hello
can you explain to me about package shapes in R software?
especially about order procGPA?
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Hi,
I have a question for gplots function heatmap.2.
In this function, is there any way to control/know the heights of two
dendrograms, such as how many pixels or how many percentage of the whole
image the dendrogram have?
I need to know the coordinates of northwest corner of real heatmap in the
Hi,
The bracket after lty=1 should be replaced with comma (,).
x<-1:15
y<--8:6
plot(x, y, type ="o", xlab="Panelist", ylab="T
value",lwd=1.5,lty=1,xlim=range(1:14),ylim=range(-8:8),las=1)
A.K.
- Original Message -
From: stefaniewind
To: r-help@r-project.org
Cc:
Sent: Friday, July
HI,
I have XML library installed in R2.15 and is working fine. I used it only a
few times, it was working. I am using Ubuntu 12.04.
A.K.
- Original Message -
From: Santosh
To: r-help
Cc:
Sent: Friday, July 20, 2012 11:03 PM
Subject: [R] library XML in R version 2.15.1
Hello Rxpe
Hello,
I guess this should be posted in the bioconductor mailing list to get better
response. I never used Gostats before, but I think BINGO and DAVID are very
good in giving these information. I would choose BINGO plugin in cytoscape
installed. But, you may have specific reasons to use Gosta
Hi,
You can try this:
x<-1:15
y<--8:6
plot(x, y, type ="o", xlab="Panelist", ylab="T value",lwd=1.5,axes=FALSE)
axis(1,at=c(0,2,4,6,8,10,12,14,16))
axis(2,at=c(-8,-6,-4,-2,0,2,4,6,8))
A.K.
From: Stefanie Wind
To: arun
Sent: Friday, July 20, 2012 11:42 PM
Hello,
When computing Sxx, Syy and you are mistaking the square of the sum for
the sum of squares. The same goes for the crossed term Sxy, it's the sum
of the products, not the product of the sums Sx and Sy.
Hope this helps,
Rui Barradas
Em 20-07-2012 23:04, cesare orsini escreveu:
Dear fr
Hello,
You can try either one of these methods::
#Simple line plot
dat1<-read.table(text="
Gene1 10 14 12 23 11 11 33 1
Gene2 4 2 1 1 3 4 1 2
Gene3 2 5 7 5 6 89 7 3
Gene4 1 9 8 3 90 8 8 5
",sep="",header=FALSE,stringsAsFactors=FALSE)
dat2<-as.data.frame(t(dat1[,-1]))
colnames(dat2)<-paste("Gene",
Hi,
So, you got the same error message for R 2.14.1 and R 2.15? Or is it only for R
2.15?
It is always good to install the current version.
Try this:
install.packages("XML",dependencies=TRUE)
#Warning message suggests dependencies.
A.K.
- Original Message -
From: Santosh
To: R he
On Saturday, July 21, 2012, Mehrab Nodehi wrote:
> hello
> can you explain to me about package shapes in R software?
> especially about order procGPA?
Not unless you read the posting guide and formulate a more specific
question.
Sarah
--
Sarah Goslee
http://www.stringpage.com
http://www.sar
On 07/18/2012 09:11 PM, Karan Anand wrote:
hi,
i am new to using R, so if u can help me in merging my csv file having
different sheets .if u can help me with the commands for it.
Hi karan,
I didn't see an answer for your question. If you are reading in several
CSV files with the same num
Hi
I want to add a row to a "data.table" in each round of a for loop.
"rbind" seems to be a inefficient way to implement this.
How would you do this? The "slow" solution:
library(data.table)
Rprof("test.out")
dt <- data.table()
for (i in (1:1)) {
# algorithm that generates a list with dif
On 07/20/2012 12:33 AM, Stuart Leask wrote:
You're right - easily tested by just re-sizing the graphics box - sort of
counter-intuitive until I remember the clue is in the name - this generates a
CIRCLE, come what may...
Stuart
From: Sarah Goslee [mailto:sarah.gos...@gmail.com]
Sent: 19 July
next for loop question.
I need a loop that removes a row from a matrix if it is worse in positions
1,2,3,4 than another row in the matrix. right now my matrix is 503028x26.
Rule to define worse position1 is smaller, position2 is smaller, position3
is higher, and position4 is smaller
Example:
r
Hi list,
I am wondering if there is a way to use EM algorithm to handle missing data and
get a completed data set in R?
I usually do it in SPSS because EM in SPSS kind of "fill in" the estimated
value for the missing data, and then the completed dataset can be saved and
used for further analy
Hi list,
I am wondering if there is a way to use EM algorithm to handle missing data and
get a completed data set in R?
I usually do it in SPSS because EM in SPSS kind of "fill in" the estimated
value for the missing data, and then the completed dataset can be saved and
used for further ana
I'm sorry I misunderstood your original request. You're right, use
subscripts for panel-specific argument values.
Peter Ehlers
On 2012-07-20 19:35, "José M. Blanco Moreno" wrote:
Sorry about that, when I asked before I meant that I had tried your
proposed syntax. That has a problem, and it is t
Search yourself!
1. Google on "Impute missing data in R"
2. See the ?RSiteSearch function
3. Go to Rseek.org and enter in keywords.
4. Download and install the sos package and use its search functionality.
R has multiple packages and functions with multiple approaches to
missing data imputation.
please don't send email to this email address:
mehdi.p...@gmail.com
lots of thanks
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PLEASE do read the posting guide http://w
Hello,
Maybe it would have been better to start a new thread, if the question
is different. To show that it's a continuation, the subject line could
be extended with "part 2" or something like that.
This solution runs in 3.6 hours.
to.keep <- function(x){
keep <- function(i, env){
Martin Ivanov abv.bg> writes:
>
> Dear R users,
>
> I have the following problem. I plot a SpatialPixelsDataFrame object with
spplot and I need to add a contourplot
> of another spatial variable.
...
You may find that posting to R-sig-geo will help. It would also help to include
a self-cont
You need to preallocate. [See the R Inferno]
n <- 1
dt <- as.data.table(matrix(0, nrow = n, ncol = 5))
for(i in seq_len(n)){
dt[i, ] <- ### Whatever
}
Note that this *might* be somewhat trickier with data.tables and their
fancy indexing. It might be easier to simply assign into the matrix
Hello Ya.
I am no expert, so I am eager to read suggestions from other people in the
mailing list. But just a few pointers I am (somewhat) sure of -
You can try using this package:
http://cran.r-project.org/web/packages/imputation/imputation.pdf
And use something like kNNImpute. KNN solving is
On 07/20/2012 10:35 PM, Andrew Miles wrote:
Hello!
I am trying to reproduce (for a publication) analyses that I ran
several months ago using lavaan, I'm not sure which version, probably
0.4-12. A sample model is given below:
pathmod='mh30days.log.w2 ~ mh30days.log + joingroup + leavegroup +
alw
Any chance I could ask for an idiots guide for function to.keep(x). I
understand how to use it but not what some of the lines are doing. Comments
would be extremely helpful.
--
View this message in context:
http://r.789695.n4.nabble.com/Speeding-up-a-loop-tp4637201p4637316.html
Sent from the R
Ok, sorry, I should have included some comments.
The function is divided in three parts, 1. intro, 2. decision, 3. keep rows.
Part 3 is the function keep(), internal to to.keep(). Let's start with 1.
1. Setup some variables first.
1.a) The variables 'a'.
If the input object 'x' is a matrix this
It is not clear what you actually want. Do you want to save imputed data
sets for further analysis? That is pretty simple. What do you mean by
combining the data sets? Are you confusing single imputation with multiple
imputation? In addition to the packages you mentioned, there are many
others. See
Hello,
In the classical function "contour" labels are drawn so that each contour line
is broken at the place of the label, so that the label does not overlap the
line. In the trellis contoourplot the labels are placed beside or over the
line, controlled by the label.style parameter, but I could
The EM algorithm does not impute missing data, rather it estimates
parameters when you have missing data (those parameters can then be
used to impute the missing values, but that is separate from the EM
algorithm).
If you create a dataset that has missing values imputed (a single
time) and then an
Dear friends,
I have two questions regarding the use of lattice. First some code:
## begin code
z <- cbind(rep(c("BIC", "ICL", "s_v", "Q_v", "sig-q",
"s_lsk", "s_lML", "s_mlsk", "s_mlML", "s_la8",
"s_haar"), each = 250), rep(c(5, 10, 20, 30, 50), each = 50))
z <- rbind(cbi
Thanks Bert.
So far I have not found any way that output a single data set which combines
all the imputed data sets (say, 50 imputed data sets). Probably I missed
something, but could you share some information about it, maybe a link?
Thank you very much for helping.
ya
From: Bert Gunter
D
Dear list,
I would like to run an ANCOVA using car::Anova with repeated measures factors,
but I can't figure out how to do it. My (between-subjects) covariate always
interacts with my within-subject factors.
As far as I understand ANCOVA, covariates usually do not interact with the
effects of
Hi,
No problem.
I was gettting -8 and 6 for the code I sent to you. I am using R 2.15.
This code gets -8 and 8 for the y axis:
x<-1:17
> y<- -8:8
> plot(x, y, type ="o", xlab="Panelist", ylab="T value",lwd=1.5,axes=FALSE)
> axis(1,at=c(0,2,4,6,8,10,12,14,16,18))
> axis(2,at=c(-8,-6,-4,-2,0
Hello,
Probably, you didn't know about this option. You could deactivate your
membership from Rhelp by clicking on the link below i.e
(https://stat.ethz.ch/mailman/listinfo/r-help).
A.K.
- Original Message -
From: mehdi azizi
To: R-help@r-project.org
Cc:
Sent: Saturday, July 21, 2
All,
1. Is there a command that tells you what libraries are loaded?
2. How do you remove a library that has been loaded?
3. If you have loaded a library that masks previously loaded objects, how
can you tell which object is being run? In Matlab, I would run "which f" to
determine the location o
They are called packages, not libraries.
On Jul 21, 2012, at 5:19 PM, darnold wrote:
> All,
>
> 1. Is there a command that tells you what libraries are loaded?
Loaded is a fluid idea** in a namespace world, but search() will let you know
what's on the search path (accessible to you)
>
> 2
Answer to you first question, try this at the start of bwplot to
specify ordering:
bwplot(Error~factor(Method, levels = unique(Method))
On Sat, Jul 21, 2012 at 2:42 PM, Ranjan Maitra
wrote:
> Dear friends,
>
> I have two questions regarding the use of lattice. First some code:
>
>
> ## begin cod
Using x/yaxp also works:
plot(x, y, type ="o", xlab="Panelist", ylab="T value", lwd=1.5,
xaxp=c(0, 18, 9), yaxp=c(-8, 8, 8), las=1)
--
David L Carlson
Associate Professor of Anthropology
Texas A&M University
College Station, TX 77843-4352
> -
All,
I believe I am running the latest version of rshape2 (1.2.1). But this code:
library(reshape2)
tmp <- melt(smiths,
id.vars=1:2,
measure.vars=c("age","weight","height"),
variable.name="myvars",
value.name="myvals"
)
names(tmp)
Produces this output:
> names(tmp)
[1] "su
Dear R community,
I'm running "a mlogit" function with a very large data set. Since the data
size is so large, I got the Error:
Error: cannot allocate vector of size 5.4 Mb
In addition: Warning messages:
1: In mapply("*", X, P, SIMPLIFY = FALSE) :
Reached total allocation of 16340Mb: see help(m
Hi David,
Your example works as expected for me (see sessionInfo below). What
version of R are you using? What other packages are loaded?
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8
Run this before the bwplot() command:
z$Method <- factor(z$Method, levels = c("BIC", "ICL", "s_v", "Q_v",
"sig-q", "s_lsk", "s_lML", "s_mlsk", "s_mlML", "s_la8", "s_haar"))
I don't have an answer for the 2nd question. Seems like it must be
possible.
---
Ista,
You are correct.
> search()
[1] ".GlobalEnv""package:reshape" "package:plyr"
[4] "package:reshape2" "tools:rstudio" "package:stats"
[7] "package:graphics" "package:grDevices" "package:utils"
[10] "package:datasets" "package:methods" "Autoloads"
[13
Take a look at useOuterStrips() in package latticeExtra.
---
David
> -Original Message-
> From: David L Carlson [mailto:dcarl...@tamu.edu]
> Sent: Saturday, July 21, 2012 6:51 PM
> To: 'jim holtman'; 'Ranjan Maitra'
> Cc: 'r-help@r-project.org'
> Subject: RE: [R] two questions re: the
Hi,
New to R. Need a bit of help. Thanks
I am trying to import data from Excel file. The package I am trying to use
requires data in Matrix format.
Excel -> R Matrix with the constraint that the very first column in Excel
file should became the names for rows of the matrix.
Example. Data has 10
There are many possibilities, but they all begin with reading the posting guide
and following the recommendations therein so we don't have to guess what your
actual configuration is. However, since your first task is to read, you might
consider reading the FAQs on memory use and Windows specifi
Hi,
Input Format: excel file (XLS)
Column 1: Gene ID (alphanumeric)
Column 2 - 10 : (numeric data).
inData = read.xls ( )
geneLabel = inData [ , 1] - column 1 stored in geneLabel
tempData = inData [ , 2: 10]
expValues = data.matrix (tempData) - convert frame into Matrix format
exp
Hi,
It works for me too. When I had reshape and reshape2 both loaded, I had the
same problem.
library(reshape2)
tmp <- melt(smiths,
id.vars=1:2,
measure.vars=c("age","weight","height"),
variable.name="myvars",
value.name="myvals"
)
names(tmp)
[1] "subject" "time"
Hello,
Try this:
You can use the read.table with sep="," if it is comma separated to read the
file.
test1<-read.table(text="
0.141 0.242 0.342
0.224 0.342 0.334
0.652 0.682 0.182
",sep="",header=FALSE)
#Read data
test1
# V1 V2 V3
#1 0.141 0.242 0.342
#2 0.224 0.342 0.334
#3 0.65
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