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Hi
is there an easy way of re-installing all packages in my user library?
I am not referring to checkBuilt=TRUE, but re-install all packages,
irrespective of the version.
Reasoning: I installed Simons patched R for Mac to use the new C
compiler, and
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On 01/09/14, 10:35 , Berwin A Turlach wrote:
G'day Rainer,
Hi Berwin,
On Thu, 09 Jan 2014 10:10:43 +0100 Rainer M Krug rai...@krugs.de
wrote:
is there an easy way of re-installing all packages in my user
library? I am not referring to
Thanks for your suggestions! Here are links to simulated data and the Epicure
syntax + reference fit:
http://dwoll.de/err/dat.txt
http://dwoll.de/err/epicure.log
The model tested in Epicure is
lambda = exp(alpha0 + alpha1*agePyr)*(1 + beta0*dosePyr*exp(beta1*agePyr))
with counts in variable
Hi,
Iam trying to run the DanteR package, but keep getting some problems.
I installed the Gtk 2.24 version on my mac and was able than to install the
RGtk2 package and load it.
After installing the DantR package I tried to load it but I keep getting
strange error massages.
library(DanteR);
** Apologies for any cross posting **
Earthzine http://www.earthzine.org/, an IEEE-sponsored online scientific
journal, is soliciting articles of 800-3,000 words for its second quarter
theme of 2014 on *Geospatial Semantic Array Programming *(GeoSemAP). We
seek contributions from all regions of
On 09/01/2014 10:41, Assa Yeroslaviz wrote:
Hi,
I am trying to run the DanteR package, but keep getting some problems.
Isn't that the expected behavior?
--
Patrick Burns
pbu...@pburns.seanet.com
twitter: @burnsstat @portfolioprobe
http://www.portfolioprobe.com/blog
What's that suppose to mean?
Do you always expect problem when you do something?
On Thu, Jan 9, 2014 at 12:11 PM, Patrick Burns pbu...@pburns.seanet.comwrote:
On 09/01/2014 10:41, Assa Yeroslaviz wrote:
Hi,
I am trying to run the DanteR package, but keep getting some problems.
Isn't
Patrick,
No error in your code, just two different ways of deriving a range of
colors ... heat.colors() and color.scale(). I modified the code to just
use color.scale(). You can tell it what two colors you want it to use for
the extremes, and it will work out the shades in between.
Jean
#
On 09/01/2014 11:18, Assa Yeroslaviz wrote:
What's that suppose to mean?
Do you always expect problem when you do something?
Actually, yes I do always expect problems, but more
pertinently it is an oblique reference to 'The R Inferno'.
http://www.burns-stat.com/documents/books/the-r-inferno/
Dear all,
I'm using the package pscl for adjusting a Zero-Inflated Negative Binomial
Regression to my data set. I would like to know if it is possible to compute
the standardised Pearson residuals from the output of this package.
Thanks in advanced.
Best regards,
Helena.
Hi there !!
I have a matrix like
mm
[,1] [,2] [,3]
[1,] 1 11 21
[2,] 2 12 22
[3,] 3 13 23
I have a list of position index like
pos
$row1
[1] 1 3
$row2
[1] 3 2
$row3
[1] 1 3 2
I have a list of values like
gty
$v1
9 3
$v2
4 8
$v3
7 4 1
On 09/01/2014 9:25 AM, Mohammad Tanvir Ahamed wrote:
Hi there !!
I have a matrix like
mm
[,1] [,2] [,3]
[1,]1 11 21
[2,]2 12 22
[3,]3 13 23
I have a list of position index like
pos
$row1
[1] 1 3
$row2
[1] 3 2
$row3
[1] 1 3 2
I have a list of values
Hi everybody,
I wrote a function where several variables
are created, and the used in a generalized
mixed model, from the glmmADMB package.
here is part of the function:
deleted lines where ni, spx and spy are created
print(length(spy))
Given a 3+ way table, I'd like a simple, elegant way to flatten the
table to a two-way
table, with some variables joined interactively to form the rows and
others forming
the columns. For example, starting with
str(UCBAdmissions)
table [1:2, 1:2, 1:6] 512 313 89 19 353 207 17 8 120 205 ...
Oh, thank you. Was this a mistaken reply from you? Because your link directs
to yahoo mail.
Al
--
View this message in context:
http://r.789695.n4.nabble.com/Different-colours-for-LatticeExtra-graphs-tp4683250p4683304.html
Sent from the R help mailing list archive at Nabble.com.
Hi,
Try:
res - do.call(rbind,lapply(seq_len(nrow(mm)),function(i) {x1 - mm[i,];
x1[pos[[i]]] - gty[[i]]; x1}))
A.K.
On Thursday, January 9, 2014 9:28 AM, Mohammad Tanvir Ahamed
mashra...@yahoo.com wrote:
Hi there !!
I have a matrix like
mm
[,1] [,2] [,3]
[1,] 1 11 21
[2,]
Hi,
You may also try:
vec1 - (seq(nrow(mm))-1)*ncol(mm)
pos2 - unlist(mapply(+,pos,vec1))
mm1 - t(mm)
mm1[pos2] - unlist(gty)
identical(res,t(mm1))
#[1] TRUE
A.K.
On Thursday, January 9, 2014 9:40 AM, arun smartpink...@yahoo.com wrote:
Hi,
Try:
res -
Great, it works perfectly! Thanks so much for the awesome help!
(Happy) patrick
On Jan 9, 2014, at 7:07, Adams, Jean jvad...@usgs.gov wrote:
Patrick,
No error in your code, just two different ways of deriving a range of colors
... heat.colors() and color.scale(). I modified the code to
Do you just want to change how the rows and columns of ftable's output are
labelled? If so, the following may do what you want: it produces a matrix
with dimnames based on the row.vars and col.vars attributes of ftable's
output.
f - function(ftable) {
makeDimNamesEl - function(x) {
Hi Michael,
It's pretty easy with reshape:
library(reshape2)
ucbm - melt(UCBAdmissions)
acast(ucbm, Admit + Gender ~ Dept)
acast(ucbm, Admit ~ Dept + Gender)
acast(ucbm, Admit + Dept + Gender ~ .)
# You can also do aggregations
acast(ucbm, Admit ~ Dept, fun = sum)
Hadley
On Thu, Jan 9, 2014
The phrase,
need to go row by row plugging this formula in to only take data from
that individual row
suggests a spreadsheet-like concept. But R does not work the way a
spreadsheet does.
Given the example data and function that Frede provided (thank you!),
a simple, and probably the most basic,
On 12/31/2013 05:00 AM, r-help-requ...@r-project.org wrote:
Thanks for your kind response Duncan. To be more specific, I'm using the
function mvrnorm from MASS. The issue is that MASS depends on survival and
I have a function in my package named tt() which conflicts with a function
in survival
You have made a good first start by keeping your data in a database
(it would be even slower if you read it in from a text file each
time).
The first suggestion is to not read in all the data, just bring in
what you need. For early steps, exploring the data, getting a feel
for what you want to
?uniroot
?optim
?optimize
and look at the Optimization and Mathematical Programming task view on CRAN.
On Wed, Jan 8, 2014 at 8:55 PM, Aurélien Philippot
aurelien.philip...@gmail.com wrote:
Dear R experts,
I want to use numerical methods to solve a complex problem. Here is a very
simple
Hi,
I am using following R version:
version
_
platform i386-w64-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 3
minor 0.1
year 2013
month 05
day16
svn rev62743
language
Hi Vivek,
res1 - read.table(positve-res1.txt,header=TRUE)
dim(res1)
#[1] 5292 4
#You could simplify the first loop as:
mean_Res2 - as.vector(rowMeans(res1))
identical(mean_Res1,mean_Res2)
#[1] TRUE
##Regarding the second loop:
pval_r2 - as.vector(apply(res1,1,function(x)
Hi, I'm having a problem with my labels.
I am reading in a data file:
df - read.csv(file = 'batch1extract_100k_sample.csv')
However, it's producing two sets of labels:
labels(df)
[[1]]
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14
15 16 17 18 19 20 21
[22] 22 23 24 25 26 27 28 29 30 31 32 33
Hello,
According to the help page for ?labels, for a data.frame it's simply the
dimnames, meaning, the row names (your numbers) and the column names.
Note that read.csv returns a data.frame, not a matrix, and data frames
allways have row names, typically numbers.
I wouldn't worry about it.
Hi Jeff,
If you read the help for labels(), it says that for a dataframe it
returns the dimnames: the first component is the row names, which by
default are numbers, and the second component of the list is the
column names.
Since you appear to want just the latter, you could use
colnames(df)
The answer most likely is in the message:
'\\homer.win.ad.jhu.edu\users$\rvaradh1\Documents'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
That path starting with a \\ is a *UNC path* (a Windows thing), which
I
Thanks for this, Bill
Your solution does just what I want. In fact, it qualifies as the
missing as.matrix() method
for n-way tables arranged with ftable(), or vcd::structable(), which
does provide an
as.matrix() method, but omits the names and dimnames.
Here it is, renamed and
using _ as
On Thu, Jan 9, 2014 at 11:04 AM, Henrik Bengtsson h...@biostat.ucsf.edu wrote:
The answer most likely is in the message:
'\\homer.win.ad.jhu.edu\users$\rvaradh1\Documents'
CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows
On 10/01/14 07:00, Greg Snow wrote:
?uniroot
?optim
?optimize
The OP will have to be careful and clever. Specifying the *intervals*
over which uniroot() and optimise() search is going to be problematic,
it seems to me.
and look at the Optimization and Mathematical Programming task
On Jan 9, 2014, at 9:47 AM, Eric Elguero wrote:
Hi everybody,
I wrote a function where several variables
are created, and the used in a generalized
mixed model, from the glmmADMB package.
here is part of the function:
deleted lines where ni, spx and spy are created
print(length(spy))
Hi:
I am trying to analyze an yeast gene expression data
http://arep.med.harvard.edu/biclustering/yeast.matrix
I need to convert the real-valued data matrix to a binary (0,1)
matrix. Is there any package available? How can it be done?
Thanks:
John
Hi,
Try:
library(emdist)
set.seed(435)
results- array(sample(1:400,120,replace=TRUE),dim=c(10,3,4))
res - sapply(seq(dim(results)[1]),function(i) {x1 - results[i,,]; x2 -
results; sapply(seq(dim(x2)[1]),function(i) emd2d(x1,x2[i,,]))})
dim(res)
#[1] 10 10
A.K.
On Thursday, January 9, 2014
Hi,
No problem.
You can use ?lower.tri() or ?upper.tri()
res[lower.tri(res)]
res[lower.tri(res,diag=TRUE)]
#Other way would be to use:
?combn
indx - combn(dim(results)[1],m=2)
res2 - sapply(seq_len(ncol(indx)),function(i) {x1 - indx[,i];
emd2d(results[x1[1],,],results[x1[2],,]) })
Why? You lose information in doing so, do you not?
I also think you might do better posting to the Bioconductor list, as
they are specifically concerned with such matters.
Cheers,
Bert
Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374
Data is not information. Information is not
Hi Silvano
I am not sure exactly what you want as I am not sure of the structure and
format going into xtable
but the structure after you have formed the table is apparently the same
structure.
This is what I suggested before (modified)
for(j in 1:25){
yourtable - ...
xx - xtable(yourtable)
Hi,
I wouldn't call it a bug, but it's a documented limitation, if you know
how to read it. As documented, the expression is evaluated with the
caller's environment as the parent environment. But here the caller is
some code in lapply, not your function f. x is not found there.
Thanks!
Hi Alex,
Try:
set.seed(345)
results- array(sample(-5:5,120,replace=TRUE),dim=c(10,3,4))
indx - !!apply(results,1,sum)
library(plyr)
results2 - laply(lapply(seq(dim(results)[1]),function(i)
results[i,,])[indx],identity)
attr(results2,dimnames) - NULL
dim(results2)
#[1] 9 3 4
A.K.
I have a 3D
Just use apply() and indexing instead!
results[,,apply(results,3,sum)TRUE]
## will do it.
However, note that numerical error may make a hash of this. So safer
would be something like:
eps - 1e-15 ## i.e. something small
results[,,abs(apply(results,3,sum))eps]
Cheers,
Bert
Bert Gunter
I figured it out:
dim(results[apply(results,1,sum)TRUE,,])
#[1] 9 3 4
A.K.
On , arun smartpink...@yahoo.com wrote:
dim(results[,,apply(results,3,sum)TRUE])
#[1] 10 3 4
dim(results[,,abs(apply(results,3,sum))eps])
#[1] 10 3 4
dim(results2)
#[1] 9 3 4
A.K.
On Friday, January 10, 2014
Hi R users,
I need to apply a function on a list of vectors. This is simple when I use
functions that returns only one numerical value such as 'mean' or
'variance'. Things get complex when I use functions returning a list of
value, such as 'acf'.
In the following example I first create a list of
Dear all,
I have a binary matrix
0 0 0 0 0
1 1 1 0 0
1 1 1 0 0
0 0 0 0 0
0 0 0 1 1
0 0 0 1 1
I want to find the location of all the square and rectangular 1 blocks, like
First block in row=2, col=1 to row=3, col=3.
Second block in row=5, col=4, to row=6, col=5.
How can I find such blocks of
Hi:
I am trying to implement a bandwidth reduction algorithm for a (M x
N) binary matrix using the GA package in R.
I am using the folloging code to get the optimal permutation for rows
and columns (optimization in two dimensions).
M - matrix(c(0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 1,
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