Dear R users:
Recently, I tried to write a program to calculate cross-validated predicted
value.
My sources are as follows. However, the R reported an error.
Could you please check the sources? Thanks.
set.seed(100)
x<-rnorm(100)
y<-sample(rep(0:1,50),replace=T)
dat<-data.frame(x,y)
library(rms)
HELLO, anybody... could you help me to check the below coding for volcano.
what is the mistake?
what the plot could not display?
#volcano_plot.r
#
#Author:Amsha Nahid, Jairus Bowne, Gerard Murray
#Purpose:Produces a volcano plot
#
#Input:Data matrix as specified
Hello Erik and Ravi,
I am curious if Erick or Ravi have a solution to Erick's question.
I have a similar problem. I wish to use auglag to solve a nonlinear
optimization problem. The cost function, grad function, and constraints are
all function of some parameters that are dependent upon the sys
No, unfortunately not. It works perfectly fine with other kinds of files.
Everything, but these ones...The program that generates them does not have
any helpful specifications regarding this format ..*.trees
On Mon, Jun 20, 2011 at 5:55 AM, Bhoom [via R] <
ml-node+3610421-1897267921-239...@n4.nabb
Hello All,
I have searched but haven't been able to find an answer to this question.
I'm writing a function that needs to be able evaluate the right-hand side of
a general non-linear formula for different parameter values, similar to what
nls() does. I looked through the nls() code but it isn't cl
Hi Jim,
Just want to make sure that I understand correctly.What do you mean by SNP =
Single Nucleotide Polymorphism?
Bhoom
On Sun, Jun 19, 2011 at 5:57 PM, Jim Silverton wrote:
> Hello, Does anyone has software to simulate SNP data? Specifically I would
> like any package that produces 2 x 3 S
Does read.nexus work for you?
Bhoom
On Sun, Jun 19, 2011 at 5:04 PM, Andra Tolbus wrote:
> Dear all,
>
> I am trying to create a consensus skyline plot using the "ape"
> package(newbie).
> I have a nexus file that looks like the one from above containing many
> trees. (my_file.trees)
Hi everyone,
I have certain values retrieved from mysql database.How can i do
certain analysis like histogram, correlational analysis tc using this data,I
tried it. But when i tried to plot a histogram it actually showed error the
data is not numeric evenif it was stored as integer data type
If I understand you correctly, you are trying to find the cumulative maximum
from the end within each level of the factor. If this is what you are trying
to do, then here is one way you might like to do it. First, define the
function:
> cumMax <- function(x) Reduce(max, x, right = TRUE, accum
try this:
> test <- data.frame(A=c("a", "a", "a", "b", "b", "c", "c", "c", "c"),
> B=c(3,2,1,3,2,2,3,1,1))
> test
A B
1 a 3
2 a 2
3 a 1
4 b 3
5 b 2
6 c 2
7 c 3
8 c 1
9 c 1
> # determine which group is not decreasing
> tapply(test$B, test$A, function(x) any(diff(x) > 0))
a b c
FA
I figured it out:
x<-sub("^.*:([[:digit:]]+)..([[:digit:]]+).*", "\\1 \\2", CTSS$V4)
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___
So if I am given some data that look like this:
> head(CTSS)
V1 V2 V3V4 V5 V6 V7
1 chr1 564563 564598 chr1:564588..564589,+ 1336
2 chr1 564620 564649 chr1:564644..564645,+ 94
3 chr1 565369 565404 chr1:565371..565372,+ 217
4 chr1 565463 5655
If I understand what you want (which I may very well not) you could use
something like this:
If this is an example of your type of data:
564589,+
substr(x, 1, 6)
as.numeric(x)
Please try to post something more thorough if you would like a better
answer.
Sam
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ht
Hello, Does anyone has software to simulate SNP data? Specifically I would
like any package that produces 2 x 3 SNP data.
--
Thanks,
Jim.
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R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/l
On 19/06/2011 7:29 PM, p_conno...@slingshot.co.nz wrote:
Quoting 王海生:
dear everyone
system:windows XP
R2.13.0
I download the windows binary from website and successfully install
it ,because I use a proxy server ,when I follow the instrction as
follows:
I set a system property R_HOME=C:\Progra
Quoting 王海生 :
dear everyone
system:windows XP
R2.13.0
I download the windows binary from website and successfully install
it ,because I use a proxy server ,when I follow the instrction as
follows:
I set a system property R_HOME=C:\Program Files\R\R-2.13.0
" R_HOME\bin\i386\Rgui.exe http_pr
This works, but I'm still hunting for a more elegant final step:
> test <- data.frame(A=c("a", "a", "a", "b", "b", "c", "c", "c", "c"),
> B=c(3,2,1,3,2,2,3,1,1))
> test2 <- lapply(split(test$B, test$A), sort, dec=TRUE)
> test3 <- data.frame(A=rep(names(test2), times=lapply(test2, length)),
> B=un
Dear R users,
I run into the following problem and hope someone can help me out. Thank you
in advance for your time.
I have a function defined recursively as follows:
recFun = function(k,x){ #i is less than 10. x can be any real number. I need
the value of recFun(k=1,2,3,4, x=0.12).
if(k==1)
i
Dear all,
I am trying to create a consensus skyline plot using the "ape"
package(newbie).
I have a nexus file that looks like the one from above containing many
trees. (my_file.trees)
#NEXUS
begin trees; [Treefile generated by sim_coal.exe (Laurent Excoffier)]
tree true_tree_1 = [
I have a data.frame as follows:
a 3
a 2
a 1
b 3
b 2
c 2
c 3
c 1
c 1
Each factor (a, b, c) should be monotonically decreasing, notice that factor
'c' is not.
I could use some help to figure out how to form a logical structure (mostly
just syntax), that will check each 'next value' for ea
Hello,
I found a problem to transfer my package on the site
ftp://cran.rproject.org/incoming/ .
Access is not allowed. Please,could you give me the settings for connecting
to your server to transfer my package using the FileZilla.
Best Regards
Fadia
[[alternative HTML version delete
Hi all,
I have a column that has the following format:
chr1:564588..564589,+ and I want to extract only the coordinates; I have
tried writing a regular expression but I couldn't figure out how I should
write it. Does anyone know?
Thank you,
Best,
Nanami
[[alternative HTML version deleted
dear everyone
system:windows XP
R2.13.0
I download the windows binary from website and successfully install it ,because
I use a proxy server ,when I follow the instrction as follows:
I set a system property R_HOME=C:\Program Files\R\R-2.13.0
" R_HOME\bin\i386\Rgui.exe http_proxy=http://211.83.1
> Date: Sun, 19 Jun 2011 19:06:20 +1200
> From: agw1...@gmail.com
> To: r-help@r-project.org
> Subject: [R] Multivariate HPD credible volume -- is it computable in R?
>
> Hi all,
>
> I'm new to the list and am hoping to get some advice. I have a set of
> multivariate data and would like to
Hello,
i'm trying to draw a dendrogram to show the clustering hierarchy. i'm
working on 2 classes but each class contains more than 3000 instances.
i'm using the hclust function to do that! but i can't read anything from
this figure.
i would like to color each class with its own color so at leas
Hi:
It's just an extra step:
y <- list(list(c(1,5),c(2,3,4)), list(c(1, 3, 4), c(5, 7)))
lapply(seq_len(length(y)), function(i) lapply(y[[i]], min))
[[1]]
[[1]][[1]]
[1] 1
[[1]][[2]]
[1] 2
[[2]]
[[2]][[1]]
[1] 1
[[2]][[2]]
[1] 5
unlist(lapply(seq_len(length(y)), function(i) lapply(y[[i]], min
I know about the current.row, current.column, and panel.number functions that
are useful within panel functions written for lattice. Are there easy ways
to obtain the names of the conditioning variables (those appearing after |)
and their values for the current panel?
Thanks
Frank
-
Frank Har
but in my case, the list is a two-variable list, list[[j]][[i]]
when i use
lapply(list, min)
it appears
"""Error in FUN(X[[1L]], ...) : invalid 'type' (list) of argument"""
thanks
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If your alternative hypothesis is unequal variances (2-sided), both F
< 1 and F > 1 are of interest, and rejection of the equal variance
null can occur on either side.
The usual ANOVA F test is 1-sided, with an alternative the numerator
variance exceeds the denominator one, so this is perhaps
Thanks Jeff and Duncan
Assign worked for me. I did not check the other methods suggested by you. I
am repreducing my code below:
##
filenames = list.files(path = ".", pattern = '.txt$', all.files = FALSE,
full.names = TRUE, ignore.case = FALSE) #all input files
numFiles = length
On 11-06-19 10:26 AM, Mary Kindall wrote:
I have a list of txt files that I want to convert into .rdata R data
object.
filenames
1. "./file1.txt"
2. "./file2.txt"
3. "./file3.txt"
4. "./file4.txt"
5. "./file5.txt"
6. "./file6.txt"
7. "./file7.txt"
8. "./file8.txt"
9. "./file9.txt"
10. "./file10.
I have a list of txt files that I want to convert into .rdata R data
object.
filenames
1. "./file1.txt"
2. "./file2.txt"
3. "./file3.txt"
4. "./file4.txt"
5. "./file5.txt"
6. "./file6.txt"
7. "./file7.txt"
8. "./file8.txt"
9. "./file9.txt"
10. "./file10.txt"
I saved these files as
for ( i in 1:1
Hi, that depends on whether you want to get the minimum within each list
element or the global minimum across all list elements. The first is
achieved by using lapply(). The second can be achieved by unlisting the list
(which assumes that all list elements are numeric) and looking for its
minimum.
true, it did work using unlist() funciton, it can be found the minimum
value.
and for further step, if i want identify the minimum value with the list,
which means the minimum value i have found is belonged to which
list[[j]][[i]].
i used the codes like this
##which(list1==min(list1))##
but
Woodcock, Helena liverpool.ac.uk> writes:
> Apologies if this is a silly question but I am a student
> and this is my first time using R so I am still trying to
> educate myself on commands, models e.t.c
>
> I have a mixed model with four dichotomous fixed factors and
> subject as a random fac
hi, r users
I'm a new r user. i want to apply kmeans into every level of the tree which
i built.
the codes for clusterring only one level of the tree.
#
d <- dist(data1, method = "euclidean")
h1 <- hclust(d, method="ward")
c1 <- cutree(h1, 100) # 100 groups which i want to cluster
cd
Funny, I was going to quote your paper with Dichmont in Fisheries Research
regarding this, then I forgot to do it, but you yourself came out and posted
the explanation.
This forum is great!
Rubén
-Original Message-
From: r-help-boun...@r-project.org on behalf of bill.venab...@csiro.au
The two commands you give below are certain to lead to very different results,
because they are fitting very different models.
The first is a gaussian model for the response with a log link, and constant
variance.
The second is a gaussian model for a log-transformed response and identity
link.
On 11-06-19 3:19 AM, Jim Lemon wrote:
On 06/18/2011 08:47 PM, Trying To learn again wrote:
Hi all,
I´m trying to "recuperate" old files I wrotte and I´m trying to execute on R
version 2.13.0 (2011-04-13), the thing is I execute my old file and nothing
happens...I suposse I need to install some
The problem is not that you are new to R. This is a conceptual issue.
Let y be the response variable and let {x_i} be a set of predictors. Your first
model (identity response and log-link) is saying that
y=f(x_1)f(x_2)...f(x_n) + e, e~Normal(0,sigma)
i.e. this is an additive observation-error
On 11-06-18 3:47 PM, Fernando (Est - UnB) wrote:
Hi,
I'm new here.
This question concerns the package rgl.
Is it possible to change the colour of a set of points drawn with
plot3d /without/ removing them from the scene?
No, you can't modify objects other than by removing and recreating them.
hi, R users
here i have one problem, if i wanna get the minimum value in the normal
data, i can do this,
## which(data1==min(data1)).
but if i want get the minimum value of a list which has two variables
##list1[[j]][[i]]##,
i tried the codes like this, but it did not work.
## which(list1
Thanks for the tips. I'll give them a try!
On Sat, Jun 18, 2011 at 12:07 PM, Dennis Murphy wrote:
> Much better..nice!
>
> Dennis
>
> On Sat, Jun 18, 2011 at 1:53 AM, Dimitris Rizopoulos
> wrote:
> > maybe another way is by reconstructing the formula using paste(), e.g.,
> >
> > data <- data.fr
Hi Muhuri,
What do you suspect the underlying distribution is of your statistic?
Contact
Details:---
Contact me: tal.gal...@gmail.com | 972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www
I'm new R-programming user, I need to use gam function.
y<-gam(a~s(b),family=gaussian(link=log),data)
y<-gam(loga~s(b), family =gaussian (link=identity),data)
why these two command results are different?
I guess these two command results are same, but actally these two command
results are differen
Hi all,
I'm new to the list and am hoping to get some advice. I have a set of
multivariate data and would like to find the densest part of the data cloud
containing 95% of the data, like a 95% HPD credible volume. Is there any R
code available to compute that?
Thank you very much! Your help and p
On 06/18/2011 08:47 PM, Trying To learn again wrote:
Hi all,
I´m trying to "recuperate" old files I wrotte and I´m trying to execute on R
version 2.13.0 (2011-04-13), the thing is I execute my old file and nothing
happens...I suposse I need to install some library but there no appears no
message
Hi,
I'm new here.
This question concerns the package rgl.
Is it possible to change the colour of a set of points drawn with
plot3d /without/ removing them from the scene?
The idea is to create a presentation of a clustering algorithm, step
by step, representing the currently assigned cluster by
Thank you for your email.
The problem is that i'm not quite sure how to specify the model using arima().
Here's an example of my problem:
I would like to fit an ARMA model, but I'm not sure exactly how to fit it.
Â
Here's an example of the problem.
Â
This is my time variable, hourly d
Hello,
I am entirely new to this list, and not very experienced with R yet (but very
excited about it!!). I am struggling with a dataset of x and y coordinate
points I am plotting as a density map as follows:
trial <- read.csv(file="F12.csv", sep=",", skip=32, head=TRUE)
trial.sub <- subset(tri
Sorry for the confusion, thank you for the correction and explanation.
Tal
Contact
Details:---
Contact me: tal.gal...@gmail.com | 972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) |
www.r-sta
Hi everyone,
Apologies if this is a silly question but I am a student and this is my first
time using R so I am still trying to educate myself on commands, models e.t.c
I have a mixed model with four dichotomous fixed factors and subject as a
random factor (as each person completed four vignett
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