similar to: random effect question and glm

I have a dataset like this: p aa index x y z sdx sdy sdz delta as ms cur sc 1 821p MET 1 -5.09688 32.8830 -5.857620 1.478200 1.73998 0.825778 13.7883 126.91 92.37 -0.1320180 111.0990 2 821p THR 2 -4.07357 28.6881 -4.838430 0.597674 1.37860 1.165780 13.7207 64.09 50.72 -0.0977129 98.5319 3 821p GLU 3 -5.86733 30.4759

consider p as random effect with 5 levels, what is difference between these two models? > p5.random.p <- lmer(Y ~p+(1|p),data=p5,family=binomial,control=list(usePQL=FALSE,msV=1)) > p5.random.p1 <- lmer(Y ~1+(1|p),data=p5,family=binomial,control=list(usePQL=FALSE,msV=1)) thanks, Aimin Yan

if I want to put fig1plot to the left, figYPplot to the right figYAaplot on the bottom. How to modify the following cod to do these? \begin{figure}[H] \centering \begin{minipage}[t]{0.5\textwidth} \centering <<label=fig1plot,fig=TRUE,echo=FALSE>>= <<fig1plot>> @ %\caption{Caption 1} \end{minipage} \begin{minipage}[t]{0.5\textwidth} \centering

Sorry, I can't reproduce the example below even on the same machine. However, the following example produces the same error as NULL values in prior examples: > setClass("FOOCLASS", +????????? representation("list") + ) > ma = new("FOOCLASS", list(M=matrix(rnorm(300), 30,10))) > isS4(ma) [1] TRUE > data.frame(a=1:3) == ma Error in

I run the following code, all other is ok, but plot(m.svm,p5.new,As~Cur) is not ok Anyone know why? install.packages("e1071") library(e1071) library(MASS) p5 <- read.csv("http://www.public.iastate.edu/~aiminy/data/p_5_2.csv") p5.new<-subset(p5,select=-Ms) p5.new$Y<-factor(p5.new$Y) levels(p5.new$Y) <- list(Out=c(1), In=c(0)) attach(p5.new)

I am trying to fit a logistic regression model for this data set. Firstly, I want to plot P(Y=1) vs As and P(Y=1) vs Aa. Does any body know how to do these in R. Thanks, Aimin > p5 <- read.csv("http://www.public.iastate.edu/~aiminy/data/p_5_2.csv") > str(p5) 'data.frame': 1030 obs. of 6 variables: $ P : Factor w/ 5 levels "821p","8ABP",..: 1

Dear R users, I'm pretty new on using lmer package. My response is binary and I have fixed treatment effect (2 treatments) and random center effect (7 centers). I want to test the effect of treatment by fitting 2 models: Model 1: center effect (random) only Model 2: trt (fixed) + center (random) + trt*center interaction. Then, I want to compare these 2 models with Likelihood Ratio Test.

Dear all, I have a question on how to set up the starting model in POLYCLASS and make sure the terms in the starting model retained in the final POLYCLASS model. In the function POLYMARS, this can be done using the STARTMODEL option. See below for example, I started with model y= b0 + b1*X1 + b2*X2 + b3*X4 + b4*X5 + b5*X2*X5 + e > m00 <- matrix(c( 1, NA, 0, NA, 1, 2,

What does thoes this means??? warn:module:load_builtin_dll failed to load .so lib for builtin L"C:\\windows\\system32\\msvfw32.dll": /home/xekhz/.wine/dosdevices/c:/windows/system32/msv fw32.dll: invalid ELF header

I have a question in R. In directory H:/Delta_angle I have 19 files like this: ALA.delta ASN.delta ASP.delta CYS.delta GLN.delta GLU.delta HIS.delta ILE.delta LEU.delta LYS.delta MET.delta PHE.delta PRO.delta SER.delta THR.delta TRP.delta TYR.delta VAL.delta I want to read these files to 19 data sets in R. All these data sets have "P","AA",index","delta"

I have a data(ABC) like this: x y A 3 4 A 1 3 B 2 6 B 4 8 C 5 4 C 6 7 I want to split this data into A: x y A 3 4 A 1 3 B B 2 6 B 4 8 C C 5 4 C 6 7 anyone knows how to do that? thanks, Aimin Yan

I try to type this in my R-winEdt. but I got these. Do you know? Aimin > install.packages('http://rh-mirror.linux.iastate.edu/CRAN/bin/windows/contrib/2.4/plotrix_2.1-6.zip') Warning in download.packages(pkgs, destdir = tmpd, available = available, : no package 'http://rh-mirror.linux.iastate.edu/CRAN/bin/windows/contrib/2.4/plotrix_2.1-6.zip' at the

I try Sweave and get Sweave-test-1.tex but hot to run LaTeX on 'Sweave-test-1.tex'? I am using WinEdt. thanks, Aimin > Sweave(testfile) Writing to file Sweave-test-1.tex Processing code chunks ... 1 : print term verbatim 2 : term hide 3 : echo print term verbatim 4 : term verbatim 5 : echo term verbatim 6 : echo term verbatim eps pdf 7 : echo term verbatim eps pdf

I have been timing a particular model fit using lmer on several different computers and came up with a peculiar result - the model fit is considerably slower on a dual-core Athlon 64 using Goto's multithreaded BLAS than on a single-core processor. Here is the timing on a single-core Athlon 64 3000+ running under today's R-devel with version 0.995-5 of the Matrix package. >

I have a full data set like this: aa bas aas bms ams bcu acu omega y 1 ALA 0 127.71 0 69.99 0 -0.2498560 79.91470 outward 2 PRO 0 68.55 0 55.44 0 -0.0949008 76.60380 outward 3 ALA 0 52.72 0 47.82 0 -0.0396550 52.19970 outward 4 PHE 0 22.62 0 31.21 0 0.1270330 169.52500 inward 5 SER 0 71.32 0 52.84 0 -0.1312380 7.47528 outward 6

Hello, I am new to R, How to delete a matrix column. Thanks,

I am trying to create a NetCDF file with bathymetry (a matrix) and then to add a grid type (an integer) as variables. This is the relevant part of the code: library(ncdf) wfile="my_file.nc" msv=-10 grdtp=2 # Dimensions d1=dim.def.ncdf("lon","degrees",as.double(lon)) d2=dim.def.ncdf("lat","degrees",as.double(lat)) # Variables

I use knncat to make a predictive model and get misclass rate > knncat.m<-knncat(training.new,k=c(10,20),classcol=5) > knncat.m Training set misclass rate: 36.88% then I try to calculate prediction accuracy by the following: > pr.knncat.train <- predict (knncat.m,training.new,training.new,train.classcol=5,newdata.classcol=5) > tb.knncat.train <-table (pr.knncat.train,

I am trying to use scatterplot function in CAR like the following: scatterplot(X~Y) I want to label X points and Y ponits using the different color. Any idea for this? Aimin

How to use "contour" function? I type "contour(th1,th2,SumofSquares,levels=c(seq(1000,4000,200)))" But I didn't see contour in the plot, I guess it is because my data is so big that contour is out of range. Does anybody know how to fix this problem? here th1 is a 1x101 array(158741.8-298529.6) th2 is another 1X101 array(-0.0058352269-0.2093140935) SumofSquares is a