Dear R Help,
I would like to use the glmer.nb function for mixed modelling using negative
binomial distribution please.
On the CRAN website apparently this function is called from the lme4 package
(version 0.9911-1).
I have downloaded the latest version of the lme4 package (version 0
I have seen several queries about parameterizing the negative binomial scale
parameter. This is called
the heterogeneous negative binomial. I have written a function called
"nbinomial" which is in the
msme package on CRAN. Type ?nbinomial to see the help file. The default
model is a negative b
I presume it's related to the fact that the X coordinate is duplciated
in the two records, and the grid generated by adehabitatHR is a single
column,
Here's a test:
require(adehabitatHR)
m <- matrix(c(5419574 ,390051, 5419490 , 390051), ncol = 2,
byrow = TRUE)
tt <- as.POSIXct(c("2012-05-
it works!Thanks!
On Fri, May 17, 2013 at 2:28 PM, Rui Barradas wrote:
> Hello,
>
> Try the following.
>
>
> dat <- read.table(text = "
>
> Var Time
> 1 51
> 2 151
> 3 251
> 4234
> 5 331
> 6351
> ", header = TRUE)
>
> dat[dat$Time
Hi,
dat1<- read.table(text="
Var Time
1 51
2 151
3 251
4 234
5 331
6 351
",sep="",header=TRUE)
dat1[!is.na(match(gsub(".*(\\d{2})$","\\1",dat1$Time),51)),]
# Var Time
#1 1 51
#2 2 151
#3 3 251
#6 6 351
#or
dat1[substr(dat1$T
On 2013-05-17 12:45, Jesse Gervais wrote:
Hi there,
I want to do several bivariate linear regressions and, than, do a
multivariate linear regression including only variables significantly
associated *(p < 0.15)* with y in bivariate analysis, without having to
look manually to those p values.
Hello,
Try the following.
dat <- read.table(text = "
Var Time
1 51
2 151
3 251
4234
5 331
6351
", header = TRUE)
dat[dat$Time %% 100 == 51, ]
Em 17-05-2013 22:01, Ye Lin escreveu:
Hey All,
I want to delete rows based on the
Hey All,
I want to delete rows based on the last 2 digits on the value in one column
but I dont know how to do that.
Suppose my data looks like this:
Var Time
1 51
2 151
3 251
*4234*
*5 331*
6351
I want to delete the rows that the
Hi,
library(plyr)
res<-dcast(dataset,Date~ScowNo,sum,value.var="EstimatedQuantity")
rownames(res)<- res[,1]
res[,-1]
# 3002 4001 4002 BR 8
#9/7/2010 2772 3535 6763 6685
#9/8/2010 0 3305 0 0
A.K.
- Original Message -
From: Tim
To: r-help@r-project.org
Cc:
Sent: Friday,
Have you tried xtable?
library( xtable )
x <- structure(list(Record = 1:3, Average = c(34L, 14L, 433L), Maximum =
c(899L,
15L, 1003L)), .Names = c("Record", "Average", "Maximum"), class = "data.frame",
row.names = c(NA,
-3L))
x <- xtable( x )
print( x )
% latex table generated in R 2.15.2 by x
On May 17, 2013, at 12:58 PM, Hermann Norpois wrote:
> Hello,
>
> I have a nice function that makes an image of an matrix
> e.g.:
> qt[1:3,1:3]
> rs655246 rs943795 rs955612
> rs655246 NA NA NA
> rs943795 9.610070e-04 NA NA
> rs955612 5.55
Hi Patrick,
Thanks for you reply. I tried adding site fixed effect as you told me, but
the program failed again (R stopped working).
Basically, what I am trying to do is to test for auto-correlation between
sites within routes. My survey takes place in routes, but each route is
divided in segments
Paul,
Inverting log(y) is just the beginning of the problem, after that you need to
teach predict.lm() that E(y |x) = exp(x'betahat + .5*sigmahat^2) and then
further
lessons are required to get it to understand how to adapt its confidence and
prediction bands… and then you need to generalize
Hello,
I have a nice function that makes an image of an matrix
e.g.:
qt[1:3,1:3]
rs655246 rs943795 rs955612
rs655246 NA NA NA
rs943795 9.610070e-04 NA NA
rs955612 5.555616e-05 7.915982e-07 NA
myimage <- function(x, cex.axis = 0.7,
Is there any way to format the headers of data frames, for printing?
I am using Sweave to generate formatted reports. In Sweave, I read in a
data.frame:
result <- read.table(path.to.table);
then display it:
print.data.frame(result);
This gives me what I expect in t
Hi there,
I want to do several bivariate linear regressions and, than, do a
multivariate linear regression including only variables significantly
associated *(p < 0.15)* with y in bivariate analysis, without having to
look manually to those p values.
So, here what I got for the moment.
Fir
On May 17, 2013, at 11:55 AM, masumeh akhgar wrote:
> hi all
> this command used tt function for all variables.
> How can i define a different function for each variable?
>> exCox.all<-coxph(Surv(SURVT,STATUS) ~
> RX+LOGWBC+SEX+tt(RX)+tt(LOGWBC)+tt(SEX),
> data=rem.data,tt=function(x,t,...) log(t
Hi,
May be this helps:
dat<- read.table(text="
Date,Parameter,Weight
2012-01-31,90,200
2012-01-31,80,400
2012-01-31,70,500
2012-01-31,60,800
2012-02-29,120,220
2012-02-29,110,410
2012-02-29,75,520
2012-02-29,65,840
2012-03-31,115,210
2012-03-31,100,405
2012-03-31,70,500
2012-03-31,60,800
",sep=",",
hi all
this command used tt function for all variables.
How can i define a different function for each variable?
> exCox.all<-coxph(Surv(SURVT,STATUS) ~
RX+LOGWBC+SEX+tt(RX)+tt(LOGWBC)+tt(SEX),
data=rem.data,tt=function(x,t,...) log(t)*x))
thank you
__
On May 17, 2013, at 11:48 AM, Chirag Maru wrote:
> I have following data for which I need to calculate the weighted aggregate
> value of the parameter at each time.
>
> Date,Parameter,Weight
> 2012-01-31,90,200
> 2012-01-31,80,400
> 2012-01-31,70,500
> 2012-01-31,60,800
> 2012-02-29,120,220
> 2
m <- as.matrix(var)
John Kane
Kingston ON Canada
> -Original Message-
> From: akhgar.masu...@gmail.com
> Sent: Fri, 17 May 2013 22:45:22 +0430
> To: r-help@r-project.org
> Subject: [R] help
>
> Hello,
>
> I fail to tranfer data from a dataframe to a matrix.
>
> var is from a datafra
On 17-05-2013, at 20:15, masumeh akhgar wrote:
> Hello,
>
> I fail to tranfer data from a dataframe to a matrix.
>
> var is from a dataframe (and belongs still to the class dataframe) and
> should look like m (see below).
>
>> var
> vec1 vec3 d1 d2
> 1 172 173 223 356
>> dput (var)
> str
On May 17, 2013, at 9:46 AM, Tim wrote:
> #question I have the following data set:
>
> Date<-c("9/7/2010","9/7/2010","9/7/2010","9/7/2010","9/7/2010","9/7/2010","9/8/2010")
>
> EstimatedQuantity<-c(3535,2772,3279,3411,3484,3274,3305)
>
> ScowNo<-c("4001","3002","4002","BR 8","4002","BR 8","400
On 05/17/2013 02:34 PM, masumeh akhgar wrote:
hi deer all
Estimate KM survival probabilities for each categories of RX means
‘treatment’ and ‘placebo’ separately
surv.Rx<-survfit(Surv(SURVT,STATUS)~strata(RX),data=rem.data)
when write that command. it doesnt run.
what should i do?
thanks
Wha
hi deer all
Estimate KM survival probabilities for each categories of RX means
‘treatment’ and ‘placebo’ separately
> surv.Rx<-survfit(Surv(SURVT,STATUS)~strata(RX),data=rem.data)
when write that command. it doesnt run.
what should i do?
thanks
__
R-help
Hello,
I fail to tranfer data from a dataframe to a matrix.
var is from a dataframe (and belongs still to the class dataframe) and
should look like m (see below).
> var
vec1 vec3 d1 d2
1 172 173 223 356
> dput (var)
structure(list(vec1 = 172L, vec3 = 173L, d1 = 223L, d2 = 356L), .Names =
c
I have following data for which I need to calculate the weighted aggregate
value of the parameter at each time.
Date,Parameter,Weight
2012-01-31,90,200
2012-01-31,80,400
2012-01-31,70,500
2012-01-31,60,800
2012-02-29,120,220
2012-02-29,110,410
2012-02-29,75,520
2012-02-29,65,840
2012-03-31,115,21
#question I have the following data set:
Date<-c("9/7/2010","9/7/2010","9/7/2010","9/7/2010","9/7/2010","9/7/2010","9/8/2010")
EstimatedQuantity<-c(3535,2772,3279,3411,3484,3274,3305)
ScowNo<-c("4001","3002","4002","BR 8","4002","BR 8","4001")
dataset<- data.frame(EstimatedQuantity,Date,ScowNo)
There was some mistakes in my previous sending. The following are correct.
This is the problematic data, especially the line 43, but when I removed that
line, it bugs at line 62 and so on.
sig1 time id
UTMnorthin UTMeasting
40 4.5
Just stating the obvious that Peter left unsaid: The OP calculated a
matrix, whose diagonal is the correlations between each variable and
itself, with the off-diagonal entries being the ones of interest.
On 17-May-13, at 11:06 AM, Peter Ehlers wrote:
On 2013-05-17 08:37, Jose Iparraguirre
Hi Andrea,
I'm not exactly sure what you're trying to do, but you've included a
random effect for a "site" coefficient that's not even in your list of
fixed effects... you're basically allowing the coefficient for site to
vary across routes, but you're never including the coefficient in the
first
This is the problematic data, especially the line 43, but when I removed that
line, it bugs at line 62 and so on.
sig1 time id UTMnorthin
UTMeasting
40 4.5766 2012.05.30 08:00:00 Ade-55419576 390052
41 4.5766
On 2013-05-17 08:37, Jose Iparraguirre wrote:
Dear Elaine,
One of the elements you obtain the P matrix, which is the matrix of asymptotic
p-values. In your case, you get that the asymptotic p-value of the association
between t_i and t_r is 0. That is, there would exist a perfect association
On May 17, 2013, at 7:44 AM, Rémi Lesmerises wrote:
> Dear all,
>
> I'm trying to get a Brownian bridge kernel (kernelbb) for each combination of
> two consecutive animal locations (see commands below) and put them, with a
> loop, inside a list. It works well at the beginning but after 42 runs
On May 17, 2013, at 7:04 AM, Martin Batholdy wrote:
> Hi,
>
> I know R is not made for this, but I still wanted to ask if there are
> possibilities to do this;
>
>
> I repeatedly collect data from a database for a given time interval.
> Now I would like to monitor the change of this data with
Thanks! I didn't know about that list. I forwarded my question there
Andrea
Bert Gunter wrote
> It would be better to post this on the r-sig-mixed-models list, I think.
>
> -- Bert
>
> On Fri, May 17, 2013 at 10:02 AM, Andrea Goijman
> <
> agoijman@.gov
> > wrote:
>> Dear R list,
>>
>> I'm at
It would be better to post this on the r-sig-mixed-models list, I think.
-- Bert
On Fri, May 17, 2013 at 10:02 AM, Andrea Goijman
wrote:
> Dear R list,
>
> I'm attaching a sample of my data which consists on the presence/absence
> ("punto6", binomial n=5 occasions)
> of different species ("sp"),
This is an R formula handling question. It arose in class. We were working
on the Animals data in the MASS package. In order to see a relationship,
you need to log brain and body weight. It's a fun one for teaching
regression, if you did not try it yet. There are outliers too!
Students wanted to
Dear R list,
I'm attaching a sample of my data which consists on the presence/absence
("punto6", binomial n=5 occasions)
of different species ("sp"), on different sites ("site") within routes
('route").
First, I want to be able to find if there is autocorrelation of the
response variable between
You are wrong... since the SQL query you wish to create is itself a string.
Of course, you cannot send a SQL fragment such as you used as an example, so be
sure to form a complete, syntactically correct SQL statement before giving it
to your database query function.
Oh, and if you need more ass
is this what you want"
> x <- c(1, 2, 3, 4, 5)
> paste0("where ASSETT in (", paste(x, collapse = ','), ")")
[1] "where ASSETT in (1,2,3,4,5)"
On Fri, May 17, 2013 at 11:46 AM, Manta wrote:
> Hi all,
>
> I have a vector of numbers, and to be able to pass it to RMySQL and use the
> IN clause I
Hi all,
I have a vector of numbers, and to be able to pass it to RMySQL and use the
IN clause I need to have this vector to be a single list numeric and comma
separated.
I saw the post below but it is about strings, which I do not need (I cannot
pass strings in this SQL query, I need something li
Dear Elaine,
One of the elements you obtain the P matrix, which is the matrix of asymptotic
p-values. In your case, you get that the asymptotic p-value of the association
between t_i and t_r is 0. That is, there would exist a perfect association
(look also at the first result, the matrix of co
No data. The list tends to strip out many kinds of attachements including csv
files. I'd suggest trying .txt or parking the data at someplace like
[url=http://www.mediafire.com/][b]MediaFire[/b][/url] or
Dropbox [url=https://www.dropbox.com/][b]Dropbox[/b][/url]
John Kane
Kingston ON Canada
>
Hello,
Try the following.
lmR <- lm(cd$Depth ~ cd$CHAOsep12RNA)
pconfR <- predict(lmR,interval="confidence")
pcR <- pconfR[order(pconfR[, 1]), ] # Add this line
plot(cd$CHAOsep12RNA,cd$Depth, ylim = rev(range(0:100)), xlab="CHAO",
ylab="Depth", pch=15, las=2, main="Sep12-RNA", cex.main=1)
a
On 2013-05-17 06:03, Ozgul Inceoglu wrote:
Dear All,
When I plot the values and linear regression line for one data set, it is fine.
But for another one I see zigzags, when I plot the confidence interval
cd
Depth CHAOsep12RNA
9,94804
25,06 1476,83
40,04 1540,561404
50,11 1575
Technically this is correct for raw R functionality.
in practice various modules impose their own limits on variables so you have
to check.
For example the coxreg package truncates all variables to 16 characters.
for example the test below
> res
Call:
coxreg(formula = Surv(vtime, vstatus) ~
abcde
Apologies to John - I should have thought to give an example. However, xpd
is what I was looking for. Thanks for the help!
On 14 May 2013 14:55, David Carlson wrote:
> Let's try again after restraining Outlook's desire to use html.
>
> set.seed(42)
> dat <- matrix(c(runif(48), 0, 0), 25, 2, b
On May 17, 2013, at 9:47 AM, Johan Lassen wrote:
> Dear community . I would like to connect r to libre office base. Does
> anyone know if and how this can be done? I think of the pendant to rodbc
> for libre office. I am using windows 7.
> Thanks in advance and best regards johan
As an FYI, th
Dear community . I would like to connect r to libre office base. Does
anyone know if and how this can be done? I think of the pendant to rodbc
for libre office. I am using windows 7.
Thanks in advance and best regards johan
[[alternative HTML version deleted]]
Dear all,
I'm trying to get a Brownian bridge kernel (kernelbb) for each combination of
two consecutive animal locations (see commands below) and put them, with a
loop, inside a list. It works well at the beginning but after 42 runs, it
appears the following warning :
>Error in seq.default(yl
Hi,
Try this:
dat1$idx<-with(dat1,ifelse(is.na(delais)|delais<45 &
delais>20, 1,ifelse(delais<60 &
delais>=45,2,ifelse(delais<=90 & delais>=60,3,NA
dat1$idx1<-c(dat1$idx[-head(dat1$idx,1)],1)
library(zoo)
res1<-do.call(rbind,lapply(split(dat1,dat1$patient_id),function(x)
{x$idx[as.logica
Hello everyone,
I am trying to undertake an item bifactor analysis of graded response data from
a questionnaire. I am using the mirt package, especially the bfactor
function.My dataset is called "data.items", it contains about 2000 observations
and 31 variables (variables represent the items in
Hi,
I know R is not made for this, but I still wanted to ask if there are
possibilities to do this;
I repeatedly collect data from a database for a given time interval.
Now I would like to monitor the change of this data with some nice plots.
I actually have to draw 15 plots to get the whole p
Hello,
It is not the correct procedure. Go to the bottom of the following webpage
to unsubscribe.
https://stat.ethz.ch/mailman/listinfo/r-help
Regards,
Pascal
2013/5/17 Mario Garrido
> Hello,
> I want to stop receiveng mails from R help forum,
> thanks.
>
> This is my data :
> Mario Garrido
Hello,
I want to stop receiveng mails from R help forum,
thanks.
This is my data :
Mario Garrido Escudero
Dpto. de Biología Animal, Ecología, Parasitología, Edafología y Qca.
Agrícola
Fac. de Farmacia
Campus Unamuno
Universidad de Salamanca
gaiarr...@usal.es
[[alternative HTML version de
Am 17.05.2013 13:36, schrieb John Fox:
Dear Knut,
This is really more a limitation than a bug. Like most of the dialogs in the
Rcmdr, the dialog to read Excel files uses existing facilities in R and R
packages. I'll see whether it's possible to add an option to read a data set
without variabl
It's difficult to see where your error is when you provide no accompanying
data for us to test your code out on (X? Y? Stand?).
However, it looks like you are making your code more complex than it needs
to be. Are you simply trying to a fit a separate linear regression to each
subset of your da
Dear All,
When I plot the values and linear regression line for one data set, it is fine.
But for another one I see zigzags, when I plot the confidence interval
>cd
Depth CHAOsep12RNA
9,94804
25,06 1476,83
40,04 1540,561404
50,11 1575,17
52,46 349,22
54,92 1941,5
57,2
Dear colleagues (especially those with an understanding of the inner
workings of R),
For some years, I have been using R's fft (Fast Fourier Transform)
routines from within C code as part of an R package.
With R-3.0.1, fft_factor and fft_work are no longer available as entry
points declared in R
Dear All,
I have a query about using log scales for filled.contour plots. I have
used log values on the x and y axes but labelled the axes with their
linear (non-log) values. I's like to do the same with the contour
values. I want the range to go from -100% to +100%. To use log I just
added 1
Thanks a lot, that is all i want. If someone is interessed, see the code
below
panel.3d.contour <-
function(x, y, z, rot.mat, distance,
nlevels = 20, zlim.scaled, ...) # les3 points de suspension
pour dire les autres paramètres sont ceux données par défaut
{
add.line <- trel
Hi,
I am a new user of R.
This is a conceptual doubt regarding screeing out outliers from the dataset
in regression.
I read up that Cook's distance can be used and if we want to remove
influential observations, we can use the metric (>4/n) (n=no of
observations) to remove any outliers.
I also ca
Hello!
I'm
using the NLPCA to reduce the
dimensionality of nine variables
(4 nominal /
3 ordinal /2 numeric)
to obtain the object-scores to be used as dependent variable in a regression
model.
I'm using the package homals (http://www.jstatsoft.org/v31/i04/paper).
The output is:
Call: homals
Dear all,
How do I obtain the number of countries that my panel models estimated by
pglm() and relogit() (the latter one is in the Zelig library) use? I
couldn't find any information on that in the help files.
Thank you very much in advance.
Best wishes
_
To make it easier for R-help readers to help you, please you provide the
before UUU[2] data using the dput() function.
dput(UUU[2])
Jean
On Thu, May 16, 2013 at 11:12 AM, Aldi wrote:
> Hi, If I have an R object UUU, where the second element is U2, based on
> "g" column of my.table
>
> my.tab
Hi,
rep(seq_along(v),v)
#[1] 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 5 5 5 6 6
A.K.
- Original Message -
From: Stefan Petersson
To: r-help@r-project.org
Cc:
Sent: Friday, May 17, 2013 6:53 AM
Subject: [R] Repeating sequence elements
I want to create a sequence, repeating each element according
Dear Knut,
This is really more a limitation than a bug. Like most of the dialogs in the
Rcmdr, the dialog to read Excel files uses existing facilities in R and R
packages. I'll see whether it's possible to add an option to read a data set
without variable names. The obvious workaround is to add
Try
rep(1:length(v), v)
HTH,
Jorge.-
On Fri, May 17, 2013 at 8:53 PM, Stefan Petersson wrote:
> I want to create a sequence, repeating each element according to a vector.
>
> I have this:
>
> v <- c(4, 4, 4, 3, 3, 2)
>
> And want to create this:
>
> 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 5 5 5 6 6
>
Hello,
At an R prompt, type
?rep
Then use
v <- c(4, 4, 4, 3, 3, 2)
rep(1:6, v)
Hope this helps,
Rui Barradas
Em 17-05-2013 11:53, Stefan Petersson escreveu:
I want to create a sequence, repeating each element according to a vector.
I have this:
v <- c(4, 4, 4, 3, 3, 2)
And want to crea
On 13-05-17 12:01 AM, David Winsemius wrote:
Do this search with your favorite search tool
Accessing the sources ligges
(Uwe Ligges is the author of a comprehensive article on the topic in R News.)
That article is also linked from the R help system. After help.start(),
look for "technical
On 13-05-16 9:56 PM, Seth Myers wrote:
Let's say I would like to look inside the function corBrownian in library
(ape). When I type in the function name I get the following, which is not
nearly the detail that goes into this function. I am wondering how to
begin cracking this function open (and
I want to create a sequence, repeating each element according to a vector.
I have this:
v <- c(4, 4, 4, 3, 3, 2)
And want to create this:
1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 5 5 5 6 6
TIA
// s
R version 3.0.0 (2013-04-03)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 L
On May 17, 2013, at 08:51 , Sparks, John James wrote:
> Dear R Helpers,
>
> I need help with a slightly unusual situation in which I am trying to
> select some columns from a data frame. I know how to use the subset
> statement with column names as in:
Notice that subset() is a convenience fun
On May 17, 2013, at 12:02 , peter dalgaard wrote:
>
> On May 17, 2013, at 08:51 , Sparks, John James wrote:
>
>> Dear R Helpers,
>>
>> I need help with a slightly unusual situation in which I am trying to
>> select some columns from a data frame. I know how to use the subset
>> statement with
Hello
I am using package Hmisc to calculate the pearson correlation and the
significant level for the matrix of t_i and t_r. (temperature minimum and
temperature range)
However, I have difficulty interpreting the result, even after checking the
manual.
Please kindly help to indicate if the p-valu
Hello,
It works for me if I replace
> ImportantVars <- as.character(ImportantVars)
by
> ImportantVars <- ImportantVars$Vars
Hope this helps,
Pascal
2013/5/17 Sparks, John James
> Dear R Helpers,
>
> I need help with a slightly unusual situation in which I am trying to
> select some colum
Am 17.05.2013 09:09, schrieb Pascal Oettli:
> Hi,
>
> Which command? But I would say that the first row is imported as
> column names.
maybe its a general problem of importing excel files.
First of all I am using only sheeets with headlines ;_) but Students do
sometimes not. ;-)
So
gdata - read
Hi,
For example:
> which(complete.cases(test))
[1] 1 3 4 6
Probably a more elegant way exists.
Regards,
Pascal
2013/5/17 jpm miao
> Hi,
>
> I have a sequence whose 1st, 3rd, 4th, 6th are non-NAs. How could I let R
> return 1,3,4,6, the indices?
>
> I know only how to find the non-NA ele
Hi,
Which command? But I would say that the first row is imported as column
names.
Regards,
Pascal
2013/5/17 Knut Krueger
> may be it is a bug:
> if a excel file is not containing headlines the first data row will not be
> imported
>
> Knut
>
> __**___
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