Dear Kristi,
You could do something like this.
ggplot(dat1, aes(x = factor(site), y = Present)) +
geom_boxplot(aes(colour = layer)) +
geom_line(data = dat2, aes(group = 1, y = present)) +
geom_point(data = dat2, aes(y = present))
Note that
- ggplot provides no second axis
- the boxplots
On 14-01-28 2:48 AM, Eva Prieto Castro wrote:
Hi everybody,
I have a doubt in relation with arguments in functions when packaging: Does it
make sense the fact of having dots as an argument when it is the only argument?.
I mean you have a package and a function that will be used directly by
But in crran page it says mac binaries ?
if I do install.library, it compiles the package. My old mac can't compile some
packages. that's why I need to install binaries directly if possible.
-Original Message-
From: Henrik Bengtsson [h...@biostat.ucsf.edu]
Date: 01/28/2014 12:30 AM
To:
Hello,
I'm using the nlme package to run non-linear mixed models!
I would like to subset the plots obtained with the code:
plot(augPred(Nlme0))
Any help is wellcome!
Cheers,
Vasco
--
Vasco A. P. Cadavez, PhD
Departamento de Ciência Animal Centro de Investigação de Montanha (CIMO)
Escola
Hi
can you be more specific? Your code gives an error without Nlme0 data.
library(nlme)
plot(augPred(Nlme0))
Error in augPred(Nlme0) : object 'Nlme0' not found
If you want to use only some selection of panels in your plot, you probably
need to dig into aug.Pred code and change it or make the
Thank you, Bert. I'll definitely ask there.
In the meantime I just wanted to ensure that my R code (my function for
bootstrap and the bootstrap run) is correct and my abnormal bootstrap
results are not a function of my erroneous code.
Thank you!
On Mon, Jan 27, 2014 at 7:09 PM, Bert Gunter
Hi, see inline
Feladó: r-help-boun...@r-project.org [r-help-boun...@r-project.org] ;
meghatalmaz#243;: Armel KAPTUE [armel.kap...@sdstate.edu]
Küldve: 2014. január 28. 8:16
To: R-help@r-project.org
Tárgy: [R] Markov chain simulation
Hi there,
I'm wonder
Dear all
I have such data
temp - structure(list(x = c(1.22640164371796, 2.06054252402081,
0.648406692116093,
0.502688462027622, 1.20971015442933, -1.33912870469085, 1.04053747125611,
1.08845105918041, 1.6409121019292, 0.596150765260052, 1.78013122654094,
0.4709422376346), y =
Hello Pikal,
I have 39 conditions (graphs) and I want to plot the 39 graphs individually!
How can I do this?
Cheers,
Vasco
On 28/01/14 13:47, PIKAL Petr wrote:
Hi
can you be more specific? Your code gives an error without Nlme0 data.
library(nlme)
plot(augPred(Nlme0))
Error in
I would like to make a plea for publication-ready figures from R.
The default figures produced by R (both traditional and lattice graphics) need
to be amended (by users) in many respects to be acceptable by publishers.
I imagine that most R users are producing figures for publication, and it
Chapman Hall/CRC: The R Series
The R Series from Chapman Hall/CRC has now been up and running for almost
three years and is growing from strength to strength. We now have eight books
published in the series, and more than twenty in development. This year looks
set to be a big year for the
The Statistical Computing Section of the American Statistical Association
announces the competition for the John M. Chambers Statistical Software Award.
In 1998 the Association for Computing Machinery presented its Software System
Award to John Chambers for the design and development of S. Dr.
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 01/28/14, 12:12 , Bebber, Dan wrote:
I would like to make a plea for publication-ready figures from R.
The default figures produced by R (both traditional and lattice
graphics) need to be amended (by users) in many respects to be
Dear R users, how I can implement Breslow and Tarone-Ware tests for
survival analysis?
Also, is there any way I can estimate and plot the hazard function,along
the lines of the survival function in Survival Package? (The package muhaz
seems that does not do what it promises, except if I could not
Hi All,
I am trying to manipulate my data in R. I have used the following code
[aggregate(latency~participant+condition+state, data=data, FUN=mean)] which
produces a summary of the variable I am interested in. However, I need to
export the crated variable into excel. Can anyone help with this
Dear Dan,
Have a look at ggplot2. It allows to define themes. I've create two theme for
our institution: one according our internal styling guide, one according to the
styling guide for Elsevier journal. Applying the Elsevier theme to all plots in
a script requires just adding
Colleagues
Frank Harrell wrote that you need to purchase Stat/Transfer, which I did many
years ago and continue to use.
But I dont understand why the sas7bdat package (or something equivalent)
cannot reverse engineer the SAS procedures so that R users can read sas7bdat
files as well as
labelling of figure parts with a, b, c etc. in the top left corner
that should be easy to achieve in R.
It is; use par(usr) to get the corners and text() to place labels inside the
plot region, as in
text(par(usr)[1], par(usr)[4], a), cex=1.5, adj=c(-0.2,1.2))
or something like
mtext(a),
Dennis,
The key difference is that with R, you are, as always, dependent upon
volunteers providing software at no charge to you, most of whom have full time
(and then some) jobs. Those jobs (and in many cases, family) will be their
priority, as I am sure is the case with Matt.
Unless they
Personally I just create a csv file using write.csv() and then read the text
file into the spreadsheet if needed. To be fancier have a look at the xlsx
package.
BTW there is no 'state' variable in your data.frame.
John Kane
Kingston ON Canada
-Original Message-
From:
Hi,
May be this helps:
set.seed(85)
mat1 - matrix(sample(seq(0,1,by=0.01),36,replace=TRUE),ncol=3)
mat2 - mat1[sprintf(%.2f,rowSums(mat1))==1.00,]
any(!rowSums(mat2))
#[1] FALSE
A.K.
Hi,
I'd like to create a matrix with three columns so that each
element is between 0 and 1 and each row
I'd like to create a matrix with three columns so that each element is
between 0 and 1 and each row always adds to 1. So, if in the same row the
You could start with expand.grid
m - expand.grid(x1=0:100, x2=0:100) #Avoids comparing floats
m - m[rowSums(m)=100,]#Throw away
Whether a package is install from source or from an available binary
is controlled by argument 'type', cf. ?install.packages. I believed
that, just as on Windows, the default on OSX was to install from
binaries, but I might be wrong, or you have changed the settings of
the below option. So,
Hi Kehl,
Thank you for your reply.
Indeed, there are many ways to simulate a markov chain sequence.
For instance, if I assume that n=20, rnd_occ1-c(0, 0, 0, 0, 0, 0, 1, 1, 0, 1,
1, 1, 0, 0, 0, 0, 1, 1, 1, 1) and rnd_occ2-c(0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0,
0, 0, 0, 0, 0, 1, 1, 0, 0) are two
Dear list,
I'm using the rms package to fit some Cox models. I run anova() on them to
obtain sequential p-values, but I'm getting strange results when I run it on a
subset of the data.
Following the example on the help page of anova.coxph:
library(rms)
data(ovarian)
fit -
Hello,
Your data.frame doesn't have a 'state' column:
aggregate(latency~participant+condition+state, data=data, FUN=mean)
Error in eval(expr, envir, enclos) : object 'state' not found
Anyway, you can use ?write.csv to write the result to a csv file, and
open it in excel, or use one of the R
On 28-01-2014, at 19:23, Kaptue Tchuente, Armel armel.kap...@sdstate.edu
wrote:
Hi Kehl,
Thank you for your reply.
Indeed, there are many ways to simulate a markov chain sequence.
For instance, if I assume that n=20, rnd_occ1-c(0, 0, 0, 0, 0, 0, 1, 1, 0,
1, 1, 1, 0, 0, 0, 0, 1, 1,
ce,
Did you try to use the menu Packages Data Package Installer, select
CRAN (binaries) from the top left option in the open menu, search for the
forecast package and then install it with the dependencies? I did this here
and it worked for me.
If it doesn't work, please run
sessionInfo()
Hi,
May be this helps you in getting started:
library(lattice)
library(grid)
xy -xyplot(decrease ~ treatment, OrchardSprays,
main= Some plot,
groups = rowpos, type = a,
scales=list(x=list(at=seq(1,8,1),labels=c('A','','C','','E','','G',''))),
page =
An alternative using runif.
x - round(runif(1, 0, 1), 2)
y - round(runif(1, 0, 1-x), 2)
z - round(1-x-y, 2)
sum1 - cbind(x, y, z)
any(!(sum1[,1] + sum1[,2] + sum1[,3]))
Richard
On Tue, Jan 28, 2014 at 9:36 AM, S Ellison s.elli...@lgcgroup.com wrote:
I'd like to create a matrix
Hi there,
I have some question about how to use this package:
My code structure is as follows:
rm(list=ls())
set.seed(2014)
library(snowfall)
#
#part 1:
generate the initial value for simulation
#part 2:
some functions will be used in the simulation
#simulation part, start from
Hi, if 50% survival probability horizontal line in a Kaplan-Meier survival
curve overlap one of the step line between 2 time points t1 and t2, the
survfit() from survival package estimates median survival as t2 (the longest
time point). But I saw some articles (page 23:
Marc
I understand that R is staffed entirely by volunteers and I appreciate the
massive efforts that have created this awesome software. My suggestion was
aiming to encourage the Core team that one weakness of the present structure is
less-than-optimal interchangeability with SAS. If this
All,
I asked over at the manipulatr group and Hadley showed me how to do it. In
case anyone is interested I will post the solution here:
target - hp
call - substitute(mutate(mtcars, scale(target)), list(target =
as.name(target)))
eval(call)
Thanks,
Roger
-Original Message-
From:
Also,
library(gtools)
x - rdirichlet(1000, c(1,1,1) )
any(!rowSums(x))
#[1] FALSE
A.K.
On Tuesday, January 28, 2014 2:20 PM, Richard Kwock richardkw...@gmail.com
wrote:
An alternative using runif.
x - round(runif(1, 0, 1), 2)
y - round(runif(1, 0, 1-x), 2)
z - round(1-x-y, 2)
sum1
Hi experts
I want to plot some plots with r in plot pane. At least two plots to six or
more.
I have this code to do this job, but in some positions the main plot gets
lost:
plot(datalistB, type=l)
while(1+window+n = length(data[,1]))
{
datalistB-datalist[n:(n+window-1)]
Hi, I wanted to remove redundant rows (with same entry in columns) in a data
frame. For example, with this data frame:
dat-cbind(x=c('a','a','b','b','c','c'),y=c('x','x','d','s','g','g'))
dat
x y
[1,] a x
[2,] a x
[3,] b d
[4,] b s
[5,] c g
[6,] c g
after removing the redundancy, the
Inline.
-- Bert
Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374
Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom.
H. Gilbert Welch
On Tue, Jan 28, 2014 at 2:06 PM, array chip arrayprof...@yahoo.com wrote:
Hi, I wanted to remove
Hi,
use ?unique
unique(dat)
A.K.
Hi, I wanted to remove redundant rows (with same entry in columns) in a data
frame. For example, with this data frame:
dat-cbind(x=c('a','a','b','b','c','c'),y=c('x','x','d','s','g','g'))
dat
x y
[1,] a x
[2,] a x
[3,] b d
[4,] b s
[5,] c g
Here is a great response I got from SO:
There is an important difference between the two importance measures:
MeanDecreaseAccuracy is calculated using out of bag (OOB) data,
MeanDecreaseGini is not. For each tree MeanDecreaseAccuracy is calculated
on observations not used to form that particular
I think that the fundamental problem is that you are using the default
value of ntree (500). You should always use at least 1500 and more if n or
p are large.
Also, this link will give you more up-to-date information on that package
and feature selection:
On Jan 27, 2014, at 7:45 AM, Bos, Roger wrote:
All,
I would like to figure out how to pass variable names to the dplyr function
mutate. For example, this works because hp is one of the variable names on
mtcars:
mutate(mtcars, scale(hp))
Let's says I want to pass in the target
David:
I privately suggested he post to manipulatr because Hadley is more
likely to see his question there first than in R-help. He originally
posted here, noted the cross-posting and referral at manipulatr and
responded back to this list when he got a successful reply from
Hadley. I don't see
On Jan 27, 2014, at 1:30 PM, Dustin Fife wrote:
Hi all,
I frequently get requests to do data analysis where the person
references an excel column. e.g., I want to analyze [insert complex
variable name], located at column AAQ in Excel. I've been doing is
gsub and inserting a part of the
Thank you for a very thorough analysis. It seems whether or not an
operation makes a full copy really depends on the specific operation,
and that it is not safe to assume that because I know something is
unchanged there will be no copy. For example, in your last case only
one element of a list
sorry.. don't know unique().. such a great function
From: Bert Gunter gunter.ber...@gene.com
Cc: r-help@r-project.org r-help@r-project.org
Sent: Tuesday, January 28, 2014 2:21 PM
Subject: Re: [R] unique rows
Inline.
-- Bert
Bert Gunter
Genentech
On Jan 28, 2014, at 7:58 AM, Endy BlackEndy wrote:
Dear R users, how I can implement Breslow and Tarone-Ware tests for
survival analysis?
Tests ... of what?
Perhaps you should learn to search:
install.packages('sos')
library(sos)
findFn(Tarone-Ware)
The 'comp' function in {survMisc}
On Jan 28, 2014, at 10:32 AM, Oscar Rueda wrote:
Dear list,
I'm using the rms package to fit some Cox models. I run anova() on them to
obtain sequential p-values, but I'm getting strange results when I run it on
a subset of the data.
Following the example on the help page of
On Jan 28, 2014, at 3:43 PM, Dennis Murphy wrote:
David:
I privately suggested he post to manipulatr because Hadley is more
likely to see his question there first than in R-help. He originally
posted here, noted the cross-posting and referral at manipulatr and
responded back to this list
On Jan 28, 2014, at 4:19 PM, Dennis Murphy wrote:
Hi David:
Do you meant [sic] the (cumulative) hazard function that is 1 minus the
survival function?
Um, 1 - S(t) = F(t), the cumulative *distribution function* of the
random variable T. The cumulative hazard function is -ln S(t) and
On Tue, Jan 28, 2014 at 6:46 PM, David Winsemius dwinsem...@comcast.netwrote:
On Jan 27, 2014, at 1:30 PM, Dustin Fife wrote:
Hi all,
I frequently get requests to do data analysis where the person
references an excel column. e.g., I want to analyze [insert complex
variable name],
On Jan 27, 2014, at 8:04 AM, Carlo Giovanni Camarda wrote:
Dear R-users,
I would like to know whether you know some trick for skipping some of
the steps in the example below (especially the last step in a way that
would make easier to be written succinctly in a text).
I could try to
please ignore. actually the median survival from survfit() is the mean of the 2
time points.
To: R help r-help@r-project.org
Sent: Tuesday, January 28, 2014 11:27 AM
Subject: [R] median survival
Hi, if 50% survival probability horizontal line in a
Hi Folks!
I have been writing a small set of utilities for dealing with files that are
hard to open correctly for one reason or another, especially because they
are too big for memory, non-rectangular, or contain odd characters or
unexpected codings, or all of these things together. Today it
On Jan 28, 2014, at 8:43 PM, andrewH wrote:
Hi Folks!
I have been writing a small set of utilities for dealing with files that are
hard to open correctly for one reason or another, especially because they
are too big for memory, non-rectangular, or contain odd characters or
unexpected
I have a data frame with variable datetime which is of class POSIXct.
Consecutive observations are separated by 30 minutes.
However, some of the differences reported by R give unexpected results.
For example consider the following two consecutive entries:
par.dat$datetime[5944]
[1] 2010-04-04
Sorry how do access this menu? R-studio? I open an xterm and type R to start R.
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-apple-darwin9.8.0 (32-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a
Thank you for advise. I am using mac osx 10.5. 8.
I am still having problems with install :
install.packages(forecast,type=mac.binary.leopard)
Warning: unable to access index for repository
http://lib.stat.cmu.edu/R/CRAN/bin/macosx/leopard/contrib/3.0
package 'forecast' is available as a
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of David Fox
Sent: Tuesday, January 28, 2014 5:15 PM
To: r-help@r-project.org
Subject: [R] Difference between two datetimes
I have a data frame with variable datetime which is of
On Jan 28, 2014 at 8:56pm, David Winsemius wrote:
On Jan 28, 2014, at 8:43 PM, andrewH wrote:
Hi Folks!
I have been writing a small set of utilities for dealing with files that
are
hard to open correctly for one reason or another, especially because they
are too big for memory,
http://r.789695.n4.nabble.com/file/n4684362/Screen_Shot_2014-01-28_at_9.23.57_PM.png
I have many .txt files all with the same format, one column for date
(/mm/dd), another column for discharge (numerical values from 0.00 to
500.00), and two coulmns that I do not need. I am working in R.
I
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