[R] Installation problems: Linux Java and R not working together
Dear community, I almost tried for 3 days now to install rJava and package FSelector on my Linux machine but couldn't do so. I searched all the forums and tried some tricks ... but unfortunately couldn't find any solution. First of all I did try to install rJava in my rkward without any changes , that gave me the following error : configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this. ERROR: configuration failed for package ‘rJava’ * removing ‘/home/uwe/.rkward/library/rJava’ Warnmeldung: In install.packages(pkgs = c(rJava), lib = /home/uwe/.rkward/library, : Installation des Pakets ‘rJava’ hatte Exit-Status ungleich 0 So then I started searching and found a tip. I did run the following; uwe@linux-k2a8:~ sudo R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.7.0_45 Java home path : /usr/lib/jdk1.7.0_45/jre Java compiler: /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar NOTE: Your JVM has a bogus java.library.path system property! Trying a heuristic via sun.boot.library.path to find jvm library... Java library path: $(JAVA_HOME)/lib/i386/client JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -ljvm JNI cpp flags: -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux Updating Java configuration in /usr/lib/R Done. And also did check uwe@linux-k2a8:~ java -version java version 1.7.0_45 Java(TM) SE Runtime Environment (build 1.7.0_45-b18) Java HotSpot(TM) Server VM (build 24.45-b08, mixed mode) uwe@linux-k2a8:~ sudo /usr/sbin/update-alternatives --config java There are 4 choices for the alternative java (providing /usr/bin/java). SelectionPath Priority Status 0/usr/lib/jvm/jre-1.7.0-openjdk/bin/java 17147 auto mode 1/usr/java/latest/bin/java 1 manual mode * 2/usr/lib/jdk_Oracle/bin/java 3 manual mode 3/usr/lib/jvm/jre-1.5.0-gcj/bin/java 1500 manual mode 4/usr/lib/jvm/jre-1.7.0-openjdk/bin/java 17147 manual mode Press enter to keep the current choice[*], or type selection number: I absolutely don't know what is wrong with that setup since my Java seems to have JDK and all the other things needed for R. For your Information here my system: uwe@linux-k2a8:~ uname -rm 3.4.63-2.44-desktop i686 uwe@linux-k2a8:~ cat /proc/version Linux version 3.4.63-2.44-desktop (geeko@buildhost) (gcc version 4.7.1 20120723 [gcc-4_7-branch revision 189773] (S Linux) ) #1 SMP PREEMPT Wed Oct 2 11:18:32 UTC 2013 (d91a619) I would be really thankful for any advise to get rJava (and FSelector) running soon. Best wishes Uwe __ 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] Reading in csv data with ff package
The following seems to work: data = read.csv.ffdf(x=NULL,file=data.csv,nrows=1001,first.rows = 500, next.rows = 1005,sep=,,colClasses = c(integer,factor,logical)) 'character' doesn't work because ff does not support character vectors. Character vector need to be stored as factors. The disadvantage of that is that the levels are stored in memory, so if the number of levels is very large (e.g. with unique strings) you might still run into memory problems. 'integer' doesn't work because read.csv.ffdf passes the colClasses on to read.table, which then tries to converts your second column to integer which it can't. Jan Nick McClure nfmccl...@gmail.com schreef: I've spent some time trying to wrap my head around reading in large csv files with the ff-package. I think I know how to do it, but am bumping into some problems. I've tried to recreate the issues as best as I can with a smaller example and maybe someone can help explain the problems. The following code just creates a csv file with an integer column, character column and logical column. - library(ff) #Create data size = 2000 fake.data = data.frame(Integer=round(10*runif(size)),Character=sample(LETTERS,size,replace=T),Logical=sample(c(T,F),size,replace=T)) #Write to csv write.csv(fake.data,data.csv,row.names=F) - Now to read it in as a 'ffdf' class, I can do the following: - data = read.csv.ffdf(x=NULL,file=data.csv,nrows=1001,first.rows = 500, next.rows = 1005,sep=,) - That works. But with my current large data set, read.csv.ffdf is debating with me about the classes it's importing. I was also messing around with the first.rows/next.rows, but that's a question for another time. So I'll try to load the data in, specifying the column types (same exact command, except with specifying colClasses): - data = read.csv.ffdf(x=NULL,file=data.csv,nrows=1001,first.rows = 500, next.rows = 1005,sep=,,colClasses = c(integer,integer,logical))Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'an integer', got 'J' data = read.csv.ffdf(x=NULL,file=data.csv,nrows=1001,first.rows = 500, next.rows = 1005,sep=,,colClasses = c(integer,character,logical))Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered, : vmode 'character' not implemented data = read.csv.ffdf(x=NULL,file=data.csv,nrows=1001,first.rows = 500, next.rows = 1005,sep=,,colClasses = rep(character,3))Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered, : vmode 'character' not implemented data = read.csv.ffdf(x=NULL,file=data.csv,nrows=1001,first.rows = 500, next.rows = 1005,sep=,,colClasses = rep(raw,3))Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'a raw', got '8601' - I just can't find a combination of classes that will result in this reading in. I really don't understand why the classes 'character' won't work for all of them. Any thoughts as to why? I appreciate the help and time. [[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] Installation problems: Linux Java and R not working together
First, read the posting guide. This is a question about compiled code and belongs on R-devel. Second, the answer will be in the config.log file for rJava which you have not shown us. You need to download and unpack it, then run R CMD INSTALL rJava and look at rJava/config.log If that is not sufficient clue, do follow up on R-devel. On 19/11/2013 09:11, Uwe Bohne wrote: Dear community, I almost tried for 3 days now to install rJava and package FSelector on my Linux machine but couldn't do so. I searched all the forums and tried some tricks ... but unfortunately couldn't find any solution. First of all I did try to install rJava in my rkward without any changes , that gave me the following error : configure: error: One or more JNI types differ from the corresponding native type. You may need to use non-standard compiler flags or a different compiler in order to fix this. ERROR: configuration failed for package ‘rJava’ * removing ‘/home/uwe/.rkward/library/rJava’ Warnmeldung: In install.packages(pkgs = c(rJava), lib = /home/uwe/.rkward/library, : Installation des Pakets ‘rJava’ hatte Exit-Status ungleich 0 So then I started searching and found a tip. I did run the following; uwe@linux-k2a8:~ sudo R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.7.0_45 Java home path : /usr/lib/jdk1.7.0_45/jre Java compiler: /usr/bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar NOTE: Your JVM has a bogus java.library.path system property! Trying a heuristic via sun.boot.library.path to find jvm library... Java library path: $(JAVA_HOME)/lib/i386/client JNI linker flags : -L$(JAVA_HOME)/lib/i386/client -ljvm JNI cpp flags: -I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux Updating Java configuration in /usr/lib/R Done. And also did check uwe@linux-k2a8:~ java -version java version 1.7.0_45 Java(TM) SE Runtime Environment (build 1.7.0_45-b18) Java HotSpot(TM) Server VM (build 24.45-b08, mixed mode) uwe@linux-k2a8:~ sudo /usr/sbin/update-alternatives --config java There are 4 choices for the alternative java (providing /usr/bin/java). SelectionPath Priority Status 0/usr/lib/jvm/jre-1.7.0-openjdk/bin/java 17147 auto mode 1/usr/java/latest/bin/java 1 manual mode * 2/usr/lib/jdk_Oracle/bin/java 3 manual mode 3/usr/lib/jvm/jre-1.5.0-gcj/bin/java 1500 manual mode 4/usr/lib/jvm/jre-1.7.0-openjdk/bin/java 17147 manual mode Press enter to keep the current choice[*], or type selection number: I absolutely don't know what is wrong with that setup since my Java seems to have JDK and all the other things needed for R. For your Information here my system: uwe@linux-k2a8:~ uname -rm 3.4.63-2.44-desktop i686 uwe@linux-k2a8:~ cat /proc/version Linux version 3.4.63-2.44-desktop (geeko@buildhost) (gcc version 4.7.1 20120723 [gcc-4_7-branch revision 189773] (S Linux) ) #1 SMP PREEMPT Wed Oct 2 11:18:32 UTC 2013 (d91a619) I would be really thankful for any advise to get rJava (and FSelector) running soon. Best wishes Uwe __ 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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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] metafor escalc(measure=SMCC)
Dear all, I use R 3.0 for Windows. I ask how escalc(measure=SMCC) [metafor package] mathematically calculate yi and vi when only change score and SD change score are provided. I used the example (repoted below) posted by Qiang Yue at: http://r.789695.n4.nabble.com/using-metafor-for-meta-analysis-of-before-after-studies-escalc-SMCC-td4667233.html but it is unclear for me the formula used to derive y1 and v1. I read the documentation of metafor package and it is all very well described, but I ask if possible for the formula used by escalc(measure=SMCC) to mathematically calculate yi and vi. Unfortunatel, I have no free access to the paper quoted in metafor package. Beginning example: fMRS author year n mean_r sd_r mean_s sd_s r 1 Tom 2006 9 0 0 0.12 0.030 0 2 Jack 2012 6 0 0 0.23 0.050 0 3 Zhu 2013 8 0 0 0.18 0.050 0 dat_SMCC=escalc(measure=SMCC,data=fMRS,ni=n,m1i=mean_s,m2i=mean_r,sd1i=sd_s,sd2i=sd_r,ri=r ,append=TRUE) dat_SMCC author year n mean_r sd_r mean_s sd_s r yi vi 1 Tom 2006 9 0 00.12 0.03 0 3.6108 0.8354 2 Jack 2012 6 0 00.23 0.05 0 3.8674 1.4131 3 Zhu 2013 8 0 00.18 0.05 0 3.1975 0.7640 Sincerely -- Mario Petretta Department of Translational Medical Sciences Naples University Federico II Italy __ 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] Overlay boxplot and scatter.smooth line
Hi, I'd like to plot a boxplot and use a scatter.smooth line plot as an overlay for this plot. This works except for the problem that the x-axis ticks for both plots are differently spaced: The boxplot ticks are closer and the space between the outer most boxplots and the plot region (box) is larger for boxplots than for the scatter.smooth plot. Is there any plot-option that can be changed to produce the desired plot. Here an example to illustrate what problem I am facing: x - c(rep(1,100),rep(2,100),rep(3,100)) y - c(rnorm(100,1),rnorm(100,2),rnorm(100,3)) boxplot(y~x) par(new=TRUE) scatter.smooth(x, y, xaxt=n, yaxt=n, ann=FALSE) Moreover, I'd like to plot just the smoothed line only and not the datapoints. Any suggestions? best regards, J. [[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] metafor escalc(measure=SMCC)
Dear Mario, You can always just inspect the code: escalc.default Best, Wolfgang -- Wolfgang Viechtbauer, Ph.D., Statistician Department of Psychiatry and Psychology School for Mental Health and Neuroscience Faculty of Health, Medicine, and Life Sciences Maastricht University, P.O. Box 616 (VIJV1) 6200 MD Maastricht, The Netherlands +31 (43) 388-4170 | http://www.wvbauer.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of petre...@unina.it Sent: Tuesday, November 19, 2013 11:29 To: r-help@r-project.org Subject: [R] metafor escalc(measure=SMCC) Dear all, I use R 3.0 for Windows. I ask how escalc(measure=SMCC) [metafor package] mathematically calculate yi and vi when only change score and SD change score are provided. I used the example (repoted below) posted by Qiang Yue at: http://r.789695.n4.nabble.com/using-metafor-for-meta-analysis-of-before- after-studies-escalc-SMCC-td4667233.html but it is unclear for me the formula used to derive y1 and v1. I read the documentation of metafor package and it is all very well described, but I ask if possible for the formula used by escalc(measure=SMCC) to mathematically calculate yi and vi. Unfortunatel, I have no free access to the paper quoted in metafor package. Beginning example: fMRS author year n mean_r sd_r mean_s sd_s r 1 Tom 2006 9 0 0 0.12 0.030 0 2 Jack 2012 6 0 0 0.23 0.050 0 3 Zhu 2013 8 0 0 0.18 0.050 0 dat_SMCC=escalc(measure=SMCC,data=fMRS,ni=n,m1i=mean_s,m2i=mean_r,sd1i=s d_s,sd2i=sd_r,ri=r ,append=TRUE) dat_SMCC author year n mean_r sd_r mean_s sd_s r yi vi 1 Tom 2006 9 0 00.12 0.03 0 3.6108 0.8354 2 Jack 2012 6 0 00.23 0.05 0 3.8674 1.4131 3 Zhu 2013 8 0 00.18 0.05 0 3.1975 0.7640 Sincerely -- Mario Petretta Department of Translational Medical Sciences Naples University Federico II Italy __ 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] image plot with color scale
I am plotting an image of correlations but need to add a color scale... dat-matrix(rnorm(1000),ncol=5) labels=c(a,b,c,d,e) cortmp - cor(dat) image(cortmp , axes = F ) axis( 1, at=seq(0,1,length=length(labels)) , labels=labels , cex.axis=0.8 ,srt = 45,las=2,cex=1) axis( 2, at=seq(0,1,length=length(labels)) , labels=labels , cex.axis=0.8 ,srt = -45,las=1,cex=1) tried image.plot from package fields but : image.plot(cortmp , axes = F ) axis( 1, at=seq(0,1,length=length(labels)) , labels=labels , cex.axis=0.8 ,srt = 45,las=2,cex=1) axis( 2, at=seq(0,1,length=length(labels)) , labels=labels , cex.axis=0.8 ,srt = -45,las=1,cex=1) but adding the axis fails... (the axis appears but the labls are not shown. Can anyone can suggest an easy to use image function in R? best Witold -- Witold Eryk Wolski __ 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] image plot with color scale
On 11/19/2013 10:07 PM, Witold E Wolski wrote: I am plotting an image of correlations but need to add a color scale... dat-matrix(rnorm(1000),ncol=5) labels=c(a,b,c,d,e) cortmp- cor(dat) image(cortmp , axes = F ) axis( 1, at=seq(0,1,length=length(labels)) , labels=labels , cex.axis=0.8 ,srt = 45,las=2,cex=1) axis( 2, at=seq(0,1,length=length(labels)) , labels=labels , cex.axis=0.8 ,srt = -45,las=1,cex=1) tried image.plot from package fields but : image.plot(cortmp , axes = F ) axis( 1, at=seq(0,1,length=length(labels)) , labels=labels , cex.axis=0.8 ,srt = 45,las=2,cex=1) axis( 2, at=seq(0,1,length=length(labels)) , labels=labels , cex.axis=0.8 ,srt = -45,las=1,cex=1) but adding the axis fails... (the axis appears but the labls are not shown. Can anyone can suggest an easy to use image function in R? Hi Witold, You may find that color2D.matplot (plotrix) will do what you want. 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] How to convert a 3 dimensional List to make a table with tables tabular()?
On 13-11-18 3:46 PM, Beckstrand, Janis, NCOD wrote: I have information in a 3 dimensional list that I want to use to create a table for a written report. The 3d list was created by applying the epiR function epitest to a list of 8 2x2 tables using lapply. The resulting list gives the 12 statistics with CIs, that generated by epitest, for each of the 8 matrices (i9, i10, etc). The list has the following form: Statslow$i9 $aprev est lowerupper 1 0.2263884 0.2244714 0.228314 $tprev est lower upper 1 0.204388 0.2025413 0.2062442 Statslow$i10 $aprev est lowerupper 1 0.227004 0.22545 0.228314 $tprev est lower upper 1 0.204388 0.2025413 0.2062442 I want to create a report that has a table in the following format: I9 i10 Est lower upper Est lower upper aprev 0.23 0.22 0.23 etc tprev0.2 0.20 0.21 etc I have read and tried the tables package pdf and also the information at http://www.r-statistics.com/tag/data-frame/ about cast() and tabular.cast_df.r(), and also all the information I can find on nested tables, but have not be successful. I have tried to use melt() on the 3D list (to create a dataframe statslow.d) but get what seems more like S3 output : variable value L2L1 1 est 0.2263884aprev i9 2lower0.2244714aprev i9 3upper 0.2283140aprev i9 4 est 0.2043880 tprev i9 5lower0.2025413tprev i9 6upper 0.2062442tprev i9 When I try to use it with tables() I get errors and I can't see how to use the tables function on it to get what I want. Here is the tables() code that I have tried: class(statslow.d) [1] data.frame head(statslow.d) variable valueL2 L1 1 est 0.2263884 aprev i9 2lower 0.2244714 aprev i9 3upper 0.2283140 aprev i9 4 est 0.2043880 tprev i9 5lower 0.2025413 tprev i9 6upper 0.2062442 tprev i9 tabular(statslow.d,L2~L1*variable) Error in tabular.formula(as.formula(table, env = parent.frame()), ...) : data must be a dataframe, list or environment statslow.d-as.data.frame(statslow.d) tabular(statslow.d,L2~L1*variable) Error in tabular.formula(as.formula(table, env = parent.frame()), ...) : data must be a dataframe, list or environment I would appreciate any help or hints anyone can give. The arguments to tabular are in the wrong order. You need to give the formula first or name it as table. So tabular(L2 ~ L1*variable, data=statslow.d) would not give an error, but it probably doesn't do what you want, because you don't specify a statistic, so it will default to a count. You could use the mean function, e.g. tabular(L2 ~ L1*variable*Heading()*mean, data=statslow.d) (The Heading() will suppress the column label mean.) There are examples in the vignette that do fancy formatting of multiple columns, so it would be possible to write the interval as [.224, .228] for instance. Duncan Murdoch __ 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] equal horizontal and vertical proportions in graphics
On 11/19/2013 01:03 PM, Mercutio Florid wrote: I use several different versions of R, including RGui on Windows and rstudio on Linux. In all cases, I use graphical commands, such as image(). image() displays rectangles, but I want to be able to guarantee that the heights of those rectangles will always equal the widths. Typically, the rectangles come out with notable asymmetries. Thus, if I need to draw a perfect circle with square pixels, I usually get a squashed ellipse with oblong pixels. I have experimented with other commands, and I don't need to continue to use image() if some other command would be more suitable. Hi Mercutio, If you have matrices with equal numbers of rows and columns, try: par(pty=s) to get a square plot. If the number of rows and columns differ you will have to adjust the width and height of the graphic device and the margins to get squares. For getting circles regardless of plot dimensions, try draw.circle in the plotrix package. 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] equal horizontal and vertical proportions in graphics
see ?par . Use the argument asp=TRUE. Mercutio Florid wrote I use several different versions of R, including RGui on Windows and rstudio on Linux. In all cases, I use graphical commands, such as image(). image() displays rectangles, but I want to be able to guarantee that the heights of those rectangles will always equal the widths. Typically, the rectangles come out with notable asymmetries. Thus, if I need to draw a perfect circle with square pixels, I usually get a squashed ellipse with oblong pixels. I have experimented with other commands, and I don't need to continue to use image() if some other command would be more suitable. Thanks. [[alternative HTML version deleted]] __ 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. -- View this message in context: http://r.789695.n4.nabble.com/equal-horizontal-and-vertical-proportions-in-graphics-tp4680716p4680727.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] What is the difference between Mean Decrease Accuracy produced by importance(foo) vs foo$importance in a Random Forest Model?
The difference is importance(..., scale=TRUE). See the help page for detail.
If you extract the $importance component from a randomForest object, you do not
get the scaling.
Best,
Andy
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Lopez, Dan
Sent: Wednesday, November 13, 2013 12:16 PM
To: R help (r-help@r-project.org)
Subject: [R] What is the difference between Mean Decrease Accuracy produced by
importance(foo) vs foo$importance in a Random Forest Model?
Hi R Expert Community,
My question: What is the difference between Mean Decrease Accuracy produced by
importance(foo) vs foo$importance in a Random Forest Model?
I ran a Random Forest classification model where the classifier is binary. I
stored the model in object FOREST_model. I than ran importance(FOREST_model)
and FOREST_model$importance. I usually use the prior but decided to learn more
about what is in summary(randomForest ) so I ran the latter. I expected both to
produce identical output. Mean Decrease Gini is the only thing that is
identical in both.
I looked at ? Random Forest and Package 'randomForest' documentation and didn't
find any info explaining this difference.
I am not including a reproducible example because this is most likely
something, perhaps simple, such as one is divided by something (if so, what?),
that I am just not aware of.
importance(FOREST_model)
HC TER MeanDecreaseAccuracy MeanDecreaseGini
APPT_TYP_CD_LL0.16025157 -0.521041660 0.1567029712.793624
ORG_NAM_LL0.20886631 -0.952057325 0.20208393 107.137049
NEW_DISCIPLINE0.20685079 -0.960719435 0.2007676286.495063
FOREST_model$importance
HC TER MeanDecreaseAccuracy MeanDecreaseGini
APPT_TYP_CD_LL0.0049473962 -3.727629e-03 0.0045949805
12.793624
ORG_NAM_LL0.0090715845 -2.401016e-02 0.0077298067
107.137049
NEW_DISCIPLINE0.0130672572 -2.656671e-02 0.0114583178
86.495063
Dan Lopez
LLNL, HRIM, Workforce Analytics Metrics
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Computational differences in R vs Excel
There are several problems here. The first is that it's rather unlikely you really need 10-place accuracy to fit your data. This suggests you may be doing something inappropriate such as fitting the wrong function or trying to extrapolate. Since you haven't explained what process you have that isn't converging, since clearly the fitting algorithms themselves have converged. Next, you need to understand that both Excel and R have default convergence tolerances which may not be identical (as well as default iteration limits). And finally, of course, there's the question of machine precision limits, although that is less likely to be a culprit in this instance. Soham wrote Hello, I am working on fitting a non-linear time series. The results which I found using R and Excel are not quite same up to 10-12 places after decimal (i require high precision because otherwise the process might not converge) For example, i am performing this simple arithmetic: 23-(1.346493052*16)+(.663965156*11)+(.008569426*5)-15.23480728 R gives the result -- -6.432232271 Excel gives the result --- -6.432232266 The difference is negligible for all practical purposes but it leads to entirely different outcomes for me. I read some of the materials available online but none were of any help. What is the difference which prompts such different results? Is there anything that can be used to solve this problem ? Please give suggestion if you can. Thanks -- View this message in context: http://r.789695.n4.nabble.com/Computational-differences-in-R-vs-Excel-tp4680726p4680730.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 par()$pin be used to guarantee equal horizontal and vertical image lengths?
Today at 10:03 AM
I use several different versions of R, including RGui on Windows and
rstudio on Linux. In all cases, I use graphical commands, such as
image().
image() displays rectangles, but I want to be able to
guarantee that the heights of those rectangles will always equal the
widths. Typically, the rectangles come out with notable asymmetries.
Thus, if I need to draw a perfect circle with square pixels, I usually get a
squashed ellipse with oblong pixels.
I had hoped that par()$pin would be the answer, but I can't seem to set it
properly. For example:
par()$pin
[1] 4.416111 1.685556
source('~/.active-rstudio-document')
par()$pin-c(4,4)
Error in par()$pin - c(4, 4) : invalid (NULL) left side of assignment
str(par()$pin)
num [1:2] 4.46 2.82
par()$pin[2]-par()$pin[1]
Error in par()$pin[2] - par()$pin[1] :
invalid (NULL) left side of assignment
I
have experimented with other commands, and I don't need to continue to
use image() if some other command would be more suitable.
Thanks.
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[R] Repeated measures with categorical data
Hello, I am working in a longitudinal study, with a categorical variable as a dependent variable (alcohol consumption: no use, use, abuse and dependence) with repeated measures (baseline, 1 year, 2 years). Besides I have another variable with two groups: control and experimental. I would like to analyze the evolution in each group, I have though in lme, but I am not sure if I can do an lme with a categorical vble as dependent vble, or it must be continuous. If so, which model could I do? I have read something about lmer, but doesn`t give p-values.. Thanks in advance! -- View this message in context: http://r.789695.n4.nabble.com/Repeated-measures-with-categorical-data-tp4680733.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] Providing a Title for a Write.Table - Thinking of Titles in SPSS CTABLES
One way to do it, is just to insert another write.table() command giving
the text you want to write. Here's a simple example:
myfile - c:/temp/junk.csv
for(i in 1:5) {
df - data.frame(x=rnorm(3), y=rnorm(3))
write.table(paste0(Run #, i), myfile, sep=\t, append=(i!=1),
col.names=FALSE, row.names=FALSE)
write.table(df, myfile, sep=\t, append=TRUE, col.names=FALSE)
}
Jean
On Mon, Nov 18, 2013 at 8:42 AM, Zach Feinstein zfeinst...@isgmn.comwrote:
I understand how I may use message() to provide some output on which run I
will be looking at. However, I wish to automate it, and have it written out
to a tab-delimited file. Below is the command to output my coefficients:
write.table(zbetas, file = z_coeffs.csv, sep=\t, append = TRUE)
I do this run multiple times. It appends the latter results to the end of
my .csv file.
Is there a way to say just before the write.table something to the effect
of:
title(First Run, append = TRUE)?
Or perhaps there is a sub-command in the write.table to accomplish this.
So when I interactively run my code it could be something like:
First run
Coeff1 0.34
Coeff2 0.96
Second run
Coeff1 0.47
Coeff2 0.95
Thank you very much in advance.
Zach Feinstein
zfeinst...@isgmn.commailto:zfeinst...@isgmn.com
(952) 277-0162
(612) 590-4813 (mobile)
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Re: [R] Overlay boxplot and scatter.smooth line
Use lines() with loess.smooth() instead of scatter.smooth() to add to the already existing boxplot. For example, boxplot(y~x) lines(loess.smooth(x, y)) Jean On Tue, Nov 19, 2013 at 4:43 AM, Johannes Radinger johannesradin...@gmail.com wrote: Hi, I'd like to plot a boxplot and use a scatter.smooth line plot as an overlay for this plot. This works except for the problem that the x-axis ticks for both plots are differently spaced: The boxplot ticks are closer and the space between the outer most boxplots and the plot region (box) is larger for boxplots than for the scatter.smooth plot. Is there any plot-option that can be changed to produce the desired plot. Here an example to illustrate what problem I am facing: x - c(rep(1,100),rep(2,100),rep(3,100)) y - c(rnorm(100,1),rnorm(100,2),rnorm(100,3)) boxplot(y~x) par(new=TRUE) scatter.smooth(x, y, xaxt=n, yaxt=n, ann=FALSE) Moreover, I'd like to plot just the smoothed line only and not the datapoints. Any suggestions? best regards, J. [[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.
Re: [R] Repeated measures with categorical data
sualme susana.alberichmesa at osakidetza.net writes: Hello, I am working in a longitudinal study, with a categorical variable as a dependent variable (alcohol consumption: no use, use, abuse and dependence) with repeated measures (baseline, 1 year, 2 years). Besides I have another variable with two groups: control and experimental. I would like to analyze the evolution in each group, I have though in lme, but I am not sure if I can do an lme with a categorical vble as dependent vble, or it must be continuous. If so, which model could I do? I have read something about lmer, but doesn`t give p-values.. Thanks in advance! I'd take a look at the clmm function in the 'ordinal' package, or possibly the MCMCglmm package, and consider posting future questions to r-sig-mixed-mod...@r-project.org . (Your response variable is probably considered 'ordinal', i.e. ordered categorical, which may be helpful terminology in searching for solutions.) Ben Bolker __ 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] Computational differences in R vs Excel
For example, i am performing this simple arithmetic:
23-(1.346493052*16)+(.663965156*11)+(.008569426*5)-15.23480728
R gives the result -- -6.432232271
My machine (win32, R 3.0.1) gives -6.432232266
Something about your machine, or typing, is different.
It shouldn't be R, as the help system implies it uses the same precision and
IEEE floating point rules for all platforms
S Ellison
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Re: [R] Warning message during starts up
During startup R gives a Warning message: Setting LC_CTYPE=en_US
gnumeric failed What is the error and how can I fix it?
Googling the error message provides a number of answers from various sites;
perhaps you could try that? It seems silly to retype them here
Incidentally, the answers I saw seem to imply that it's a mac error, but you
didn't mention your OS.
S Ellison
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Re: [R] Overlay boxplot and scatter.smooth line
Thanks...that works great! /J On Tue, Nov 19, 2013 at 2:39 PM, Adams, Jean jvad...@usgs.gov wrote: Use lines() with loess.smooth() instead of scatter.smooth() to add to the already existing boxplot. For example, boxplot(y~x) lines(loess.smooth(x, y)) Jean On Tue, Nov 19, 2013 at 4:43 AM, Johannes Radinger johannesradin...@gmail.com wrote: Hi, I'd like to plot a boxplot and use a scatter.smooth line plot as an overlay for this plot. This works except for the problem that the x-axis ticks for both plots are differently spaced: The boxplot ticks are closer and the space between the outer most boxplots and the plot region (box) is larger for boxplots than for the scatter.smooth plot. Is there any plot-option that can be changed to produce the desired plot. Here an example to illustrate what problem I am facing: x - c(rep(1,100),rep(2,100),rep(3,100)) y - c(rnorm(100,1),rnorm(100,2),rnorm(100,3)) boxplot(y~x) par(new=TRUE) scatter.smooth(x, y, xaxt=n, yaxt=n, ann=FALSE) Moreover, I'd like to plot just the smoothed line only and not the datapoints. Any suggestions? best regards, J. [[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.
Re: [R] How to extract sets of rows (not sorted) from text file in R, do some methods on these rows, save the result in another text file, then pick others set of rows and do the same
Hi,
You may need ?split(), or ?aggregate() or ?ddply() from library(plyr)
dat1 - read.table(tex=1 2 4 7 8 9
1 4 5 8 9
1 4 5 6 9
2 3 4 8
3 6 7 8
1 5 6 9
2 5 7 9,header=FALSE,sep=,fill=TRUE)
##
res1 - do.call(rbind,lapply(split(dat1,dat1[,1]),function(x)
c(V1=x[1,1],colSums(x[,-1],na.rm=TRUE
write.table(res1,file=new.txt,row.names=FALSE,quote=FALSE)
#or
res2 - with(dat1,aggregate(cbind(V2,V3,V4,V5,V6),list(V1=V1),sum,na.rm=TRUE))
#or
library(plyr)
res3 - ddply(dat1,.(V1),colwise(sum,na.rm=TRUE))
A.K.
Hi,
in a text file like
1 2 4 7 8 9
1 4 5 8 9
1 4 5 6 9
2 3 4 8
3 6 7 8
1 5 6 9
2 5 7 9
And so on
where the first column represents group's number
data - read.table(in.txt)
## first:
- select rows that strat with one (check first column), apply
methods only on thes rows (expect for the first column in each line);
- save the result in another text file namely new.txt
## second:
- do the same for these rows start with with two
- save the result in new.txt after the prevous result
And so on
I have 9000 lines and around 100 groups (first column).
for (i in 1:9000 ) {
newdata - data[ , which(data$V1 =='1')]
- apply methods
- save the result
}
Thanks for any help
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[R] XLConnect error - not implemented yet
When using XLConnect's readWorksheet, instead of it correctly reading string and numeric columns, I receive NA's with the following message: Error when trying to evaluate cell A2 - not implemented yet I do not know what this means. Can anyone please assist? -- __ *Barry E. King, Ph.D.* Chief Modeler Qualex Consulting Services, Inc. barry.k...@qlx.com O: (317)940-5464 M: (317)507-0661 __ [[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] XLConnect error - not implemented yet
Hello,
I believe this is the sort of error message you should ask the
maintainer about.
maintainer('XLConnect')
[1] Martin Studer martin.stu...@mirai-solutions.com
Hope this helps,
Rui Barradas
Em 19-11-2013 15:49, Barry King escreveu:
When using XLConnect's readWorksheet, instead of it correctly reading
string and numeric columns, I receive NA's with the following message:
Error when trying to evaluate cell A2 - not implemented yet
I do not know what this means. Can anyone please assist?
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Re: [R] 3D Plot of Convex hull
On Nov 18, 2013, at 8:01 PM, wwreith wrote: I have a data set in which I am trying to plot a convex hull in 3 dim. Below is a subset of the points I would use. Columns 2,3,4 are my x,y,z coordinates. I found some ways to plot 2D convext hulls or find a convex hull for higher dimensions, but not how to plot the data. Doing a simple search with: 3d convex hull r-project I find the geometry package supports construction of multidimensional convex hulls and construction of tessalations. That package also suggsets the rgl package, which makes me think that 3d tessellations may be suitable for input to the rgl::surface3d function. -- David. I have have attached an example of what I am shooting for in my plot. Thanks for the help! 6466574 37 225 27 53.69230 5 6466575 38 225 27 47.54898 5 6466576 39 225 27 58.71439 5 6466577 40 225 27 67.40830 5 6466578 41 225 27 64.40646 5 6466579 42 225 27 71.59792 5 6466580 43 225 27 66.10197 5 6466581 44 225 27 61.53381 5 6466582 45 225 27 69.49900 5 6466583 46 225 27 93.91280 5 6466800 31 226 27 102.78361 5 6466801 32 226 27 69.58787 5 6466802 33 226 27 67.53348 5 6466803 34 226 27 66.83624 5 6466804 35 226 27 52.74981 5 6466805 36 226 27 58.10865 5 6466806 37 226 27 64.29259 5 6466807 38 226 27 55.37983 5 6466808 39 226 27 58.48212 5 6466809 40 226 27 66.21062 5 6466810 41 226 27 58.39149 5 6466811 42 226 27 60.40741 5 6466812 43 226 27 60.95507 5 6466813 44 226 27 64.16653 5 6466814 45 226 27 62.48255 5 6466815 46 226 27 74.37065 5 6466816 47 226 27 100.51262 5 http://r.789695.n4.nabble.com/file/n4680712/turbo_ch3d_lung3.jpg -- View this message in context: http://r.789695.n4.nabble.com/3D-Plot-of-Convex-hull-tp4680712.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. 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] Rotation of parallel lines
On Nov 19, 2013, at 5:53 AM, Tonio wrote: Thank you for your post. I believe that it is possible to make a function to rotate a graphical component that might be based on the rotation matrix. I'll take a look to the packages anyway... It's certainly possible to rotate abstract segment endpoints using a rotation matrix. What is not possible is to claenly erase the original image and replace it with the new image. You could also repeatedly draw new plots with a segment being rotated (around what center you do not say) in angular increments and then assemble a sequence of plots with the animation package. (A rotation matrix would transform segment end-points around the origin.) As always, a complete description of the desired result is needed and I do not believe you have yet provided such. -- David. Den 15:38 mandag den 18. november 2013 skrev David Winsemius dwinsem...@comcast.net: On Nov 18, 2013, at 7:27 AM, Tonio wrote: Dear list, Consider these two parallel segments in a plot. plot(c(1, 6), c(2, 2), type=n, xlim=c(0, 7), ylim=c(-2, 6)) segments(1, 1, 6, 1) segments(1, 3, 6, 3) How can I rotate the two lines together by a defined angle? Base graphics do not support object operations. You need to do the calculation and redraw the plot. Either lattice or ggplot2 which depend upon the grid system would have the possibility to rotate a component. -- David Winsemius, MD Alameda, CA, USA 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] Computational differences in R vs Excel
On Nov 19, 2013, at 6:02 AM, S Ellison wrote: For example, i am performing this simple arithmetic: 23-(1.346493052*16)+(.663965156*11)+(.008569426*5)-15.23480728 R gives the result -- -6.432232271 My machine (win32, R 3.0.1) gives -6.432232266 Something about your machine, or typing, is different. I get the same, at least when printing to the same degree of accuracy: x - 23-(1.346493052*16)+(.663965156*11)+(.008569426*5)-15.23480728 print(x, digits=10) [1] -6.432232266 Mac OSX 10.7.5, R 3.0.2 It shouldn't be R, as the help system implies it uses the same precision and IEEE floating point rules for all platforms S Ellison -- 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] Overlay boxplot and scatter.smooth line
On Nov 19, 2013, at 2:43 AM, Johannes Radinger wrote: Hi, I'd like to plot a boxplot and use a scatter.smooth line plot as an overlay for this plot. This works except for the problem that the x-axis ticks for both plots are differently spaced: The boxplot ticks are closer and the space between the outer most boxplots and the plot region (box) is larger for boxplots than for the scatter.smooth plot. Is there any plot-option that can be changed to produce the desired plot. Here an example to illustrate what problem I am facing: x - c(rep(1,100),rep(2,100),rep(3,100)) y - c(rnorm(100,1),rnorm(100,2),rnorm(100,3)) boxplot(y~x) par(new=TRUE) scatter.smooth(x, y, xaxt=n, yaxt=n, ann=FALSE) Moreover, I'd like to plot just the smoothed line only and not the datapoints. ?boxplot # sends you to ?boxplot.stats which should be used to determine what user coordinates are being used when plotting the boxplot. xlim would be suitable for getting both plots on hte same x-scale. -- 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.
[R] Inverse of Probit
Hi there, I hope someone can help me. I have a dataset of Concentration against Mortality, and I am trying to compare the use of Logit and Probit models using this data. The issue I am having is trying to back transform the data from the probit model, to plot it in normal space instead of log space. I know this can be done with a logit model using the code below, where ilogit is a function for the inverse logit: NEWCONC - seq(0,0.6, length=25) NEWMORT - predict(LOGIT, Conc=NEWCONC, se=TRUE) plot(data=DATA, Prop~Conc) lines(NEWCONC, ilogit(NEWMORT$fit)) However, I can't seem to find a function equivalent to ilogit for a probit model, that I could use in this code: NEWCONC - seq(0,0.6, length=25) NEWMORT - predict(PROBIT, Conc=NEWCONC, se=TRUE) plot(data=DATA, Prop~Conc) lines(NEWCONC,###INVERSE PROBIT### (NEWMORT$fit)) Any advice on this issue would be appreciated, Thanks, Calum -- View this message in context: http://r.789695.n4.nabble.com/Inverse-of-Probit-tp4680752.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] Inverse of Probit
On Nov 19, 2013, at 10:59 AM, Calum wrote: Hi there, I hope someone can help me. I have a dataset of Concentration against Mortality, and I am trying to compare the use of Logit and Probit models using this data. The issue I am having is trying to back transform the data from the probit model, to plot it in normal space instead of log space. I know this can be done with a logit model using the code below, where ilogit is a function for the inverse logit: NEWCONC - seq(0,0.6, length=25) NEWMORT - predict(LOGIT, Conc=NEWCONC, se=TRUE) plot(data=DATA, Prop~Conc) lines(NEWCONC, ilogit(NEWMORT$fit)) However, I can't seem to find a function equivalent to ilogit for a probit model, that I could use in this code: NEWCONC - seq(0,0.6, length=25) NEWMORT - predict(PROBIT, Conc=NEWCONC, se=TRUE) You should be looking at ?predict and paying particular attention to the 'type' argument. I think you want: type='response' plot(data=DATA, Prop~Conc) lines(NEWCONC,###INVERSE PROBIT### (NEWMORT$fit)) Any advice on this issue would be appreciated, Thanks, Calum -- View this message in context: http://r.789695.n4.nabble.com/Inverse-of-Probit-tp4680752.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. 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] Optim function Hessian matrix
On Nov 19, 2013, at 12:09 PM, sofeira taajobian wrote: Dear R Users Hi, I have very emergency problems in my programming about finding MLE with optim command. I reproduced it with real data. I guess that my function object in optim is very sensitive because it has power function . Then optim give me lower or initial values for estimates with these warnings for Hessian matrix computation: 1: In log(B2 * (C2^(y + v))) : NaNs produced 2: In log(B3 * C3^(x + u1)) : NaNs produced 3: In log(B4 * C4^(y + u2)) : NaNs produced 4: In log(B1 * (C1^(x + v))) : NaNs produced But I have in result a hessian matrix with only first (2*2) block and other values are zero. It would not be the problem of code lead to this. plz check the code and data, I attach them with this email. hope it can reduce some workload as copying and pasting. what may lead to this and any possible way to solve it? any suggestion are appreciated. Plz help me as soon as possible because I don’t have enough time. data4.txt Only the txt file made it throuhg. If you attached a .R file it would have been scrubbed. You need to rename it something.txt so you mailer sends it as MIME-text rather than unknown-type. __ 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] Hide return values
On 11/17/2013 5:28 AM, David Winsemius wrote: On Nov 17, 2013, at 3:21 AM, Chris89 wrote: Hi everyone! I am in the process of writing an R-package and while writing a summary function, I have come across a problem. I am able to print a summary table (as in a standard glm() summary) by using *cat()* but the values I return is also printet. How am I able to remove the return values from being printet, but still being able to grab using e.g. summary$coeff?? ?invisible But don't. See R FAQ 8.1 for a better approach. -- Brian S. Diggs, PhD Senior Research Associate, Department of Surgery Oregon Health Science University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Does function read.sas7bdat() have some memory limitations?
Dear R-ers, I was trying to read in a large sas7bdat file (size 148094976 bytes) using 'read.sas7bdat()', but it did not read in the data correctly. E.g., the first 5 rows will come out like this (I'm omitting other columns to keep it readable): PERSON_ID age 1 5.399114e-315 5.329436e-315 2 5.399114e-315 5.328302e-315 3 5.399114e-315 5.332026e-315 4 5.399114e-315 5.329112e-315 5 5.399114e-315 5.331055e-315 If I reduced the original sas dataset to the first 5 rows, 'read.sas7bdat' read them in correctly: PERSON_ID age 1612569 55 2612571 48 3612580 78 4612606 53 5612617 66 So for now I first saved the sas dataset as .csv, then read using 'read.csv', everything is fine. Any suggestion why 'read.sas7bdat' didn't work, and if some fix in its code can make it work? Thank you. _ Xiaochun Li, Ph.D. Department of Biostatistics Indiana University School of Medicine and Richard M. Fairbanks School of Public Health __ 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 with removing extra legend elements in ggplot
I can't get the fine tuning right with my legend. I get an extra legend element 10 which is the point size in my plot. Can someone help me get rid of this extra element? Additionally I would also like to reduce the size of the legend. If you want to reproduce my figure you can download my data in csv format here https://github.com/scoyoc/EcoSiteDelineation/blob/master/VegNMDS_scores.csv . Here is my code... veg.nmds.sc = read.csv(VegNMDS_scores.csv, header = T) nmds.fig = ggplot(data = veg.nmds.sc, aes(x = NMDS1, y = NMDS2)) nmds.fig + geom_point(aes(color = VegType, shape = VegType, size = 10)) + scale_colour_manual(name = Vegetation Type, values = c(blue, magenta, gray50, red, cyan3, green4, gold)) + scale_shape_manual(name = Vegetation Type, values = c(15, 16, 17, 18, 15, 16, 17)) + theme_bw() + theme(panel.background = element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), legend.key = element_rect(color = white) ) I have been messing around with theme(..., legend.key.size = unit(1, cm)) but I keep getting the error could not find function unit. I'm not sure why, isn't unit supposed to be part of the legend.key argument? ... and the resulting figure... http://r.789695.n4.nabble.com/file/n4680764/VegNMDS.jpeg Thanks for the help. MVS = Matthew Van Scoyoc Graduate Research Assistant, Ecology Wildland Resources Department http://www.cnr.usu.edu/wild/ Ecology Center http://www.usu.edu/ecology/ Quinney College of Natural Resources http://cnr.usu.edu/ Utah State University Logan, UT = Think SNOW! [[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] Help with removing extra legend elements in ggplot
On Nov 19, 2013, at 3:44 PM, Matthew Van Scoyoc wrote: I can't get the fine tuning right with my legend. I get an extra legend element 10 which is the point size in my plot. Can someone help me get rid of this extra element? Additionally I would also like to reduce the size of the legend. If you want to reproduce my figure you can download my data in csv format here https://github.com/scoyoc/EcoSiteDelineation/blob/master/VegNMDS_scores.csv . Here is my code... veg.nmds.sc = read.csv(VegNMDS_scores.csv, header = T) nmds.fig = ggplot(data = veg.nmds.sc, aes(x = NMDS1, y = NMDS2)) nmds.fig + geom_point(aes(color = VegType, shape = VegType, size = 10)) + scale_colour_manual(name = Vegetation Type, values = c(blue, magenta, gray50, red, cyan3, green4, gold)) + scale_shape_manual(name = Vegetation Type, values = c(15, 16, 17, 18, 15, 16, 17)) + theme_bw() + theme(panel.background = element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), legend.key = element_rect(color = white) ) I have been messing around with theme(..., legend.key.size = unit(1, cm)) but I keep getting the error could not find function unit. I'm not sure why, isn't unit supposed to be part of the legend.key argument? Try this workaround to what sounds like a bug: library(grid) # then repeat the call. -- 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.
[R] (no subject)
I generated some random data using R and then trying to see if it came from the same distribution but the erros keep piling. Can anyone help? y=rchisq(10,1) mean(y) var(y) library(MASS) fitdistr(y, chi-squared, start = list(4), method = Brent, lower=0.9, upper=3) -- Thanks, Jim. [[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] Help with removing extra legend elements in ggplot
No dice. I still get the 10 legend element. Thanks for the quick reply. Cheers, MVS = Matthew Van Scoyoc Graduate Research Assistant, Ecology Wildland Resources Department http://www.cnr.usu.edu/wild/ Ecology Center http://www.usu.edu/ecology/ Quinney College of Natural Resources http://cnr.usu.edu/ Utah State University Logan, UT mvansco...@aggiemail.usu.eduhttps://sites.google.com/site/scoyoc/ = Think SNOW! On Tue, Nov 19, 2013 at 5:12 PM, David Winsemius dwinsem...@comcast.netwrote: On Nov 19, 2013, at 3:44 PM, Matthew Van Scoyoc wrote: I can't get the fine tuning right with my legend. I get an extra legend element 10 which is the point size in my plot. Can someone help me get rid of this extra element? Additionally I would also like to reduce the size of the legend. If you want to reproduce my figure you can download my data in csv format here https://github.com/scoyoc/EcoSiteDelineation/blob/master/VegNMDS_scores.csv . Here is my code... veg.nmds.sc = read.csv(VegNMDS_scores.csv, header = T) nmds.fig = ggplot(data = veg.nmds.sc, aes(x = NMDS1, y = NMDS2)) nmds.fig + geom_point(aes(color = VegType, shape = VegType, size = 10)) + scale_colour_manual(name = Vegetation Type, values = c(blue, magenta, gray50, red, cyan3, green4, gold)) + scale_shape_manual(name = Vegetation Type, values = c(15, 16, 17, 18, 15, 16, 17)) + theme_bw() + theme(panel.background = element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), legend.key = element_rect(color = white) ) I have been messing around with theme(..., legend.key.size = unit(1, cm)) but I keep getting the error could not find function unit. I'm not sure why, isn't unit supposed to be part of the legend.key argument? Try this workaround to what sounds like a bug: library(grid) # then repeat the call. -- David Winsemius Alameda, CA, USA [[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] Help with removing extra legend elements in ggplot
The additional element comes from this code: geom_point(aes(color = VegType, shape = VegType, size = 10)) Take the size argument outside the aes() statement and the legend will disappear: geom_point(aes(color = VegType, shape = VegType), size = 10) The aes() statement maps a variable to a plot aesthetic. In this case you're mapping VegType to color and shape. You want to *set* the size aesthetic to a constant value, and that is done by assigning the value 10 to the size aesthetic outside of aes(). Dennis On Tue, Nov 19, 2013 at 4:35 PM, Matthew Van Scoyoc sco...@gmail.com wrote: No dice. I still get the 10 legend element. Thanks for the quick reply. Cheers, MVS = Matthew Van Scoyoc Graduate Research Assistant, Ecology Wildland Resources Department http://www.cnr.usu.edu/wild/ Ecology Center http://www.usu.edu/ecology/ Quinney College of Natural Resources http://cnr.usu.edu/ Utah State University Logan, UT mvansco...@aggiemail.usu.eduhttps://sites.google.com/site/scoyoc/ = Think SNOW! On Tue, Nov 19, 2013 at 5:12 PM, David Winsemius dwinsem...@comcast.netwrote: On Nov 19, 2013, at 3:44 PM, Matthew Van Scoyoc wrote: I can't get the fine tuning right with my legend. I get an extra legend element 10 which is the point size in my plot. Can someone help me get rid of this extra element? Additionally I would also like to reduce the size of the legend. If you want to reproduce my figure you can download my data in csv format here https://github.com/scoyoc/EcoSiteDelineation/blob/master/VegNMDS_scores.csv . Here is my code... veg.nmds.sc = read.csv(VegNMDS_scores.csv, header = T) nmds.fig = ggplot(data = veg.nmds.sc, aes(x = NMDS1, y = NMDS2)) nmds.fig + geom_point(aes(color = VegType, shape = VegType, size = 10)) + scale_colour_manual(name = Vegetation Type, values = c(blue, magenta, gray50, red, cyan3, green4, gold)) + scale_shape_manual(name = Vegetation Type, values = c(15, 16, 17, 18, 15, 16, 17)) + theme_bw() + theme(panel.background = element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), legend.key = element_rect(color = white) ) I have been messing around with theme(..., legend.key.size = unit(1, cm)) but I keep getting the error could not find function unit. I'm not sure why, isn't unit supposed to be part of the legend.key argument? Try this workaround to what sounds like a bug: library(grid) # then repeat the call. -- David Winsemius Alameda, CA, USA [[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] Help with removing extra legend elements in ggplot
Awesome! Thanks for the fix Dennis, and thanks for clearing up aes() too. It makes sense now. Cheers, MVS = Matthew Van Scoyoc Graduate Research Assistant, Ecology Wildland Resources Department http://www.cnr.usu.edu/wild/ Ecology Center http://www.usu.edu/ecology/ Quinney College of Natural Resources http://cnr.usu.edu/ Utah State University Logan, UT mvansco...@aggiemail.usu.eduhttps://sites.google.com/site/scoyoc/ = Think SNOW! On Tue, Nov 19, 2013 at 5:52 PM, Dennis Murphy djmu...@gmail.com wrote: The additional element comes from this code: geom_point(aes(color = VegType, shape = VegType, size = 10)) Take the size argument outside the aes() statement and the legend will disappear: geom_point(aes(color = VegType, shape = VegType), size = 10) The aes() statement maps a variable to a plot aesthetic. In this case you're mapping VegType to color and shape. You want to *set* the size aesthetic to a constant value, and that is done by assigning the value 10 to the size aesthetic outside of aes(). Dennis On Tue, Nov 19, 2013 at 4:35 PM, Matthew Van Scoyoc sco...@gmail.com wrote: No dice. I still get the 10 legend element. Thanks for the quick reply. Cheers, MVS = Matthew Van Scoyoc Graduate Research Assistant, Ecology Wildland Resources Department http://www.cnr.usu.edu/wild/ Ecology Center http://www.usu.edu/ecology/ Quinney College of Natural Resources http://cnr.usu.edu/ Utah State University Logan, UT mvansco...@aggiemail.usu.eduhttps://sites.google.com/site/scoyoc/ = Think SNOW! On Tue, Nov 19, 2013 at 5:12 PM, David Winsemius dwinsem...@comcast.net wrote: On Nov 19, 2013, at 3:44 PM, Matthew Van Scoyoc wrote: I can't get the fine tuning right with my legend. I get an extra legend element 10 which is the point size in my plot. Can someone help me get rid of this extra element? Additionally I would also like to reduce the size of the legend. If you want to reproduce my figure you can download my data in csv format here https://github.com/scoyoc/EcoSiteDelineation/blob/master/VegNMDS_scores.csv . Here is my code... veg.nmds.sc = read.csv(VegNMDS_scores.csv, header = T) nmds.fig = ggplot(data = veg.nmds.sc, aes(x = NMDS1, y = NMDS2)) nmds.fig + geom_point(aes(color = VegType, shape = VegType, size = 10)) + scale_colour_manual(name = Vegetation Type, values = c(blue, magenta, gray50, red, cyan3, green4, gold)) + scale_shape_manual(name = Vegetation Type, values = c(15, 16, 17, 18, 15, 16, 17)) + theme_bw() + theme(panel.background = element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), legend.key = element_rect(color = white) ) I have been messing around with theme(..., legend.key.size = unit(1, cm)) but I keep getting the error could not find function unit. I'm not sure why, isn't unit supposed to be part of the legend.key argument? Try this workaround to what sounds like a bug: library(grid) # then repeat the call. -- David Winsemius Alameda, CA, USA [[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.
Re: [R] (no subject)
Hello, The value for 'start' is not correct. According to the help for fitdistr, 'start' should contain the paramaters used by the random function (?rchisq) Hope this helps, Pascal On 20 November 2013 09:29, Jim Silverton jim.silver...@gmail.com wrote: I generated some random data using R and then trying to see if it came from the same distribution but the erros keep piling. Can anyone help? y=rchisq(10,1) mean(y) var(y) library(MASS) fitdistr(y, chi-squared, start = list(4), method = Brent, lower=0.9, upper=3) -- Thanks, Jim. [[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. -- Pascal Oettli Project Scientist JAMSTEC Yokohama, Japan __ 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] if else in R
Dear R users,
I am a R beginner and I am having trouble in using If Else in R. Here is
an example:
## create a data frame
a-c(1,2,3,4)
b-c(2,0,5,0)
ab-data.frame(cbind(a,b))
##calculate c, which is the ratio between a and b
if(ab$b0) {
ab$c-ab$a/ab$b
} else {
ab$c-0
}
here is the error I got:
Warning message:
In if (ab$b 0) { :
the condition has length 1 and only the first element will be used.
Any help is appreciated!
Gary
[[alternative HTML version deleted]]
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] if else in R
Hi,
This would be an issue with if() as well as if/else. ab$b has 4
numbers in it, so ab$b 0 evaluates to TRUE TRUE FALSE TRUE or
whatever. if() can only take a single true or false. Cheers! Nick
On Tue, Nov 19, 2013 at 8:30 PM, Gary Dong pdxgary...@gmail.com wrote:
Dear R users,
I am a R beginner and I am having trouble in using If Else in R. Here is
an example:
## create a data frame
a-c(1,2,3,4)
b-c(2,0,5,0)
ab-data.frame(cbind(a,b))
##calculate c, which is the ratio between a and b
if(ab$b0) {
ab$c-ab$a/ab$b
} else {
ab$c-0
}
here is the error I got:
Warning message:
In if (ab$b 0) { :
the condition has length 1 and only the first element will be used.
Any help is appreciated!
Gary
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] if else in R
Hi,
On Nov 19, 2013, at 9:41 PM, Nick Matzke mat...@berkeley.edu wrote:
Hi,
This would be an issue with if() as well as if/else. ab$b has 4
numbers in it, so ab$b 0 evaluates to TRUE TRUE FALSE TRUE or
whatever. if() can only take a single true or false. Cheers! Nick
As a follow up, you could make a logical index for the condition as Nick
suggests.
a-c(1,2,3,4)
b-c(2,0,5,0)
ab-data.frame(a,b)
ix - ab[,'b'] 0
ix
# [1] TRUE FALSE TRUE FALSE
ab[ix,'c'] - ab[ix,'a']/ab[ix,'b']
ab[!ix,'c'] - 0
ab
# a b c
# 1 1 2 0.5
# 2 2 0 0.0
# 3 3 5 0.6
# 4 4 0 0.0
I'm not a big fan of the ab$b form of subsetting, I find ab[,'b'] more readable
for my fading eyesight. But you could do it your way, too.
ab$c[ix] - ab$a[ix]/ab$b[ix]
Cheers,
Ben
On Tue, Nov 19, 2013 at 8:30 PM, Gary Dong pdxgary...@gmail.com wrote:
Dear R users,
I am a R beginner and I am having trouble in using If Else in R. Here is
an example:
## create a data frame
a-c(1,2,3,4)
b-c(2,0,5,0)
ab-data.frame(cbind(a,b))
##calculate c, which is the ratio between a and b
if(ab$b0) {
ab$c-ab$a/ab$b
} else {
ab$c-0
}
here is the error I got:
Warning message:
In if (ab$b 0) { :
the condition has length 1 and only the first element will be used.
Any help is appreciated!
Gary
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org
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Re: [R] if else in R
Hi,
Try:
within(ab, {c - ifelse(b0, a/b,0)})
A.K.
On Tuesday, November 19, 2013 8:51 PM, Gary Dong pdxgary...@gmail.com wrote:
Dear R users,
I am a R beginner and I am having trouble in using If Else in R. Here is
an example:
## create a data frame
a-c(1,2,3,4)
b-c(2,0,5,0)
ab-data.frame(cbind(a,b))
##calculate c, which is the ratio between a and b
if(ab$b0) {
ab$c-ab$a/ab$b
} else {
ab$c-0
}
here is the error I got:
Warning message:
In if (ab$b 0) { :
the condition has length 1 and only the first element will be used.
Any help is appreciated!
Gary
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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Re: [R] if else in R
Which means you should use the ifelse function...
ab$c - ifelse( ab$b0, ab$a/ab$b, 0 )
---
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Nick Matzke mat...@berkeley.edu wrote:
Hi,
This would be an issue with if() as well as if/else. ab$b has 4
numbers in it, so ab$b 0 evaluates to TRUE TRUE FALSE TRUE or
whatever. if() can only take a single true or false. Cheers! Nick
On Tue, Nov 19, 2013 at 8:30 PM, Gary Dong pdxgary...@gmail.com
wrote:
Dear R users,
I am a R beginner and I am having trouble in using If Else in R.
Here is
an example:
## create a data frame
a-c(1,2,3,4)
b-c(2,0,5,0)
ab-data.frame(cbind(a,b))
##calculate c, which is the ratio between a and b
if(ab$b0) {
ab$c-ab$a/ab$b
} else {
ab$c-0
}
here is the error I got:
Warning message:
In if (ab$b 0) { :
the condition has length 1 and only the first element will be
used.
Any help is appreciated!
Gary
[[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.
__
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and provide commented, minimal, self-contained, reproducible code.
[R] If commands in a while loop
Unfortunately, the while loop in the following code doesn't seem to work. It
would be very nice
if someone might help me, thanks in advance:
z = 0*c(1:1000)
while (sum(z) 751){
for(mu in (900:1100)/1){
for(i in(1:1000)) {
z[i] - V5[i]*exp(5*mu)
if (z[i] = 1276281) {z[i] - 1}
else{z[i] - 0}
}
}
}
--
View this message in context:
http://r.789695.n4.nabble.com/If-commands-in-a-while-loop-tp4680775.html
Sent from the R help mailing list archive at Nabble.com.
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and provide commented, minimal, self-contained, reproducible code.
[R] R- package for Parametric Survival Analysis with Left-censored data
Dear All, I am new to R. Can someone please direct me to an R package using which I can estimate a Parametric Survival Analysis model with Left-censored (delayed entry) data in it. I recently received reviewers comment on my submitted article, where the reviewer suggested that only R has capabilities of estimating above mentioned survival model. However, I am not able to figure which specific package in R, the reviewer was referring to. Any pointer would be greatly appreciated !! cheers, Vinod Mishra __ 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] if else in R
On Nov 19, 2013, at 5:30 PM, Gary Dong wrote:
Dear R users,
I am a R beginner and I am having trouble in using If Else in R. Here is
an example:
## create a data frame
a-c(1,2,3,4)
b-c(2,0,5,0)
ab-data.frame(cbind(a,b))
##calculate c, which is the ratio between a and b
if(ab$b0) {
ab$c-ab$a/ab$b
} else {
ab$c-0
}
here is the error I got:
Consider this alternative:
ab$c - (ab 0 ) * ab$a/ab$b
Although in general, you will probably use `ifelse`.
?ifelse # different than ?if
--
David Winsemius
Alameda, CA, USA
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] If commands in a while loop
On Nov 19, 2013, at 5:22 PM, Hlebtomane wrote:
Unfortunately, the while loop in the following code doesn't seem to work. It
would be very nice
if someone might help me, thanks in advance:
z = 0*c(1:1000)
I think it is more likely that you don't know what z looks like. Try `head(z)`
while (sum(z) 751){
for(mu in (900:1100)/1){
for(i in(1:1000)) {
z[i] - V5[i]*exp(5*mu)
if (z[i] = 1276281) {z[i] - 1}
else{z[i] - 0}
}
}
}
--
David Winsemius
Alameda, CA, USA
__
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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] R- package for Parametric Survival Analysis with Left-censored data
On Nov 19, 2013, at 5:30 PM, Vinod Mishra wrote: Dear All, I am new to R. Can someone please direct me to an R package using which I can estimate a Parametric Survival Analysis model with Left-censored (delayed entry) data in it. I recently received reviewers comment on my submitted article, where the reviewer suggested that only R has capabilities of estimating above mentioned survival model. However, I am not able to figure which specific package in R, the reviewer was referring to. Look at: ?Surv ... after loading the survival package. (I do think you would be advised to seek statistical consultation.) -- 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] Datatable manipulation
Hi, Try: dat1 - read.table(text=a b c x 1 4 7 y 2 5 8 z 3 6 9,header=TRUE) dat2 - dat1 #either library(reshape2) res1 - within(melt(dat1,id.var=ID),cell-as.character(interaction(variable,ID,sep=_)))[,c(4,3)] #or indx - which(dat20,arr.ind=TRUE) res2 - data.frame(cell=paste(colnames(dat2)[indx[,2]],rownames(dat2)[indx[,1]],sep=_),value=dat2[indx],stringsAsFactors=FALSE) identical(res1,res2) #[1] TRUE A.K. On Tuesday, November 19, 2013 11:07 PM, Nitisha jha nitisha...@gmail.com wrote: Hi could you please let me know the solution? Thanks On Wed, Nov 20, 2013 at 4:13 AM, smartpink...@yahoo.com wrote: Hi, If this is a data.frame(), then I have some solution for this problem. Also, you need to post it in R-help if that is the case. Thanks. A.K. quote author='nuts' Sample input dataset where a,b,c are col names. x y z are row names. a b c x 1 4 7 y 2 5 8 z 3 6 9 I want output to be like this after manipulating the dataset. cell value a_x 1 a_y 2 a_z 3 b_x 4 b_y 5 b_z 6 c_x 7 c_y 8 c_z 9 where cell and value are the colnames. How do I achieve this? I am at a loss here. /quote Quoted from: http://r.789695.n4.nabble.com/Datatable-manipulation-tp4680747.html _ Sent from http://r.789695.n4.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] Optim function Hessian matrix
This is the code that was attached. I arrived in the copy sent to my email
address:
#--
L1=function(X){
B1=X[1]
C1=X[2]
B2=X[3]
C2=X[4]
mu=X[5]
S=-(B1*(C1^x)*((C1^v)-1)/log(C1))
+(d2*log(B1*(C1^(x+v
-(B2*(C2^y)*((C2^v)-1)/log(C2))
+(d1*log(B2*(C2^(y+v
-(v*mu)
+(d3*log(mu))
return(sum(S))
}
L2=function(X){
B3=X[1]
C3=X[2]
sum(-(B3*(C3^(x+u1)-C3^(x))) + h1*log(B3*C3^(x+u1)))
}
L3=function(X){
B4=X[1]
C4=X[2]
sum(-(B4*(C4^(y+u2)-C4^(y))) + h2*log(B4*C4^(y+u2)))
}
L=function(X){
B1=X[1]
C1=X[2]
B2=X[3]
C2=X[4]
mu=X[5]
B3=X[6]
C3=X[7]
B4=X[8]
C4=X[9]
L=L1(c(B1,C1,B2,C2,mu))
+L2(c(B3,C3))
+L3(c(B4,C4))
-L
}
Sol=nlminb(c(7.741*10^(-7),1.155,2.422*10^(-5),1.0889,.001307,2.51*10^(-5),1.0712,3.7654*10^(-4),1.0561),L,
lower=c(7.000*10^(-7),1.055,2.122*10^(-5),1.0689,.001107,2.13*10^(-5),1.0088,3.5437*10^(-4),1.0612),
upper=c(1.0299*10^(-6),1.214,2.822*10^(-5),1.0989,.015407,2.77*10^(-5),1.1888,3.8737*10^(-4),1.0812),control=list(iter.max=1500))
par=Sol$par
optim(par,L,method=L-BFGS-B,
lower=c(7.000*10^(-7),1.055,2.122*10^(-5),1.0689,.001107,2.13*10^(-5),1.0088,3.5437*10^(-4),1.0612),
upper=c(1.0299*10^(-6),1.214,2.822*10^(-5),1.0989,.015407,2.77*10^(-5),1.0888,3.8737*10^(-4),1.0712),control=list(maxit=1500,pgtol=10^(-7)),hessian=TRUE)
--
David.
On Nov 19, 2013, at 12:09 PM, sofeira taajobian wrote:
Dear R Users
Hi,
I have very emergency problems in my programming about finding MLE
with optim command. I reproduced it with real data. I guess that my
function object in optim is very sensitive because it has power
function .
Then optim give me lower or initial values for estimates with these
warnings for Hessian matrix computation:
1: In log(B2 * (C2^(y + v))) : NaNs produced
2: In log(B3 * C3^(x + u1)) : NaNs produced
3: In log(B4 * C4^(y + u2)) : NaNs produced
4: In log(B1 * (C1^(x + v))) : NaNs produced
But I have in result a hessian matrix with only first (2*2) block and
other values are zero.
It would not be the problem of code lead to this. plz check the code
and data, I attach them with this email. hope it can reduce some
workload as copying and pasting.
what may lead to this and any possible way to solve it? any suggestion
are appreciated. Plz help me as soon as possible because I don’t have
enough time.
data4.txt__
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] R- package for Parametric Survival Analysis with Left-censored data
On 20 Nov 2013, at 04:15 , David Winsemius dwinsem...@comcast.net wrote: On Nov 19, 2013, at 5:30 PM, Vinod Mishra wrote: Dear All, I am new to R. Can someone please direct me to an R package using which I can estimate a Parametric Survival Analysis model with Left-censored (delayed entry) data in it. I recently received reviewers comment on my submitted article, where the reviewer suggested that only R has capabilities of estimating above mentioned survival model. However, I am not able to figure which specific package in R, the reviewer was referring to. Look at: ?Surv ... after loading the survival package. (I do think you would be advised to seek statistical consultation.) In particular, notice the difference between left censoring (some patients are known to have died at an unknown time before t0) and left truncation (we only know survival times for patients alive at t0). Delayed entry is the latter. -- 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. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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] save table to txt file in a printable form
Hi there, I would like to save tabular (in R just matrices) in a txt file but in a way that they would be somehow readable. That means keeping columns aligned and rows so one can read easily for example the 2,3 element. IS there a way to do that in R? capture.output for example does not produce tables in the way I want to have those. Regards Alex [[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] save table to txt file in a printable form
On Wed, 20 Nov 2013, Alaios ala...@yahoo.com writes: Hi there, I would like to save tabular (in R just matrices) in a txt file but in a way that they would be somehow readable. That means keeping columns aligned and rows so one can read easily for example the 2,3 element. IS there a way to do that in R? capture.output for example does not produce tables in the way I want to have those. Please provide an example that shows what you want to achieve, and why capture.output does not work. A - rnorm(12) dim(A) - c(4,3) colnames(A) - LETTERS[1:3] A # A B C # [1,] 1.3883785 1.7264519 -0.1340838 # [2,] 1.0601385 -0.2378076 0.2078081 # [3,] 0.7278065 -0.1279776 -1.1674676 # [4,] 1.3321629 -1.4082142 0.9145042 capture.output(A) # [1] A B C # [2] [1,] 1.3883785 1.7264519 -0.1340838 # [3] [2,] 1.0601385 -0.2378076 0.2078081 # [4] [3,] 0.7278065 -0.1279776 -1.1674676 # [5] [4,] 1.3321629 -1.4082142 0.9145042 # writeLines(capture.output(A), matrix.txt) ## or similar Regards Alex [[alternative HTML version deleted]] Please send plain-text emails. -- Enrico Schumann Lucerne, Switzerland http://enricoschumann.net __ 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.
