Re: [R] is this an ANOVA ?
You may try the following to perform anova:
anova(lm(y~x))
or
summary(aov(y~x))
2011/4/13 Ubuntu Diego ubuntu.di...@gmail.com
Hi all,
I have a very easy questions (I hope). I had measure a property of
plants, growing in three different substrates (A, B and C). The rest of the
conditions remained constant. There was very high variation on the results.
I want to do address, whether there is any difference in the
response (my measurement) from substrate to substrate?
x-c('A','A','A','A','A','B','B','B','B','B','C','C','C','C','C') #
Substrate type
y - c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15) # Results of the measurement
MD-data.frame(x,y)
I wrote a linear model for this:
summary(lm(y~x,data=MD))
This is the output:
Call:
lm(formula = y ~ x, data = MD)
Residuals:
Min 1Q Median 3QMax
-2.000e+00 -1.000e+00 5.551e-17 1.000e+00 2.000e+00
Coefficients:
Estimate Std. Error t value Pr(|t|)
(Intercept) 3. 0.7071 4.243 0.001142 **
xB5. 1. 5.000 0.000309 ***
xC 10. 1. 10.000 3.58e-07 ***
---
Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1
Residual standard error: 1.581 on 12 degrees of freedom
Multiple R-squared: 0.8929, Adjusted R-squared: 0.875
F-statistic:50 on 2 and 12 DF, p-value: 1.513e-06
I conclude that there is an effect of substrate type (x).
NOW the questions :
1) Do the fact that the all p-values are significant means
that all the groups are different from each other ?
2) Is there a (easy) way to plot, mean plus/minus 2*sd for
each substrate type ? (with asterisks denoting significant differences ?)
THANKS !
version
platform x86_64-apple-darwin9.8.0
arch x86_64
os darwin9.8.0
system x86_64, darwin9.8.0
status
major 2
minor 11.1
year 2010
month 05
day31
svn rev52157
language R
version.string R version 2.11.1 (2010-05-31)
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Dump the source code of data frame
Dear R experts, I remember a similar function existed and have been mentioned in R-help before. I tried my best to search but I really can't find it out. suppose I have an data frame like this: somedata - data.frame(age.min = 1, age.max = 1.5, male = TRUE, l = -1.013, m=16.133, s=0.07656) In order to back up the data and I don't want to use write.table(), I would like to back up the source code of the data frame. When I apply that function (let's call it dumpdf() ), the function will reproduce the source code that creates the data.frame. For example: dumpdf(somedata) somedata - data.frame(age.min = 1, age.max = 1.5, male = TRUE, l = -1.013, m=16.133, s=0.07656) Is there any function similar to the dumpdf() above? Thank you so much! Regards, CH -- CH Chan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Dump the source code of data frame
Hi CH, Take a look at ?dput HTH, Jorge On Wed, Apr 13, 2011 at 3:09 AM, C.H. wrote: Dear R experts, I remember a similar function existed and have been mentioned in R-help before. I tried my best to search but I really can't find it out. suppose I have an data frame like this: somedata - data.frame(age.min = 1, age.max = 1.5, male = TRUE, l = -1.013, m=16.133, s=0.07656) In order to back up the data and I don't want to use write.table(), I would like to back up the source code of the data frame. When I apply that function (let's call it dumpdf() ), the function will reproduce the source code that creates the data.frame. For example: dumpdf(somedata) somedata - data.frame(age.min = 1, age.max = 1.5, male = TRUE, l = -1.013, m=16.133, s=0.07656) Is there any function similar to the dumpdf() above? Thank you so much! Regards, CH -- CH Chan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Compatibility with Work Load/Resource Managers
I was wondering if anyone knew whether R is capable of integrating with the following work load/resource managers TORQUE, OpenPBS, PBS Pro, LSF, and SGE? I am running R scripts in our cluster under SGE on a regular basis and have also done that under Platform LSF in the past but I am not sure what you mean by integrating with these systems. cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] forest + igraph ?
Sure. Here is an example:
library(metafor)
data(dat.bcg)
windows(height=8, width=6, pointsize=10)
par(mfrow=c(2,1))
dat - escalc(measure=RR, ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat.bcg)
res - rma(yi, vi, data=dat)
forest(res, atransf=exp)
title(Forest Plot of Relative Risks)
dat - escalc(measure=OR, ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat.bcg)
res - rma(yi, vi, data=dat)
forest(res, atransf=exp)
title(Forest Plot of Odds Ratios)
Best,
--
Wolfgang Viechtbauer
Department of Psychiatry and Neuropsychology
School for Mental Health and Neuroscience
Maastricht University, P.O. Box 616
6200 MD Maastricht, The Netherlands
Tel: +31 (43) 368-5248
Fax: +31 (43) 368-8689
Web: http://www.wvbauer.com
-Original Message-
From: Samor Gandhi [mailto:samorgan...@yahoo.com]
Sent: Tuesday, April 12, 2011 15:59
To: r-h...@stat.math.ethz.ch; Viechtbauer Wolfgang (STAT)
Subject: RE: [R] forest + igraph ?
Thanks, That is a nice one. Is there any option that I can plot the pooled
estimate?
Regards,
Samor
--- On Tue, 12/4/11, Viechtbauer Wolfgang (STAT)
wolfgang.viechtba...@maastrichtuniversity.nl wrote:
From: Viechtbauer Wolfgang (STAT)
wolfgang.viechtba...@maastrichtuniversity.nl
Subject: RE: [R] forest + igraph ?
To: Samor Gandhi samorgan...@yahoo.com, r-h...@stat.math.ethz.ch r-
h...@stat.math.ethz.ch
Date: Tuesday, 12 April, 2011, 15:54
You said that you do NOT want to use par(mfrow=c(2,1)). Why not?
Isn't this (below) what you want?
library(metafor)
data(dat.bcg)
windows(height=8, width=6, pointsize=10)
par(mfrow=c(2,1))
dat - escalc(measure=RR, ai=tpos, bi=tneg, ci=cpos, di=cneg,
data=dat.bcg)
forest(dat$yi, dat$vi, atransf=exp)
title(Forest Plot of Relative Risks)
dat - escalc(measure=OR, ai=tpos, bi=tneg, ci=cpos, di=cneg,
data=dat.bcg)
forest(dat$yi, dat$vi, atransf=exp)
title(Forest Plot of Odds Ratios)
Best,
--
Wolfgang Viechtbauer
Department of Psychiatry and Neuropsychology
School for Mental Health and Neuroscience
Maastricht University, P.O. Box 616
6200 MD Maastricht, The Netherlands
Tel: +31 (43) 368-5248
Fax: +31 (43) 368-8689
Web: http://www.wvbauer.com
-Original Message-
From: Samor Gandhi [mailto:samorgan...@yahoo.com]
Sent: Tuesday, April 12, 2011 11:52
To: r-h...@stat.math.ethz.ch; Viechtbauer Wolfgang (STAT)
Subject: RE: [R] forest + igraph ?
Thank you for your reply. I would like to have two forest plots one on
top
and the other on the bottom. I am using R version 2.12.2 (32-bit)
Windows.
The code you sent me still plotting two windows one after the other?
Best wishes and many thanks,
Samor
--- On Tue, 12/4/11, Viechtbauer Wolfgang (STAT)
wolfgang.viechtba...@maastrichtuniversity.nl wrote:
From: Viechtbauer Wolfgang (STAT)
wolfgang.viechtba...@maastrichtuniversity.nl
Subject: RE: [R] forest + igraph ?
To: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch
Cc: Samor Gandhi samorgan...@yahoo.com
Date: Tuesday, 12 April, 2011, 13:42
It is not clear (at least to me) what exactly you want. You want two
forest plots in one graph but apparently not side-by-side or one on
top
and the other on the bottom. So, you want to superimpose them? How do
you
want to do that without creating an illegible mess? Or do you want one
graph, where you can scroll through various plots? Then try this:
library(metafor)
data(dat.bcg)
if (interactive()) {
windows(record=TRUE)
dat - escalc(measure=RR, ai=tpos, bi=tneg, ci=cpos, di=cneg,
data=dat.bcg)
forest(dat$yi, dat$vi)
dat - escalc(measure=OR, ai=tpos, bi=tneg, ci=cpos, di=cneg,
data=dat.bcg)
forest(dat$yi, dat$vi)
}
and then use PageUp and PageDown to switch between the figures.
(I don't know what OS you are using, so windows() may not work).
Best,
--
Wolfgang Viechtbauer
Department of Psychiatry and Neuropsychology
School for Mental Health and Neuroscience
Maastricht University, P.O. Box 616
6200 MD Maastricht, The Netherlands
Tel: +31 (43) 368-5248
Fax: +31 (43) 368-8689
Web: http://www.wvbauer.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org]
On Behalf Of Samor Gandhi
Sent: Monday, April 11, 2011 18:25
To: r-h...@stat.math.ethz.ch
Subject: [R] forest + igraph ?
Hello,
Is it possible to have two meta-plots in one graph (not
par(mfrow=c(2,1))?
But somthing like
library(metafor)
library(igraph)
if (interactive()) {
forest(dat.Treat$RR, ci.lb=dat.Treat$lower, ci.ub=dat.Treat$upper,
xlab=Relative Risk,slab=dat.Treat$ID,refline=1)
forest(dat.Control$RR, ci.lb=dat.Control$lower,
ci.ub=dat.Control$upper, xlab=Relative
Risk,slab=dat.Control$ID,refline=1)
}
i.e. both metaplots on the same graph!
Regards,
Samor
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[R] R 2.13.0 is released
I've rolled up R-2.13.0.tar.gz a short while ago. This is a development release which contains a number of new features. Also, a number of mostly minor bugs have been fixed (but notice that serious build issues were fixed in 2.12.2). See the full list of changes below. You can get it from http://cran.r-project.org/src/base/R-2/R-2.13.0.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: MD5 (AUTHORS) = ac9746b4845ae81f51cfc99262f5 MD5 (COPYING) = eb723b61539feef013de476e68b5c50a MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343 MD5 (FAQ) = 3cbcd5d33708d03431cd13f695d1bcb0 MD5 (INSTALL) = 70447ae7f2c35233d3065b004aa4f331 MD5 (NEWS) = de39d09adf2c02e573722507c610d0f6 MD5 (ONEWS) = 0c3e10eef74439786e5fceddd06dac71 MD5 (OONEWS) = b0d650eba25fc5664980528c147a20db MD5 (R-latest.tar.gz) = ecfb928067cfd932e75135f8b8bba3e7 MD5 (README) = 296871fcf14f49787910c57b92655c76 MD5 (RESOURCES) = 020479f381d5f9038dcb18708997f5da MD5 (THANKS) = 03d783ff71270c77d497fd573d711fd8 MD5 (R-2/R-2.13.0.tar.gz) = ecfb928067cfd932e75135f8b8bba3e7 This is the relevant part of the NEWS file: R News CHANGES IN R VERSION 2.13.0: SIGNIFICANT USER-VISIBLE CHANGES: • replicate() (by default) and vapply() (always) now return a higher-dimensional array instead of a matrix in the case where the inner function value is an array of dimension = 2. • Printing and formatting of floating point numbers is now using the correct number of digits, where it previously rarely differed by a few digits. (See “scientific” entry below.) This affects _many_ *.Rout.save checks in packages. NEW FEATURES: • normalizePath() has been moved to the base package (from utils): this is so it can be used by library() and friends. It now does tilde expansion. It gains new arguments winslash (to select the separator on Windows) and mustWork to control the action if a canonical path cannot be found. • The previously barely documented limit of 256 bytes on a symbol name has been raised to 10,000 bytes (a sanity check). Long symbol names can sometimes occur when deparsing expressions (for example, in model.frame). • reformulate() gains a intercept argument. • cmdscale(add = FALSE) now uses the more common definition that there is a representation in n-1 or less dimensions, and only dimensions corresponding to positive eigenvalues are used. (Avoids confusion such as PR#14397.) • Names used by c(), unlist(), cbind() and rbind() are marked with an encoding when this can be ascertained. • R colours are now defined to refer to the sRGB color space. The PDF, PostScript, and Quartz graphics devices record this fact. X11 (and Cairo) and Windows just assume that your screen conforms. • system.file() gains a mustWork argument (suggestion of Bill Dunlap). • new.env(hash = TRUE) is now the default. • list2env(envir = NULL) defaults to hashing (with a suitably sized environment) for lists of more than 100 elements. • text() gains a formula method. • IQR() now has a type argument which is passed to quantile(). • as.vector(), as.double() etc duplicate less when they leave the mode unchanged but remove attributes. as.vector(mode = any) no longer duplicates when it does not remove attributes. This helps memory usage in matrix() and array(). matrix() duplicates less if data is an atomic vector with attributes such as names (but no class). dim(x) - NULL duplicates less if x has neither dimensions nor names (since this operation removes names and dimnames). • setRepositories() gains an addURLs argument. • chisq.test() now also returns a stdres component, for standardized residuals (which have unit variance, unlike the Pearson residuals). • write.table() and friends gain a fileEncoding argument, to simplify writing files for use on other OSes (e.g. a spreadsheet intended for Windows or Mac OS X Excel). • Assignment expressions of the form foo::bar(x) - y and foo:::bar(x) - y now work; the replacement functions used are foo::`bar-` and foo:::`bar-`. • Sys.getenv() gains a names argument so Sys.getenv(x, names = FALSE) can replace the common idiom of as.vector(Sys.getenv()). The default has been changed to not name a length-one result. • Lazy loading of environments now preserves attributes and locked status. (The locked status of bindings and active bindings are still not preserved; this may be addressed in the future). • options(install.lock) may be set to FALSE so that install.packages()
[R] R plots pdf() does not allow spotcolors?
Hi We are about to publish a book, which contains figures made with R plots. An important detail that we did not take into account is that the book will not be printed in 4 colors (cmyk mode), but only 2 (black +spotcolor). The spotcolor we use is part of the big Pantone family. The problem is that both pdf() and postscript() offer either rgb or cmyk, but no spotcolors such as pantone. I'm afraid this constraint can't be solved at all, and we can't use R for creating these plots? I did not find any package that would extend the colormodel to include spot colors... Did anyone had a similar experience? Thanks!! Matthieu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] MLE where loglikelihood function is a function of numerical solutions
Albyn and others,
Thank you for your replies.
In order to be more specific I've constructed my program. I know it's long
and in some places quite messy. It works until the last part where the
log-likelihood function has to be defined and maximized wrt the parameters.
The log-likelihood has the form L = 1/T*sum_t=0^T[log(transdens(v_t,
r_t))-log(Jac(r_t,v_t))], where the functions transdens(v_t, r_t) and
Jac(r_t,v_t) are defined below.
The problem remains the same, how do I construct the log-likelihood function
such that the numerical procedures employed are updated in the maximization
procedure?
I was thinking something along the lines of
minuslogLik - function(x,x2)
{f - rep(NA, length(x))
for(i in 1:T)
{
f[1] - -1/T*sum(log(transdens(parameters = parameters, x =
c(v[i],v[i+1])))-log(Jac(outmat=outmat, x2=c(v[i],r[i])))
}
f
}
Thank you in advance.
Kristian
--Program starts
here--
# Solving ODEs
parameters - c(K_vv- 0.0047,
K_rv--0.0268,
K_rr-0.3384,
theta_v - 50,
theta_r -5.68,
Sigma_rv-0.0436,
Sigma_rr-0.1145,
lambda_v-0,
lambda_r--0.0764,
k_v-K_vv*theta_v,
k_r- K_rv*theta_v+K_rr*theta_r,
alpha_r - 0,
B_rv- (Sigma_rr+Sigma_rv)^2)
#declaring state variables i.e. the functions and their intial conditions
state - c(b_1 = 0,
b_2 = 0,
a = 0)
#delclaring function and system of equations.
Kristian - function(t, state, parameters)
{
with(as.list(c(state, parameters)),
{
db_1 =
-((K_vv+lambda_v)*b_1+(K_rv+Sigma_rv*lambda_v+Sigma_rr*lambda_r)*b_2+0.5*(b_1)^2+Sigma_rv*b_1*b_2+0.5*((Sigma_rv)^2+(Sigma_rr)^2)*(b_2)^2
)
db_2 = -K_rr*b_2+1
da = K_vv*theta_v*b_1+(K_rv*theta_v+K_rr*theta_r)*b_2
list(c(db_1, db_2, da))
})
}
# time making a sequence from t to T evaluated at each delta seq(t, T, by =
delta)
times - seq(0, 10, by = 0.5)
#solving the model using the deSolve function ode
library(deSolve)
outmat - ode(y = state, times = times, func = Kristian, parms = parameters)
#print(outmat)
#Solving 2 equations in 2 unknowns using nleslv
# simulating data for testing
c2 - matrix(data = rnorm(20, mean =0, sd =1)+2, nrow = 20, ncol =1)
c10 - matrix(data = rnorm(20, mean =0, sd =1)+5, nrow = 20, ncol =1)
besselinput - matrix(data = 0, nrow =20, ncol = 1)
vncChi - matrix(data = 0, nrow =20, ncol = 1)
v - matrix(data = 0, nrow =20, ncol = 1)
r - matrix(data = 0, nrow =20, ncol = 1)
for(i in 1:20)
{
Bo - function(x, s, outmat)
{
f - rep(NA, length(x))
z - - outmat[,2:4] %*% c(x[2],x[1],1)
f[1] - (1-exp(z[4]))/sum(exp(z[1:4])) - s[1]
f[2] - (1-exp(z[20]))/sum(exp(z)) - s[2]
f
}
s - c(c2[i],c10[i] )
p - c(50, 5)
# loading nleqslv package
library(nleqslv)
ans.nlq - nleqslv(x=p, fn=Bo, s=s, outmat=outmat, control = list(matxit
=10))
v[i] - ans.nlq$x[1]
r[i] - ans.nlq$x[2]
#print(ans.nlq$termcd)
#ans.nlq$fvec
}
#calculating transition density as a function of parameters
transdens - function(parameters, x)
{
delta -1
c - 2*K_vv*(1-exp(-K_vv*delta))^(-1) #2.004704
q - 2*k_v-1 #0.00959666
f - rep(NA, 1)
#besselinput[2] - 2*c*(x[2]*x[1]*exp(-K_vv*delta))^(0.5)
f[1]-
c*exp(c*(x[2]+exp(-K_vv*delta)*x[1]))*(x[2]/(exp(-K_vv*delta)*x[1]))^(q/2)*besselI(2*c*(x[2]*x[1]*exp(-K_vv*delta))^(0.5),
q, expon.scaled = FALSE)
f
}
vncChi - transdens(parameters = parameters, x=c(v[1],v[2]))
print(vncChi)
#calculating Determinant of Jacobian as a function of outmat.
Jac - function(outmat, x2){
f - rep(NA, 1)
y - - outmat[,2:4] %*% c(x2[1],x2[2],1)
w1 - outmat[,2]*exp(-outmat[,2:4] %*% c(x2[1],x2[2],1))
w2 - outmat[,3]*exp(-outmat[,2:4] %*% c(x2[1],x2[2],1))
f[1] - abs((outmat[5,2]*exp(y[4])/(sum(exp(y[1:4])))+
(1-exp(y[4]))*sum(w1[1:4])/(sum(exp(y[1:4])))^2)*(outmat[21,3]
*exp(y[21])/(sum(exp(y)))+(1-exp(y[21]))*sum(w2)/
(sum(exp(y)))^2)-(outmat[21,2]*exp(y[21])/(sum(exp(y)))
+(1-exp(y[21]))*sum(w1)/(sum(exp(y)))^2)*(outmat[5,3]
*exp(y[4])/(sum(exp(y[1:4])))+(1-exp(y[4]))*sum(w2[1:4])
/(sum(exp(y[1:4])))^2))
f
}
#--Program works as it is
supposed to until here
#Maximum likelihood estimation using mle package
library(stats4)
#defining loglikelighood function
#T - length(v)
#minuslogLik - function(x,x2)
#{f - rep(NA, length(x))
#for(i in 1:T)
#{
#f[1] - -1/T*sum(log(transdens(parameters = parameters, x =
c(v[i],v[i+1])))-log(Jac(outmat=outmat, x2=c(v[i],r[i])))
#}
#f
}
2011/4/10 Albyn Jones jo...@reed.edu
to clarify: by if you knew that LL(psi+eps) were well
[R] strategy for writing out file with lines header initiated with comment sign
Dear all, I have data.frame object in R. I want to export it in tab-delimited file with several lines of header initiated with comment sign (#). I do not know how to do that in R. Could you please give helps on this problem? Thanks in advance. Best, Jian-Feng, ## The lines I want to write in the header lines look like, with words in the last line (here the line #CHROM POS IDREF ALTQUAL FILTER INFO FORMAT NA1) be separated by tab : ##fileformat=VCFv4.1 ##fileDate=20090805 ##source=myImputationProgramV3.1 ##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta ##contig=ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species=Homo sapiens,taxonomy=x ##phasing=partial ##INFO=ID=NS,Number=1,Type=Integer,Description=Number of Samples With Data ##INFO=ID=DP,Number=1,Type=Integer,Description=Total Depth ##INFO=ID=AF,Number=A,Type=Float,Description=Allele Frequency ##INFO=ID=AA,Number=1,Type=String,Description=Ancestral Allele ##INFO=ID=DB,Number=0,Type=Flag,Description=dbSNP membership, build 129 ##INFO=ID=H2,Number=0,Type=Flag,Description=HapMap2 membership ##FILTER=ID=q10,Description=Quality below 10 ##FILTER=ID=s50,Description=Less than 50% of samples have data ##FORMAT=ID=GT,Number=1,Type=String,Description=Genotype ##FORMAT=ID=GQ,Number=1,Type=Integer,Description=Genotype Quality ##FORMAT=ID=DP,Number=1,Type=Integer,Description=Read Depth ##FORMAT=ID=HQ,Number=2,Type=Integer,Description=Haplotype Quality #CHROM POS IDREF ALTQUAL FILTER INFO FORMAT NA1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is there a better way to parse strings than this?
Hi:
Here's one approach:
strings - c(
A5.Brands.bought...Dulux,
A5.Brands.bought...Haymes,
A5.Brands.bought...Solver,
A5.Brands.bought...Taubmans.or.Bristol,
A5.Brands.bought...Wattyl,
A5.Brands.bought...Other)
slist - strsplit(strings, '\\.\\.\\.')
# Conversion to data frame:
library(plyr)
ldply(slist, rbind)
V1 V2
1 A5.Brands.bought Dulux
2 A5.Brands.bought Haymes
3 A5.Brands.bought Solver
4 A5.Brands.bought Taubmans.or.Bristol
5 A5.Brands.bought Wattyl
6 A5.Brands.bought Other
# Conversion to matrix:
laply(slist, rbind)
do.call(rbind, slist)
...and one can subselect from there.
HTH,
Dennis
On Tue, Apr 12, 2011 at 9:07 PM, Chris Howden
ch...@trickysolutions.com.auwrote:
Hi Everyone,
I needed to parse some strings recently.
The code I've wound up using seems rather clunky, and I was wondering if
anyone had any suggestions on a better way?
Basically I do the following:
1) Use substr() to do the parsing
2) Use regexpr() to find the location of the string I want to parse on, I
then pass this onto substr()
3) Use nchar() as the stop input to substr() where necessary
I've got a simple example of the parsing code I used below. It takes
questionnaire variable names that includes the question and the brand it
was answered for and then parses it so the variable name and the brand are
in separate columns. I then use this to restructure the data from
unstacked to stacked, but that's another story.
# this is the data set
test
[1] A5.Brands.bought...Dulux
[2] A5.Brands.bought...Haymes
[3] A5.Brands.bought...Solver
[4] A5.Brands.bought...Taubmans.or.Bristol
[5] A5.Brands.bought...Wattyl
[6] A5.Brands.bought...Other
# Where do I want to parse?
break1 - regexpr('...',test, fixed=TRUE)
break1
[1] 17 17 17 17 17 17
attr(,match.length)
[1] 3 3 3 3 3 3
# Put Variable name in a variable
str1 - substr(test,1,break1-1)
str1
[1] A5.Brands.bought A5.Brands.bought A5.Brands.bought
A5.Brands.bought
[5] A5.Brands.bought A5.Brands.bought
# Put Brand name in a variable
str2 - substr(test,break1+3, nchar(test))
str2
[1] Dulux Haymes Solver
[4] Taubmans.or.Bristol Wattyl Other
Thanks for any and all suggestions
Chris Howden
Founding Partner
Tricky Solutions
Tricky Solutions 4 Tricky Problems
Evidence Based Strategic Development, IP Commercialisation and Innovation,
Data Analysis, Modelling and Training
(mobile) 0410 689 945
(fax / office) (+618) 8952 7878
ch...@trickysolutions.com.au
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http://www.R-project.org/posting-guide.html
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] The three routines in R that calculate the wilcoxon signed-rank test give different p-values.......which is correct?
On 2011-04-12 16:57, Michael G Rupert wrote: I have a question concerning the Wilcoxon signed-rank test, and specifically, which R subroutine I should use for my particular dataset. There are three different commands in R (that I'm aware of) that calculate the Wilcoxon signed-rank test; wilcox.test, wilcox.exact, and wilcoxsign_test. When I run the three commands on the same dataset, I get different p-values. I'm hoping that someone can give me guidance on the strengths and weaknesses of each command, why they produce different p-values, and which one is the most appropriate for my particular needs. First, let me describe the dataset I am working with. The project I am working on collected water samples from groups/networks of about 30 water wells and analyzed them for nitrate, major ions, and other chemical constituents. We revisited those same wells about 10 years later and analyzed the water samples for the same chemical constituents. I now have a paired dataset, and the question I would like to answer is whether there was a significant change in concentrations of those chemical constituents (such as nitrate or chloride). Concentrations measured in water from some wells have increased, some have decreased, and some have stayed the same over the ten-year time period. In water from some wells, the concentrations were below the laboratory detection limits, so those concentrations are tied at the reporting level. The following is an example of the data I am evaluating. x- c(13.60, 9.10, 22.01, 9.08, 1.97, 2.81, 0.66, 0.97, 0.21, 2.23, 0.08, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 3.44, 15.18, 5.25, 4.27, 17.81) y- c( 4.32, 3.39, 16.36, 7.10, 0.08, 2.02, 0.19, 0.59, 0.06, 2.15, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 4.02, 16.13, 7.30, 7.98, 24.37) The nonparametric Wilcoxon signed-rank test seems to be the most appropriate test for these data. There are two different methods to calculate the signed-rank test. The first is by Wilcoxon (1945), who discards any tied data and then calculates the signed ranks. The second method incorporates tied values in the ranking procedure (see J.W. Pratt, 1959, Remarks on zeros and ties in the Wilcoxon signed rank procedure: Journal of the American Statistical Association, Vol. 54, No. 287, pp. 655-667). There are two commands in R that calculate the original method by Wilcoxon (that I know of), wilcox.test and wilcoxsign_test (make sure to include the argument zero.method = c(Wilcoxon)). There are two other commands in R that incorporate ties in the signed-rank test, wilcox.exact and wilcoxsign_test (make sure to include the argumentzero.method = c(Pratt)). Here's my problem. I get different p-values from each of the 4 signed-rank tests in R, and I don't know which one to believe. Wilcox.test and wilcoxsign_test(zero.method = c(Wilcoxon) calculate the standard Wilcoxon signed-rank test. Even though they are not designed to deal with tied data, they should at least calculate the same p-value, but they do not. I ran the same datasets in SYSTAT and Minitab to check on the results from R. Minitab gives the same results as wilcox.test, and SYSTAT gives the same results as wilcoxsign_test(zero.method = c(Wilcoxon). Similarly, wilcox.exact and wilcoxsign_test(zero.method = c(Pratt)) are designed to incorporate ties, but they give different p-values from each other. The signed-rank test procedure is relatively straightforward, so I'm surprised I'm not getting identical results. To check on these R commands, I calculated the signed-rank tests using the dataset shown on page 658-659 of Pratt (1959). These R routines do not produce the same results as that listed in Pratt, which makes me think that the R routines are not calculating the statistics correctly. Ahem that's a pretty strong claim. Actually, the problem is user misunderstanding and the relevant help pages do tell you where the differences lie. Let's take the 3 functions one at a time, using your x,y data from Pratt: 1. wilcox.test() in the stats package This function automatically switches to using a Normal approximation when there are ties in the data: wilcox.test(x, y, paired=TRUE)$p.value #[1] 0.05802402 (You can suppress the warning (due to ties) by specifying the argument 'exact=FALSE'.) This function also uses a continuity correction unless told not to: wilcox.test(x, y, paired=TRUE, correct=FALSE)$p.value #[1] 0.05061243 2. wilcox.exact() in pkg exactRankTests This function can handle ties (using the Wilcoxon method) with an 'exact' calculation: wilcox.exact(x, y, paired=TRUE)$p.value #[1] 0.0546875 If you want the Normal approximation: wilcox.exact(x, y, paired=TRUE, exact=FALSE)$p.value #[1] 0.05061243 -- cf. above 3. wilcoxsign_test() in pkg coin This is the most comprehensive of these functions. It is also the only one that offers the Pratt method of handling ties. It will default to this
Re: [R] The three routines in R that calculate the wilcoxon signed-rank test give different p-values.......which is correct?
On Apr 13, 2011, at 01:57 , Michael G Rupert wrote: I have a question concerning the Wilcoxon signed-rank test, and specifically, which R subroutine I should use for my particular dataset. There are three different commands in R (that I'm aware of) that calculate the Wilcoxon signed-rank test; wilcox.test, wilcox.exact, and wilcoxsign_test. When I run the three commands on the same dataset, I get different p-values. I'm hoping that someone can give me guidance on the strengths and weaknesses of each command, why they produce different p-values, and which one is the most appropriate for my particular needs. Well, there are two version of zero-handling, and for each of these, you can have exact p values or asymptotic p values with or without continuity correction, so that's 6 possibilities already. First, let me describe the dataset I am working with. The project I am working on collected water samples from groups/networks of about 30 water wells and analyzed them for nitrate, major ions, and other chemical constituents. We revisited those same wells about 10 years later and analyzed the water samples for the same chemical constituents. I now have a paired dataset, and the question I would like to answer is whether there was a significant change in concentrations of those chemical constituents (such as nitrate or chloride). Concentrations measured in water from some wells have increased, some have decreased, and some have stayed the same over the ten-year time period. In water from some wells, the concentrations were below the laboratory detection limits, so those concentrations are tied at the reporting level. The following is an example of the data I am evaluating. x - c(13.60, 9.10, 22.01, 9.08, 1.97, 2.81, 0.66, 0.97, 0.21, 2.23, 0.08, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 3.44, 15.18, 5.25, 4.27, 17.81) y - c( 4.32, 3.39, 16.36, 7.10, 0.08, 2.02, 0.19, 0.59, 0.06, 2.15, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 0.06, 4.02, 16.13, 7.30, 7.98, 24.37) The nonparametric Wilcoxon signed-rank test seems to be the most appropriate test for these data. There are two different methods to calculate the signed-rank test. The first is by Wilcoxon (1945), who discards any tied data and then calculates the signed ranks. The second method incorporates tied values in the ranking procedure (see J.W. Pratt, 1959, Remarks on zeros and ties in the Wilcoxon signed rank procedure: Journal of the American Statistical Association, Vol. 54, No. 287, pp. 655-667). There are two commands in R that calculate the original method by Wilcoxon (that I know of), wilcox.test and wilcoxsign_test (make sure to include the argument zero.method = c(Wilcoxon)). There are two other commands in R that incorporate ties in the signed-rank test, wilcox.exact and wilcoxsign_test (make sure to include the argumentzero.method = c(Pratt)). Here's my problem. I get different p-values from each of the 4 signed-rank tests in R, and I don't know which one to believe. Wilcox.test and wilcoxsign_test(zero.method = c(Wilcoxon) calculate the standard Wilcoxon signed-rank test. Even though they are not designed to deal with tied data, they should at least calculate the same p-value, but they do not. They do if you turn off the continuity correction in wilcox.test: wilcox.test(x, y, alternative='two.sided', paired=TRUE, correct=F) Wilcoxon signed rank test data: x and y V = 39, p-value = 0.05061 alternative hypothesis: true location shift is not equal to 0 I ran the same datasets in SYSTAT and Minitab to check on the results from R. Minitab gives the same results as wilcox.test, and SYSTAT gives the same results as wilcoxsign_test(zero.method = c(Wilcoxon). So one does continuity correction and the other not. Similarly, wilcox.exact and wilcoxsign_test(zero.method = c(Pratt)) are designed to incorporate ties, but they give different p-values from each other. They still handle zeros differently. wilcox.exact does not handle the Pratt ranking. To get exact p values for Pratt ranks, try perm.test(c(-3,-4,-5,6:11)) 1-sample Permutation Test data: c(-3, -4, -5, 6:11) T = 51, p-value = 0.08984 alternative hypothesis: true mu is not equal to 0 ... and for the asymptotic counterpart: perm.test(c(-3,-4,-5,6:11), exact=F) Asymptotic 1-sample Permutation Test data: c(-3, -4, -5, 6:11) T = 51, p-value = 0.08144 alternative hypothesis: true mu is not equal to 0 The signed-rank test procedure is relatively straightforward, so I'm surprised I'm not getting identical results. To check on these R commands, I calculated the signed-rank tests using the dataset shown on page 658-659 of Pratt (1959). Not found. Apparently, you _constructed_ a data set to get the same set of ranks. These R routines do not
Re: [R] Layout within levelplot from the lattice package
Hi Dieter,
Thank you for that! Your post helped me on my way by introducing me to the
padding settings within lattice, and I'm nearly there now.
My new problem related to this graph is that I would like to add a polygon to
one of the panels, but it seems that my code also adds the polygon to the
paired panel. Is there a way to condition it so that it only appears on the
top panel in column 3?
Here is my updated code:
start = expand.grid(1:10,1:14)
start2 = rbind(start,start,start,start,start,start)
z = rnorm(840)
factor.1 = c(rep(A, 280), rep(B, 280), rep(C, 280))
factor.2 = c(rep(1, 140), rep(2, 140), rep(1, 140), rep(2, 140),
rep(1, 140), rep(2, 140))
data = data.frame(start2, z, factor.1, factor.2)
names(data)[1:2] = c(x, y)
data.A = data[data$factor.1 == A,]
data.B = data[data$factor.1 == B,]
data.C = data[data$factor.1 == C,]
plot.A = levelplot(z~x*y|1*factor.2,data.A,col.regions=heat.colors, strip =
FALSE, asp=iso,xlab = , ylab = , colorkey = list(space=bottom),
scales=list(y=list(draw=F),x=list(draw=F)))
plot.B = levelplot(z~x*y|1*factor.2,data.B,col.regions=topo.colors, strip =
FALSE, asp=iso,xlab = , ylab = , colorkey = list(space=bottom),
scales=list(y=list(draw=F),x=list(draw=F)))
plot.C = levelplot(z~x*y|1*factor.2,data.C,col.regions=terrain.colors, strip =
FALSE, asp=iso,xlab = , ylab = , colorkey = list(space=bottom),
scales=list(y=list(draw=F),x=list(draw=F)),
panel = function(x, y, subscripts, ...) {
panel.levelplot(x, y, subscripts, ...)
panel.polygon(c(2, 5, 5, 2), c(3, 3, 8, 8), col=blue)
}
)
print(plot.A, split=c(1,1,3,1))
print(plot.B, split=c(2,1,3,1), newpage = FALSE)
print(plot.C, split=c(3,1,3,1), newpage = FALSE)
Thanks again for your help!
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[R] AR(1)
Dear all, I would like to ask you if you know any AR(1) function that can create a sequence of values for different time lags. The AR(1) based on a starting value and with the gaussian error can produce this time lags. Could you please help me find a function that can do and does not depend on any sequence? I would like to thank you in advance for your help Best Regards Alex __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] FW: [r] how to enclose two xyplot
Dear R-users, I have to plot two xyplot, and I wish to enclose this two graphs with just one headline, the same x scale, the same grid etc. These parameters should tie in, in order to obtain, visually, a unique graph formed by two xyplot. I try to give an idea: xyplot1: |_|_|_| xyplot2: |_|_|_| what i want: | | | | |_|_|_| I tried to use the command par, but it's doesn't work with xyplot. The two plot have, by default, the same x-axis scale. I know it's just a visual solution, but it could be nice for a paper! Thanks a lot, Francesco Nutini PhD student [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to set the dimension of a matrix correctly?
Lin Pei-Ling barthealin at hotmail.com writes:
Hi all, I use kriging to interpolate the precipitation from
stations, but the map of this results show lots of stripes. (please
see the attachment)I think there's something wrong with the setting
of the dimension of this matrix, however, I have no idea how to know
or test to see if this setting is correct or not.I've tried to
switch the latitude and longitude, but still got the same results
(stripes). Hope anyone can take a look at it and give me some
suggestion. Thanks for help,Peiling
My main suggestion is that you try to boil your example down
to something smaller, simpler, and reproducible. The attention
span of R-helpers is only about 10 minutes, maximum (maybe a little
longer for problems they are particularly interested in), and
it took me almost that long just to reformat your R code so
it was readable.
Often the process of trying to simplify the problem leads
you to discover your own problem.
good luck,
Ben Bolker
--
library(geoR) #functions for geostatistical data analysis
coords- as.matrix(read.table('/Users/R/Code/stncoords.dat'))
ppt- as.matrix(read.table('/Users/R/Code/ppt_15day.dat'))
xx - dim(ppt) # (77,528)
plat - seq(37.5,42,by=0.07273)
plon - seq(-105.5,-93.5,by=0.07273)
pgrid - expand.grid(x=plon,y=plat)
pdim - dim(pgrid) # (10230,2)
#plot(pgrid, cex=0.5)
lat - coords[,1]
lon - coords[,2]
ppt1 - ppt[,1:xx[2]] # 1:528
pptpred - matrix(0,ncol=xx[2],nrow=1)
# Only test one period data##
ptemp - ppt1[,3]
ll - which(ptemp0)
ppt2 - matrix(0,nrow=length(ll),ncol=3) # (lon,lat,ptemp)
ppt2[,1] - lat[ll] # y-axis
ppt2[,2] - lon[ll] # x-axis
ppt2[,3] - ptemp[ll] # ppt
pptd - as.geodata(ppt2)
bin1 - variog(pptd)
## plot(bin1) # fig1
bin2 - variog(pptd,estimator.type=modulus)
## plot(bin2) # fig2
ini1 - max(bin1$v)
ols - variofit(bin1, fix.nugget = FALSE,
weights=cressie,ini.cov.pars=c(ini1,4))
kc - krige.conv(pptd,loc=pgrid,
krige=krige.control(type.krige=OK,trend.d=2nd,
trend.l=2nd,cov.pars=ols[2]$cov.pars))
pvalxx - which(kc$predict 0)
kc$predict[pvalxx] - 0
## ?? something got mangled here ??
## pptpred - kc$predict}else{
## pptpred - 0*(1:pdim[1])}}
## need to fit the lat/lon frame
newpptpred - matrix(pptpred, nrow=62, ncol=165)
plat - seq(37.5,42,by=0.07273) ## repeat from above?
plon - seq(-105.5,-93.5,by=0.07273) ## repeat from above?
lat2 - which((plat 37)(plat 42))
lon2 - which((plon -106)(plon -93))
## fixed ? typos ?
newpptpred - pptpred[lat2,lon2]
nLevel - 60
quartz()
filled.contour(plon,plat,t(newpredppt),
col=rainbow(nLevel),plot.axes={axis(1);axis(2)})
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R plots pdf() does not allow spotcolors?
Matthieu Stigler matthieu.stigler at gmail.com writes: Hi We are about to publish a book, which contains figures made with R plots. An important detail that we did not take into account is that the book will not be printed in 4 colors (cmyk mode), but only 2 (black +spotcolor). The spotcolor we use is part of the big Pantone family. The problem is that both pdf() and postscript() offer either rgb or cmyk, but no spotcolors such as pantone. I'm afraid this constraint can't be solved at all, and we can't use R for creating these plots? I did not find any package that would extend the colormodel to include spot colors... Did anyone had a similar experience? Wasn't aware of spotcolors, but I bet you could hack the PDF reasonably easily (if you have many figures you might have to use awk/sed/perl ?) ... if you don't use R, what is your alternative for creating the figures? Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is there a better way to parse strings than this?
On Wed, Apr 13, 2011 at 5:18 AM, Dennis Murphy djmu...@gmail.com wrote: Hi: Here's one approach: strings - c( A5.Brands.bought...Dulux, A5.Brands.bought...Haymes, A5.Brands.bought...Solver, A5.Brands.bought...Taubmans.or.Bristol, A5.Brands.bought...Wattyl, A5.Brands.bought...Other) slist - strsplit(strings, '\\.\\.\\.') Or with stringr: library(stringr) str_split_fixed(strings, fixed(...), n = 2) # or maybe str_match(strings, (..).*\\.\\.\\.(.*)) Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is there a better way to parse strings than this?
On Wed, Apr 13, 2011 at 12:07 AM, Chris Howden
ch...@trickysolutions.com.au wrote:
Hi Everyone,
I needed to parse some strings recently.
The code I've wound up using seems rather clunky, and I was wondering if
anyone had any suggestions on a better way?
Basically I do the following:
1) Use substr() to do the parsing
2) Use regexpr() to find the location of the string I want to parse on, I
then pass this onto substr()
3) Use nchar() as the stop input to substr() where necessary
I've got a simple example of the parsing code I used below. It takes
questionnaire variable names that includes the question and the brand it
was answered for and then parses it so the variable name and the brand are
in separate columns. I then use this to restructure the data from
unstacked to stacked, but that's another story.
# this is the data set
test
[1] A5.Brands.bought...Dulux
[2] A5.Brands.bought...Haymes
[3] A5.Brands.bought...Solver
[4] A5.Brands.bought...Taubmans.or.Bristol
[5] A5.Brands.bought...Wattyl
[6] A5.Brands.bought...Other
# Where do I want to parse?
break1 - regexpr('...',test, fixed=TRUE)
break1
[1] 17 17 17 17 17 17
attr(,match.length)
[1] 3 3 3 3 3 3
# Put Variable name in a variable
str1 - substr(test,1,break1-1)
str1
[1] A5.Brands.bought A5.Brands.bought A5.Brands.bought
A5.Brands.bought
[5] A5.Brands.bought A5.Brands.bought
# Put Brand name in a variable
str2 - substr(test,break1+3, nchar(test))
str2
[1] Dulux Haymes Solver
[4] Taubmans.or.Bristol Wattyl Other
Try this:
x - c(A5.Brands.bought...Dulux, A5.Brands.bought...Haymes,
+ A5.Brands.bought...Solver)
do.call(rbind, strsplit(x, ..., fixed = TRUE))
[,1] [,2]
[1,] A5.Brands.bought Dulux
[2,] A5.Brands.bought Haymes
[3,] A5.Brands.bought Solver
# or
xa - sub(..., \1, x, fixed = TRUE)
read.table(textConnection(xa), sep = \1, as.is = TRUE)
V1 V2
1 A5.Brands.bought Dulux
2 A5.Brands.bought Haymes
3 A5.Brands.bought Solver
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
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and provide commented, minimal, self-contained, reproducible code.
[R] BackCast and Forecast with stats.arima and forecast.Arima
Hello everyone, I am experiencng some problems in producing forecasts and backcast from an ARIMA(1,0,0) model. I need to produce an insample backcast and a seasonal normal backcast and forecast. I have a seasonal consumption function. By using actual data I get actual demand. By passing Seasonal Normal regressors I need to obtain seasonal normal demand. I tested backcasting in arima by passing data used in the estimation back to the model through predict. This didnt work as the output was different from the fitted value I could see for the estimated model. In other words, in arima I am not able to produce my seasonal normal backcast. I then started looking at Arima in Forecast. By passing the estimated model to Arima I can reproduce the fitted value from the model. My problem comes when I try to apply that model to different dependent (y) data, as the y is supposed to be passed to Arima, so essentially I can do only an in sample backcast for same dependent variable. Is there a way I can get a Seasonal Normal backcast based on the model estimated on actual data but by passing Seasonal Normal regressors? Thanks, Paolo [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] strategy for writing out file with lines header initiated with comment sign
Here is an outline of how to do it using connections:
con - file('/temp/mytemp.txt', 'w')
writeLines(c(#comment, # lines, # in the file), con = con)
# create some data to be output as 'tab' separated
myData - as.data.frame(matrix(letters[1:25], 5))
write.table(myData, file = con, sep = '\t')
close(con)
con - file('/temp/mytemp.txt', 'w')
writeLines(c(#comment, # lines, # in the file), con = con)
# create some data to be output as 'tab' separated
myData - as.data.frame(matrix(letters[1:25], 5))
write.table(myData, file = con, sep = '\t')
close(con)
On Wed, Apr 13, 2011 at 6:15 AM, Mao Jianfeng jianfeng@gmail.com wrote:
Dear all,
I have data.frame object in R. I want to export it in tab-delimited
file with several lines of header initiated with comment sign (#). I
do not know how to do that in R. Could you please give helps on this
problem?
Thanks in advance.
Best,
Jian-Feng,
##
The lines I want to write in the header lines look like, with words in
the last line (here the line #CHROM POS ID REF ALT QUAL
FILTER INFO FORMAT NA1) be
separated by tab :
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species=Homo
sapiens,taxonomy=x
##phasing=partial
##INFO=ID=NS,Number=1,Type=Integer,Description=Number of Samples With Data
##INFO=ID=DP,Number=1,Type=Integer,Description=Total Depth
##INFO=ID=AF,Number=A,Type=Float,Description=Allele Frequency
##INFO=ID=AA,Number=1,Type=String,Description=Ancestral Allele
##INFO=ID=DB,Number=0,Type=Flag,Description=dbSNP membership, build 129
##INFO=ID=H2,Number=0,Type=Flag,Description=HapMap2 membership
##FILTER=ID=q10,Description=Quality below 10
##FILTER=ID=s50,Description=Less than 50% of samples have data
##FORMAT=ID=GT,Number=1,Type=String,Description=Genotype
##FORMAT=ID=GQ,Number=1,Type=Integer,Description=Genotype Quality
##FORMAT=ID=DP,Number=1,Type=Integer,Description=Read Depth
##FORMAT=ID=HQ,Number=2,Type=Integer,Description=Haplotype Quality
#CHROM POS ID REF ALT QUAL FILTER INFO
FORMAT NA1
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
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Data Munger Guru
What is the problem that you are trying to solve?
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R plots pdf() does not allow spotcolors?
On 13-Apr-11 12:30:26, Ben Bolker wrote: Matthieu Stigler matthieu.stigler at gmail.com writes: Hi We are about to publish a book, which contains figures made with R plots. An important detail that we did not take into account is that the book will not be printed in 4 colors (cmyk mode), but only 2 (black +spotcolor). The spotcolor we use is part of the big Pantone family. The problem is that both pdf() and postscript() offer either rgb or cmyk, but no spotcolors such as pantone. I'm afraid this constraint can't be solved at all, and we can't use R for creating these plots? I did not find any package that would extend the colormodel to include spot colors... Did anyone had a similar experience? Wasn't aware of spotcolors, but I bet you could hack the PDF reasonably easily (if you have many figures you might have to use awk/sed/perl ?) ... if you don't use R, what is your alternative for creating the figures? Ben Bolker Don't expect to hack PDF reasonably easily -- for many reasons, one of which is that in PDF different bits of a document can be (and usually are) encapsulated in PDF objects, whose physical location in the PDF file can be pretty random (there is a kind of hash index at the beginning which points to them). So a PDF file can be heavily fragmented (as also can a PS file, though usually not nearly so heavily). In theory it would be possible for every single character in a textual document to be in a separate PDF object and located in random order in the file! As a general comment (which unfortunately doesn't address the main problem raised by Matthieu), it can often be better to use independent software to create figures/diagrams based on numerical results computed by R. R's plots are quite nicely done by default, but tweaking them to achieve a preferred layout in R itself can be painfully time-consuming. Myself, I farm this out to the 'pic' preprocessor in troff/groff, using which any details whatever can be arranged exactly to one's taste. Since spotcolour printing is a multi-pass procedure, one can prepare the separate layers in the respective colours, along with any necessary crop-marks or bulls-eyes, quite easily. However, this too generates PS output in the first instance (convertible to PDF of course), so suffers the same binding to the RGB/CMYK colour paradigm. So Pantone would not be available in the first instance (except insofar as a subset of the Pantone spectrum corresponds to colours in CMYK). However, I presume it is highly likely that there is software which can take a file (PS or PDF) prepared using RGB/CMYK, and convert this to a Pantone-compatible file. Even so, this would depend on what your publisher/printer requires in what you submit. It would be important to obtain from them a full and exact specification of what they require for colour printing in files submitted to them for printing. Hoping this is of some help ... Ted. E-Mail: (Ted Harding) ted.hard...@wlandres.net Fax-to-email: +44 (0)870 094 0861 Date: 13-Apr-11 Time: 14:17:56 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] strategy for writing out file with lines header initiated with comment sign
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 13/04/11 15:15, jim holtman wrote:
Here is an outline of how to do it using connections:
con - file('/temp/mytemp.txt', 'w')
writeLines(c(#comment, # lines, # in the file), con = con)
# create some data to be output as 'tab' separated
myData - as.data.frame(matrix(letters[1:25], 5))
write.table(myData, file = con, sep = '\t')
close(con)
con - file('/temp/mytemp.txt', 'w')
writeLines(c(#comment, # lines, # in the file), con = con)
# create some data to be output as 'tab' separated
myData - as.data.frame(matrix(letters[1:25], 5))
write.table(myData, file = con, sep = '\t')
close(con)
or:
myData - as.data.frame(matrix(letters[1:25], 5))
writeLines(c(#comment, # lines, # in the file), con = ./test.csv)
write.table(myData, ./test.csv, append=TRUE)
Cheers,
Rainer
On Wed, Apr 13, 2011 at 6:15 AM, Mao Jianfeng jianfeng@gmail.com wrote:
Dear all,
I have data.frame object in R. I want to export it in tab-delimited
file with several lines of header initiated with comment sign (#). I
do not know how to do that in R. Could you please give helps on this
problem?
Thanks in advance.
Best,
Jian-Feng,
##
The lines I want to write in the header lines look like, with words in
the last line (here the line #CHROM POS IDREF ALTQUAL
FILTER INFO FORMAT NA1) be
separated by tab :
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species=Homo
sapiens,taxonomy=x
##phasing=partial
##INFO=ID=NS,Number=1,Type=Integer,Description=Number of Samples With
Data
##INFO=ID=DP,Number=1,Type=Integer,Description=Total Depth
##INFO=ID=AF,Number=A,Type=Float,Description=Allele Frequency
##INFO=ID=AA,Number=1,Type=String,Description=Ancestral Allele
##INFO=ID=DB,Number=0,Type=Flag,Description=dbSNP membership, build 129
##INFO=ID=H2,Number=0,Type=Flag,Description=HapMap2 membership
##FILTER=ID=q10,Description=Quality below 10
##FILTER=ID=s50,Description=Less than 50% of samples have data
##FORMAT=ID=GT,Number=1,Type=String,Description=Genotype
##FORMAT=ID=GQ,Number=1,Type=Integer,Description=Genotype Quality
##FORMAT=ID=DP,Number=1,Type=Integer,Description=Read Depth
##FORMAT=ID=HQ,Number=2,Type=Integer,Description=Haplotype Quality
#CHROM POS IDREF ALTQUAL FILTER INFO
FORMAT NA1
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
- --
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D):+49 - (0)3 21 21 25 22 44
email: rai...@krugs.de
Skype: RMkrug
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Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iEYEARECAAYFAk2lo98ACgkQoYgNqgF2egovxwCeN7G2It+1petLynKW37fIqKbW
YIkAmwfMSgfLLZwTGDHJ2dNsVp5muj+7
=Cfj2
-END PGP SIGNATURE-
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R plots pdf() does not allow spotcolors?
On Wed, 13 Apr 2011, Ben Bolker wrote: Matthieu Stigler matthieu.stigler at gmail.com writes: Hi We are about to publish a book, which contains figures made with R plots. An important detail that we did not take into account is that the book will not be printed in 4 colors (cmyk mode), but only 2 (black +spotcolor). The spotcolor we use is part of the big Pantone family. The problem is that both pdf() and postscript() offer either rgb or cmyk, but no spotcolors such as pantone. Well, how could it? R's colour model is sRGB, and it has not other way to refer to colours. The colour model is not at the level of a package I'm afraid this constraint can't be solved at all, and we can't use R for creating these plots? I did not find any package that would extend the colormodel to include spot colors... Did anyone had a similar experience? Wasn't aware of spotcolors, but I bet you could hack the PDF reasonably easily (if you have many figures you might have to use awk/sed/perl ?) ... if you don't use R, what is your alternative for creating the figures? No, PDF is not a text format and not easy to hack. It has a binary index of byte positions so you edit it at your peril. However, this is exactly what professionals have PDF editing tools for. I believe I used Acrobat (not Reader) to do it when I needed to for my books. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] strategy for writing out file with lines header initiated with comment sign
Dear Jim and Rainer,
I learned much from you all. It is my first time to experience the
functions, like file(), writeLines(), close().
Thanks a lot.
Best,
Jian-Feng,
2011/4/13 Rainer M Krug r.m.k...@gmail.com:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 13/04/11 15:15, jim holtman wrote:
Here is an outline of how to do it using connections:
con - file('/temp/mytemp.txt', 'w')
writeLines(c(#comment, # lines, # in the file), con = con)
# create some data to be output as 'tab' separated
myData - as.data.frame(matrix(letters[1:25], 5))
write.table(myData, file = con, sep = '\t')
close(con)
con - file('/temp/mytemp.txt', 'w')
writeLines(c(#comment, # lines, # in the file), con = con)
# create some data to be output as 'tab' separated
myData - as.data.frame(matrix(letters[1:25], 5))
write.table(myData, file = con, sep = '\t')
close(con)
or:
myData - as.data.frame(matrix(letters[1:25], 5))
writeLines(c(#comment, # lines, # in the file), con = ./test.csv)
write.table(myData, ./test.csv, append=TRUE)
Cheers,
Rainer
On Wed, Apr 13, 2011 at 6:15 AM, Mao Jianfeng jianfeng@gmail.com wrote:
Dear all,
I have data.frame object in R. I want to export it in tab-delimited
file with several lines of header initiated with comment sign (#). I
do not know how to do that in R. Could you please give helps on this
problem?
Thanks in advance.
Best,
Jian-Feng,
##
The lines I want to write in the header lines look like, with words in
the last line (here the line #CHROM POS ID REF ALT QUAL
FILTER INFO FORMAT NA1) be
separated by tab :
##fileformat=VCFv4.1
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species=Homo
sapiens,taxonomy=x
##phasing=partial
##INFO=ID=NS,Number=1,Type=Integer,Description=Number of Samples With
Data
##INFO=ID=DP,Number=1,Type=Integer,Description=Total Depth
##INFO=ID=AF,Number=A,Type=Float,Description=Allele Frequency
##INFO=ID=AA,Number=1,Type=String,Description=Ancestral Allele
##INFO=ID=DB,Number=0,Type=Flag,Description=dbSNP membership, build 129
##INFO=ID=H2,Number=0,Type=Flag,Description=HapMap2 membership
##FILTER=ID=q10,Description=Quality below 10
##FILTER=ID=s50,Description=Less than 50% of samples have data
##FORMAT=ID=GT,Number=1,Type=String,Description=Genotype
##FORMAT=ID=GQ,Number=1,Type=Integer,Description=Genotype Quality
##FORMAT=ID=DP,Number=1,Type=Integer,Description=Read Depth
##FORMAT=ID=HQ,Number=2,Type=Integer,Description=Haplotype Quality
#CHROM POS ID REF ALT QUAL FILTER INFO
FORMAT NA1
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
- --
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D): +49 - (0)3 21 21 25 22 44
email: rai...@krugs.de
Skype: RMkrug
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
iEYEARECAAYFAk2lo98ACgkQoYgNqgF2egovxwCeN7G2It+1petLynKW37fIqKbW
YIkAmwfMSgfLLZwTGDHJ2dNsVp5muj+7
=Cfj2
-END PGP SIGNATURE-
--
Jian-Feng, Mao
the Institute of Botany,
Chinese Academy of Botany,
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R plots pdf() does not allow spotcolors?
Prof Brian Ripley ripley at stats.ox.ac.uk writes: On Wed, 13 Apr 2011, Ben Bolker wrote: Matthieu Stigler matthieu.stigler at gmail.com writes: Hi We are about to publish a book, which contains figures made with R plots. An important detail that we did not take into account is that the book will not be printed in 4 colors (cmyk mode), but only 2 (black +spotcolor). The spotcolor we use is part of the big Pantone family. The problem is that both pdf() and postscript() offer either rgb or cmyk, but no spotcolors such as pantone. Well, how could it? R's colour model is sRGB, and it has not other way to refer to colours. The colour model is not at the level of a package I'm afraid this constraint can't be solved at all, and we can't use R for creating these plots? I did not find any package that would extend the colormodel to include spot colors... Did anyone had a similar experience? Wasn't aware of spotcolors, but I bet you could hack the PDF reasonably easily (if you have many figures you might have to use awk/sed/perl ?) ... if you don't use R, what is your alternative for creating the figures? No, PDF is not a text format and not easy to hack. It has a binary index of byte positions so you edit it at your peril. However, this is exactly what professionals have PDF editing tools for. I believe I used Acrobat (not Reader) to do it when I needed to for my books. OK. I was misremembering the good old days when I used to hack the PostScript coming out of gnuplot. I must admit that when I look at PDFs coming out of R, as in pdf(test.pdf) plot(1:10,1:10,pch=16,col=rep(1:5,2),cex=2) dev.off() I still see text-like bits like /sRGB cs 0.000 0.804 0.000 scn that are clearly (by experiment) hackable. That doesn't mean it's easy or a good idea in practice. Re Ted's comment that it's better to compute in R and draw figures outside: that really depends on one's comfort level with various tools and the tradeoffs between (1) command-line control and reproducibility (2) the ability to do subtle visual design adjustments by hand. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] MLE where loglikelihood function is a function of numerical solutions
Questions:
1. why are you defining Bo within a loop?
2. Why are you doing library(nleqslv) within the loop?
Doing both those statements outside the loop once is more efficient.
In your transdens function you are not using the function argument
parameters, why?
Shouldn't there be a with(parameters) since otherwise where is for example
K_vv supposed to come from?
I can't believe that the code worked: in the call of nleqslv you have ...
control=list(matxit=10) ...
It should be maxit and nleqslv will issue an error message and stop (at
least in the latest versions).
And why 10? If that is required, something is not ok with starting
values and/or functions.
Finally the likelihood function at the end of your code
#Maximum likelihood estimation using mle package
library(stats4)
#defining loglikelighood function
#T - length(v)
#minuslogLik - function(x,x2)
#{f - rep(NA, length(x))
#for(i in 1:T)
#{
#f[1] - -1/T*sum(log(transdens(parameters = parameters, x =
c(v[i],v[i+1])))-log(Jac(outmat=outmat, x2=c(v[i],r[i])))
#}
#f
# }
How do the arguments of your function x and x2 influence the calculations in
the likelihood function?
As written now with argument x and x2 not being used in the body of the
function, there is nothing to optimize.
Shouldn't f[1] be f[i] because otherwise the question is why are looping
for( i in 1:T)?
But then returning f as a vector seems wrong here. Shouldn't a likelihood
function return a scalar?
Berend
--
View this message in context:
http://r.789695.n4.nabble.com/MLE-where-loglikelihood-function-is-a-function-of-numerical-solutions-tp3439436p3447224.html
Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R plots pdf() does not allow spotcolors?
Even so, this would depend on what your publisher/printer requires in what you submit. It would be important to obtain from them a full and exact specification of what they require for colour printing in files submitted to them for printing. No one else has mentioned this, but the publisher is trying to make money, not make your life easier. Sometimes the right thing to do is say Hey - you guys are the experts at this, you convert my RGB pdfs to the correct format. It's worthwhile to push back a bit to publishers and get them to do their job. Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Quiz: Who finds the nicest form of X_1^\prime?
Marius Hofert wrote: Haha, I found a hack (using the letter l): plot(0,0,main=expression(italic(X)[1]^bolditalic(l))) Why cheat when you can use a *real* prime character: plot(0, 0, main=expression(paste(italic(X)[1],\u2032))) -- Karl Ove Hufthammer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Merge matrix
Hi Kevin, Sorry.it is not Bt ? A and B are two independent Matrices with equal number rows and different number of columns. dim (A) [1] 30380 104 dim(B) [1] 3038063 I want to combine both A and B to matrix C wheredim(C) [1] 30380 167 So I got the answer C-cbind(A,B) Thanks and regards, Pankaj Regards, Pankaj On Tue, Apr 12, 2011 at 5:36 PM, Kevin E. Thorpe kevin.tho...@utoronto.cawrote: On 04/12/2011 10:54 AM, pankaj borah wrote: I have two matrices A and B dim (A) [1] 30380 104 dim(Bt) [1] 3038063 I want to combine both A and B to matrix C where dim(C) [1] 30380 167 How do I do that ? Assuming that Bt is the transpose of B and you want C = [A|Bt] you could do: C - cbind(A,t(B)) Regards, Pankaj Barah Department of Biology, Norwegian University of Science Technology (NTNU) Realfagbygget, N-7491 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Dalla Lana School of Public Health University of Toronto email: kevin.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.3016 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] iterative method in R software
In confirmatory factor analysis,we need to estimate unknown parameters . I read a book about it,which needs iterative method to estimate parameters,but I don't know it.Does someone konw it?Thank u! -- View this message in context: http://r.789695.n4.nabble.com/iterative-method-in-R-software-tp3446918p3446918.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] split string into individual valus while reading in R
Sorry NULL in V8 should be corrected as NA On Wed, Apr 13, 2011 at 7:33 AM, Ram H. Sharma sharma.ra...@gmail.comwrote: It looks like my question is not clear, I have not get any suggestion, yet let me reiterate my problem: My data looks like this to be read from a text file. As I provided earlier the A, B, and H in V4 column has much longer chain. V1 V2 V3V4 1_1ch1 0.0 AHAH 1_2ch1 0.20 AHAAA ...so on I want to read this as (splitting AHBinto individual characters) V1 V2 V3 V4 V5V6 V7 V8 1_1ch1 0.0 AH AHNA 1_2ch1 0.20 AH AAA Any trick to do this? Thanks; Ram H On Tue, Apr 12, 2011 at 5:19 PM, Ram H. Sharma sharma.ra...@gmail.comwrote: Dear R experts Sorry for posting: I have text file that I need to read into R (this is out from different program). A portion of data look like: ;example data 1_1 ch1 0.0 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_2 ch1 0.1 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_3 ch1 0.1 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_4 ch1 0.2 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_5 ch1 0.2 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_6 ch1 0.3 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_7 ch1 0.3 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_8 ch1 0.4 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_9 ch1 0.4 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_10 ch1 0.5 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_11 ch1 0.5 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_12 ch1 0.6 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHH 1_13 ch1 0.6 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHH 1_14 ch1 0.7 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHH 1_15 ch1 0.7 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHH read_data - read.table (my_text_file.txt,header=F,comment=;) How can I read this into table where columns first five column are maintained as such (e.g. 1_1 ch1 0.0 H ) where as the long single column (filled with A, H, B) split into individual columns. Or alternatively first read using the following command and then able to split the variable 4. Thank you for help; Ram H -- Ram H -- Ram H [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 1 continuous non-normal variable ~ 4 factors + 1 continuous covariate (with interactions)
Thanks, I guess I can do that, and it actually seem appropriate for one of my variable. But can you do post-hoc tests on a survival analysis? Use contrasts or something? -- View this message in context: http://r.789695.n4.nabble.com/1-continuous-non-normal-variable-4-factors-1-continuous-covariate-with-interactions-tp3444378p3446782.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Find characters in a matrix and return a TRUE-FALSE vector
I have the following problem: My data is a matrix of multiple columns and rows. The column I am interested in looks like that (I think it is a column in a matrix that contains a vector each?): [[1]] [1] A B C [4] D E [[2]] [1] A D E [[3]] [1] C E F [4] G I now want to look for a special word (for example C; in my case the single entries are words, not single letters) and return a vector, like [1] TRUE FALSE TRUE Is there an easy way to do it? Sorry, I am really a beginner and I did not really solve the problem by looking into other threads... Thanks a lot, Nina -- View this message in context: http://r.789695.n4.nabble.com/Find-characters-in-a-matrix-and-return-a-TRUE-FALSE-vector-tp3446868p3446868.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] split string into individual valus while reading in R
It looks like my question is not clear, I have not get any suggestion, yet let me reiterate my problem: My data looks like this to be read from a text file. As I provided earlier the A, B, and H in V4 column has much longer chain. V1 V2 V3V4 1_1ch1 0.0 AHAH 1_2ch1 0.20 AHAAA ...so on I want to read this as (splitting AHBinto individual characters) V1 V2 V3 V4 V5V6 V7 V8 1_1ch1 0.0 AH AHNULL 1_2ch1 0.20 AH AAA Any trick to do this? Thanks; Ram H On Tue, Apr 12, 2011 at 5:19 PM, Ram H. Sharma sharma.ra...@gmail.comwrote: Dear R experts Sorry for posting: I have text file that I need to read into R (this is out from different program). A portion of data look like: ;example data 1_1 ch1 0.0 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_2 ch1 0.1 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_3 ch1 0.1 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_4 ch1 0.2 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_5 ch1 0.2 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_6 ch1 0.3 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_7 ch1 0.3 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_8 ch1 0.4 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_9 ch1 0.4 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_10 ch1 0.5 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_11 ch1 0.5 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_12 ch1 0.6 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHH 1_13 ch1 0.6 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHH 1_14 ch1 0.7 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHH 1_15 ch1 0.7 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHH read_data - read.table (my_text_file.txt,header=F,comment=;) How can I read this into table where columns first five column are maintained as such (e.g. 1_1 ch1 0.0 H ) where as the long single column (filled with A, H, B) split into individual columns. Or alternatively first read using the following command and then able to split the variable 4. Thank you for help; Ram H -- Ram H [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ddply and nlminb
Hello
I'm new to R (one week) so please excuse any obvious mistakes in my code
or posting.
I am attempting to fit a non linear function defining the relationship
between dependent variable A and the variables PAR and T grouped by the
condition Di.
The following steps are taken in the Rcode below:
1) load the data (not shown)
2) define the function to be fit
3) define the starting values of the fit parameters and their upper and
lower limits
4) fit the function using all data using nlminb (Di groupings not
considered)
5) estimate the parameter standard errors
6) fit the function with the data grouped by Di using ddply
The first 5 steps appear to be working alright and produce reasonable
fit parameters and parameter errors.
However, when attempting to fit the function with the data grouped by Di
the parameters are returned with the same value for each grouping:
R3Dpar
Di V1 V2
V3 V4V5 V6
1 0.033461 0.06081973 -2.119109e-05 31.75188 -2.631321 17.32565 0.821518
2 0.082682 0.06081973 -2.119109e-05 31.75188 -2.631321 17.32565 0.821518
3 0.133670 0.06081973 -2.119109e-05 31.75188 -2.631321 17.32565 0.821518
4 0.195940 0.06081973 -2.119109e-05 31.75188 -2.631321 17.32565 0.821518
5 0.272430 0.06081973 -2.119109e-05 31.75188 -2.631321 17.32565 0.821518
6 0.368960 0.06081973 -2.119109e-05 31.75188 -2.631321 17.32565 0.821518
7 0.500150 0.06081973 -2.119109e-05 31.75188 -2.631321 17.32565 0.821518
8 0.748380 0.06081973 -2.119109e-05 31.75188 -2.631321 17.32565 0.821518
Can someone point out the error in my ways, and also the correct way to
return both the parameter estimates and the parameter errors.
Thank you
Robert
# END OF CODE
--
# Data loaded in data frame M2 and attached - not shown.
# Define function
fnonRecHypT - function(x){
qeo = x[1]
dqe = x[2]
Fmo = x[3]
TL= x[4]
To= x[5]
TH= 45
theta = x[6]
qe = qeo + dqe*T
theta =
phi = (TH-To)/(To-TL)
Fm = Fmo*((T-TL)*(TH-T)^ phi) / ((To-TL)*(TH-To)^ phi)
Aest = (qe*PAR + Fm - ((qe*PAR + Fm)^2 - 4*theta*qe*PAR*Fm)^0.5)/(2.*theta)
result = sum((Aest-A)^2 )
}
# Define parameter starting values and limits
startval = c(0.05,-0.01,20, -5,15,0.5)
lowval = c(0.01,-0.05, 5,-15, 7,0.1)
uppval = c(0.2, 0.02,50, 0,25,0.99)
# Fit using entire data set
R3 - nlminb(startval, fnonRecHypT, control=list(trace=1),
lower=lowval, upper = uppval)
# estimate fit parameter standard errors
x = R3$par
D3 = hessian(fnonRecHypT,x)
e3 = sqrt(diag(solve(D3)))
# attempt to fit by grouping variable, Di (Di is a real
vector with 8 possible values)
R3Dpar= ddply(M2,
.(Di),
function(x) {res - nlminb(startval, fnonRecHypT,
control=list(trace=1), lower=lowval, upper = uppval)
return(res$par)
}
)
# - END OF CODE
-
--
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University of Edinburgh
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Edinburgh
Scotland
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[R] Boxplot with two or more Y vectors
Hi, for a simple boxplot in R, in the formula is it possible to include two or more Y vectors directly. Or is that only possibility by aggregating the data first? -- Håvard Wahl Kongsgård Peace Research Institute Oslo (PRIO) http://havard.security-review.net/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ordinal predictor in anova
Hi, I have a dataset with a continuous response variable and, among other predictors, an ordinal variable. Here is what it could look like treatment - factor(rep(c(AA, AC, AD,AE, AB), each = 10)) length - c(75, 67, 70, 75, 65, 71, 67, 67, 76, 68, 57, 58, 60, 59, 62, 60, 60, 57, 59, 61, 58, 61, 56, 58, 57, 56, 61, 60, 57, 58, 58, 59, 58, 61, 57, 56, 58, 57, 57, 59, 62, 66, 65, 63, 64, 62, 65, 65, 62, 67) This ordinal variable (treatment) contains 5 classes and can not be recoded as a numerical variable (for example 1, 2,3,4 and 5) because I have no information on the relative difference between classes (it could as well be 1, 24, 25, 50,55). Coding it simply as a categorical variable is also not ok because there is a hierarchy between the groups. This is the definition of ordinal variable. I have defined the ordinal variable (the order is from a priori prediction) #NOW DEFINING THE ORDERED VARIABLE: sugars$treatment_ordered-ordered(sugars$treatment,c(AA, AB,AC, AD,AE)) The problem is that when I run the ANOVA or perform model comparison, R is giving me the same results if I use either treatment as a predictor in the model or treatment_ordered. anova(lm(length ~ treatment_ordered, sugars));anova(lm(length ~ treatment, sugars)) I've thought about using planned contrasts but I do not manage to translate the prediction (AAABAC ADAE) would it be (AA(AB,AC,AD,AE))((AA,AB)(AC,AD,AE))etc etc (-1,0.25,0.25,0.25,0.25)(-0.5,-0.5,0.33,0.33,0.33)... OR (AAAB)(AB,AC)... (-1,1,0,0,0)(0,-1,1,0,0)... and anyway you can only test one matrix at a time. To make thinks a bit more complicated, I also have another factor, categorical variable and I'd like to test the interaction with the ordinal factor (of course sample sizes are higher in the real dataset): treatment - factor(rep(c(AA, AC, AD,AE, AB), each = 10)) length - c(75, 67, 70, 75, 65, 71, 67, 67, 76, 68, 57, 58, 60, 59, 62, 60, 60, 57, 59, 61, 58, 61, 56, 58, 57, 56, 61, 60, 57, 58, 58, 59, 58, 61, 57, 56, 58, 57, 57, 59, 62, 66, 65, 63, 64, 62, 65, 65, 62, 67) treatment2 - c(BA, BA, BB, BB, BC, BC, BD, BD, BE, BE, BA, BA, BB, BB, BC, BC, BD, BD, BE, BE, BA, BA, BB, BB, BC, BC, BD, BD, BE, BE, BA, BA, BB, BB, BC, BC, BD, BD, BE, BE, BA, BA, BB, BB, BC, BC, BD, BD, BE, BE) sugars - data.frame(treatment, length,treatment2) sugars$treatment_ordered-ordered(sugars$treatment,c(AA, AB,AC, AD,AE)) anova(lm(length ~ treatment_ordered+treatment2+treatment_ordered:treatment2, sugars)) Any suggestions? Thanks, V. -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. - End forwarded message - -- Vincent STASZEWSKI Institute of Infection and Immunology Research Ashworth Laboratories Kings' Buildings EH9 3JT Edinburgh Scotland, UK Tel: 0044(0)131 650 8682 webpage: http://reece.bio.ed.ac.uk/vincent-staszewski.html -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Find characters in a matrix and return a TRUE-FALSE vector
Hi Nina, You might try sapply(yourdata, function(x) any(x == C)) See ?sapply for more details. HTH, Jorge On Wed, Apr 13, 2011 at 7:17 AM, Vitrifizierung wrote: I have the following problem: My data is a matrix of multiple columns and rows. The column I am interested in looks like that (I think it is a column in a matrix that contains a vector each?): [[1]] [1] A B C [4] D E [[2]] [1] A D E [[3]] [1] C E F [4] G I now want to look for a special word (for example C; in my case the single entries are words, not single letters) and return a vector, like [1] TRUE FALSE TRUE Is there an easy way to do it? Sorry, I am really a beginner and I did not really solve the problem by looking into other threads... Thanks a lot, Nina -- View this message in context: http://r.789695.n4.nabble.com/Find-characters-in-a-matrix-and-return-a-TRUE-FALSE-vector-tp3446868p3446868.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Overcoming warning in package zoo
Dear R users,I have a long program that I am trying to run--I am using RStudio as my interface with R. The pieces of the program run well individually but when I try to run everything in sequence it bogs down because of a warning after using rollmax from package zoo. Here is the warning: In rollmax.zoo(zoo(Pmat), 7, na.pad = FALSE, align = right) : na.pad is deprecated. Use fill. The code that generates this warning islibrary(zoo)Pmax - as.data.frame(rollmax(zoo(Pmat), 7, na.pad = FALSE, align = right)) I also obtain the same warning when I run Pmax - as.data.frame(rollmax(zoo(Pmat), 7, na.pad = TRUE, align = right)) Note that Pmat is a 136x271 double matrix and Pmax is a dataframe (265 obs. of 136 variables). The function rollmax is doing exactly what I want it to do, so my data is as it's supposed to be and everything is fine, except for the warning, that is... The version of zoo that I am running was obtained by running install.packages(zoo, repos = http://r-forge.r-project.org;) So, my ultimate goal is to either find a way for R to ignore this warning and move on to the next step or fix the problem that is causing the warning. Any thoughts or suggestions? Thanks so much and have a great day! Rita If you think education is expensive, try ignorance--Derek Bok [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Overcoming warning in package zoo
On Wed, Apr 13, 2011 at 10:38 AM, Rita Carreira ritacarre...@hotmail.com wrote: Dear R users,I have a long program that I am trying to run--I am using RStudio as my interface with R. The pieces of the program run well individually but when I try to run everything in sequence it bogs down because of a warning after using rollmax from package zoo. Here is the warning: In rollmax.zoo(zoo(Pmat), 7, na.pad = FALSE, align = right) : na.pad is deprecated. Use fill. The code that generates this warning islibrary(zoo)Pmax - as.data.frame(rollmax(zoo(Pmat), 7, na.pad = FALSE, align = right)) I also obtain the same warning when I run Pmax - as.data.frame(rollmax(zoo(Pmat), 7, na.pad = TRUE, align = right)) Note that Pmat is a 136x271 double matrix and Pmax is a dataframe (265 obs. of 136 variables). The function rollmax is doing exactly what I want it to do, so my data is as it's supposed to be and everything is fine, except for the warning, that is... The version of zoo that I am running was obtained by running install.packages(zoo, repos = http://r-forge.r-project.org;) So, my ultimate goal is to either find a way for R to ignore this warning and move on to the next step or fix the problem that is causing the warning. Any thoughts or suggestions? Thanks so much and have a great day! Use the CRAN version of zoo. If you do want to use the development version then surely the error message is pretty explicit in what you have to do. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Removing objects and clearing memory
Hey guys thanks very much for al your responses. It was very helpful.
Jim
On Tue, Apr 12, 2011 at 6:59 PM, Peter Ehlers ehl...@ucalgary.ca wrote:
On 2011-04-12 15:52, seeliger.c...@epamail.epa.gov wrote:
How do I remove all objects except one in R?
rm(list=ls()) #will remove ALL objects
But he wanted to remove all objects ***except one***!!! So what's the
point of this answer?
I can't see any way except a rather round-about kludge to do what the
OP wants. ...
That might work. Or try this, replacing QQQ with the name of the object
you want to keep.
rm(list=ls()[!grepl('^QQQ$',ls())])
cur
package gdata has function keep() which does just what the OP asks for.
Peter Ehlers
--
Thanks,
Jim.
[[alternative HTML version deleted]]
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[R] Wilcoxon rank sum in unbalanced design
Hi everyone! I need to perform a Wilcoxon rank sum test, but I have some ties and the groups have different size also. When I deal with ties I use the wilcox.exact function, how can I solve the different size problem using this function? thanks net -- View this message in context: http://r.789695.n4.nabble.com/Wilcoxon-rank-sum-in-unbalanced-design-tp3447400p3447400.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Decimals in R/SQL
Hello, When I am writing in sqldf or RSQLite I lose the decimals in my matrix. The only way I can get decimals is by multiplying by 1.0, etc. I have tried manipulating the options, but it is only effective once I multiply by 1.. I appreciate any suggestions! Thanks! Example: z - sqldf (select ST, SUM(AGEP*PWGTP)*1.0/SUM(PWGTP)*1.00 as wgtage from ss09 group by ST) z shouldn't be whole numbers. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] glmnet
Hello, I´m trying to in install the package 'glmnet' but I get always the error massage package ‘Matrix’ is not available. I search on you site, but I coundn´t find the package there either. Is their still a package called Matrix? Or how can I use glmnet? Thank You in advance. Kind regards J.Hemmersbach __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] split string into individual valus while reading in R
Hi Ram, Try this on your V4: d - yourdf$V4 unlist(lapply(1:nchar(d),function(x) substr(d,x,x))) HTH steve -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Ram H. Sharma Sent: Wednesday, April 13, 2011 7:34 AM To: r-help@r-project.org Subject: Re: [R] split string into individual valus while reading in R It looks like my question is not clear, I have not get any suggestion, yet let me reiterate my problem: My data looks like this to be read from a text file. As I provided earlier the A, B, and H in V4 column has much longer chain. V1 V2 V3V4 1_1ch1 0.0 AHAH 1_2ch1 0.20 AHAAA ...so on I want to read this as (splitting AHBinto individual characters) V1 V2 V3 V4 V5V6 V7 V8 1_1ch1 0.0 AH AHNULL 1_2ch1 0.20 AH AAA Any trick to do this? Thanks; Ram H On Tue, Apr 12, 2011 at 5:19 PM, Ram H. Sharma sharma.ra...@gmail.comwrote: Dear R experts Sorry for posting: I have text file that I need to read into R (this is out from different program). A portion of data look like: ;example data 1_1 ch1 0.0 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_2 ch1 0.1 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_3 ch1 0.1 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_4 ch1 0.2 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_5 ch1 0.2 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_6 ch1 0.3 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_7 ch1 0.3 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_8 ch1 0.4 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_9 ch1 0.4 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_10 ch1 0.5 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_11 ch1 0.5 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHA 1_12 ch1 0.6 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHH 1_13 ch1 0.6 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHH 1_14 ch1 0.7 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHH 1_15 ch1 0.7 HAAAHHAAAHHAHHAHHAHAHHHAAHHAHHAAAHHAHHAAHAHHHAAAHHHAAAHHAHHHAAAH HHHAHHAAHHAHAAAHAHHAAHAAHAAHHHAHAHHAHH read_data - read.table (my_text_file.txt,header=F,comment=;) How can I read this into table where columns first five column are maintained as such (e.g. 1_1 ch1 0.0 H ) where as the long single column (filled with A, H, B) split into individual columns. Or alternatively first read using the following command and then able to split the variable 4. Thank you for help; Ram H -- Ram H [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R plots pdf() does not allow spotcolors?
Jim Thanks for your feedback! The problem is that the people those responsible for layout are us... We are doing the book in Latex, and till now did not need any other software. But I am scared we will need use kind of Indesign co softwares to be able to use our R plots, since R can't export into spotcolor... Thanks! Mat Le 13/04/2011 13:41, Jim Lemon a écrit : On 04/13/2011 07:15 PM, Matthieu Stigler wrote: Hi We are about to publish a book, which contains figures made with R plots. An important detail that we did not take into account is that the book will not be printed in 4 colors (cmyk mode), but only 2 (black +spotcolor). The spotcolor we use is part of the big Pantone family. The problem is that both pdf() and postscript() offer either rgb or cmyk, but no spotcolors such as pantone. I'm afraid this constraint can't be solved at all, and we can't use R for creating these plots? I did not find any package that would extend the colormodel to include spot colors... Did anyone had a similar experience? Hi Matthieu, I have occasionally had to handle this. In every case, those responsible for the actual layout would take grayscale figures (black, white and some gray level) and then convert the gray level to the desired color in the illustrations. I have always supplied Postscript in these cases. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] glmnet
Janina Hemmersbach janina.hemmersbach at scai.fraunhofer.de writes: Hello, I´m trying to in install the package 'glmnet' but I get always the error massage package ‘Matrix’ is not available. I search on you site, but I coundn´t find the package there either. Is their still a package called Matrix? Or how can I use glmnet? We need more information. What are the results of sessionInfo()? Are you using the latest version of R (at least R 2.12.x)? What repository are you using or trying to use? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plotting line graphs for output from crosstabs function
Hi R-users, This is a generic question, is there a way to plot a line graph for the output from crosstable function? one of the inputs to the crosstab function is categorical. Taby -- [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] glmnet
Am 13.04.2011 16:58, schrieb Janina Hemmersbach: Hello, I´m trying to in install the package 'glmnet' but I get always the error massage package ‘Matrix’ is not available. I search on you site, but I coundn´t find the package there either. Is their still a package called Matrix? Or how can I use glmnet? I had the same error when I tried install.packages(glmnet) However, it worked when I first installed Matrix and then glmnet: install.packages(Matrix) install.packages(glmnet) Have you tried this? -- Alex __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to get the names of all the packages that depend on a give package?
Dear All, I want to check what packages depends on a given package. For example, glmnet depends on Matrix. I want get the names of all the packages that depend on Matrix on CRAN. Is there a way to do so? Thanks! library(glmnet) Loading required package: Matrix Loading required package: lattice -- Tom __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Decimals in R/SQL
You at least have to provide a subset of 'ss09' so we can see what the
original data looks like. I have not had any problems with decimals
in using sqldf.
x - as.data.frame(matrix(runif(100)*100, 10))
x$key - sample(1:3, 10, TRUE)
require(sqldf)
xsum - sqldf('
+ select key, sum(V1 * V2) / sum(V3)
+ from x
+ group by key
+ ')
xsum
key sum(V1 * V2) / sum(V3)
1 1 19.38166
2 2 17.40503
3 3 71.48818
dput(xsum)
structure(list(key = 1:3, `sum(V1 * V2) / sum(V3)` = c(19.3816573628268,
17.4050302312273, 71.4881812227571)), .Names = c(key, sum(V1 * V2) / sum(V3)
), row.names = c(NA, 3L), class = data.frame)
On Wed, Apr 13, 2011 at 11:10 AM, Rachel Licata rach...@kff.org wrote:
Hello,
When I am writing in sqldf or RSQLite I lose the decimals in my matrix.
The only way I can get decimals is by multiplying by 1.0, etc. I
have tried manipulating the options, but it is only effective once I
multiply by 1..
I appreciate any suggestions!
Thanks!
Example:
z - sqldf (select ST,
SUM(AGEP*PWGTP)*1.0/SUM(PWGTP)*1.00 as wgtage from
ss09 group by ST)
z shouldn't be whole numbers.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R plots pdf() does not allow spotcolors?
2011/4/13 Matthieu Stigler matthieu.stig...@gmail.com:
Jim
Thanks for your feedback! The problem is that the people those responsible
for layout are us... We are doing the book in Latex, and till now did not
need any other software.
But I am scared we will need use kind of Indesign co softwares to be able
to use our R plots, since R can't export into spotcolor...
I've just had a look into how PostScript handles spot colours, having
been hacking PS files for many years its not something I'd played with
before.
This page gave me a PS file that used spot colours:
http://pslib.sourceforge.net/examples.php
and it seems that you can set a colour using a colour space array:
[ /Separation (PANTONE Violet C)
/DeviceCMYK { dup 0.75 mul exch dup 0.94 mul exch dup
0.00 mul exch 0.00 mul }
] setcolorspace 1.00 setcolor
Now, my screen previewer has no idea what colour PANTONE Violet C is,
so there's an alternative CMYK colour space version. In fact PANTONE
Violet C is just a label. The idea is that when processed for colour
separations the software will use the separation colours.
Now, to get this into R is tricky. Either you have to rewrite the PS
driver or hack the PS output file. I produced a simple R plot with one
purple (col=#FF00FF) blob and saved to a PS file. The bit of the PS
that set the colour was this:
/bg { 1 0 1 rgb } def
1 0 1 rgb
- the two settings here are for the outline and fill of the blob,
which was created using pch=19.
To specify this as a spot colour (with a CMYK alternative for
preview), I changed that to this:
/pvc {
[ /Separation (PANTONE Violet C)
/DeviceCMYK { dup 0.75 mul exch dup 0.94 mul exch dup
0.00 mul exch 0.00 mul }
] setcolorspace
} def
/bg {
pvc 1.00 setcolor
} def
pvc 1.00 setcolor
Now if you only have one or two spot colours and only a few places
where they occur then it might be possible for you to do this kind of
edit/replacement - either manually or automatically. And beware I'm
not even sure this is right or that your publisher would be happy
anyway.
Anyway, thats enough PS hacking for one day.
Barry
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R plots pdf() does not allow spotcolors?
Scribus claims to be able to convert RGB/CMYK colors to spot colors: http://documentation.scribus.net/index.php/Spot_Colors I've never used Scribus, but it's floss. Jeremy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Decimals in R/SQL
Thanks Jim. It appears the issue may only be in SQLite. SS09 is a large table
and here is a subset of the variables I am working with.
SS09
ST AGEPPWGTP
33323130 130
33324110 186
333251 2 162
33326180 93
33327129 135
33328166 54
33329162 54
0121 138
1129 103
21 7 144
31 5 143
z - dbGetQuery( connSQLite , select ST, SUM(AGEP*PWGTP/SUM(PWGTP) as wgtage
from ss09 group by ST)
ST wgtage
1 1 37
2 2 33
3 4 36
4 5 37
5 6 35
z - dbGetQuery( connSQLite , select ST,
SUM(AGEP*PWGTP)*1.0/SUM(PWGTP)*1.00 as wgtage from ss09
group by ST)
ST wgtage
1 1 37.57083
2 2 33.94322
3 4 36.14499
4 5 37.51233
5 6 35.65581
-Original Message-
From: jim holtman [mailto:jholt...@gmail.com]
Sent: Wednesday, April 13, 2011 12:16 PM
To: Rachel Licata
Cc: r-help@r-project.org
Subject: Re: [R] Decimals in R/SQL
You at least have to provide a subset of 'ss09' so we can see what the
original data looks like. I have not had any problems with decimals
in using sqldf.
x - as.data.frame(matrix(runif(100)*100, 10))
x$key - sample(1:3, 10, TRUE)
require(sqldf)
xsum - sqldf('
+ select key, sum(V1 * V2) / sum(V3)
+ from x
+ group by key
+ ')
xsum
key sum(V1 * V2) / sum(V3)
1 1 19.38166
2 2 17.40503
3 3 71.48818
dput(xsum)
structure(list(key = 1:3, `sum(V1 * V2) / sum(V3)` = c(19.3816573628268,
17.4050302312273, 71.4881812227571)), .Names = c(key, sum(V1 * V2) / sum(V3)
), row.names = c(NA, 3L), class = data.frame)
On Wed, Apr 13, 2011 at 11:10 AM, Rachel Licata rach...@kff.org wrote:
Hello,
When I am writing in sqldf or RSQLite I lose the decimals in my matrix.
The only way I can get decimals is by multiplying by 1.0, etc. I
have tried manipulating the options, but it is only effective once I
multiply by 1..
I appreciate any suggestions!
Thanks!
Example:
z - sqldf (select ST,
SUM(AGEP*PWGTP)*1.0/SUM(PWGTP)*1.00 as wgtage from
ss09 group by ST)
z shouldn't be whole numbers.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R plots pdf() does not allow spotcolors?
On Wed, Apr 13, 2011 at 5:26 PM, Jeremy Hetzel jthet...@gmail.com wrote: Scribus claims to be able to convert RGB/CMYK colors to spot colors: http://documentation.scribus.net/index.php/Spot_Colors I've never used Scribus, but it's floss. Scribus can import output from R's svg driver (with at least some degree of success). I just imported a simple plot to Scribus, specified some spot colours, and saved as EPS - the colours were specified as /Separation colours as described in my earlier message. I did try inkscape for this, but forgot about scribus. Inkscape doesnt seem to have such colour management. Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Decimals in R/SQL
The problem is that you data is 'integer' and I assume that the
database is keeping everything integer. You can do what you are
doing, or convert to 'numeric':
x - read.table(textConnection( ST AGEP
PWGTP
+ 33323130 130
+ 33324110 186
+ 333251 2 162
+ 33326180 93
+ 33327129 135
+ 33328166 54
+ 33329162 54
+ 0121 138
+ 1129 103
+ 21 7 144
+ 31 5 143), header = TRUE)
closeAllConnections()
str(x)
'data.frame': 11 obs. of 3 variables:
$ ST : int 1 1 1 1 1 1 1 1 1 1 ...
$ AGEP : int 30 10 2 80 29 66 62 21 29 7 ...
$ PWGTP: int 130 186 162 93 135 54 54 138 103 144 ...
require(sqldf)
xsum - sqldf('
+ select ST, sum(AGEP * PWGTP) / sum(PWGTP)
+ from x
+ group by ST
+ ')
xsum
ST sum(AGEP * PWGTP) / sum(PWGTP)
1 1 23
# change to numeric instead of integer
x$AGEP - as.numeric(x$AGEP)
str(x)
'data.frame': 11 obs. of 3 variables:
$ ST : int 1 1 1 1 1 1 1 1 1 1 ...
$ AGEP : num 30 10 2 80 29 66 62 21 29 7 ...
$ PWGTP: int 130 186 162 93 135 54 54 138 103 144 ...
xsum - sqldf('
+ select ST, sum(AGEP * PWGTP) / sum(PWGTP)
+ from x
+ group by ST
+ ')
xsum
ST sum(AGEP * PWGTP) / sum(PWGTP)
1 1 23.81446
On Wed, Apr 13, 2011 at 12:42 PM, Rachel Licata rach...@kff.org wrote:
Thanks Jim. It appears the issue may only be in SQLite. SS09 is a large
table and here is a subset of the variables I am working with.
SS09
ST AGEP PWGTP
33323 1 30 130
33324 1 10 186
33325 1 2 162
33326 1 80 93
33327 1 29 135
33328 1 66 54
33329 1 62 54
0 1 21 138
1 1 29 103
2 1 7 144
3 1 5 143
z - dbGetQuery( connSQLite , select ST, SUM(AGEP*PWGTP/SUM(PWGTP) as wgtage
from ss09 group by ST)
ST wgtage
1 1 37
2 2 33
3 4 36
4 5 37
5 6 35
z - dbGetQuery( connSQLite , select ST,
SUM(AGEP*PWGTP)*1.0/SUM(PWGTP)*1.00 as wgtage from ss09
group by ST)
ST wgtage
1 1 37.57083
2 2 33.94322
3 4 36.14499
4 5 37.51233
5 6 35.65581
-Original Message-
From: jim holtman [mailto:jholt...@gmail.com]
Sent: Wednesday, April 13, 2011 12:16 PM
To: Rachel Licata
Cc: r-help@r-project.org
Subject: Re: [R] Decimals in R/SQL
You at least have to provide a subset of 'ss09' so we can see what the
original data looks like. I have not had any problems with decimals
in using sqldf.
x - as.data.frame(matrix(runif(100)*100, 10))
x$key - sample(1:3, 10, TRUE)
require(sqldf)
xsum - sqldf('
+ select key, sum(V1 * V2) / sum(V3)
+ from x
+ group by key
+ ')
xsum
key sum(V1 * V2) / sum(V3)
1 1 19.38166
2 2 17.40503
3 3 71.48818
dput(xsum)
structure(list(key = 1:3, `sum(V1 * V2) / sum(V3)` = c(19.3816573628268,
17.4050302312273, 71.4881812227571)), .Names = c(key, sum(V1 * V2) /
sum(V3)
), row.names = c(NA, 3L), class = data.frame)
On Wed, Apr 13, 2011 at 11:10 AM, Rachel Licata rach...@kff.org wrote:
Hello,
When I am writing in sqldf or RSQLite I lose the decimals in my matrix.
The only way I can get decimals is by multiplying by 1.0, etc. I
have tried manipulating the options, but it is only effective once I
multiply by 1..
I appreciate any suggestions!
Thanks!
Example:
z - sqldf (select ST,
SUM(AGEP*PWGTP)*1.0/SUM(PWGTP)*1.00 as wgtage from
ss09 group by ST)
z shouldn't be whole numbers.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
Re: [R] How to get the names of all the packages that depend on a give package?
Hi: Here's one way, assuming Matrix (or whichever package you want to investigate) is installed on your system: u - installed.packages() u['Matrix', 'Depends'] [1] R (= 2.10.0), stats, methods, utils, lattice HTH, Dennis On Wed, Apr 13, 2011 at 8:57 AM, thmsfuller...@gmail.com thmsfuller...@gmail.com wrote: Dear All, I want to check what packages depends on a given package. For example, glmnet depends on Matrix. I want get the names of all the packages that depend on Matrix on CRAN. Is there a way to do so? Thanks! library(glmnet) Loading required package: Matrix Loading required package: lattice -- Tom __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to get the names of all the packages that depend on a give package?
On Wed, Apr 13, 2011 at 11:57 AM, thmsfuller...@gmail.com thmsfuller...@gmail.com wrote: Dear All, I want to check what packages depends on a given package. For example, glmnet depends on Matrix. I want get the names of all the packages that depend on Matrix on CRAN. Is there a way to do so? Thanks! library(glmnet) Loading required package: Matrix Loading required package: lattice Look at the bottom of this page: http://cran.r-project.org/web/packages/Matrix/index.html -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] B %*% t(B) = R , then solve for B
Correct. In the example I gave you yesterday, I used a different matrix, but showed this solution because it also answered the other question you had about doing it on non-square matrices. Of course, Spencer Graves also gave a very useful answer suggesting QR decomposition. I also gave you the example in the context of linear regression because that is commonly why statisticians will use these factorizations. If your matrix is small, chol() works fine. If your matrix is big and sparse, see Cholesky() in the matrix package (a package that I often refer to as a God-send) -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Shawn Koppenhoefer Sent: Tuesday, April 12, 2011 12:33 PM To: r-help@r-project.org Subject: Re: [R] B %*% t(B) = R , then solve for B Importance: High Solution found... Sorry for not having known this,... Apparently, what I was after is called a Choleski factorization. The solution pops right out of R, as follows: M-matrix(c(0.6098601, 0.2557882, 0.1857773, + 0.2557882, 0.5127065, -0.1384238, + 0.1857773, -0.1384238, 0.9351089 ), + nrow=3, ncol=3, byrow=TRUE) chol(M) [,1] [,2] [,3] [1,] 0.7809354 0.3275408 0.2378907 [2,] 0.000 0.6367288 -0.3397722 [3,] 0.000 0.000 0.8735398 Thanks again for all your help! /shawn __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R plots pdf() does not allow spotcolors?
By the way, I had trouble importing PDFs into Scribus 1.3.3. However, Scribus 1.4.0rc3 had no problem opening multi-page PDFs, assuming the appropriate Ghostscript was also installed (I'm on Windows 7 at the moment). So Matthieu might be able to combine all of his figures into a single PDF, convert to spot color in Scribus, then break the PDF apart again for Latex. Jeremy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] latex, eps graphics and transparent colors
I have a diagram to be included in latex, where all my figures are .eps
graphics (so pdflatex is not an
option) and I want to achieve something
like the following: three concentric filled circles varying in lightness
or saturation. It is easiest to do this using
transparency, but in my test using the postscript driver, the
transparent color fills do not appear. Is it
correct that postscript() does not support transparency?
circle -function (radius = 1, segments=61) {
angles - (0:segments)*2*pi/segments
radius * cbind( cos(angles), sin(angles))
}
plot(1:5, 1:5, type='n', xlim=c(-1,5), ylim=c(-1,5), xlab='', ylab='',
asp=1, xaxt=n, yaxt=n)
#clrs - trans.colors(lightblue, alpha=c(.2, .4, .6)) ## from heplots
package
clrs - c(#ADD8E633, #ADD8E666, #ADD8E699)
c1 - circle(3)
polygon(c1, col=clrs[1], border=lightblue)
polygon(.67*c1, col=clrs[2], border=lightblue)
polygon(.33*c1, col=clrs[3], border=lightblue)
arrows(-1, 0, 5, 0, angle=10, length=.2, lwd=2, col=darkgray)
arrows( 0, -1, 0, 5, angle=10, length=.2, lwd=2, col=darkgray)
One alternative that sort of works is to use the png() driver, and then
convert fig.png fig.eps
but I need very high resolution to make the real diagram legible.
It might suffice to use hcl() colors to approximate what I've done with
transparency,
but I don't know how to start with a given color (lightblue) and
achieve roughly
similar resuts.
--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele StreetWeb: http://www.datavis.ca
Toronto, ONT M3J 1P3 CANADA
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Re: [R] Fwd: CRAN problem with plyr-1.4.1
On 12.04.2011 17:29, Hadley Wickham wrote: Then, can we have the ERROR message, please? Otherwise the only explanation I can guess is that a mirror grabs the contents of a repository exactly in the second the repository is updated and that is unlikely, particularly if more than one mirror is involved. Isn't one possible explanation that PACKAGES.gz on the mirror was updated before the package directory was? It is in the same directory. Uwe That would seem to me a plausible hypothesis to me, because rsync seems to send files in the top level directory before files in directories below. Hadley __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Previously attainable fisher's exact test
I have a matrix say, 1 4 23 30 and I want to find the previously attainable fisher's exact test p-value. Is there a way to do this in R? -- Thanks, Jim. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to get the names of all the packages that depend on a give package?
Dennis Murphy djmuser at gmail.com writes: Hi: Here's one way, assuming Matrix (or whichever package you want to investigate) is installed on your system: u - installed.packages() u['Matrix', 'Depends'] [1] R (= 2.10.0), stats, methods, utils, lattice HTH, Dennis Or, if it's not installed locally, use u - available.packages() u['Matrix', 'Depends'] instead. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Wilcoxon rank sum in unbalanced design
On Apr 13, 2011, at 17:07 , netrunner wrote: Hi everyone! I need to perform a Wilcoxon rank sum test, but I have some ties and the groups have different size also. When I deal with ties I use the wilcox.exact function, how can I solve the different size problem using this function? What problem? Wilcoxon tests work quite happily with unequal group sizes. There's some loss of power due to imbalance, but the only way around _that_ is to move observations from one group to the other... (And exact testing actually solves a slightly different problem than the tie issue, but never mind.) thanks net -- View this message in context: http://r.789695.n4.nabble.com/Wilcoxon-rank-sum-in-unbalanced-design-tp3447400p3447400.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Removing objects and clearing memory
On Wed, Apr 13, 2011 at 11:12 AM, Jim Silverton jim.silver...@gmail.comwrote:
Hey guys thanks very much for al your responses. It was very helpful.
Jim
On Tue, Apr 12, 2011 at 6:59 PM, Peter Ehlers ehl...@ucalgary.ca wrote:
On 2011-04-12 15:52, seeliger.c...@epamail.epa.gov wrote:
How do I remove all objects except one in R?
rm(list=ls()) #will remove ALL objects
But he wanted to remove all objects ***except one***!!! So what's the
point of this answer?
I can't see any way except a rather round-about kludge to do what the
OP wants. ...
That might work. Or try this, replacing QQQ with the name of the object
you want to keep.
rm(list=ls()[!grepl('^QQQ$',ls())])
cur
package gdata has function keep() which does just what the OP asks for.
Peter Ehlers
--
Thanks,
Jim.
--
Thanks,
Jim.
[[alternative HTML version deleted]]
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[R] Data with different time lines for one analysis
Hello I have one data set that is in the range from 1950 to 2009 with yearly values (one value per year), and another one from 1959 to 1983 with 364 values, which means 15 values per year. Now I want to use both sets in some analysis, one for example ccf, but also other analyses. What would you recommend as way to analyze the data? Should I use the lowest date as t=0 and then use days as base for data exploration? And later recreate the real date values from that? I found out that strptime can help me in converting the dates as string into internal POSIX representation, but I now stcuk with how to go on. Ciao, Oliver __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R plots pdf() does not allow spotcolors?
Hi, I may be wrong, but I have the impression that tikz (a LaTeX drawing package) can handle spot colors (that's what Google seemed to tell me [*]). If this is the case you could output R graphics using the tikzDevice package, post-process the output (readable, plain text file), and eventually have LaTeX produce the pdf image with spot colors. Worth a try, perhaps. baptiste [*] http://wiki.contextgarden.net/Colors#In_TikZ On 13 April 2011 21:15, Matthieu Stigler matthieu.stig...@gmail.com wrote: Hi We are about to publish a book, which contains figures made with R plots. An important detail that we did not take into account is that the book will not be printed in 4 colors (cmyk mode), but only 2 (black +spotcolor). The spotcolor we use is part of the big Pantone family. The problem is that both pdf() and postscript() offer either rgb or cmyk, but no spotcolors such as pantone. I'm afraid this constraint can't be solved at all, and we can't use R for creating these plots? I did not find any package that would extend the colormodel to include spot colors... Did anyone had a similar experience? Thanks!! Matthieu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R plots pdf() does not allow spotcolors?
Barry, thanks a lot for checking for this!! Find below answers.
Le 13. 04. 11 18:26, Barry Rowlingson a écrit :
2011/4/13 Matthieu Stiglermatthieu.stig...@gmail.com:
Jim
Thanks for your feedback! The problem is that the people those responsible
for layout are us... We are doing the book in Latex, and till now did not
need any other software.
But I am scared we will need use kind of Indesign co softwares to be able
to use our R plots, since R can't export into spotcolor...
I've just had a look into how PostScript handles spot colours, having
been hacking PS files for many years its not something I'd played with
before.
This page gave me a PS file that used spot colours:
http://pslib.sourceforge.net/examples.php
and it seems that you can set a colour using a colour space array:
[ /Separation (PANTONE Violet C)
/DeviceCMYK { dup 0.75 mul exch dup 0.94 mul exch dup
0.00 mul exch 0.00 mul }
] setcolorspace 1.00 setcolor
Now, my screen previewer has no idea what colour PANTONE Violet C is,
so there's an alternative CMYK colour space version. In fact PANTONE
Violet C is just a label. The idea is that when processed for colour
separations the software will use the separation colours.
Now, to get this into R is tricky. Either you have to rewrite the PS
driver or hack the PS output file. I produced a simple R plot with one
purple (col=#FF00FF) blob and saved to a PS file. The bit of the PS
that set the colour was this:
/bg { 1 0 1 rgb } def
1 0 1 rgb
I do no get something similar... I used:
set.seed(123)
a-runif(100)
postscript(RplotRGB.ps, colormodel=rgb)
plot(a, col=#FF00FF)
dev.off()
Interestingly, I compared with:
postscript(RplotCMYK.ps, colormodel=cmyk)
plot(a, col=#FF00FF)
dev.off()
and making a diff, I see only:
87c87,88
1 0 1 rgb
---
0 1 0 0 setcmykcolor
194c195,196
0 setgray
---
0 0 0 1 setcmykcolor
278c280,281
0 setgray
---
0 0 0 1 setcmykcolor
does not look so similar to what you obtained...
- the two settings here are for the outline and fill of the blob,
which was created using pch=19.
may I ask you what are outline and fill?
To specify this as a spot colour (with a CMYK alternative for
preview), I changed that to this:
/pvc {
[ /Separation (PANTONE Violet C)
/DeviceCMYK { dup 0.75 mul exch dup 0.94 mul exch dup
0.00 mul exch 0.00 mul }
] setcolorspace
} def
/bg {
pvc 1.00 setcolor
} def
pvc 1.00 setcolor
Now if you only have one or two spot colours and only a few places
where they occur then it might be possible for you to do this kind of
edit/replacement - either manually or automatically. And beware I'm
not even sure this is right or that your publisher would be happy
anyway.
no but seems quite a nice solution, as I have only known cmyk colors (5)
for which I can find Pentone matching. Could setup small script then!
Just need to figure out why we do not get similar results you and me!!
Thanks so much!!
Anyway, thats enough PS hacking for one day.
Barry
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[R] Line plots in base graphics
Am I missing something obvious on how to draw multi-line plots in base graphics? In ggplot2, I can do: data(Oxboys, package = nlme) library(ggplot2) qplot(age, height, data = Oxboys, geom = line, group = Subject) But in base graphics, the best I can come up with is this: with(Oxboys, plot(age, height, type = n)) lapply(split(Oxboys[c(age, height)], Oxboys$Subject), lines) Am I missing something obvious? Thanks! Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] latex, eps graphics and transparent colors
Michael Friendly friendly at yorku.ca writes:
I have a diagram to be included in latex, where all my figures are .eps
graphics (so pdflatex is not an
option) and I want to achieve something
like the following: three concentric filled circles varying in lightness
or saturation. It is easiest to do this using
transparency, but in my test using the postscript driver, the
transparent color fills do not appear. Is it
correct that postscript() does not support transparency?
circle -function (radius = 1, segments=61) {
angles - (0:segments)*2*pi/segments
radius * cbind( cos(angles), sin(angles))
}
plot(1:5, 1:5, type='n', xlim=c(-1,5), ylim=c(-1,5), xlab='', ylab='',
asp=1, xaxt=n, yaxt=n)
#clrs - trans.colors(lightblue, alpha=c(.2, .4, .6)) ## from heplots
package
clrs - c(#ADD8E633, #ADD8E666, #ADD8E699)
c1 - circle(3)
polygon(c1, col=clrs[1], border=lightblue)
polygon(.67*c1, col=clrs[2], border=lightblue)
polygon(.33*c1, col=clrs[3], border=lightblue)
arrows(-1, 0, 5, 0, angle=10, length=.2, lwd=2, col=darkgray)
arrows( 0, -1, 0, 5, angle=10, length=.2, lwd=2, col=darkgray)
One alternative that sort of works is to use the png() driver, and then
convert fig.png fig.eps
but I need very high resolution to make the real diagram legible.
It might suffice to use hcl() colors to approximate what I've done with
transparency,
but I don't know how to start with a given color (lightblue) and
achieve roughly
similar resuts.
If you really only want to lighten a specified colour (rather
than overlaying multiple colours), then something like this ought
to do the trick:
testfun - function(clrs=c(#ADD8E633, #ADD8E666, #ADD8E699)) {
plot(1:5, 1:5, type='n', xlim=c(-1,5), ylim=c(-1,5), xlab='', ylab='',
asp=1, xaxt=n, yaxt=n)
c1 - circle(3)
polygon(c1, col=clrs[1], border=lightblue)
polygon(.67*c1, col=clrs[2], border=lightblue)
polygon(.33*c1, col=clrs[3], border=lightblue)
arrows(-1, 0, 5, 0, angle=10, length=.2, lwd=2, col=darkgray)
arrows( 0, -1, 0, 5, angle=10, length=.2, lwd=2, col=darkgray)
}
postscript(testalpha1.ps)
testfun()
dev.off()
lblue - #ADD8E6
alphafy - function(col,alpha=1) {
rr - 1-alpha*(1-c(col2rgb(col)/255))
rgb(rr[1],rr[2],rr[3])
}
alphafy(#ADD8E6)
alphafy(#ADD8E6,alpha=0)
postscript(testalpha2.ps)
testfun(clrs=c(alphafy(lblue,0.2),alphafy(lblue,0.4),alphafy(lblue,0.6)))
dev.off()
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Re: [R] Line plots in base graphics
Hadley Wickham hadley at rice.edu writes: Am I missing something obvious on how to draw multi-line plots in base graphics? In ggplot2, I can do: data(Oxboys, package = nlme) library(ggplot2) qplot(age, height, data = Oxboys, geom = line, group = Subject) But in base graphics, the best I can come up with is this: with(Oxboys, plot(age, height, type = n)) lapply(split(Oxboys[c(age, height)], Oxboys$Subject), lines) [quoting removed to fool gmane] Am I missing something obvious? reshape to wide format and matplot()? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] latex, eps graphics and transparent colors
On Thu, Apr 14, 2011 at 5:30 AM, Michael Friendly frien...@yorku.ca wrote:
I have a diagram to be included in latex, where all my figures are .eps
graphics (so pdflatex is not an
option)
You could use the pdf() device and then use pdf2ps to convert to PostScript.
and I want to achieve something
like the following: three concentric filled circles varying in lightness or
saturation. It is easiest to do this using
transparency, but in my test using the postscript driver, the transparent
color fills do not appear. Is it
correct that postscript() does not support transparency?
circle -function (radius = 1, segments=61) {
angles - (0:segments)*2*pi/segments
radius * cbind( cos(angles), sin(angles))
}
plot(1:5, 1:5, type='n', xlim=c(-1,5), ylim=c(-1,5), xlab='', ylab='',
asp=1, xaxt=n, yaxt=n)
#clrs - trans.colors(lightblue, alpha=c(.2, .4, .6)) ## from heplots
There's now an adjustcolor() function in base R to do this.
package
clrs - c(#ADD8E633, #ADD8E666, #ADD8E699)
c1 - circle(3)
polygon( c1, col=clrs[1], border=lightblue)
polygon(.67*c1, col=clrs[2], border=lightblue)
polygon(.33*c1, col=clrs[3], border=lightblue)
arrows(-1, 0, 5, 0, angle=10, length=.2, lwd=2, col=darkgray)
arrows( 0, -1, 0, 5, angle=10, length=.2, lwd=2, col=darkgray)
One alternative that sort of works is to use the png() driver, and then
convert fig.png fig.eps
but I need very high resolution to make the real diagram legible.
It might suffice to use hcl() colors to approximate what I've done with
transparency,
but I don't know how to start with a given color (lightblue) and achieve
roughly
similar resuts.
It would be useful to have an alpha-blending function for this sort of
purpose, but I don't think we have one.
-thomas
--
Thomas Lumley
Professor of Biostatistics
University of Auckland
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Re: [R] Decimals in R/SQL
Thanks again Jim - that is really helpful and I apologize that I am new to R.
How can I convert to numeric in SQL and when I am working on a table in a
database? The file is huge so that is why I am using SQL and the database to
work through it.
Thanks!
-Original Message-
From: jim holtman [mailto:jholt...@gmail.com]
Sent: Wednesday, April 13, 2011 12:52 PM
To: Rachel Licata
Cc: r-help@r-project.org
Subject: Re: [R] Decimals in R/SQL
The problem is that you data is 'integer' and I assume that the
database is keeping everything integer. You can do what you are
doing, or convert to 'numeric':
x - read.table(textConnection( ST AGEP
PWGTP
+ 33323130 130
+ 33324110 186
+ 333251 2 162
+ 33326180 93
+ 33327129 135
+ 33328166 54
+ 33329162 54
+ 0121 138
+ 1129 103
+ 21 7 144
+ 31 5 143), header = TRUE)
closeAllConnections()
str(x)
'data.frame': 11 obs. of 3 variables:
$ ST : int 1 1 1 1 1 1 1 1 1 1 ...
$ AGEP : int 30 10 2 80 29 66 62 21 29 7 ...
$ PWGTP: int 130 186 162 93 135 54 54 138 103 144 ...
require(sqldf)
xsum - sqldf('
+ select ST, sum(AGEP * PWGTP) / sum(PWGTP)
+ from x
+ group by ST
+ ')
xsum
ST sum(AGEP * PWGTP) / sum(PWGTP)
1 1 23
# change to numeric instead of integer
x$AGEP - as.numeric(x$AGEP)
str(x)
'data.frame': 11 obs. of 3 variables:
$ ST : int 1 1 1 1 1 1 1 1 1 1 ...
$ AGEP : num 30 10 2 80 29 66 62 21 29 7 ...
$ PWGTP: int 130 186 162 93 135 54 54 138 103 144 ...
xsum - sqldf('
+ select ST, sum(AGEP * PWGTP) / sum(PWGTP)
+ from x
+ group by ST
+ ')
xsum
ST sum(AGEP * PWGTP) / sum(PWGTP)
1 1 23.81446
On Wed, Apr 13, 2011 at 12:42 PM, Rachel Licata rach...@kff.org wrote:
Thanks Jim. It appears the issue may only be in SQLite. SS09 is a large
table and here is a subset of the variables I am working with.
SS09
ST AGEP PWGTP
33323 1 30 130
33324 1 10 186
33325 1 2 162
33326 1 80 93
33327 1 29 135
33328 1 66 54
33329 1 62 54
0 1 21 138
1 1 29 103
2 1 7 144
3 1 5 143
z - dbGetQuery( connSQLite , select ST, SUM(AGEP*PWGTP/SUM(PWGTP) as wgtage
from ss09 group by ST)
ST wgtage
1 1 37
2 2 33
3 4 36
4 5 37
5 6 35
z - dbGetQuery( connSQLite , select ST,
SUM(AGEP*PWGTP)*1.0/SUM(PWGTP)*1.00 as wgtage from ss09
group by ST)
ST wgtage
1 1 37.57083
2 2 33.94322
3 4 36.14499
4 5 37.51233
5 6 35.65581
-Original Message-
From: jim holtman [mailto:jholt...@gmail.com]
Sent: Wednesday, April 13, 2011 12:16 PM
To: Rachel Licata
Cc: r-help@r-project.org
Subject: Re: [R] Decimals in R/SQL
You at least have to provide a subset of 'ss09' so we can see what the
original data looks like. I have not had any problems with decimals
in using sqldf.
x - as.data.frame(matrix(runif(100)*100, 10))
x$key - sample(1:3, 10, TRUE)
require(sqldf)
xsum - sqldf('
+ select key, sum(V1 * V2) / sum(V3)
+ from x
+ group by key
+ ')
xsum
key sum(V1 * V2) / sum(V3)
1 1 19.38166
2 2 17.40503
3 3 71.48818
dput(xsum)
structure(list(key = 1:3, `sum(V1 * V2) / sum(V3)` = c(19.3816573628268,
17.4050302312273, 71.4881812227571)), .Names = c(key, sum(V1 * V2) /
sum(V3)
), row.names = c(NA, 3L), class = data.frame)
On Wed, Apr 13, 2011 at 11:10 AM, Rachel Licata rach...@kff.org wrote:
Hello,
When I am writing in sqldf or RSQLite I lose the decimals in my matrix.
The only way I can get decimals is by multiplying by 1.0, etc. I
have tried manipulating the options, but it is only effective once I
multiply by 1..
I appreciate any suggestions!
Thanks!
Example:
z - sqldf (select ST,
SUM(AGEP*PWGTP)*1.0/SUM(PWGTP)*1.00 as wgtage from
ss09 group by ST)
z shouldn't be whole numbers.
[[alternative HTML version deleted]]
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Re: [R] Decimals in R/SQL
On Wed, Apr 13, 2011 at 4:34 PM, Rachel Licata rach...@kff.org wrote: Thanks again Jim - that is really helpful and I apologize that I am new to R. How can I convert to numeric in SQL and when I am working on a table in a database? The file is huge so that is why I am using SQL and the database to work through it. Thanks! There are some examples here (a few of them, as noted, require the development version of sqldf): http://code.google.com/p/sqldf/#15._Why_do_certain_calculations_come_out_as_integer_rather_than -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem with all/all.equal
The help pages for identical() and all.equal() have information that will make it clear why they don't do what you want. In the meantime, I tend to use a construct such as: length(unique(x))==1 But be careful if x is not a vector. No doubt there are other ways. -Don -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 -Original Message- From: Laura Smith smithlaura...@gmail.com Date: Wed, 6 Apr 2011 15:09:14 -0700 To: r-help@r-project.org r-help@r-project.org Subject: [R] problem with all/all.equal Hi! In a function, I may have an instance in which all elements are equal. x - rep(1,5) x [1] 1 1 1 1 1 identical(x) Error in .Internal(identical(x, y, num.eq, single.NA, attrib.as.set)) : 'y' is missing all.equal(x) Error in is.expression(x) : 'x' is missing I don't care what particular value it is, I just want to know if they are all equal. What am I doing wrong, please? Thanks, Laura [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] FW: [r] how to enclose two xyplot
Hi, Have you tried ?c.trellis in the latticeExtra package? HTH, baptiste On 13 April 2011 23:36, Francesco Nutini nutini.france...@gmail.com wrote: Dear R-users, I have to plot two xyplot, and I wish to enclose this two graphs with just one headline, the same x scale, the same grid etc. These parameters should tie in, in order to obtain, visually, a unique graph formed by two xyplot. I try to give an idea: xyplot1: |_|_|_| xyplot2: |_|_|_| what i want: | | | | |_|_|_| I tried to use the command par, but it's doesn't work with xyplot. The two plot have, by default, the same x-axis scale. I know it's just a visual solution, but it could be nice for a paper! Thanks a lot, Francesco Nutini PhD student [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] latex, eps graphics and transparent colors
Thomas Lumley tlumley at uw.edu writes: On Thu, Apr 14, 2011 at 5:30 AM, Michael Friendly friendly at yorku.ca wrote: I have a diagram to be included in latex, where all my figures are .eps graphics (so pdflatex is not an option) You could use the pdf() device and then use pdf2ps to convert to PostScript. Clever. [snip] There's now an adjustcolor() function in base R to do this. That makes my solution more or less obsolete. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Line plots in base graphics
On Wed, Apr 13, 2011 at 2:58 PM, Ben Bolker bbol...@gmail.com wrote: Hadley Wickham hadley at rice.edu writes: Am I missing something obvious on how to draw multi-line plots in base graphics? In ggplot2, I can do: data(Oxboys, package = nlme) library(ggplot2) qplot(age, height, data = Oxboys, geom = line, group = Subject) But in base graphics, the best I can come up with is this: with(Oxboys, plot(age, height, type = n)) lapply(split(Oxboys[c(age, height)], Oxboys$Subject), lines) [quoting removed to fool gmane] Am I missing something obvious? reshape to wide format and matplot()? Hmmm, that doesn't work if your measurements are at different times e.g: Oxboys2 - transform(Oxboys, age = age + runif(234)) Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Decimals in R/SQL
On Wed, Apr 13, 2011 at 1:34 PM, Rachel Licata rach...@kff.org wrote: Thanks again Jim - that is really helpful and I apologize that I am new to R. How can I convert to numeric in SQL and when I am working on a table in a database? The file is huge so that is why I am using SQL and the database to work through it. I believe that RSQLite will do the right thing if you provide the correct types in your schema. So for a new database, you want to make sure that the columns that you want to be numeric are created like: CREATE table sometable (my_data REAL); You should be able to create a new table from an existing table using SQL where the new table has the types you want. + seth -- Seth Falcon | @sfalcon | http://userprimary.net/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] File Save As...
On 13/04/2011 5:20 PM, Gene Leynes wrote:
as of right now
x = function(a) print(a)
attr(x, srcref)
returns NULL in 2.13, am I doing something wrong?
There's a limitation to the debug information: it can't be attached to
a function whose body consists of a single simple expression like
print(a). If you put braces around print(a), it will be attached to the
body of x:
Put this line into a file, and source it:
x - function(a) { print(a) }
source(test.R)
attr(body(x), srcref)
In case you're interested, the reason for this limitation is that there
are some objects in R (NULL is the most obvious one) which can be a
function body but which can't hold attributes. At the time the debug
info is added, the function hasn't been created, but its body has, so
the attribute has to go there.
Duncan Murdoch
(also, should I post this to a new thread, or the development thread?)
About me: I like long walks on the beach, and this is my current version
of R:
t(as.data.frame(R.Version()))
[,1]
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status RC
major 2
minor 13.0
year 2011
month 04
day 11
svn.rev 55409
language R
version.string R version 2.13.0 RC (2011-04-11 r55409)
On Wed, Mar 16, 2011 at 2:44 PM, Gene Leynes gleyne...@gmail.com
mailto:gleynes%...@gmail.com wrote:
Thanks for showing me the link to the code / your response / your
work in general.
It seems that the real magic is happening in the call to the
function attributes, via the line
attr(x, srcref)
I'm guessing that attributes must be defined somewhere deep inside
the R machinery (since I didn't find it as a file in base)... And
there's probably not much benefit for me to know more beyond that.
So, I'll be looking forward to 2.13!
On Tue, Mar 15, 2011 at 3:37 PM, Duncan Murdoch
murdoch.dun...@gmail.com mailto:murdoch.dun...@gmail.com wrote:
On 15/03/2011 2:56 PM, Gene Leynes wrote:
The getSrcFilename function is exactly what I was trying
to describe, and
I'm excited to know that it's on it way!
I have tried to create that type of function, but I didn't
think it was
possible with currently available functions. I would be
interested in
seeing how the new function works, maybe I'll check it out
using the google
code search
toolhttp://www.google.com/codesearch?hl=enlr=q=lang%3Ar+sbtn=Search
http://www.google.com/codesearch?hl=enlr=q=lang%3Ar+sbtn=Search(although
I usually have a hard time making sense of that code).
The source is available in
https://svn.r-project.org/R/trunk/src/library/utils/R/sourceutils.R
Duncan Murdoch
Please let me briefly clarify this part:
But it can. If you open a script and choose save, it
will be saved to the
same place.
I just mean that when you do save as... R doesn't seem to
use the same
information that it uses during a normal save (the directory
or script
name). In other applications like Microsoft Word, or
Python's IDLE (screen
shot attached) the user is shown a dialogue box with the
file name in the
current directory of that file.
This is a very minor annoyance though. I only brought it up
because I
thought it would be easier to explain than asking about a
function that
would do the job of getSrcFilename, which is really what I
was after.
I rarely upgrade my R versions, but this will definitely be
an occasion when
I do!
This makes me want to go back and look at the past release
notes to see what
other goodies I've been overlooking.
Thanks again,
Gene
On Mon, Mar 14, 2011 at 8:17 PM, Duncan
Murdochmurdoch.dun...@gmail.com
mailto:murdoch.dun...@gmail.comwrote:
On 11-03-14 8:12 PM, Gene Leynes wrote:
Yes, I understand. Normally I use Eclipse, which does
what I want for
save as...
The bigger issue is that R can't tell the location of
an open script,
which makes it harder to create new versions of
existing work
But it can. If you open a script and choose save, it
will be saved to the
same place. Or do you mean an executing script? There
are indirect ways to
find the name of the executing script. For example,
in R-devel (to become 2.13.0 next month), you can do this:
[R] for loop performance
Dear list I am running some simulations in R involving reading in several hundred datasets, performing some statistics and outputting those statistics to file. I have noticed that it seems that the time it takes to process of a dataset (or, say, a set of 100 datasets) seems to take longer as the simulation progresses. Has anyone else noticed this? I am curious to know if this has to do with how R processes code in loops or if it might be due to memory usage issues (e.g., repeatedly reading data into the same matrix). Thanks in advance Barth PRIVILEGED AND CONFIDENTIAL INFORMATION This transmittal and any attachments may contain PRIVILEGED AND CONFIDENTIAL information and is intended only for the use of the addressee. If you are not the designated recipient, or an employee or agent authorized to deliver such transmittals to the designated recipient, you are hereby notified that any dissemination, copying or publication of this transmittal is strictly prohibited. If you have received this transmittal in error, please notify us immediately by replying to the sender and delete this copy from your system. You may also call us at (309) 827-6026 for assistance. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] File Save As...
That's very interesting. It's not what I was thinking about or expecting,
but I'm glad to know about it (and it will probably be useful at some
point).
Initially, I was asking for a method to find out the name of the current
script. I mean, the current script that you're editing / running.
However, this is useful. Just by putting a few lines of code, you can
change the working directory with a simple drag and drop. Put the following
lines into a script, and drop it into the R GUI.
curpath = dirname(getSrcFilename(function(){}, full=TRUE))
setwd(curpath)
cat('Now in ', curpath, '\n')
What I was looking for is almost accomplished by this:
filepath = getSrcFilename(function(){}, full=TRUE)
setwd(dirname(filepath))
browser()
Of course, you wouldn't want to stay in browser mode forever...
It would be nice to get the name of your current script with something like
this.file(). Of course, I don't know how that would work if someone typed
it into the console.
I'm genuinely excited to explore the new updates in 2.13. Either it's a
good update, or I'm just now learning enough to appreciate the updates.
Thanks
Gene
On Wed, Apr 13, 2011 at 4:33 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote:
On 13/04/2011 5:20 PM, Gene Leynes wrote:
as of right now
x = function(a) print(a)
attr(x, srcref)
returns NULL in 2.13, am I doing something wrong?
There's a limitation to the debug information: it can't be attached to a
function whose body consists of a single simple expression like print(a).
If you put braces around print(a), it will be attached to the body of x:
Put this line into a file, and source it:
x - function(a) { print(a) }
source(test.R)
attr(body(x), srcref)
In case you're interested, the reason for this limitation is that there are
some objects in R (NULL is the most obvious one) which can be a function
body but which can't hold attributes. At the time the debug info is added,
the function hasn't been created, but its body has, so the attribute has to
go there.
Duncan Murdoch
(also, should I post this to a new thread, or the development thread?)
About me: I like long walks on the beach, and this is my current version
of R:
t(as.data.frame(R.Version()))
[,1]
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status RC
major 2
minor 13.0
year 2011
month 04
day 11
svn.rev 55409
language R
version.string R version 2.13.0 RC (2011-04-11 r55409)
On Wed, Mar 16, 2011 at 2:44 PM, Gene Leynes gleyne...@gmail.com
mailto:gleynes%...@gmail.com wrote:
Thanks for showing me the link to the code / your response / your
work in general.
It seems that the real magic is happening in the call to the
function attributes, via the line
attr(x, srcref)
I'm guessing that attributes must be defined somewhere deep inside
the R machinery (since I didn't find it as a file in base)... And
there's probably not much benefit for me to know more beyond that.
So, I'll be looking forward to 2.13!
On Tue, Mar 15, 2011 at 3:37 PM, Duncan Murdoch
murdoch.dun...@gmail.com mailto:murdoch.dun...@gmail.com wrote:
On 15/03/2011 2:56 PM, Gene Leynes wrote:
The getSrcFilename function is exactly what I was trying
to describe, and
I'm excited to know that it's on it way!
I have tried to create that type of function, but I didn't
think it was
possible with currently available functions. I would be
interested in
seeing how the new function works, maybe I'll check it out
using the google
code search
tool
http://www.google.com/codesearch?hl=enlr=q=lang%3Ar+sbtn=Search
http://www.google.com/codesearch?hl=enlr=q=lang%3Ar+sbtn=Search
(although
I usually have a hard time making sense of that code).
The source is available in
https://svn.r-project.org/R/trunk/src/library/utils/R/sourceutils.R
Duncan Murdoch
Please let me briefly clarify this part:
But it can. If you open a script and choose save, it
will be saved to the
same place.
I just mean that when you do save as... R doesn't seem to
use the same
information that it uses during a normal save (the directory
or script
name). In other applications like Microsoft Word, or
Python's IDLE (screen
shot attached) the user is shown a dialogue box with the
file name in the
current directory of that file.
This is a very minor annoyance though. I only brought it up
because I
thought it would be easier to explain than asking about a
function that
would do the job of getSrcFilename, which is really what I
Re: [R] area under roc curve
ROC area does not measure goodness of prediction but does measure pure predictive discrimination. The generalization of the ROC area is the C-index for continuous or censored Y. See for example the rcorr.cens function in the Hmisc package. Frank agent dunham wrote: Dear all, I want to measure the goodness of prediction of my linear model. That's why I was thinking about the area under roc curve. I'm trying the following, but I don't know how to avoid the error. Any help would be appreciated. library(ROCR) model.lm - lm(log(outcome)~log(v1)+log(v2)+factor1) pred-predict(model.lm) pred-prediction(as.numeric(pred), as.numeric(log(outcome))) auc-performance(pred,auc) Error en prediction(as.numeric(pred), as.numeric(log(outcome))) : Number of classes is not equal to 2. ROCR currently supports only evaluation of binary classification tasks. u...@host.com - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/area-under-roc-curve-tp3447420p3448377.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] is this an ANOVA ?
You probably want to do something like this:
fm - lm(y ~ x, MD)
anova(fm)
Analysis of Variance Table
Response: y
Df Sum Sq Mean Sq F valuePr(F)
x 2250 125.0 50 1.513e-06
Residuals 12 30 2.5
Answers to questions:
1. No.
2. Yes.
(whoever you are).
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Ubuntu Diego
Sent: Wednesday, 13 April 2011 10:10 AM
To: r-help@r-project.org
Subject: [R] is this an ANOVA ?
Hi all,
I have a very easy questions (I hope). I had measure a property of
plants, growing in three different substrates (A, B and C). The rest of the
conditions remained constant. There was very high variation on the results.
I want to do address, whether there is any difference in the response
(my measurement) from substrate to substrate?
x-c('A','A','A','A','A','B','B','B','B','B','C','C','C','C','C') # Substrate
type
y - c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15) # Results of the measurement
MD-data.frame(x,y)
I wrote a linear model for this:
summary(lm(y~x,data=MD))
This is the output:
Call:
lm(formula = y ~ x, data = MD)
Residuals:
Min 1Q Median 3QMax
-2.000e+00 -1.000e+00 5.551e-17 1.000e+00 2.000e+00
Coefficients:
Estimate Std. Error t value Pr(|t|)
(Intercept) 3. 0.7071 4.243 0.001142 **
xB5. 1. 5.000 0.000309 ***
xC 10. 1. 10.000 3.58e-07 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 1.581 on 12 degrees of freedom
Multiple R-squared: 0.8929, Adjusted R-squared: 0.875
F-statistic:50 on 2 and 12 DF, p-value: 1.513e-06
I conclude that there is an effect of substrate type (x).
NOW the questions :
1) Do the fact that the all p-values are significant means that
all the groups are different from each other ?
2) Is there a (easy) way to plot, mean plus/minus 2*sd for
each substrate type ? (with asterisks denoting significant differences ?)
THANKS !
version
platform x86_64-apple-darwin9.8.0
arch x86_64
os darwin9.8.0
system x86_64, darwin9.8.0
status
major 2
minor 11.1
year 2010
month 05
day31
svn rev52157
language R
version.string R version 2.11.1 (2010-05-31)
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Line plots in base graphics
Hadley Wickham hadley at rice.edu writes: On Wed, Apr 13, 2011 at 2:58 PM, Ben Bolker bbolker at gmail.com wrote: Hadley Wickham hadley at rice.edu writes: Am I missing something obvious on how to draw multi-line plots in base graphics? [snip] But in base graphics, the best I can come up with is this: with(Oxboys, plot(age, height, type = n)) lapply(split(Oxboys[c(age, height)], Oxboys$Subject), lines) [quoting removed to fool gmane] Am I missing something obvious? reshape to wide format and matplot()? Hmmm, that doesn't work if your measurements are at different times e.g: Oxboys2 - transform(Oxboys, age = age + runif(234)) In that case I think you're stuck with your lapply() approach, or (I think) using lattice graphics with the group= argument (that's not base though). Ben __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Line plots in base graphics
On 14 April 2011 07:51, Hadley Wickham had...@rice.edu wrote: Am I missing something obvious on how to draw multi-line plots in base graphics? In ggplot2, I can do: It appears you've been infected with what I like to call the Dijkstra syndrome [*], quoting The tools we use have a profound (and devious!) influence on our thinking habits, and, therefore, on our thinking abilities. You can probably blame ggplot2 here, messing with our minds and spoiling us. I can't seem able to think like spreadsheets anymore either, because of R. Thanks though, baptiste [*] http://www.cs.virginia.edu/~evans/cs655/readings/ewd498.html data(Oxboys, package = nlme) library(ggplot2) qplot(age, height, data = Oxboys, geom = line, group = Subject) But in base graphics, the best I can come up with is this: with(Oxboys, plot(age, height, type = n)) lapply(split(Oxboys[c(age, height)], Oxboys$Subject), lines) Am I missing something obvious? Thanks! Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Previously attainable fisher's exact test
On 13-Apr-11 17:40:53, Jim Silverton wrote: I have a matrix say, 1 4 23 30 and I want to find the previously attainable fisher's exact test p-value. Is there a way to do this in R? -- Thanks, Jim. I do not understand what you mean by previously attainable. As far as that particular matrix is concerned, the fisher.test() function will yield its exact Fisher P-value: M - matrix(c(1, 4, 23, 30), byrow=TRUE, nrow=2) M # [,1] [,2] # [1,]14 # [2,] 23 30 fisher.test(M) # Fisher's Exact Test for Count Data # data: M # p-value = 0.3918 # alternative hypothesis: true odds ratio is not equal to 1 # 95 percent confidence interval: # 0.006355278 3.653391412 # sample estimates: # odds ratio # 0.3316483 So the P-value is 0.3918 (as attained now, and as attainable at any time previously if you had done the above ... !). Ted. E-Mail: (Ted Harding) ted.hard...@wlandres.net Fax-to-email: +44 (0)870 094 0861 Date: 14-Apr-11 Time: 00:28:59 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Density estimation and plots
I have two columns of data, one is a subset of the other. All the data lie beteen 0 and 1 inclusive. I want to fit both densities on the same graph. I would also like the ability to extract the fitted values of both smoothed density (using the best method of course). For example, if h = c( runif(1000, 0, 1), rbeta(500, 3,9)) and k = rbeta(500,3,9) then how do I get both density plots on the same diagram and if I want the actual y values (fitted values) for each of the x values in h and k, how do I get these? -- Thanks, Jim. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] add names to data frame
Hi, I have a vector V of values I used to create a distance matrix using dist() function with diag=TRUE and upper=TRUE parameters. I would like to assign names in another vector on top of each column instead of 1 2 3 4 ... How can we do that ? is the distance matrix generated a data frame or a matrix ? Regards -- *Radhouane * [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] any package for Heckman selection model when the outcome equation also probit ?
Hi, all Can anybody hint if there is extant package or function to deal with Heckman selection model where the outcome model is also probit? In stata, it is called heckprob. Thank you yong __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
