print(dotplot(ranef(fm1,post=TRUE), scales = list(x = list(relation = free)))[[1]]) qmt1- qqmath(ranef(fm1, postVar=TRUE)) print(qmt1[[1]]) A.K. From: Usha Gurunathan usha.nat...@gmail.com To: arun smartpink...@yahoo.com Cc: R help r-help@r-project.org Sent: Monday, January 14, 2013 6:32 AM Subject: Re: [R] random effects model Hi AK I have been trying to create some plots. All being categorical variables, I am not getting any luck with plots. The few ones that have worked are below: barchart(~table(HiBP)|Obese,data=BP.sub3) ## BP.sub3 is the stacked data without missing values barchart(~table(HiBP)|Overweight,data=BP.sub3) plot(jitter(hibp14,factor=2)~jitter(Obese14,factor=2),col=gray,cex=0.7, data=Copy.of.BP_2) ## Copy.of.BP_2 is the original wide format ## not producing any good plots with mixed models as well. summary(lme.3 - lme(HiBP~time, data=BP.sub3,random=~1|CODEA, na.action=na.omit)) anova(lme.3) head(ranef(lme.3)) print(plot(ranef(lme.3))) ## Thanks for any help. On Mon, Jan 14, 2013 at 4:33 AM, arun smartpink...@yahoo.com wrote: HI, I think I mentioned to you before that when you reshape the columns excluding the response variable, response variable gets repeated (in this case hibp14 or hibp21) and creates the error I run your code, there are obvious problems in the code so I didn't reach up to BP.gee BP_2b-read.csv(BP_2b.csv,sep=\t) BP.stack3 - reshape(BP_2b,idvar=CODEA,timevar=time,sep=_,varying=list(c(Obese14,Obese21),c(Overweight14,Overweight21)),v.names=c(Obese,Overweight),times=factor(c(1,2)),direction=long) BP.stack3 - transform(BP.stack3,CODEA=factor(CODEA),Sex=factor(Sex,labels=c(Male,Female)),MaternalAge=factor(MaternalAge,labels=c(39years or less,40-49 years,50 years or older)),Education=factor(Education,labels=c(Primary/special,Started secondary,Completed grade10, Completed grade12, College,University)),Birthplace=factor(Birthplace,labels=c(Australia,Other English-speaking,Other))) BP.stack3$Sex - factor(BP.stack3$Sex,levels=levels(BP.stack3$Sex)[c(2,1)]) BP.sub3a - subset(BP.stack3,subset=!(is.na(Sex)| is.na(Education)|is.na(Birthplace)|is.na(Education)|is.na(hibp14)| is.na(hibp21))) nrow(BP.sub3a) #[1] 3364 BP.sub5a - BP.sub3a[order(BP.sub3a$CODEA),] # your code was BP.sub5a - BP.sub3a[order(BP.sub5a$CODEA),] ^ was not defined before #Next line BPsub3$Categ[BPsub6$Overweight==1BPsub3$time==1BPsub3$Obese==0]- Overweight14 #It should be BP.sub3 and what is BPsub6, it was not defined previously. #Error in BPsub3$Categ[BPsub6$Overweight == 1 BPsub3$time == 1 BPsub3$Obese == : #object 'BPsub3' not found A.K. From: Usha Gurunathan usha.nat...@gmail.com To: arun smartpink...@yahoo.com Sent: Sunday, January 13, 2013 1:51 AM Subject: Re: [R] random effects model HI AK Thanks a lot for explaining that. 1. With the chi sq. ( in
Re: [R] GPIB-compatible instrument control with R
I don't know of any tools within R to do something like this, but one possibility is to use other software that will interface with your device and can then talk with R, one possibility for an intermediate program is here: http://www.windmill.co.uk/index.html. On Fri, Jan 11, 2013 at 4:41 PM, Marko Tadjer marko.tad...@gmail.comwrote: Hello, Does an R package exist for communication with instruments using GPIB (IEEE 488) protocol? Something similar exists in python for control of instruments over GPIB, RS232, or USB buses (http://pyvisa.sourceforge.net/) Thanks, Marko __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to get F values for a Generalized Linear Model?
Geraldine: On Tue, Jan 15, 2013 at 1:51 AM, Geraldine Werhahn geri...@yahoo.com wrote: Dear All, I have fitted generalized linear models with the glm() function from the package lme4. The statistical values it returns are the z-value and the p-value. Now I am searching for a way to get the F-values for my models to use for reporting - as to my knowledge Your knowledge is insufficient. Your expectations are incorrect. Either consult someone locally who has sufficient statistical expertise or do some studying of GLM's. As this is a statistics not an R question, you might also wish to try posting to a statistics list instead, like stats.stackexchange.com. Cheers, Bert reporting z-values is not very useful and the F-values together with the p-values would be desired for the report. I tried the commands summary(model) , anova(model) noranova.glm(model), but couldnt get the F-values that way. Is the command stat.anova(table, test = F, scale, df.scale, n) the right choice? If yes, for this I need the 'residual mean square' to use as scale. But how to extract the 'residual mean square' out of my glm in R? I am very thankful for your comments and advice! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Hist with Dates
If all you want is frequencies, could you use table()? dd - c(2001-01-02, 2001-01-02, 2001-01-02, 2001-01-02, 2001-01-02, 2001-01-02, 2001-01-02, 2001-01-02, 2001-01-02, 2001-01-03, 2001-01-03, 2001-01-03, 2001-01-03, 2001-01-03, 2001-01-03, 2001-01-03, 2001-01-03, 2001-01-04, 2001-01-04) ddd - as.Date(dd) str(ddd) table(ddd) as.numeric(table(ddd)) --Chris Ryan SUNY Upstate Medical University Binghamton, NY USA On Tue, Jan 15, 2013 at 7:45 AM, Dominic Roye dominic.r...@gmail.com wrote: Hello R-Helpers, I would like to generate the frequencies of dates (data.RData). str(data) Date[1:43748], format: 2001-01-01 2001-01-01 2001-01-01 2001-01-01 ... test - hist(data,days,freq=T) test$counts [1] 27 17 12 15 6 4 5 13 5 13 15 9 7 10 11 21 10 10 9 11 15 7 10 14 but the count is wrong, because i have only 9 times 01/01/2001 etc. data[1:30] [1] 2001-01-01 2001-01-01 2001-01-01 2001-01-01 2001-01-01 [6] 2001-01-01 2001-01-01 2001-01-01 2001-01-01 2001-01-02 [11] 2001-01-02 2001-01-02 2001-01-02 2001-01-02 2001-01-02 [16] 2001-01-02 2001-01-02 2001-01-02 2001-01-02 2001-01-02 [21] 2001-01-03 2001-01-03 2001-01-03 2001-01-03 2001-01-03 [26] 2001-01-03 2001-01-03 2001-01-03 2001-01-03 2001-01-03 Now, when i give R the breaks. br - seq(as.Date(31.12.2000,format=%d.%m.%Y),as.Date(01.01.2012,format=%d.%m.%Y),by=1) test2- hist(data,br,freq=T) test2$counts[1:10] [1] 12 15 17 12 15 6 4 5 13 5 In this case, neither get the right counts but limiting i get the correct counts: test3- hist(data[1:50],br[1:6],freq=T) test3$counts [1] 9 11 13 9 8 I hope someone can help me with this problem. Thank you very much!! Best regards, Dominic __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Code to fetch summary info from vector
Thanks everyone, I've used the code Will supplied - this worked well. Thanks to all the others who contributed. Ben Gillespie Research Postgraduate School of Geography University of Leeds Leeds LS2 9JT Tel: +44(0)113 34 33345 Mob: +44(0)770 868 7641 http://www.geog.leeds.ac.uk/ From: William Dunlap [wdun...@tibco.com] Sent: 15 January 2013 16:51 To: Benjamin Gillespie; r-help@r-project.org Subject: RE: Code to fetch summary info from vector I don't completely understand the question, but if you are looking for the lengths of the runs of values greater than 1 then rle() would help: b - c(1,1,1,2,3,4,3,2,1,1,1,1,1,2,3,4,5,4,3.5,3,2,1,1,1) r - rle(b1) r Run Length Encoding lengths: int [1:5] 3 5 5 8 3 values : logi [1:5] FALSE TRUE FALSE TRUE FALSE r$lengths[r$values] [1] 5 8 To get the maximum of each run of values greater than one, something like the following may do (there are more elegant ways, but I don't want to spend the time on it until I know what the question is): runNumber - cumsum( c(b[1]1, (b[-1]1) (b[-length(b)]=1)) ) runNumber[b=1] - NA tapply(b, runNumber, max) 1 2 4 5 Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Benjamin Gillespie Sent: Tuesday, January 15, 2013 8:16 AM To: r-help@r-project.org Subject: [R] Code to fetch summary info from vector Hi all, Thanks in advance for any help. I have a vector b: b=c(1,1,1,2,3,4,3,2,1,1,1,1,1,2,3,4,5,4,3.5,3,2,1,1,1) Imagine b is river flow throughout time. I would like some code that will generate the following information: number of individual 'periods' where b1 (= 2 in this case) period 1 length = 5, max = 4 period 2 length = 8, max = 5 I can't figure anything useful out. Thanks, Ben Gillespie Research Postgraduate School of Geography University of Leeds Leeds LS2 9JT http://www.geog.leeds.ac.uk/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Histogram plot spacing
On 15.01.2013 12:35, Julie Collet wrote: Dear all, I'd like to remove the space between the x-axis and the 0 of the y-axis in the hist function. I saw the previous post https://stat.ethz.ch/pipermail/r-help/2012-September/324177.html suggesting adding the x-axis at position 0 (or the lowest value of y) after making the histogram. Unfortunately, it doesn't work in my case as I want to use it with a histogram with a ylim starting above 0, so that the x-axis ends up superposing the histogram bars. Any suggestion? For info, I've been using: hist(univariateCV$varcomp, ylim=c(10300,11100), xlim=c(-0.002,0.40), breaks=seq(0,1,0.004), axes=FALSE, main=, ylab=, xlab=,col='blue', xaxt=n) axis(1, at=seq(0,0.40,0.05), labels=seq(0,0.40,0.05), pos=10300) which gives the x axis superposed with the histogram bars. par(yaxs=i) hist(rnorm(100)) Uwe Ligges Many thanks Julie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sparse dataframes?
Dear Folks-- Is there a data frame analog to sparse matrices? I am working with a panel data set that has a large number of variables that are redefined repeatedly or exist for only a few years (out of 48). In my current structure, where variables are columns and rows are years, more than 90 percent of the cells and more than 3/4 of the total size of my file are NAs. I am wondering if there is an alternate file specification currently available that still allows numeric, character and factor data to be stored. Besides just using a database. A pointer in the right direction (or a solid no if that is the truth) would be greatly appreciated. Sincerely, andrewH -- View this message in context: http://r.789695.n4.nabble.com/Sparse-dataframes-tp4655614.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Hist with Dates
You should read the help for hist carefully: ?hist.Date hist has very specific rules for applying breaks that are often different than tabulation (tapply or aggregate, with or without using the cut function first). --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Dominic Roye dominic.r...@gmail.com wrote: Hello R-Helpers, I would like to generate the frequencies of dates (data.RData). str(data) Date[1:43748], format: 2001-01-01 2001-01-01 2001-01-01 2001-01-01 ... test - hist(data,days,freq=T) test$counts [1] 27 17 12 15 6 4 5 13 5 13 15 9 7 10 11 21 10 10 9 11 15 7 10 14 but the count is wrong, because i have only 9 times 01/01/2001 etc. data[1:30] [1] 2001-01-01 2001-01-01 2001-01-01 2001-01-01 2001-01-01 [6] 2001-01-01 2001-01-01 2001-01-01 2001-01-01 2001-01-02 [11] 2001-01-02 2001-01-02 2001-01-02 2001-01-02 2001-01-02 [16] 2001-01-02 2001-01-02 2001-01-02 2001-01-02 2001-01-02 [21] 2001-01-03 2001-01-03 2001-01-03 2001-01-03 2001-01-03 [26] 2001-01-03 2001-01-03 2001-01-03 2001-01-03 2001-01-03 Now, when i give R the breaks. br - seq(as.Date(31.12.2000,format=%d.%m.%Y),as.Date(01.01.2012,format=%d.%m.%Y),by=1) test2- hist(data,br,freq=T) test2$counts[1:10] [1] 12 15 17 12 15 6 4 5 13 5 In this case, neither get the right counts but limiting i get the correct counts: test3- hist(data[1:50],br[1:6],freq=T) test3$counts [1] 9 11 13 9 8 I hope someone can help me with this problem. Thank you very much!! Best regards, Dominic __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Code to fetch summary info from vector
Hello, Continuing Jessica's code, to get the maximum of each group just use b - c(1,1,1,2,3,4,3,2,1,1,1,1,1,2,3,4,5,4,3.5,3,2,1,1,1) r - rle(b 1) groups - rep(1:length(r$lengths),r$lengths) tapply(b, groups, FUN = max) # To get just the groups where b 1, mx - tapply(b, groups, FUN = max) mx[mx 1] # And you can combine both like in cbind(length = r$lengths[r$values], max = mx[mx 1]) Hope this helps, Rui Barradas Em 15-01-2013 16:57, Jessica Streicher escreveu: Maybe rle can help a little here rle(b1) Run Length Encoding lengths: int [1:5] 3 5 5 8 3 values : logi [1:5] FALSE TRUE FALSE TRUE FALSE r-rle(b1) r$lengths[r$values] [1] 5 8 # started for the maximum but need to go home now, sorry. Will continue tomorrow if noone else finishes it. groups - rep(1:length(r$lengths),r$lengths) On 15.01.2013, at 17:16, Benjamin Gillespie wrote: Hi all, Thanks in advance for any help. I have a vector b: b=c(1,1,1,2,3,4,3,2,1,1,1,1,1,2,3,4,5,4,3.5,3,2,1,1,1) Imagine b is river flow throughout time. I would like some code that will generate the following information: number of individual 'periods' where b1 (= 2 in this case) period 1 length = 5, max = 4 period 2 length = 8, max = 5 I can't figure anything useful out. Thanks, Ben Gillespie Research Postgraduate School of Geography University of Leeds Leeds LS2 9JT http://www.geog.leeds.ac.uk/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Code to fetch summary info from vector
On Jan 15, 2013, at 8:16 AM, Benjamin Gillespie wrote: Hi all, Thanks in advance for any help. I have a vector b: b=c(1,1,1,2,3,4,3,2,1,1,1,1,1,2,3,4,5,4,3.5,3,2,1,1,1) Imagine b is river flow throughout time. I would like some code that will generate the following information: number of individual 'periods' where b1 (= 2 in this case) period 1 length = 5, max = 4 period 2 length = 8, max = 5 I can't figure anything useful out. Look at: rle(b1) ?rle Should get you started. -- David David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tukey HSD plot with lines indicating (non-)significance
Thanks for the suggested code! It’s a very nice way of displaying most aspects of the data and the HSD tests/CIs. The graphical display is probably to big for inclusion in journal articles, but works well for displaying the results when working with the data. Regards, Karl Ove Hufthammer ty. den 15. 01. 2013 klokka 06.43 (-0500) skreiv Richard M. Heiberger: Karl, Thank you for this interesting challenge. It turns out to be reasonably straightforward. This code does it for the first example in ?MMC. ## This example is based on the example in ?HH:::MMC library(HH) ## pairwise comparisons data(catalystm) ## A. individual plots ## base graphics box plot boxplot(concent ~ catalyst, data=catalystm, xlab=catalyst, ylab=concentration, las=1) ## aov catalystm1.aov - aov(concent ~ catalyst, data=catalystm) summary(catalystm1.aov) ## MMC plot old.omd - par(omd=c(0,.95,0,1)) catalystm.mmc - mmc(catalystm1.aov, linfct = mcp(catalyst = Tukey)) catalystm.mmc plot(catalystm.mmc, ry=c(50,58), x.offset=1.8) ## tiebreaker plot plotMatchMMC(catalystm.mmc$mca, xlabel.print=FALSE) ## B. coordinate scales of all three plots by adjusting par values and ##the frame sizes def.par - par(no.readonly = TRUE) # save default, for resetting... ## allocate figure 1 the right 2/3 and top 2/3 of the plotting region ## allocate figure 2 the right 2/3 and bottom 1/3 of the plotting region ## allocate figure 3 the left 1/3 and top 2/3 of the plotting region frame() layout(matrix(c(3,1, 0,2), 2, 2, byrow = TRUE),widths=c(1,2), heights=c(2,1)) ## show the regions that have been allocated to each plot layout.show(3) omd.old - par(omd=c(0,.95,0,1)) plot(catalystm.mmc, ry=c(50,59), x.offset=1.8) usr.mmc - par()$usr mar.old - par(mar=c(5,4,0,2)+.1) plotMatchMMC(catalystm.mmc$mca, xlabel.print=FALSE) par(mar.old) boxplot(concent ~ catalyst, data=catalystm, xlab=catalyst, ylab=concentration, las=1, ylim=usr.mmc[3:4], yaxs=i) ## If you have a set of plots that don't fit comfortably into the ## space illustrated here, then you will need to increase the plotting ## device window from the default 7in x 7in because the cex is ## hardwired into the plot.mmc.multicomp function. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Using system() to dump HDF to text file?
Hi all -- I am working on 64-bit Windows XP. I'm not a very technical person when it comes to the command line stuff, so please forgive me if this is a stupid question. I have a bunch of HDF files, and I want to dump a single PM25 data layer from each file to .txt by invoking ncdump.exe from system(). Here's a sample command string: C:/ncdump -v PM25 C:/01aug2010.hdf C:/01aug2010.txt This works perfectly in Python, but does not actually generate the .txt file in R when: system(command) It does show the output on the console, if flagged to do so, and I can capture the output to an R object with intern = T. I assume there is some problem with the way I have specified how to get the output to the text file (i.e. the ), but experimentation with other options has not gone well. Can anyone advise? Thanks! Sarah [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using system() to dump HDF to text file?
Use shell() instead of system(). E.g., I have a bunch of Unix-like executables in c:\cygwin\bin and I can use pipe and redirection signs with them using shell(): tf - tempfile() file.exists(tf) [1] FALSE shell(paste(c:\\cygwin\\bin\\ls | c:\\cygwin\\bin\\head -5 , shQuote(tf, cmd))) readLines(tf) [1] R.dll R.exe RSetReg.exe Rblas.dll Rcmd.exe getwd() [1] C:/Program Files/R/R-2.15.2/bin/x64 dir() [1] open.exe R.dll R.exe Rblas.dll Rcmd.exe Rgraphapp.dll Rgui.exe Riconv.dllRlapack.dll Rscript.exe RSetReg.exe [12] Rterm.exe Rzlib.dll Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Sarah Henderson Sent: Tuesday, January 15, 2013 10:28 AM To: R List Subject: [R] Using system() to dump HDF to text file? Hi all -- I am working on 64-bit Windows XP. I'm not a very technical person when it comes to the command line stuff, so please forgive me if this is a stupid question. I have a bunch of HDF files, and I want to dump a single PM25 data layer from each file to .txt by invoking ncdump.exe from system(). Here's a sample command string: C:/ncdump -v PM25 C:/01aug2010.hdf C:/01aug2010.txt This works perfectly in Python, but does not actually generate the .txt file in R when: system(command) It does show the output on the console, if flagged to do so, and I can capture the output to an R object with intern = T. I assume there is some problem with the way I have specified how to get the output to the text file (i.e. the ), but experimentation with other options has not gone well. Can anyone advise? Thanks! Sarah [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] removing loops from code in making data.frame
Dear all,
I am working on an author network and to do so I have to arrange a data.frame
(tutu) crossing author names (rows) per publication number (column). The
participation of the author to a study is indicated by a 1 and 0 otherwise.
I have a vector (xaulist) of all the names of authors and a data.frame (tata)
with all the publications in row and the authors in columns. I have writen a
loop to obtain my data.frame but it takes a long time when the number of
studies increases. I was looking for a more efficient code.
Here is a minimal working example (my code is terrible i know...):
#-
au1 - c('deb', 'art', 'deb', 'seb', 'deb', 'deb', 'mar', 'mar', 'joy', 'deb')
au2 - c('art', 'deb', 'soy', 'deb', 'joy', 'ani', 'deb', 'deb', 'nem', 'mar')
au3 - c('mar', 'lio', 'mil', 'mar', 'ani', 'lul', 'nem', 'art', 'deb', 'tat')
tata - data.frame(au1, au2, au3)
xaulist2 - levels(factor(unlist(tata[,])))
xaulist - levels(as.factor(xaulist2))
tutu - matrix(NA, nrow=length(xaulist), ncol=dim(tata)[1]) # row are authors
and col are papers
for (i in 1:length(xaulist))
{
for (j in 1:dim(tata)[1])
{
ifelse('TRUE' %in% as.character(tata[j,]==xaulist[i]), tutu[i,j] - 1,
tutu[i,j] - 0)
}
}
tutu[is.na(tutu)] - 0
#-
I am looking at some more efficient way to build 'tutu'.
Thank you very much,
David
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Re: [R] Random Forest Error for Factor to Character column
Andrew, That did the trick. Thank you. Dan From: Andrew Robinson [mailto:mensuration...@gmail.com] Sent: Monday, January 14, 2013 6:06 PM To: Lopez, Dan Cc: R help (r-help@r-project.org) Subject: Re: [R] Random Forest Error for Factor to Character column After you subset the data, did you redeclare the factor? If not then R still thinks it has the potential for all those levels. TRAINSET$JOBTITLE - factor(TRAINSET$JOBTITLE) I hope this helps Andrew On Tuesday, January 15, 2013, Lopez, Dan wrote: Hi, Can someone please offer me some guidance? I imported some data. One of the columns called JOBTITLE when imported was imported as a factor column with 416 levels. I subset the data in such a way that only 4 levels have data in JOBTITLE and tried running randomForest but it complained about JOBTITLE having more than 32 categories. I know that is the limit in randomForest but I guess I don't understand enough about factors because I thought by subsetting the data this no longer would be an issue. BTW I can run randomForest on this dataset if I exclude JOBTITLE. So I then converted that column to a character vector: TRAINSET$JOBTITLE-as.character(TRAINSET$JOBTITLE) I ran Random Forest and got the below error. Why isn't this working? What do I need to do to get this working? library(randomForest) FOREST_model - randomForest(as.factor(TARGET)~., data=trainset, mtry=4, ntree=1000, +importance=TRUE, do.trace=100) Error in randomForest.default(m, y, ...) : NA/NaN/Inf in foreign function call (arg 1) In addition: Warning message: In data.matrix(x) : NAs introduced by coercion Your help will be greatly appreciated. Dan [[alternative HTML version deleted]] __ R-help@r-project.orgjavascript:; 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. -- Andrew Robinson Director (A/g), ACERA Department of Mathematics and StatisticsTel: +61-3-8344-6410 University of Melbourne, VIC 3010 Australia (prefer email) http://www.ms.unimelb.edu.au/~andrewprhttp://www.ms.unimelb.edu.au/%7Eandrewpr Fax: +61-3-8344-4599 http://www.acera.unimelb.edu.au/ FAwR: http://www.ms.unimelb.edu.au/~andrewpr/FAwR/http://www.ms.unimelb.edu.au/%7Eandrewpr/FAwR/ SPuR: http://www.ms.unimelb.edu.au/spuRs/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] readHTMLTable (XML package)
Hi,
I am using XML::readHTMLTable and getting the below error. Does anyone know
why? Does this function not work with https? I didn't see anything in help
about that.
library(XML)
wampage-readHTMLTable('https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html',1)
Error in htmlParse(doc) :
File https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html does not exist
Dan
[[alternative HTML version deleted]]
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[R] grouping elements of a data frame
Hi everyone, I have a question on selecting and grouping elements of a data frame. For example: A.df- [ a c 0.9 b x 0.8 b z 0.5 c y 0.9 c x 0.7 c z 0.6] I want to create a list of a data frame that gives me the unique values of column 1 of A.df so that i can create intersects. That is: B[a]- [ c 0.9] B[b]- [ x 0.8 z 0.5] B[c]- [ y 0.9 x 0.7 z 0.6] B[c] n B[b] - c(x,z) How can I accomplish this? Thanks, Al __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] e1071 SVM, cross-validation and overfitting
I am accustomed to the LIBSVM package, which provides cross-validation
on training with the -v option
% svm-train -v 5 ...
This does 5 fold cross validation while building the model and avoids
over-fitting.
But I don't see how to accomplish that in the e1071 package. (I
learned that svm(... cross=5 ...) only _tests_ using cross-validation
-- it doesn't affect the training.) Can someone clue me in how to do
something equivalent to LIBSVM's -v option?
Thanks!
- ff
P.S.: My test case follows. If you run the code, the tuned output
shows clear signs of over-fitting. I'd like to eliminate that.
require('e1071')
colors - c(2, 3, 4, 5, 6)
set.seed(23) # set random seed for repeatability
# log(x) + cos(x) + noise
f - function(x) log(x) + cos(x)
x - seq(0.1, 5, by = 0.05)
y - f(x) + rnorm(x, sd = 0.2)
plot(x, y, col=gray80)
legend(topleft,
c(log(x) + cos(x), SVM, untuned, SVM, tuned),
bty=n,
col=colors,
pch=20)
lines(x, f(x), col = colors[1]) # overlay noiseless data
# SVM, untuned
svmmodel1 - svm(x, y)
print(summary(svmmodel1))
y1 - predict(svmmodel1, x)
lines(x, y1, col = colors[2])
# SVM with tuning
tuning - tune.svm(x, y, gamma = 2^(-4:4), cost = 2^(-2:2))
svmmodel2 - tuning$best.model
print(summary(svmmodel2))
y2 - predict(svmmodel2, x)
lines(x, y2, col = colors[3])
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sparse dataframes?
andrewH skreiv: Is there a data frame analog to sparse matrices? I am working with a panel data set that has a large number of variables that are redefined repeatedly or exist for only a few years (out of 48). In my current structure, where variables are columns and rows are years, more than 90 percent of the cells and more than 3/4 of the total size of my file are NAs. I am wondering if there is an alternate file specification currently available that still allows numeric, character and factor data to be stored. Besides just using a database. How about storing the data in a ‘long’ format, like you get when you apply melt() (with na.rm=TRUE) from the ‘reshape2’ package to your data frame? Parts of the data frame (the ID part) will be repeated on each row, which may make the data take up more space, but no rows are stored for NA cells, so for somewhat sparse data it will be a win. It also makes it very easy to reshape and analyse the data. Here’s an introduction (to the older ‘reshape’ package, but ‘reshape2’ is very similar): http://www.jstatsoft.org/v21/i12 You might also be interested in this paper on ‘tidy’ data: http://vita.had.co.nz/papers/tidy-data.pdf -- Karl Ove Hufthammer E-mail: k...@huftis.org Jabber: huf...@jabber.no __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Drawing a dotted circle.
There is also the my.symbols and ms.polygon functions in the TeachingDemos package that have syntax similar to the symbols function: library(TeachingDemos) x - runif(10) y - rnorm(10) my.symbols(x, y, ms.polygon, inches=0.3, n=400, add=FALSE, lty=3) On Sat, Jan 12, 2013 at 7:42 PM, Ved P. Sharma vedsha...@gmail.com wrote: Thanks everyone for suggesting the alternative draw.circle. Ved On Sat, Jan 12, 2013 at 12:50 PM, Jose Iparraguirre jose.iparragui...@ageuk.org.uk wrote: Don't know, but you can use the function draw.circle in the plotrix package. Hope this helps, Jose From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Ved P. Sharma [vedsha...@gmail.com] Sent: 12 January 2013 07:43 To: r-help@r-project.org Subject: [R] Drawing a dotted circle. Hi, I am trying to draw a dotted circle by using symbols command: symbols(0, 0, circles = 1, inches = FALSE, fg = 'gray', lty=2) But it gives me a solid line. I was just wondering whether am I making a mistake? Ved [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Wrap Up and Run 10k is back! Also, new for 2013 2km intergenerational walks at selected venues. So recruit a buddy, dust off the trainers and beat the winter blues by signing up now: http://www.ageuk.org.uk/10k Milton Keynes | Oxford | Sheffield | Crystal Palace | Exeter | Harewood House, Leeds | Tatton Park, Cheshire | Southampton | Coventry Age UK Improving later life http://www.ageuk.org.uk --- Age UK is a registered charity and company limited by guarantee, (registered charity number 1128267, registered company number 6825798). Registered office: Tavis House, 1-6 Tavistock Square, London WC1H 9NA. For the purposes of promoting Age UK Insurance, Age UK is an Appointed Representative of Age UK Enterprises Limited, Age UK is an Introducer Appointed Representative of JLT Benefit Solutions Limited and Simplyhealth Access for the purposes of introducing potential annuity and health cash plans customers respectively. Age UK Enterprises Limited, JLT Benefit Solutions Limited and Simplyhealth Access are all authorised and regulated by the Financial Services Authority. -- This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you receive a message in error, please advise the sender and delete immediately. Except where this email is sent in the usual course of our business, any opinions expressed in this email are those of the author and do not necessarily reflect the opinions of Age UK or its subsidiaries and associated companies. Age UK monitors all e-mail transmissions passing through its network and may block or modify mails which are deemed to be unsuitable. Age Concern England (charity number 261794) and Help the Aged (charity number 272786) and their trading and other associated companies merged on 1st April 2009. Together they have formed the Age UK Group, dedicated to improving the lives of people in later life. The three national Age Concerns in Scotland, Northern Ireland and Wales have also merged with Help the Aged in these nations to form three registered charities: Age Scotland, Age NI, Age Cymru. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] readHTMLTable (XML package)
Hi Dan,
A couple of things: first, I think that file really does not exist (at
least I can't open it in my web browser). Second, even if it did,
url() cannot download from https, according to the details section of
?url, which points you to RCurl. So, once you verify that you url
actually exists you can do something like
library(XML)
library(RCurl)
tabs -
readHTMLTable(getURL(http://en.wikipedia.org/wiki/List_of_countries_by_population;))
Best,
Ista
On Tue, Jan 15, 2013 at 2:59 PM, Lopez, Dan lopez...@llnl.gov wrote:
Hi,
I am using XML::readHTMLTable and getting the below error. Does anyone know
why? Does this function not work with https? I didn't see anything in help
about that.
library(XML)
wampage-readHTMLTable('https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html',1)
Error in htmlParse(doc) :
File https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html does not exist
Dan
[[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.
__
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and provide commented, minimal, self-contained, reproducible code.
[R] SQLDF column errors
I am trying to exclude integer values from a small data frame 1, d1 that have matching hits in data frame 2, d2 (Very big) which involves matching those hits first. I am trying to use sqldf on the df's in the following fashion: df1: V1 12675 14753 16222 18765 df2: head(df2) V1 V2 13647 rd1500 14753 rd1580 15987 rd1590 16222 rd2020. df1_new-sqldf(select df1.V1, df2.V2 where rs10.V1 = d10.pos) - Ideally I would like to try to use delete or not equal to != though I can only find that delete works with sqldf. but it returns this error: Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: no such column: df1.V1) I am also trying this: df1_new-sqldf(select V1 from df1, V2 from df2 where df1.V1 = df2.V1) which returns this error: Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: near from: syntax error) If anyone with sqldf knowledge could lend me a hand that would be great. Thanks! Matt [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Regular expression
gsub([',], , 'asd'f) Error: unexpected ']' in gsub([',] What is the right way to include the 'double quote' in the search field? The 'search field' is a string and to put a double quote into a double-quote delimited string you need to escape it with a backslash so it is not interpreted as the ending quote on the string. gsub([',\], , 'asd'f) [1] asdf Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Christofer Bogaso Sent: Tuesday, January 15, 2013 1:39 PM To: r-help Subject: [R] Regular expression Hello again, I am having a problem on Regular expression. Let say I have following code: gsub([',], , 'asd'f) [1] asdf This is perfect. However I am having problem if I include (i.e. the double quote) in the first argument as the pattern search: gsub([',], , 'asd'f) Error: unexpected ']' in gsub([',] What is the right way to include the 'double quote' in the search field? Thanks for your help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] removing loops from code in making data.frame
Hi,
May be this helps:
res-do.call(rbind,lapply(xaulist,function(x)
as.integer(apply(tata,1,function(i) any(i==x)
res[]-sapply(res,as.numeric)
identical(res,tutu)
#[1] TRUE
A.K.
- Original Message -
From: Biau David djmb...@yahoo.fr
To: r help list r-help@r-project.org
Cc:
Sent: Tuesday, January 15, 2013 2:41 PM
Subject: [R] removing loops from code in making data.frame
Dear all,
I am working on an author network and to do so I have to arrange a data.frame
(tutu) crossing author names (rows) per publication number (column). The
participation of the author to a study is indicated by a 1 and 0 otherwise.
I have a vector (xaulist) of all the names of authors and a data.frame (tata)
with all the publications in row and the authors in columns. I have writen a
loop to obtain my data.frame but it takes a long time when the number of
studies increases. I was looking for a more efficient code.
Here is a minimal working example (my code is terrible i know...):
#-
au1 - c('deb', 'art', 'deb', 'seb', 'deb', 'deb', 'mar', 'mar', 'joy', 'deb')
au2 - c('art', 'deb', 'soy', 'deb', 'joy', 'ani', 'deb', 'deb', 'nem', 'mar')
au3 - c('mar', 'lio', 'mil', 'mar', 'ani', 'lul', 'nem', 'art', 'deb', 'tat')
tata - data.frame(au1, au2, au3)
xaulist2 - levels(factor(unlist(tata[,])))
xaulist - levels(as.factor(xaulist2))
tutu - matrix(NA, nrow=length(xaulist), ncol=dim(tata)[1]) # row are authors
and col are papers
for (i in 1:length(xaulist))
{
for (j in 1:dim(tata)[1])
{
ifelse('TRUE' %in% as.character(tata[j,]==xaulist[i]), tutu[i,j] - 1,
tutu[i,j] - 0)
}
}
tutu[is.na(tutu)] - 0
#-
I am looking at some more efficient way to build 'tutu'.
Thank you very much,
David
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] grouping elements of a data frame
On Jan 15, 2013, at 9:10 AM, Nuri Alpay Temiz wrote: Hi everyone, I have a question on selecting and grouping elements of a data frame. For example: A.df- [ a c 0.9 b x 0.8 b z 0.5 c y 0.9 c x 0.7 c z 0.6] That is not R code. Matlab?, Python? I want to create a list of a data frame that gives me the unique values of column 1 of A.df so that i can create intersects. That is: B[a]- [ c 0.9] B[b]- [ x 0.8 z 0.5] B[c]- [ y 0.9 x 0.7 z 0.6] B[c] n B[b] - c(x,z) That's some sort of coded message? We are supposed to know what the n operation will do when assigned a vector? Assuming your really do have a dataframe named B: intersect(B$c, B$b) Please code up examples in R in the future. -- David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] removing loops from code in making data.frame
Hi,
You could also do this:
res1-do.call(rbind,lapply(xaulist,function(x)
as.numeric(apply(t(mapply(`==`,tata,x)),2,any
identical(res1,tutu)
#[1] TRUE
A.K.
- Original Message -
From: Biau David djmb...@yahoo.fr
To: r help list r-help@r-project.org
Cc:
Sent: Tuesday, January 15, 2013 2:41 PM
Subject: [R] removing loops from code in making data.frame
Dear all,
I am working on an author network and to do so I have to arrange a data.frame
(tutu) crossing author names (rows) per publication number (column). The
participation of the author to a study is indicated by a 1 and 0 otherwise.
I have a vector (xaulist) of all the names of authors and a data.frame (tata)
with all the publications in row and the authors in columns. I have writen a
loop to obtain my data.frame but it takes a long time when the number of
studies increases. I was looking for a more efficient code.
Here is a minimal working example (my code is terrible i know...):
#-
au1 - c('deb', 'art', 'deb', 'seb', 'deb', 'deb', 'mar', 'mar', 'joy', 'deb')
au2 - c('art', 'deb', 'soy', 'deb', 'joy', 'ani', 'deb', 'deb', 'nem', 'mar')
au3 - c('mar', 'lio', 'mil', 'mar', 'ani', 'lul', 'nem', 'art', 'deb', 'tat')
tata - data.frame(au1, au2, au3)
xaulist2 - levels(factor(unlist(tata[,])))
xaulist - levels(as.factor(xaulist2))
tutu - matrix(NA, nrow=length(xaulist), ncol=dim(tata)[1]) # row are authors
and col are papers
for (i in 1:length(xaulist))
{
for (j in 1:dim(tata)[1])
{
ifelse('TRUE' %in% as.character(tata[j,]==xaulist[i]), tutu[i,j] - 1,
tutu[i,j] - 0)
}
}
tutu[is.na(tutu)] - 0
#-
I am looking at some more efficient way to build 'tutu'.
Thank you very much,
David
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Re: [R] SQLDF column errors
i think this is what you want.. :) http://stackoverflow.com/questions/4765936/using-joined-tables-to-exclude-certain-records library(sqldf) # use the mtcars example table mtcars # keep the first eight records in a second, separate data set x - mtcars[ 1:8 , ] # keep all the records from mtcars where the mpg value doesn't match a record in the `x` data table y - sqldf( select * from mtcars where not exists ( select * from x where x.mpg == mtcars.mpg ) ) # the above example assumes your tables won't fit in RAM. # if they do, this method is obviously much easier y - mtcars[ !( mtcars$mpg %in% x$mpg ) , ] On Tue, Jan 15, 2013 at 4:02 PM, Matthew Liebers mr...@cornell.edu wrote: I am trying to exclude integer values from a small data frame 1, d1 that have matching hits in data frame 2, d2 (Very big) which involves matching those hits first. I am trying to use sqldf on the df's in the following fashion: df1: V1 12675 14753 16222 18765 df2: head(df2) V1 V2 13647 rd1500 14753 rd1580 15987 rd1590 16222 rd2020. df1_new-sqldf(select df1.V1, df2.V2 where rs10.V1 = d10.pos) - Ideally I would like to try to use delete or not equal to != though I can only find that delete works with sqldf. but it returns this error: Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: no such column: df1.V1) I am also trying this: df1_new-sqldf(select V1 from df1, V2 from df2 where df1.V1 = df2.V1) which returns this error: Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: near from: syntax error) If anyone with sqldf knowledge could lend me a hand that would be great. Thanks! Matt [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] configure/build R on Windows
Hello, Does anyone knows if there is a Documentation or any wiki that could help me to configure and build R using cygwin with the Intel Compilers on Windows? Thanks, Humberto. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Regular expression
HI, vec1-'asd'f vec2-'asdf' gsub([\],,vec2) #[1] asdf gsub(['],,vec1) #[1] asdf A.K. - Original Message - From: Christofer Bogaso bogaso.christo...@gmail.com To: r-help r-help@r-project.org Cc: Sent: Tuesday, January 15, 2013 4:38 PM Subject: [R] Regular expression Hello again, I am having a problem on Regular expression. Let say I have following code: gsub([',], , 'asd'f) [1] asdf This is perfect. However I am having problem if I include (i.e. the double quote) in the first argument as the pattern search: gsub([',], , 'asd'f) Error: unexpected ']' in gsub([',] What is the right way to include the 'double quote' in the search field? Thanks for your help. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Need help: R for repetitive tasks
This is fairly straight forward, you can do something like:
myfiles - scan('files.txt', what=)
base - sub(\\.[^.]*$, , myfiles)
lapply( seq_along(myfiles), function(i) {
mydat - read.table( myfiles[i] )
sink( sprintf('%sSummary.txt', base[i]) )
summary(mydat)
sink()
bmp( sprintf(%sPlot.bmp, base[i]) )
with(mydat, plot(x,y))
dev.off()
} )
Of course modifying things to include what you want to use. If you want
the summary information and plots together in a single output file (pdf
file, word document, html, etc.) then you should look at the knitr package
as a way to set up a template and possibly the pandoc program as a way to
convert the results to another format, then do the processing in a loop
like above.
On Tue, Jan 15, 2013 at 5:30 AM, Simonas Kecorius simolas2...@gmail.comwrote:
Dear R users,
First of all I would like to thank all of you who replayed to my previous
questions and problems. Thank you a lot for being great and helpful
community. I highly appreciate your suggestions and ideas even if I do not
respond after my question! But it means that your help was exactly what I
needed. Thank you again!
Now the following question I need help:
Suppose I do have a file.txt in the working directory. This file contains
the names of other files in the same directory:
First.txt
Second.txt
Third.txt
etc...
Files First.txt, Second.txt...are data files.
What I need R to do, is to read this file.txt line by line, open files
which names are listed ( First.txt, Second.txt...) and process it: lets say
make a FirstPlot.bmp, FirstSummary.txt and save it to working directory,
then automatically open Second.txt, do the same, Third.txt etc. until the
end of the names in file.txt.
This would help me with the following task: I do measurements each day, and
I need to process my data: draw some plots, make some analysis. When I
have 30 days of measurements each 1 second, there are huge amount of
numbers I am dealing with. If you could suggest some automation via R, it
would be perfect.
Thank you in advance.
Cheers.
--
Simonas Kecorius
**Lithuania
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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.
--
Gregory (Greg) L. Snow Ph.D.
538...@gmail.com
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] readHTMLTable (XML package)
Hi Ista,
It does exist. It’s a page in our company intranet.
It is https so it looks like I can't use RCurl either. I tried RCurl BTW and
got the below error.
Do you have experience with pulling a table of an https site? If so how do I do
that?
tabs -
readHTMLTable(getURL(https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html;))
Error in
readHTMLTable(getURL(https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html;))
:
error in evaluating the argument 'doc' in selecting a method for function
'readHTMLTable': Error in function (type, msg, asError = TRUE) :
SSL certificate problem, verify that the CA cert is OK. Details:
error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify
failed
Thanks.
Dan
-Original Message-
From: Ista Zahn [mailto:istaz...@gmail.com]
Sent: Tuesday, January 15, 2013 12:22 PM
To: Lopez, Dan
Cc: R help (r-help@r-project.org)
Subject: Re: [R] readHTMLTable (XML package)
Hi Dan,
A couple of things: first, I think that file really does not exist (at least I
can't open it in my web browser). Second, even if it did,
url() cannot download from https, according to the details section of ?url,
which points you to RCurl. So, once you verify that you url actually exists you
can do something like
library(XML)
library(RCurl)
tabs -
readHTMLTable(getURL(http://en.wikipedia.org/wiki/List_of_countries_by_population;))
Best,
Ista
On Tue, Jan 15, 2013 at 2:59 PM, Lopez, Dan lopez...@llnl.gov wrote:
Hi,
I am using XML::readHTMLTable and getting the below error. Does anyone know
why? Does this function not work with https? I didn't see anything in help
about that.
library(XML)
wampage-readHTMLTable('https://hr-workforce-analytics.llnl.gov/wf_pi
_pop.html',1)
Error in htmlParse(doc) :
File https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html does not
exist
Dan
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Plot Header
Any recommendations for how I can embed my title below in a single red strip/box across the plot area in the outer margin? I would like to avoid the color appearing in any other area defined by the oma. # Example Plot par(mfrow=c(2,2),mar=c(4,4,2,2), oma = c(1, 1, 3, 1)) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) # Title title(MY TITLE, outer = TRUE, cex = 1.5, adj=0, col=blue, font=2) Thanks for any pointers Pete -- View this message in context: http://r.789695.n4.nabble.com/Plot-Header-tp4655654.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Can not load Rcmdr
I am getting the error message: library(Rcmdr) Loading required package: car Loading required package: MASS Loading required package: nnet Error : .onAttach failed in attachNamespace() for 'Rcmdr', details: call: structure(.External(dotTclObjv, objv, PACKAGE = tcltk), class = tclObj) error: [tcl] invalid command name image. Error: package/namespace load failed for 'Rcmdr' If I try and load tcltk separately, it loads, but I get a warning. library(tcltk) Loading Tcl/Tk interface ... done Warning message: In fun(libname, pkgname) : couldn't connect to display /tmp/launch-pCcdvk/:0 _X11TransSocketINETConnect() can't get address for /tmp/launch-pCcdvk/:6000: nodename nor servname provided, or not known I want to run BiodiversityR. Which runs, but ultimately I get an error. library(BiodiversityR) Loading required package: vegan Loading required package: permute This is vegan 2.0-5 BiodiversityRGUI() Loading required package: Rcmdr Error : .onAttach failed in attachNamespace() for 'Rcmdr', details: call: structure(.External(dotTclObjv, objv, PACKAGE = tcltk), class = tclObj) error: [tcl] invalid command name image. Error in BiodiversityRGUI() : needs Rcmdr [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] grouping elements of a data frame
Hi, Try this: The last part was not clear. A.df-read.table(text= a c 0.9 b x 0.8 b z 0.5 c y 0.9 c x 0.7 c z 0.6 ,sep=,header=FALSE,stringsAsFactors=FALSE) lst1-split(A.df[,-1],A.df$V1) lst1 #$a # V2 V3 #1 c 0.9 # #$b # V2 V3 #2 x 0.8 #3 z 0.5 # #$c # V2 V3 #4 y 0.9 #5 x 0.7 #6 z 0.6 A.K. - Original Message - From: Nuri Alpay Temiz alpayte...@outlook.com To: R-help@r-project.org Cc: Sent: Tuesday, January 15, 2013 12:10 PM Subject: [R] grouping elements of a data frame Hi everyone, I have a question on selecting and grouping elements of a data frame. For example: A.df- [ a c 0.9 b x 0.8 b z 0.5 c y 0.9 c x 0.7 c z 0.6] I want to create a list of a data frame that gives me the unique values of column 1 of A.df so that i can create intersects. That is: B[a]- [ c 0.9] B[b]- [ x 0.8 z 0.5] B[c]- [ y 0.9 x 0.7 z 0.6] B[c] n B[b] - c(x,z) How can I accomplish this? Thanks, Al __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] readHTMLTable (XML package)
On Jan 15, 2013, at 2:31 PM, Lopez, Dan wrote:
Hi Ista,
It does exist. It’s a page in our company intranet.
It is https so it looks like I can't use RCurl either. I tried RCurl BTW and
got the below error.
Do you have experience with pulling a table of an https site? If so how do I
do that?
Why not use a browser and save it locally?
--
David.
tabs -
readHTMLTable(getURL(https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html;))
Error in
readHTMLTable(getURL(https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html;))
:
error in evaluating the argument 'doc' in selecting a method for function
'readHTMLTable': Error in function (type, msg, asError = TRUE) :
SSL certificate problem, verify that the CA cert is OK. Details:
error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify
failed
Thanks.
Dan
-Original Message-
From: Ista Zahn [mailto:istaz...@gmail.com]
Sent: Tuesday, January 15, 2013 12:22 PM
To: Lopez, Dan
Cc: R help (r-help@r-project.org)
Subject: Re: [R] readHTMLTable (XML package)
Hi Dan,
A couple of things: first, I think that file really does not exist (at least
I can't open it in my web browser). Second, even if it did,
url() cannot download from https, according to the details section of ?url,
which points you to RCurl. So, once you verify that you url actually exists
you can do something like
library(XML)
library(RCurl)
tabs -
readHTMLTable(getURL(http://en.wikipedia.org/wiki/List_of_countries_by_population;))
Best,
Ista
On Tue, Jan 15, 2013 at 2:59 PM, Lopez, Dan lopez...@llnl.gov wrote:
Hi,
I am using XML::readHTMLTable and getting the below error. Does anyone know
why? Does this function not work with https? I didn't see anything in help
about that.
library(XML)
wampage-readHTMLTable('https://hr-workforce-analytics.llnl.gov/wf_pi
_pop.html',1)
Error in htmlParse(doc) :
File https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html does not
exist
Dan
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] readHTMLTable (XML package)
David,
Because there is some data on various webpages that I use periodically that
this would be convenient for me to use.
Copying and pasting is messy . And obtaining direct database access for the
data on some these pages is not possible for me (i.e. won't get approved...but
I can use what is out there)
Dan
-Original Message-
From: David Winsemius [mailto:dwinsem...@comcast.net]
Sent: Tuesday, January 15, 2013 3:00 PM
To: Lopez, Dan
Cc: Ista Zahn; R help (r-help@r-project.org)
Subject: Re: [R] readHTMLTable (XML package)
On Jan 15, 2013, at 2:31 PM, Lopez, Dan wrote:
Hi Ista,
It does exist. It's a page in our company intranet.
It is https so it looks like I can't use RCurl either. I tried RCurl BTW and
got the below error.
Do you have experience with pulling a table of an https site? If so how do I
do that?
Why not use a browser and save it locally?
--
David.
tabs -
readHTMLTable(getURL(https://hr-workforce-analytics.llnl.gov/wf_pi_p
op.html))
Error in
readHTMLTable(getURL(https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html;))
:
error in evaluating the argument 'doc' in selecting a method for function
'readHTMLTable': Error in function (type, msg, asError = TRUE) :
SSL certificate problem, verify that the CA cert is OK. Details:
error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate
verify failed
Thanks.
Dan
-Original Message-
From: Ista Zahn [mailto:istaz...@gmail.com]
Sent: Tuesday, January 15, 2013 12:22 PM
To: Lopez, Dan
Cc: R help (r-help@r-project.org)
Subject: Re: [R] readHTMLTable (XML package)
Hi Dan,
A couple of things: first, I think that file really does not exist (at
least I can't open it in my web browser). Second, even if it did,
url() cannot download from https, according to the details section of
?url, which points you to RCurl. So, once you verify that you url
actually exists you can do something like
library(XML)
library(RCurl)
tabs -
readHTMLTable(getURL(http://en.wikipedia.org/wiki/List_of_countries_b
y_population))
Best,
Ista
On Tue, Jan 15, 2013 at 2:59 PM, Lopez, Dan lopez...@llnl.gov wrote:
Hi,
I am using XML::readHTMLTable and getting the below error. Does anyone know
why? Does this function not work with https? I didn't see anything in help
about that.
library(XML)
wampage-readHTMLTable('https://hr-workforce-analytics.llnl.gov/wf_p
i
_pop.html',1)
Error in htmlParse(doc) :
File https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html does not
exist
Dan
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] function coverage [solved?]
On Mon, 2013-01-14 at 13:08 -0800, Ross Boylan wrote:
Is there an easy way to identify all the functions called as a result of
invoking a function? Getting the calling hierarchy too would be nice,
but is definitely not essential.
I'm trying to understand someone else's package, which is in a namespace
and has some S3 functions. I could probably live without tracing the S3
functions. All the functions I want to trace are in R. The code passes
functions around as arguments, so that the function being called is not
always obvious from inspection of the source immediately around the
call.
I can imagine a solution that went something like this:
1. identify all functions by searching the sources for - function(
(probably only at the left margin, to avoid attempting to trace
functions defined inside of functions).
2. Write a function that wraps another function to record the fact that
it has been called.
3. Somehow replace all functions with their wrapped equivalents.
4. make the top level call.
5. inspect the data constructed by the wrapper.
The code is recursive and iterative; manual stepping does not seem
feasible. The package includes a lot of earlier versions of the code,
and so I suspect that a lot of the code is not active.
Thanks.
Ross Boylan
Inspired particularly by Michael Weylandt's suggestion I developed the
following functions, with a typical usage indicated int he comments.
The file is cover.R. I'm not sure if attachments are allowed, so here
it is inline
---
# cover.R determine functions called
# GPL 3.0 license
# Typical use
# mylog - gzfile(try2.gz, w)
# monitorNamespace(missreg2, mylog)
# call one or more functions
# unmonitorNamespace(missreg2)
# close(mylog)
# monitor f (type character, name of function) in environmnet env for calls
# log results to connection con (type character, name of global variable)
monitor - function(f, con, env=parent.frame()) {
tin - parse(text=paste('writeLines(', f, ' in, ', con,), sep=))
tout - parse(text=paste('writeLines(', f, ' out, ', con,), sep=))
trace(f, tin, tout, print=FALSE, where=env)
tout
}
unmonitor - function(f, env=parent.frame()) {
untrace(f, where=env)
}
# monitor all functions in ns
# con is a global variable that receives the log
monitorNamespace - function(ns, con){
e - getNamespace(ns)
invisible(sapply(ls(e), function(nm) if (is.function(get(nm, envir=e,
inherits=FALSE)))
monitor(nm, con, env=e)))
}
unmonitorNamespace - function(ns){
e - getNamespace(ns)
lapply(ls(e), function(nm) unmonitor(nm, env=e))
}
--
This mostly seemed to work, but for some reason the outerlevel call I
made is not recorded in the log. I thought this might be a result of
previous calls to trace or debug, or perhaps my having edited the
function and stuck it in my global namespace. I tried
detach(missreg2, unload=TRUE) and reloading the library; it didn't
help. And the function loaation looks like all the others that were
traced:
getAnywhere(rclusbin3)
getAnywhere(rclusbin3)
2 differing objects matching ‘rclusbin3’ were found
in the following places
package:missreg2
namespace:missreg2
which is exactly the same as other functions it did trace.
Thanks also to Duncan and Hadley for their ideas. I figured with the
profiler I'd always wonder if I'd missed something, and so went this low
tech route. Because of the missing log entry for the outer level
function, I'm still wondering if I got everything (since the reason the
outer level function wasn't traced might apply to others).
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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 Header
On Jan 15, 2013, at 2:49 PM, Pete Brecknock wrote: Any recommendations for how I can embed my title below in a single red strip/box across the plot area in the outer margin? I would like to avoid the color appearing in any other area defined by the oma. The code used blue ... not sure what that last sentence meant. Or what the single strip was supposed to look like. # Example Plot par(mfrow=c(2,2),mar=c(4,4,2,2), oma = c(1, 1, 3, 1)) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) # Title title(MY TITLE, outer = TRUE, cex = 1.5, adj=0, col=blue, font=2) opar - par(mfrow=c(2,2),mar=c(4,4,2,2), oma = c(1, 1, 3, 1)) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) title(MY TITLE, outer = TRUE, cex = 1.5, adj=0, col.main=blue, font=2, adj=0.5) par(opar) -- David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] readHTMLTable (XML package)
Hi Dan,
On Tue, Jan 15, 2013 at 5:31 PM, Lopez, Dan lopez...@llnl.gov wrote:
Hi Ista,
It does exist. It’s a page in our company intranet.
Ah, good.
It is https so it looks like I can't use RCurl either. I tried RCurl BTW and
got the below error.
Well that error is not because RCurl doesn't work with https protocol.
In my original example I meant to show
tabs -
readHTMLTable(getURL(https://en.wikipedia.org/wiki/List_of_countries_by_population;))
i.e., getURL() does work with https. (Well, maybe depending on your
version of libcurl. See the getURL help page for details.)
Do you have experience with pulling a table of an https site?
Yes, I do :)
If so how do I do that?
See below
tabs -
readHTMLTable(getURL(https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html;))
Error in
readHTMLTable(getURL(https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html;))
:
error in evaluating the argument 'doc' in selecting a method for function
'readHTMLTable': Error in function (type, msg, asError = TRUE) :
SSL certificate problem, verify that the CA cert is OK. Details:
error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify
failed
This is an RCurl FAQ (see http://www.omegahat.org/RCurl/FAQ.html). The
quick and dirty way is
getURL(https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html;,
ssl.verifypeer = FALSE)
Best,
Ista
Thanks.
Dan
-Original Message-
From: Ista Zahn [mailto:istaz...@gmail.com]
Sent: Tuesday, January 15, 2013 12:22 PM
To: Lopez, Dan
Cc: R help (r-help@r-project.org)
Subject: Re: [R] readHTMLTable (XML package)
Hi Dan,
A couple of things: first, I think that file really does not exist (at least
I can't open it in my web browser). Second, even if it did,
url() cannot download from https, according to the details section of ?url,
which points you to RCurl. So, once you verify that you url actually exists
you can do something like
library(XML)
library(RCurl)
tabs -
readHTMLTable(getURL(http://en.wikipedia.org/wiki/List_of_countries_by_population;))
Best,
Ista
On Tue, Jan 15, 2013 at 2:59 PM, Lopez, Dan lopez...@llnl.gov wrote:
Hi,
I am using XML::readHTMLTable and getting the below error. Does anyone know
why? Does this function not work with https? I didn't see anything in help
about that.
library(XML)
wampage-readHTMLTable('https://hr-workforce-analytics.llnl.gov/wf_pi
_pop.html',1)
Error in htmlParse(doc) :
File https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html does not
exist
Dan
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] readHTMLTable (XML package)
Ista,
Thank you. That more or less did the trick. I got the data though it's in a
weird format compared to how it appears on the page and needs a lot of clean
up. But I was kind of expecting that.
Dan
-Original Message-
From: Ista Zahn [mailto:istaz...@gmail.com]
Sent: Tuesday, January 15, 2013 3:18 PM
To: Lopez, Dan
Cc: R help (r-help@r-project.org)
Subject: Re: [R] readHTMLTable (XML package)
Hi Dan,
On Tue, Jan 15, 2013 at 5:31 PM, Lopez, Dan lopez...@llnl.gov wrote:
Hi Ista,
It does exist. It’s a page in our company intranet.
Ah, good.
It is https so it looks like I can't use RCurl either. I tried RCurl BTW and
got the below error.
Well that error is not because RCurl doesn't work with https protocol.
In my original example I meant to show
tabs -
readHTMLTable(getURL(https://en.wikipedia.org/wiki/List_of_countries_by_population;))
i.e., getURL() does work with https. (Well, maybe depending on your version of
libcurl. See the getURL help page for details.)
Do you have experience with pulling a table of an https site?
Yes, I do :)
If so how do I do that?
See below
tabs -
readHTMLTable(getURL(https://hr-workforce-analytics.llnl.gov/wf_pi_p
op.html))
Error in
readHTMLTable(getURL(https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html;))
:
error in evaluating the argument 'doc' in selecting a method for function
'readHTMLTable': Error in function (type, msg, asError = TRUE) :
SSL certificate problem, verify that the CA cert is OK. Details:
error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate
verify failed
This is an RCurl FAQ (see http://www.omegahat.org/RCurl/FAQ.html). The quick
and dirty way is
getURL(https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html;,
ssl.verifypeer = FALSE)
Best,
Ista
Thanks.
Dan
-Original Message-
From: Ista Zahn [mailto:istaz...@gmail.com]
Sent: Tuesday, January 15, 2013 12:22 PM
To: Lopez, Dan
Cc: R help (r-help@r-project.org)
Subject: Re: [R] readHTMLTable (XML package)
Hi Dan,
A couple of things: first, I think that file really does not exist (at
least I can't open it in my web browser). Second, even if it did,
url() cannot download from https, according to the details section of
?url, which points you to RCurl. So, once you verify that you url
actually exists you can do something like
library(XML)
library(RCurl)
tabs -
readHTMLTable(getURL(http://en.wikipedia.org/wiki/List_of_countries_b
y_population))
Best,
Ista
On Tue, Jan 15, 2013 at 2:59 PM, Lopez, Dan lopez...@llnl.gov wrote:
Hi,
I am using XML::readHTMLTable and getting the below error. Does anyone know
why? Does this function not work with https? I didn't see anything in help
about that.
library(XML)
wampage-readHTMLTable('https://hr-workforce-analytics.llnl.gov/wf_p
i
_pop.html',1)
Error in htmlParse(doc) :
File https://hr-workforce-analytics.llnl.gov/wf_pi_pop.html does
not exist
Dan
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot Header
David Winsemius wrote On Jan 15, 2013, at 2:49 PM, Pete Brecknock wrote: Any recommendations for how I can embed my title below in a single red strip/box across the plot area in the outer margin? I would like to avoid the color appearing in any other area defined by the oma. The code used blue ... not sure what that last sentence meant. Or what the single strip was supposed to look like. # Example Plot par(mfrow=c(2,2),mar=c(4,4,2,2), oma = c(1, 1, 3, 1)) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) # Title title(MY TITLE, outer = TRUE, cex = 1.5, adj=0, col=blue, font=2) opar - par(mfrow=c(2,2),mar=c(4,4,2,2), oma = c(1, 1, 3, 1)) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) title(MY TITLE, outer = TRUE, cex = 1.5, adj=0, col.main=blue, font=2, adj=0.5) par(opar) -- David Winsemius Alameda, CA, USA __ 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. Thanks for the reply. Apologies for the poor description. Let me try again. The code produces 4 charts in a 2 by 2 matrix Above these charts I have a single, left justified title in the outer margin. I would like to embed this title in a box which should run from the left hand side of the screen to the right and be say 10 lines high. I would like to color the box background red, the title MY TITLE would appear in blue inside the box. This could be described as a header. Any better? -- View this message in context: http://r.789695.n4.nabble.com/Plot-Header-tp4655654p4655665.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot Header
On Jan 15, 2013, at 3:25 PM, Pete Brecknock wrote: David Winsemius wrote On Jan 15, 2013, at 2:49 PM, Pete Brecknock wrote: Any recommendations for how I can embed my title below in a single red strip/box across the plot area in the outer margin? I would like to avoid the color appearing in any other area defined by the oma. The code used blue ... not sure what that last sentence meant. Or what the single strip was supposed to look like. # Example Plot par(mfrow=c(2,2),mar=c(4,4,2,2), oma = c(1, 1, 3, 1)) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) # Title title(MY TITLE, outer = TRUE, cex = 1.5, adj=0, col=blue, font=2) opar - par(mfrow=c(2,2),mar=c(4,4,2,2), oma = c(1, 1, 3, 1)) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) title(MY TITLE, outer = TRUE, cex = 1.5, adj=0, col.main=blue, font=2, adj=0.5) par(opar) -- David Winsemius Alameda, CA, USA __ 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. Thanks for the reply. Apologies for the poor description. Let me try again. The code produces 4 charts in a 2 by 2 matrix Above these charts I have a single, left justified title in the outer margin. I would like to embed this title in a box which should run from the left hand side of the screen to the right and be say 10 lines high. I would like to color the box background red, the title MY TITLE would appear in blue inside the box. This could be described as a header. Admittedly a hack: opar - par(mfrow=c(2,2),mar=c(4,4,2,2), oma = c(1, 1, 3, 1)) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) par(opar) rect(-5, 110, 5, 120, col=red, xpd=NA) title(MY TITLE, outer = TRUE, cex = 1.5, adj=0, col.main=blue, font=2, adj=0.5,line=-2) -- David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] readJPEG function cannot open jpeg files
On 01/15/2013 08:04 AM, Duncan Murdoch wrote: SNIP I've never understood why Microsoft thinks it is good to display incomplete filenames. This practice causes so many problems. SNIP Personally, I never understand Why Microsoft?. cheers, Rolf Turner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot Header
David Winsemius wrote On Jan 15, 2013, at 3:25 PM, Pete Brecknock wrote: David Winsemius wrote On Jan 15, 2013, at 2:49 PM, Pete Brecknock wrote: Any recommendations for how I can embed my title below in a single red strip/box across the plot area in the outer margin? I would like to avoid the color appearing in any other area defined by the oma. The code used blue ... not sure what that last sentence meant. Or what the single strip was supposed to look like. # Example Plot par(mfrow=c(2,2),mar=c(4,4,2,2), oma = c(1, 1, 3, 1)) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) # Title title(MY TITLE, outer = TRUE, cex = 1.5, adj=0, col=blue, font=2) opar - par(mfrow=c(2,2),mar=c(4,4,2,2), oma = c(1, 1, 3, 1)) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) title(MY TITLE, outer = TRUE, cex = 1.5, adj=0, col.main=blue, font=2, adj=0.5) par(opar) -- David Winsemius Alameda, CA, USA __ 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. Thanks for the reply. Apologies for the poor description. Let me try again. The code produces 4 charts in a 2 by 2 matrix Above these charts I have a single, left justified title in the outer margin. I would like to embed this title in a box which should run from the left hand side of the screen to the right and be say 10 lines high. I would like to color the box background red, the title MY TITLE would appear in blue inside the box. This could be described as a header. Admittedly a hack: opar - par(mfrow=c(2,2),mar=c(4,4,2,2), oma = c(1, 1, 3, 1)) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) plot(rnorm(100),1:100) par(opar) rect(-5, 110, 5, 120, col=red, xpd=NA) title(MY TITLE, outer = TRUE, cex = 1.5, adj=0, col.main=blue, font=2, adj=0.5,line=-2) -- David Winsemius Alameda, CA, USA __ 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. Thanks David. That will do nicely. Best regards Pete -- View this message in context: http://r.789695.n4.nabble.com/Plot-Header-tp4655654p4655676.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Get a percent variable based on group
Dear all, I'd like to get a percentage variable based on a group, but without creating a new data frame. For example: data(iris) iris$percent -unlist(tapply(iris$Sepal.Length,iris$Species,function(x) x/sum(x, na.rm=TRUE))) This does not work, I should have only three standard values, respectively for setosa, versicolor, and virginica. How can I do this? MANY THANKS, Karine [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Get a percent variable based on group
On Jan 15, 2013, at 6:30 PM, Karine Charlebois wrote: Dear all, I'd like to get a percentage variable based on a group, but without creating a new data frame. For example: data(iris) iris$percent -unlist(tapply(iris$Sepal.Length,iris$Species,function(x) x/sum(x, na.rm=TRUE))) A percentage is 100 times a fraction whose nominal value is unity. My guess is that you want a percentage of the group mean? So this would just be: iris$percent -ave(iris$Sepal.Length, iris$Species, FUN=function(x) 100*x/mean(x, na.rm=TRUE)) head(iris) This does not work, I should have only three standard values, respectively for setosa, versicolor, and virginica. How can I do this? If you just want three values, then I do not see how these are percentages. tapply(iris$Sepal.Length,iris$Species,function(x) mean(x, na.rm=TRUE)) setosa versicolor virginica 5.006 5.936 6.588 -- David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Get a percent variable based on group
HI, Not sure if this is what you meant. tapply(iris$Sepal.Length,iris$Species,FUN=function(x) sum(x)/sum(iris$Sepal.Length)*100) # setosa versicolor virginica # 28.55676 33.86195 37.58129 A.K. - Original Message - From: Karine Charlebois karine.charleb...@outlook.com To: r-help@r-project.org r-help@r-project.org Cc: Sent: Tuesday, January 15, 2013 9:30 PM Subject: [R] Get a percent variable based on group Dear all, I'd like to get a percentage variable based on a group, but without creating a new data frame. For example: data(iris) iris$percent -unlist(tapply(iris$Sepal.Length,iris$Species,function(x) x/sum(x, na.rm=TRUE))) This does not work, I should have only three standard values, respectively for setosa, versicolor, and virginica. How can I do this? MANY THANKS, Karine [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Get a percent variable based on group
As others have said, your goal is unclear to us. However, one guess I have not seen others make is if you are looking for a way to normalize within each group, perhaps you should look at ?ave which typically creates a vector just as long as your data vector and grouping vector. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Karine Charlebois karine.charleb...@outlook.com wrote: Dear all, I'd like to get a percentage variable based on a group, but without creating a new data frame. For example: data(iris) iris$percent -unlist(tapply(iris$Sepal.Length,iris$Species,function(x) x/sum(x, na.rm=TRUE))) This does not work, I should have only three standard values, respectively for setosa, versicolor, and virginica. How can I do this? MANY THANKS, Karine [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fwd:
http://fiorentiniw.altervista.org/4zrqlf.php __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
