Displaying 20 results from an estimated 100 matches similar to: "How to use PC1 of PCA and dim1 of MCA as a predictor in logistic regression model for data reduction"
2009 Aug 26
1
Within factor & random factor
Hi,
I am quite new to R and trying to analyze the following data. I have 28
controls and 25 patients. I measured X values of 4 different locations
(A,B,C,D) in the brain image of each subject. And X ranges from 0 to 1.
I think "control or patient" is a between subject factor and location is
a within subject factor. So,
controls: 28
patients: 25 (unbalanced data set)
respone measure:
2005 Aug 26
3
parts of data frames: subset vs. [-c()]
Dear all
I have a problem with splitting up a data frame called ReVerb:
?? str(ReVerb)
`data.frame': 92713 obs. of 16 variables:
$ CHILD : Factor w/ 7 levels "ABE","ADA","EVE",..: 1 1 1 1 1 1 1 1 1 1 ...
$ AGE : Factor w/ 484 levels "1;06.00","1;06.16",..: 43 43 43 99 99 99 99 99 99 99 ...
$ AGE_Q : num 2.0 2.0 2.0 2.4 2.4
2012 Jun 15
1
Customizing a Plot in Correspondence Analysis
Hello,
Using the Correspondence Analysis package (ca), I wonder if there is a way
to further customize the plot beyond the options given in plot.ca provided
by the mentioned package.
The correspondence analysis I am doing consists of two datasets sharing
only the rows, so the plot draw the total of columns (from both datasets)
in the graph and the rows as expected. However, as in my case the
2010 Jan 20
1
Change an array into a dataset of four variables, dim1, dim2, dim3 and its elements
Hi,
See my example below.
a<-array(1:12,c(2,3,2))
> a
, , 1
[,1] [,2] [,3]
[1,] 1 3 5
[2,] 2 4 6
, , 2
[,1] [,2] [,3]
[1,] 7 9 11
[2,] 8 10 12
I want to get a result something like
dim1 dim2 dim3 elements
1 1 1
1 2 1
1 3 2
2 1 2
I tried the data.frame and expand.grid functions,
2011 May 15
5
Question on approximations of full logistic regression model
Hi,
I am trying to construct a logistic regression model from my data (104
patients and 25 events). I build a full model consisting of five
predictors with the use of penalization by rms package (lrm, pentrace
etc) because of events per variable issue. Then, I tried to approximate
the full model by step-down technique predicting L from all of the
componet variables using ordinary least squares
2010 Jan 03
2
Scores in Dimensions in Correspondence Analysis
Hi R,
I was experimenting with the CA package for correspondence analysis.
data(author)
ca(author)
plot(ca(author))
How can I get the values used by the plot for the two axis for biplot?
In other words, how will I be able to obtain the scores in the
dimensions (which are obtained by PCA) of the graphs? Thanks.
Thanks and Regards,
Shubha
This e-mail may contain
2011 May 22
1
How to calculate confidence interval of C statistic by rcorr.cens
Hi,
I'm trying to calculate 95% confidence interval of C statistic of
logistic regression model using rcorr.cens in rms package. I wrote a
brief function for this purpose as the followings;
CstatisticCI <- function(x) # x is object of rcorr.cens.
{
se <- x["S.D."]/sqrt(x["n"])
Low95 <- x["C Index"] - 1.96*se
Upper95 <- x["C
2012 Dec 10
3
equivalent of group command of the egen function in Stata
Dear R listers,
I am trying to create a new variable that uniquely identifies groups of
observations in a dataset. So far I couldn't figure out how to do this in
R. In Stata I would simply type:
egen newvar = group(dim1, dim2, dim3)
Please, find below a quick example to show what I am dealing with:
I have a dataset with 4 variables:
var <- runif(50) ## a variable that I want to group
2010 Feb 10
2
system.time provides inaccurate sys.child (PR#14210)
Full_Name: Manuel L?pez-Ib??ez
Version: R version 2.6.2 (2008-02-08)
OS: linux-gnu
Submission from: (NULL) (164.15.10.156)
This is only relevant for CPU intensive child processes. Otherwise, the problem
is not obvious.
Therefore, we need a CPU intensive program like this one:
/************************************/
/*** Compile with: gcc -o timer-test -O0 timer-test.c -lm */
#include
2011 Aug 17
1
multinomRob - error message
Hi,
I would like to use the multinomRob function to test election results.
However, depending on which independent variables I include and how
many categories I have in the dependent variable, the model cannot be
estimated.
My data look like this (there are 68 observations):
> head(database)
RESTE09 GAUCHE09 PDC09 PLR09 UDC09 MCG09 RESTE05 GAUCHE05 PDC05
D1 1455
2001 Dec 31
2
Extracting/setting elements from/in a matrix/array
Dear all,
I had to extracts/set elements from/in a matrix. Let say I have two
vectors dim1 and dim2 of indices in the respective two dimensions of a
matrix: I want to extract all the corresponding elements. I the case of a
nxn matrix, dim1 <- 1:n and dim2 <- 1:n would extract the diagonal.
I know one way would be to use the functions 'row' and 'col', but the
matrixes I
2010 Nov 08
1
unknown dimensions for loglm
Dear R-help community,
I am working with multidimensional contingency tables and I am having
trouble getting loglm to run on all dimensions without typing out each
dimension.
I have generated random data and provided output for the results I want
below:
d1.c1 <- rnorm(20, .10, .02)
d1.c2 <- rnorm(20, .10, .02)
d2.c1 <- rnorm(20, .09, .02)
d2.c2 <- rnorm(20, .09, .02)
d3.c1 <-
2012 Dec 07
1
points3d and ordirgl
Hello all, I have been using the function ordirgl to plot 3D dynamic
ordinations. The ordirgl function works just fine. IN fact, I was even
able to write a function that allows me to identify points in the 3D plot:
identify.rgl<-function(env_var,ord,dim1,dim2,dim3)
{
tmp<-select3d(button="left")
tmp.keep<-tmp(ord[,dim1],ord[,dim2],ord[,dim3])
2012 Feb 25
5
which is the fastest way to make data.frame out of a three-dimensional array?
foo <- rnorm(30*34*12)
dim(foo) <- c(30, 34, 12)
I want to make a data.frame out of this three-dimensional array. Each dimension will be a variabel (column) in the data.frame.
I know how this can be done in a very slow way using for loops, like this:
x <- rep(seq(from = 1, to = 30), 34)
y <- as.vector(sapply(1:34, function(x) {rep(x, 30)}))
month <- as.vector(sapply(1:12,
2007 Dec 09
1
List comprehensions for R
Below is code that introduces a list comprehension syntax into R,
allowing expressions like:
> .[ sin(x) ~ x <- (0:11)/11 ]
[1] 0.00000000 0.09078392 0.18081808 0.26935891 0.35567516 0.43905397
[7] 0.51880673 0.59427479 0.66483486 0.72990422 0.78894546 0.84147098
> .[ .[x*y ~ x <- 0:3] ~ y <- 0:4]
[,1] [,2] [,3] [,4] [,5]
[1,] 0 0 0 0 0
[2,] 0 1 2
2006 Dec 17
2
question
Dear R users,
I'am using marray and Limma packages to analyze genepix output.
1) how can I filter bad spots from my data (data contains 3 types of bad
spots).
my experiment contains 12 samples and the bad spot are not associated to the
same probes
2) how can I remove control probes from my data ?
I'm sorry, i'm new with R and I can't find answer in packages doc.
best regards,
2010 Dec 03
3
recode letters to numbers
Hello,
I have a dataframe assigning various scores on around 20 variables to a list of
countries. The scores are rated on a scale of (D, C, B, A) and there are also
some not rated ones (NR) and others are left blank (NA). I now wanted to
transfer the scores into numeric values (such as NR=0, D=25, C=50, B=27, A=100),
while also leaving the NA in the dataframe. Can I transform the whole
2011 May 10
3
metaMDS and envfit: Help reading output
Hello R experts,
I've used metaMDS to run NMDS on some fish abundance data, and am also working on correlating environmental data to the NMDS coordinates. I'm fairly new to metaMDS and NMDS in general, so I have what are probably some very basic questions. My fish abundance data consists of 66 sites for which up to 20 species of fish were identified and counted. I ran metaMDS on this data
2007 Dec 19
3
array addition
Hi
suppose I have two arrays x1,x2 of dimensions a1,b1,c1 and
a2,b2,c2 respectively.
I want x = x1 "+" x2 with dimensions c(max(a1,a2), max(b1,b2),max
(c1,c2))
with
x[a,b,c] = x1[a1,b1,c1] + x2[a2,b2,c2] if a <=min(a1,a2) , b<=min
(b1,b2), c<=min(c1,c2)
and the other bits either x1 or x2 or zero according to whether the
coordinates
are "in range" for
2012 Apr 05
0
Multi part problem...array manipulation and sampling
Ok, I have a new, multipart problem that I need help figuring out.
Part 1. I have a three dimensional array (species, sites, repeat counts
within sites). Sampling effort per site varies so the array should be
ragged.
Maximum number of visits at any site = 22
Number of species = 161
Number of sites = 56
I generated the array first by;