Re: [R] Error running predict

You forgot to put the comma after "-intrain" in the following assignment: testing <- spam[-intrain, ] "make" is one of the data columns of spam dataset. > colnames(spam) [1] "make" -- GG [[alternative HTML version deleted]] __ R-help@r-pro

[R] Trycatch in R

Hi All, Please help me in the below code: tryCatch({ x <- capture.output(XML::xmlParse(y)) }, warning = function(w) { x <- capture.output(w) }, error = function(e) { x <-capture.output(e) }, finally = { }) I am using Tibco Enterprise Runtime for R to get value of the parsed XML in vector f

[R] problem with the use of parallel foreach

Hi, I am having a problem with the use of the foreach package. It is strange that my code works when i use the %do% function but not with %dopar%. Let me explain. I am new to parallel and foreach packages. I have data in the form of very large files, and they are in the form of data tables. I have

Re: [R] Checkpoints in Caret

I found some information about parallel processing in R that might be of your interest: http://topepo.github.io/caret/parallel.html http://www.vikparuchuri.com/blog/parallel-r-model-prediction-building/ https://www.r-project.org/nosvn/conferences/useR-2013/Tutorials/kuhn/user_caret_2up.pdf htt

Re: [R] clogit and weights

How should the weights be treated? If they are multiple observation weights (a weight of "3" is shorthand for 3 subjects) that leads to a different likelihood than sampling weights ("3" means to give this one subject more influence). The clogit command can't read your mind and so has chosen no

[R] Fwd:

Dear all, I am hoping to use the mt.maxT package, so I'm trying to understand how the maxT algorithm works in the multtest package. I have an example of data: SNP1 p value= 0.02 SNP1 permutation p values = 0.03, 0.03, 0.03, 0.04, 0.04. SNP2 p value =0.03 SNP2 permutation p values = 0.4,0.5,0

Re: [R] Checkpoints in Caret

Further, trying to be more specific about checkpoint with R, I may suggest the following readings. Look for "checkpoint models" in: http://h2o-release.s3.amazonaws.com/h2o/rel-tibshirani/8/docs-website/h2o-docs/booklets/DeepLearning_Vignette.pdf Look for "checkpointing" i

[R] Regular R freezes

Dear List, some days ago my R started to regularily freezes, especially during these operations: mso(,permutations=999), package vegan anova.cca(), package vegan forward.sel(), package packfor I am running R on a 64-bit Windows 7 installation, 4 cores, 8 GB RAM. I just today updated R to 3.2.

Re: [R] geomorph: adding confidence ellipses

Look at scatter3d() in the car package. It has an option to add a confidence ellipsoid to an interactive 3d plot. - David L Carlson Department of Anthropology Texas A&M University College Station, TX 77840-4352 -Original Message- From: R-help [mailto:

[R] How to conduct a PERMANOVA using a dissimilarity matrix

Dear R-List members, I have to compare how similar two types of forest (old growth=O) and (young forest=Y) in terms of moth communities are. I sampled moths at 4 O and 4 Y sites. I need to analyse the data using a PERMANOVA approach. But I am having a really hard time to do this in R. I found o

[R] mice error: data

Hi All, I used mice to impute NA values in a data frame like this: envdata = complete(mice(envdata,m=1,maxit=1)). It seems that the mice function can only works well with 1st and 2nd envdata. When enter the 3rd data, it triggers an error: data. iter imp variable 1 1 data data10

Re: [R] [FORGED] qqPlot vs qqcomp

Hi Rolf Thank you for your reply and time.Please let me provide more information about my problem. My data is like this (I obtained itwith the kind support of WCC), it shows the number of counted cars for eachinterval like this: timenum,count 1,1800 2,1400 4,1000 .. 1,86868 It means I ha

[R] colour input in ribbon plots (geom ribbon)

Hallow everybody I want to know if there is any command for input colour in the ribbon plot (geom ribbon) of ggplot2. Unless that, the mean line and the standard error can not be distinguished. Please help me if anyone have any idea. -- Pushan Chakraborty CSIR - SRF Center for Pollination Studie

[R] Trying to avoid the loop while merging two data frames

Hello! I have a solution for my task that is based on a loop. However, it's too slow for my real-life problem that is much larger in scope. However, I cannot use merge. Any advice on how to do it faster? Thanks a lot for any hint on how to speed it up! # I have 'mydata' data frame: set.seed(123) m

[R] vjust unresponsive (ggplot2)

Hi all, I cannot for the life of me get my axis titles to adjust vertically in a ggplot. I've seen several posts about this and have tried everything: keeping vjust within 0 and 1, adjusting the margins, etc. hjust is behaving just as it should but vjust just mocks me in silence. No error message

Re: [R] vjust unresponsive (ggplot2)

That looks to me like it might be buggy. At least I would have expected vjust to do _something_. In terms of the practical issue, you can adjust the distance between the title and the axis with margin, e.g. ggplot(data=x,aes(x=V2,y=V2))+theme(axis.title.y=element_text(margin = margin(0, 5, 0, 0))

Re: [R] vjust unresponsive (ggplot2)

Are you sure it is not working for you? Your example code did not work for me at all until I removed the plot .margin parameter (unit wasn't recognized). Once I did that hjust and vjust worked as expected. However, values between .1 and .9 for vjust don't really move the axis title very much

Re: [R] [FORGED] qqPlot vs qqcomp

> On 22 Dec 2015, at 07:30 , mohsen hs via R-help wrote: > > The above command gives me a differentplot. I am not sure what part I am > doing wrong. I appreciate your time forconsidering my request and your > feedback is highly appreciated. Please find the plots attached. The right one > is f

Re: [R] vjust unresponsive (ggplot2)

Hi Dan, Chances are that you haven't yet upgraded to ggplot2 version 2.0. unit (as well as arrow and alpha) are now re-exported from ggplot2. Using the latest release I also see that vjust doesn't seem to do anything. Best, Ista On Tue, Dec 22, 2015 at 1:37 PM, Nordlund, Dan (DSHS/RDA) wrote:

Re: [R] vjust unresponsive (ggplot2)

Ista, You are correct, I was not at the latest release of ggplot2. I updated to the latest version and am now seeing the same result as you and the OP. So it does look like an issue with the latest version of ggplot2. Dan Daniel Nordlund, PhD Research and Data Analysis Division Services & En

Re: [R] Trying to avoid the loop while merging two data frames

You seem to be saving 'myid' and then overwriting it with the last statement: result[[i]] <- result[[i]][c(5, 1:4)] Why doesn't 'merge' work for you? I tried it on your data, and seem to get back the same number of rows; may not be in the same order, but the content looks the same, and it does

Re: [R] Trying to avoid the loop while merging two data frames

Library dplyr to use arrange() for ordering, in the case. library(dplyr) result.order <- arrange(result, d, version, a, b, c) dim(result.order) [1] 30005 head(result.order) d versiona b c 1 -2.986456069 1 0.2236414154 0.004258038663 1.089

Re: [R] colour input in ribbon plots (geom ribbon)

It is not clear what you are doing. Please provide some code and data if possible. Otherwise adding something like colour = "red" in the aes() should do something. John Kane Kingston ON Canada > -Original Message- > From: pushan.zool...@gmail.com > Sent: Tue, 22 Dec 2015 14:26:03 +0

Re: [R] colour input in ribbon plots (geom ribbon)

Um, NOT in the aesthetic... as a direct argument to geom_ribbon. But yes, examples are critical for communication about R questions, and posting on plain text format is critical for getting the example through the list server undamaged. -- Sent from my phone. Please excuse my brevity. On Dec

Re: [R] Trying to avoid the loop while merging two data frames

I know I am overwriting. merge doesn't solve it because each version in mydata is given to more than one id. Hence, I thought I can't merge by version. I am not sure how to answer the question about "the problem". I described the current state and the desired state. If possible, I'd like to get fro

Re: [R] Trying to avoid the loop while merging two data frames

You are right, guys, merge is working. Somehow I was under the erroneous impression that because the second data frame (myinfo) contains no column 'myid' merge will not work. Below is the cleaner code and comparison: # ### Example with smaller data frames ##

Re: [R] Trying to avoid the loop while merging two data frames

Actually, the correct merge line should be: my.merge <- merge(myinfo, mydata, by="version", all.x = T, all.y = F) On Tue, Dec 22, 2015 at 3:50 PM, Dimitri Liakhovitski wrote: > You are right, guys, merge is working. Somehow I was under the > erroneous impression that because the second data frame

[R] R studio installation and running

Dear group I used to run Rstudio on windows. currently  I want to run Rstudio on Ubuntu server, start its GUI . kindly, is there a guide on how to do this step by step, I already searched and installed R .. but confused ..should I install Rstudio for desktop or server ? how to start it?, I am the

Re: [R] Trying to avoid the loop while merging two data frames

Taking it back - no need for all.x = T, all.y = F On Tue, Dec 22, 2015 at 3:56 PM, Dimitri Liakhovitski wrote: > Actually, the correct merge line should be: > my.merge <- merge(myinfo, mydata, by="version", all.x = T, all.y = F) > > On Tue, Dec 22, 2015 at 3:50 PM, Dimitri Liakhovitski > wrote:

Re: [R] R studio installation and running

This is not the support area for RStudio. FWIW if you will be sitting in front of this computer then you probably want the desktop version. -- Sent from my phone. Please excuse my brevity. On December 22, 2015 1:10:58 PM PST, Ragia Ibrahim wrote: >Dear group >I used to run Rstudio on windows.

[R] Expanding matrix into dummies

# I have a matrix x: k <- 20 N <- 5 set.seed(123) x <- matrix(c(sample(1:k, N, replace = F), sample(1:k, N, replace = F), sample(1:k, N, replace = F), sample(1:k, N, replace = F), sample(1:k, N, replace = F), sample(1:k, N, repl

Re: [R] Expanding matrix into dummies

> On Dec 22, 2015, at 4:42 PM, Dimitri Liakhovitski > wrote: > > # I have a matrix x: > > k <- 20 > N <- 5 > set.seed(123) > x <- matrix(c(sample(1:k, N, replace = F), > sample(1:k, N, replace = F), > sample(1:k, N, replace = F), > sample(1:k, N, replace

Re: [R] Expanding matrix into dummies

... Perhaps worth noting is that the row indices can be created directly without row(): result[cbind(rep.int(seq_len(6),5), as.vector(x))] <- 1 but the downside is that you have to know that a matrix is a vector "stored" in column major order. I find this arcane detail quite handy, though. Cheer

Re: [R] colour input in ribbon plots (geom ribbon)

Please keep the discussion on the mailing list by using reply-to-all. That function makes no line representing "mean". If you want a line in the middle then you need to add it yourself. The color attribute for geom_ribbon affects the outline of that ribbon area. -- Sent from my phone. Please e

[R] Colour input in geom line

Thanks for the help in my previous quarry, I want to know is it possible to change the colour in geom line? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/li

Re: [R] Colour input in geom line

Yes. This forum works best when you provide example code. For questions like this you really should use a web search engine. Google comes up with many results, including [1]. [1] http://www.ucl.ac.uk/~zctpep9/Archived%20webpages/Cookbook%20for%20R%20%C2%BB%20Colors%20(ggplot2).htm -- Sent f

[R] Caret - Recursive Feature Elimination Error

Hi, I am trying to use caret, for feature selection on glmnet. I get a strange error like below - "arguments imply differing number of rows: 2, 3". x <- data.matrix(train[,features]) y <- train$quoteconversion_flag > str(x) num [1:260753, 1:297] NA NA NA NA NA NA NA NA NA NA ... - attr(

[R] colour input in geom line ggplote2

Dear list I want to put a line command in the following and also want to attribute colour in the geom line command line. It would be a ribbon plot showing the mean line. Is there any help? p <- ggplot(mtcars, aes(x=carb, y=mpg)) + geom_point() p + stat_summary(geom="ribbon", fun.ymin="min", fun

Re: [R] Regular R freezes

On Tue, 22 Dec 2015 16:13:07 +0100 Tim Richter-Heitmann wrote: > Dear List, > > some days ago my R started to regularily freezes, especially during > these operations: > > mso(,permutations=999), package vegan > anova.cca(), package vegan > forward.sel(), package packfor > > I am running R on