similar to: Problems with augPlot and for loops

Hi, I am currently writing code to input a few thousand files, run them through the Random Forests package, and then output corresponding results. When I use the code below: zz<-textConnection("ex.lm.out", "w") sink(zz)

I am trying to run a partialPlot with Random Forest (as I have done many times before). First I run my forest... Cell is a 6 level factor that is the dependent variable - all other variables are predictors, most of these are factors as well. predCell<-randomForest(x=tempdata[-match("Cell",names(tempdata))],y=tempdata$Cell,importance=T) Then I try my partial plot to look at the

I have a dataFrame variable: L1 L2 L3 ... v1 v2 ... 1 2 3 4 ... I want to process subsets of it as defined by combinations of L1-L2-L3. I do it successfully using nested loops: for (i in valuesOfL1 { for (j in valuesOfL2) { for (k in valuesOfL3) { tempData <- subset(dataFrame, (L1 == i & L2 == j & L3 == k, select=c(v1,v2) )) if

# Here is the solution: require(fBasics) # Be sure that R is running in time zone GMT. # Set your Windows environment variable to "GMT" # Your PC Windows clock can still run in any other time zone! # My clock is now running in Zurich in Europe. Date = c("2003-10-09", "2003-10-10", "2003-10-13", "2003-10-14") Open = c(1.27, 1.25, 1.27,

Dear All, wonder if you have some thoughts on running the with() function (and perhaps including the pool() function to get the results?) in glmulti? In other words, how to run glmulti with a data set that is produced by mice()? publicly available code: data <- airquality data[4:10,3] <- rep(NA,7) data[1:5,4] <- NA data <- data[-c(5,6)] library(mice) library(glmulti) the following

Hi : I have old Splus code that I am trying to turn into R ( I am using windows Xp and R 2.20 ) and I am getting a warning from one of my statements because the behavior of R is different from Splus. below, tempdata is a matrix of numbers and I have the following command which basically runs through the columns and returns the minimum index of the column where an NA occurs.

hi everyone : i'm not sure if my previous mail about this got sent. i was typing and erroneosuyl hit a button and lost what i was typing. anyway, i have the code below ( it works ) in which i run through the rows of a dataframe, taking out the first two fields which are characters strings ( with some extra spacing so i yuse gsub) and appending these character strings to a list so that i can

Hi, Input Format: excel file (XLS) Column 1: Gene ID (alphanumeric) Column 2 - 10 : (numeric data). inData = read.xls ( <fileName>) geneLabel = inData [ , 1] - column 1 stored in geneLabel tempData = inData [ , 2: 10] expValues = data.matrix (tempData) - convert frame into Matrix format expValues has the matrix format needed for analysis. I need to bind gene labels as . I

Hi. I?m trying to use the speex library in c#, everything seems to works right, when I call the speex_encode_int function it always return 0, any help would be appreciated. Here?s the sequence of calls: //Initialization _Mode = speex_lib_get_mode(0); _State = speex_encoder_init(_Mode); fixed (int* __FrameSize = &_FrameSize, __Complexity =

I have many "sample" datasets (e.g. sample 5, sample 6, etc), each identified by a number as a suffix. These datasets are saved as individual R objects on my hard drive. (e.g."Wind.5.r" . "Wind.6.r","Solar.5.r","Solar.6.r") For example purposes, I have written code that creates similar data files using the "airquality" dataset. (see

Hello list, Thank you very much for replying to my earlier questions. I have a few new questions about R plots: Example: tempdata: RDate Price 2009-12-09 12:00 100 2009-12-09 15:00 99 2009-12-09 18:00 102 .... 2009-12-10 8:00 120 2009-12-10 10:00 110 2009-12-10 16:00 105 My code: (RDate already in R date-time class) plot (price~RDate, data=tempdata, "l") axis.POSIXct(1,

Dear Gabor, Thanks for your reply. however: > tail(DJd) ^DJI.Close 2010-04-01 10927.07 2010-04-05 10973.55 2010-04-06 10969.99 2010-04-07 10897.52 2010-04-08 10927.07 *2010-04-09 10997.35* > tail(ag) 2009-11-30 10344.84 2009-12-31 10428.05 2010-01-31 10067.33 2010-02-28 10325.26 2010-03-31 10856.63 *2010-04-30 10997.35 * It seems the script "makes up"

Hello All, Recently developed the code below for graphing patterns of chemotherapy administration. As someone just starting to use R in their work, I managed to figure out some parts of the code but needed help with others. setwd("N:/Regimen Coding/0906/Plots Test") getwd() TestData <- structure(list(profile_key = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3), line = c(1, 1,

All, I have a question RE plotting the prediction lines of a random effects model via augPred. I'll illustrate via the Pixel dataset within the nlme package: library(nlme) attach(Pixel) fm1Pixel = lme(pixel ~ day + I(day^2), data = Pixel, random = list(Dog = ~ 1)) plot(augPred(fm1Pixel)) ### 10 fitted lines since there are 10 dogs fm2Pixel = update(fm1Pixel, . ~ . + Side)

Following problem: Say you have a bunch of parameters and want to produce results for all combinations of those: height<-c("high","low") width<-c("slim","wide") then what i used to do was something like this: l<-list() for(h in height){ l[[h]]<-list() for(w in width){ l[[h]][[w]] <- doSomething() } } Now those parameters aren't

All, I'm trying to create an augPred plot in the nlme library, similar to the plot on p.43 of Pinheiro & Bates (Mixed Effects Models in S and S-Plus) for their Pixel data. My data structure is the same as the example but I still get the error msg below. > comp.adj.UKV <- groupedData(adj.UKV ~ Time | Patient_no/Lisinopril, data = comp.adj.UKV.frm, order.groups = F) >

Dear all as I did not get any response on my post about abline and plot(augPred)) I try again. I hope I do not break some posting guide rules. I would try to contact package maintainer directly but there is stated to be R-core people, so I feel R-help list shall be OK. I need to draw straight lines through augPred plotted panels (vertical or horizontal) at specified point. I know I shall

Dear R-users, I am a newbie to this site and a relative new-comer to S/R, so please tread lightly, for you tread... There have been several posting relating to problems with augPred() from the nlme library. Here is a "fix" for one of these problems which may lie at the root of others. In my case the problem with augPred() lay in gsummary(), which augPred() uses, causing it to fail.

I read the posts about augPred with lme, but does anyone know if there is a correlate for augPred for lmer? Specifically, I want to be able to use it to plot projections for all groups in an lmer class object using plot(augPred(lmer.object)). Thanks, Kyle *************************************** J. Kyle Roberts, Ph.D. Baylor College of Medicine Center for Educational Outreach One Baylor Plaza,

Hello, I want to use lme to fit two (or more) models, and then compare the fits on each individual. I know how to write my own code to do this (for each individual, plot the raw data, followed by lines() to plot each fitted curve) but I would like to use plot(augPred(... as it produces a nice trellis plot. I thought I could do this with par(new=T) but it does not seem to work.