Re: [R] How to make a prior graph
Hello, I believe that you're talking about beta-binomial models and that the Jeffrey's prior you're talking about is a Beta(1/2, 1/2). If so, try the following. jeffrey - function(x) dbeta(x, shape1 = 1/2, shape2 = 1/2) curve(dunif, from = 0, to = 1) curve(jeffrey, from = 0, to = 1, add = TRUE) Hope this helps, Rui Barradas Em 16-12-2012 04:02, Tania escreveu: Hello, could you tell me which is the command for create graphics of this prior distributions: Uniform (flat prior) Jeffrey's Thanks, Tania Sent from my iPod __ 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] averaging X of specific Y (latitude)
It is better to use dput() in R to create a text version of your data for us to work with. The aggregate command below gives you the mean ranges by butterfly species and latititude and saves the result as Bfly. The colnames() command simply renames the columns: dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L)) Bfly - aggregate(Range~Species+floor(Latitude), dta, mean) colnames(Bfly) - c(Species, Latitude, Mean) Bfly Species LatitudeMean 1 Butterfly A19 130.50 2 Butterfly A39 1102.38 3 Butterfly A2 10 450.68 4 Butterfly B1 10 820.20 5 Butterfly B2 10 872.20 6 Butterfly B5 12 982.78 7 Butterfly C1 12 720.32 8 Butterfly A4 16 893.34 9 Butterfly B3 16 488.20 10 Butterfly B4 18 620.11 11 Butterfly C2 18 912.20 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Elaine Kuo Sent: Saturday, December 15, 2012 10:15 PM To: r-help@r-project.org; r-sig-geo Subject: [R] averaging X of specific Y (latitude) Hello I have a table describing butterfly range traits. It is composed of three columns as below Species name range size (X)latitude of range midpoint (Y) There are 11 kinds of butterflies. Each has its range size, and the latitude of each range midpoint ranges from 9 to 19. I would like to have the average range size of every degree of latitude. For example, the average range size of latitude degree 10 (10.0-10.99: Butterfly A2, B1, B2) Please kindly help with R code to calculate the average values. Thank you. Elaine The details are as followed. Butterfly A1 130.5 9.45 Butterfly A2 450.68 10.2 Butterfly A3 1102.389.3 Butterfly A4893.34 16.4 Butterfly B1 820.2 10.54 Butterfly B2872.2 10.87 Butterfly B3488.2 16.79 Butterfly B4620.11 18.3 Butterfly B5982.78 12.98 Butterfly C1 720.32 12.67 Butterfly C2912.2 18.07 [[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.
[R] interfacing with .Call
Hi
My code is as following:
#include R.h
#include Rinternals.h
//* the Projector part *//
void Projector(double *L, int *dimL, double *G, int *dimG, double *W, int
*dimW, int *xymod, int *dimxy, double *modif, int *dimif, double *Lsum)
{ ...}
//* the interface part *//
#define getDim(A) INTEGER(coerceVector(getAttrib(A,R_DimSymbol), INTSXP))
SEXP Projector5(SEXP L, SEXP G, SEXP W, SEXP xymod, SEXP modif)
{
//* digest SEXPs from R *//
int *dimL, *dimG, *dimW, *dimxy, *dimif;
double *lptr, *gptr, *wptr, *ifptr;
int *xyptr;
dimL=getDim(L);
PROTECT(L=coerceVector(L, REALSXP));
lptr=REAL(L);
dimG=getDim(G);
PROTECT(G=coerceVector(G, REALSXP));
gptr=REAL(G);
dimW=getDim(W);
PROTECT(W=coerceVector(W, REALSXP));
wptr=REAL(W);
dimxy=getDim(xymod);
PROTECT(xymod=coerceVector(xymod, INTSXP));
xyptr=INTEGER(xymod);
dimif=getDim(modif);
PROTECT(modif=coerceVector(modif, REALSXP));
ifptr=REAL(modif);
//* create SEXP to hold the answer *//
SEXP ans;
double *ansptr;
PROTECT(ans=allocMatrix(REALSXP, dimG[1], dimG[0]));
ansptr=REAL(ans);
//* calculate the result *//
Projector(lptr, dimL, gptr, dimG, wptr, dimW, xyptr, dimxy, ifptr,
dimif, ansptr);
//* wrap up and return the result to R *//
UNPROTECT(6);
return(ans);
}
The function Projector works well and actually the interface with .C
works OK.
The question is that I can compile it in R, but .Call returns different
result each time with same inputs. Could anybody tell me why? Thanks!
Regards
Shangru
--
Department of Mathematics,
National University of Singapore,
Blk S17, 10 Lower Kent Ridge Road,
119076
--
Department of Mathematics,
National University of Singapore,
Blk S17, 10 Lower Kent Ridge Road,
119076
[[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.
Re: [R] interfacing with .Call
On Sun, Dec 16, 2012 at 6:20 PM, Shangru Li lishan...@gmail.com wrote: Hi The function Projector works well and actually the interface with .C works OK. The question is that I can compile it in R, but .Call returns different result each time with same inputs. Could anybody tell me why? Thanks! I haven't read through your code but .C and .Call are actually pretty different -- is there any reason you'd expect code written for one interface to work for the other? You might just be seeing random bits of memory returned by .Call MW __ 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] interfacing with .Call
The problem almost certainly lies in the parts of the code that you have
not shown, the R-language code including the .Call or, more likely in my
opinion, the C++ code for Projector. You can get different values in
Projector's Lsum matrix if
(a) Projector doesn't assign values to all of them (allocMatrix allocates
memory
with random contents - you must fill it with values)
(b) Projector reads or writes memory that it doesn't own.
Using valgrind can help find both sorts of errors.
I am suspicious about your reversal of the dimensions of Lsum when
you allocate it, using dimG[1],dimG[0]. Does this mean you are doing
some odd pointer arithmetic in Projector that doesn't agree with R's
conventions?
I tried adding a simple Projector() and saw no problems aside from
the random numbers in the unassigned elements of Lsum and some
of the usual unassign values in the guts of Rprintf's formatting code.
extern C {
SEXP Projector5(SEXP L, SEXP G, SEXP W, SEXP xymod, SEXP modif);
}
//* the Projector part *//
void Projector(double *L, int *dimL, double *G, int *dimG, double *W, int *dimW,
int *xymod, int *dimxy, double *modif, int *dimif, double *Lsum)
{
Rprintf(dimG=c(%d,%d)\n, dimG[0], dimG[1]);
double* pLsum = Lsum;
bool even = true ;
for(int j=0 ; j dimG[0] ; j++) {
for(int i=0 ; i dimG[1] ; i++) {
if (even) {
*pLsum = 1000 * (i+1) + (j+1);
} else {
// do not touch odd elements of pLsum
}
even = !even;
pLsum++;
}
}
}
called with
.Call(Projector5, matrix(1:6,2,3), matrix(701:720,4,5),
matrix(2^(1:12),2,6), 1:7, 1:10)
dimG=c(4,5)
[,1] [,2] [,3] [,4]
[1,] 1001 7.954e-322 1003 4.002e-322
[2,]0 2.002e+030 2.004e+03
[3,] 3001 0.000e+00 3003 0.000e+00
[4,]0 4.002e+030 4.004e+03
[5,] 5001 0.000e+00 5003 0.000e+00
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf
Of Shangru Li
Sent: Sunday, December 16, 2012 10:20 AM
To: r-help@r-project.org
Subject: [R] interfacing with .Call
Hi
My code is as following:
#include R.h
#include Rinternals.h
//* the Projector part *//
void Projector(double *L, int *dimL, double *G, int *dimG, double *W, int
*dimW, int *xymod, int *dimxy, double *modif, int *dimif, double *Lsum)
{ ...}
//* the interface part *//
#define getDim(A) INTEGER(coerceVector(getAttrib(A,R_DimSymbol), INTSXP))
SEXP Projector5(SEXP L, SEXP G, SEXP W, SEXP xymod, SEXP modif)
{
//* digest SEXPs from R *//
int *dimL, *dimG, *dimW, *dimxy, *dimif;
double *lptr, *gptr, *wptr, *ifptr;
int *xyptr;
dimL=getDim(L);
PROTECT(L=coerceVector(L, REALSXP));
lptr=REAL(L);
dimG=getDim(G);
PROTECT(G=coerceVector(G, REALSXP));
gptr=REAL(G);
dimW=getDim(W);
PROTECT(W=coerceVector(W, REALSXP));
wptr=REAL(W);
dimxy=getDim(xymod);
PROTECT(xymod=coerceVector(xymod, INTSXP));
xyptr=INTEGER(xymod);
dimif=getDim(modif);
PROTECT(modif=coerceVector(modif, REALSXP));
ifptr=REAL(modif);
//* create SEXP to hold the answer *//
SEXP ans;
double *ansptr;
PROTECT(ans=allocMatrix(REALSXP, dimG[1], dimG[0]));
ansptr=REAL(ans);
//* calculate the result *//
Projector(lptr, dimL, gptr, dimG, wptr, dimW, xyptr, dimxy, ifptr,
dimif, ansptr);
//* wrap up and return the result to R *//
UNPROTECT(6);
return(ans);
}
The function Projector works well and actually the interface with .C
works OK.
The question is that I can compile it in R, but .Call returns different
result each time with same inputs. Could anybody tell me why? Thanks!
Regards
Shangru
--
Department of Mathematics,
National University of Singapore,
Blk S17, 10 Lower Kent Ridge Road,
119076
--
Department of Mathematics,
National University of Singapore,
Blk S17, 10 Lower Kent Ridge Road,
119076
[[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.
[R] sweave and lessR
Hello I am using sweave with the Density() function from lessR package. However, unlike the older color.density() function, Density() does not work with the standard graphic output functions in R, such as pdf. Is there away to include figures fgenerated rom lessR in sweave documents? thank you __ 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] averaging X of specific Y (latitude)
Hi, You could also use ?ave(): dta$Lat1-floor(dta$Latitude) # ?trunc(), ?round(), ?signif() could also replace ?floor() dta$Mean-ave(dta$Range,dta$Species,dta$Lat1,FUN=mean) dta A.K. - Original Message - From: David L Carlson dcarl...@tamu.edu To: 'Elaine Kuo' elaine.kuo...@gmail.com; r-help@r-project.org; 'r-sig-geo' r-sig-...@stat.math.ethz.ch Cc: Sent: Sunday, December 16, 2012 11:32 AM Subject: Re: [R] averaging X of specific Y (latitude) It is better to use dput() in R to create a text version of your data for us to work with. The aggregate command below gives you the mean ranges by butterfly species and latititude and saves the result as Bfly. The colnames() command simply renames the columns: dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L)) Bfly - aggregate(Range~Species+floor(Latitude), dta, mean) colnames(Bfly) - c(Species, Latitude, Mean) Bfly Species Latitude Mean 1 Butterfly A1 9 130.50 2 Butterfly A3 9 1102.38 3 Butterfly A2 10 450.68 4 Butterfly B1 10 820.20 5 Butterfly B2 10 872.20 6 Butterfly B5 12 982.78 7 Butterfly C1 12 720.32 8 Butterfly A4 16 893.34 9 Butterfly B3 16 488.20 10 Butterfly B4 18 620.11 11 Butterfly C2 18 912.20 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Elaine Kuo Sent: Saturday, December 15, 2012 10:15 PM To: r-help@r-project.org; r-sig-geo Subject: [R] averaging X of specific Y (latitude) Hello I have a table describing butterfly range traits. It is composed of three columns as below Species name range size (X) latitude of range midpoint (Y) There are 11 kinds of butterflies. Each has its range size, and the latitude of each range midpoint ranges from 9 to 19. I would like to have the average range size of every degree of latitude. For example, the average range size of latitude degree 10 (10.0-10.99: Butterfly A2, B1, B2) Please kindly help with R code to calculate the average values. Thank you. Elaine The details are as followed. Butterfly A1 130.5 9.45 Butterfly A2 450.68 10.2 Butterfly A3 1102.38 9.3 Butterfly A4 893.34 16.4 Butterfly B1 820.2 10.54 Butterfly B2 872.2 10.87 Butterfly B3 488.2 16.79 Butterfly B4 620.11 18.3 Butterfly B5 982.78 12.98 Butterfly C1 720.32 12.67 Butterfly C2 912.2 18.07 [[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. __ 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] sweave and lessR
On 12-12-16 12:42 PM, Scott Cushman wrote:
Hello
I am using sweave with the Density() function from lessR package. However,
unlike the older color.density() function, Density() does not work with
the standard graphic output functions in R, such as pdf. Is there away to
include figures fgenerated rom lessR in sweave documents?
Tell Density to write to foo.pdf, then just use \includegraphics{foo}
in your Sweave document. (This assumes you're using pdflatex; it looks
as though you can't do it at all if you can't handle PDF figures.)
Duncan Murdoch
__
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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] sweave and lessR
On 12-12-16 3:12 PM, Scott Cushman wrote:
Thank you for the reply. With many calls to Density() I miss Sweave taking care
of the naming of the files and the generating of the \includegraphics
statements, but I guess this will work.
You (or the lessR author) could possibly write your own custom graphics
device driver to work with Sweave; see Graphics devices in the Sweave
vignette. Or perhaps lessR could be configured to use the regular pdf()
graphics driver.
Duncan Murdoch
On Dec 16, 2012, at 2:54 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote:
On 12-12-16 12:42 PM, Scott Cushman wrote:
Hello
I am using sweave with the Density() function from lessR package. However,
unlike the older color.density() function, Density() does not work with
the standard graphic output functions in R, such as pdf. Is there away to
include figures fgenerated rom lessR in sweave documents?
Tell Density to write to foo.pdf, then just use \includegraphics{foo} in your
Sweave document. (This assumes you're using pdflatex; it looks as though you can't do it
at all if you can't handle PDF figures.)
Duncan Murdoch
__
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.
Re: [R] sweave and lessR
Thank you for the reply. With many calls to Density() I miss Sweave taking care
of the naming of the files and the generating of the \includegraphics
statements, but I guess this will work.
On Dec 16, 2012, at 2:54 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote:
On 12-12-16 12:42 PM, Scott Cushman wrote:
Hello
I am using sweave with the Density() function from lessR package. However,
unlike the older color.density() function, Density() does not work with
the standard graphic output functions in R, such as pdf. Is there away to
include figures fgenerated rom lessR in sweave documents?
Tell Density to write to foo.pdf, then just use \includegraphics{foo} in
your Sweave document. (This assumes you're using pdflatex; it looks as
though you can't do it at all if you can't handle PDF figures.)
Duncan Murdoch
__
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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.
Re: [R] kruskalmc, significant differences while median values are the same
On Sat, Dec 15, 2012 at 10:04 PM, Omphalodes Verna omphalodes.ve...@yahoo.com wrote: Dear list! I work with multiple Kruskal-Wallis test (kruskalmc, package pgirmess), which evaluates differences in medians among groups (5 groups). A result of a test is significant differences among some groups, while median values are the same for 4 groups (using tapply). Why? The Kruskal-Wallis test *doesn't* evaluate differences in medians, so there is quite likely nothing wrong in a formal sense. However, this does suggest that your groups may not be stochastically ordered, which means the results of the Kruskal-Wallis test could be quite misleading. I'd suggest that you at least look at pairwise Wilcoxon tests to make sure the direction agrees with what the Kruskal-Wallis test implies. Box plots might also be a good idea. Or, if you really want differences in medians, look at differences in medians. A permutation test or a bootstrap confidence interval is probably the best way to do this. -thomas -- Thomas Lumley Professor of Biostatistics University of Auckland [[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] averaging X of specific Y (latitude)
Thank you, David. Your answer reminded me of rearranging the order according to the latitude before running the calculation. One more question, please kindly help with the code to calculate the mean of the ranges of the same latitude? Or should any re-arrangement be noticed before the mean calculation? Thank you. Elaine - Original Message - From: David L Carlson dcarl...@tamu.edu To: 'Elaine Kuo' elaine.kuo...@gmail.com; r-help@r-project.org; 'r-sig-geo' r-sig-...@stat.math.ethz.ch Cc: Sent: Sunday, December 16, 2012 11:32 AM Subject: Re: [R] averaging X of specific Y (latitude) It is better to use dput() in R to create a text version of your data for us to work with. The aggregate command below gives you the mean ranges by butterfly species and latititude and saves the result as Bfly. The colnames() command simply renames the columns: dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L)) Bfly - aggregate(Range~Species+floor(Latitude), dta, mean) colnames(Bfly) - c(Species, Latitude, Mean) Bfly Species LatitudeMean 1 Butterfly A19 130.50 2 Butterfly A39 1102.38 3 Butterfly A2 10 450.68 4 Butterfly B1 10 820.20 5 Butterfly B2 10 872.20 6 Butterfly B5 12 982.78 7 Butterfly C1 12 720.32 8 Butterfly A4 16 893.34 9 Butterfly B3 16 488.20 10 Butterfly B4 18 620.11 11 Butterfly C2 18 912.20 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Elaine Kuo Sent: Saturday, December 15, 2012 10:15 PM To: r-help@r-project.org; r-sig-geo Subject: [R] averaging X of specific Y (latitude) Hello I have a table describing butterfly range traits. It is composed of three columns as below Species name range size (X)latitude of range midpoint (Y) There are 11 kinds of butterflies. Each has its range size, and the latitude of each range midpoint ranges from 9 to 19. I would like to have the average range size of every degree of latitude. For example, the average range size of latitude degree 10 (10.0-10.99: Butterfly A2, B1, B2) Please kindly help with R code to calculate the average values. Thank you. Elaine The details are as followed. Butterfly A1 130.5 9.45 Butterfly A2 450.68 10.2 Butterfly A3 1102.389.3 Butterfly A4893.34 16.4 Butterfly B1 820.2 10.54 Butterfly B2872.2 10.87 Butterfly B3488.2 16.79 Butterfly B4620.11 18.3 Butterfly B5982.78 12.98 Butterfly C1 720.32 12.67 Butterfly C2912.2 18.07 [[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. [[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] nls for sum of exponentials
Hi there, I am trying to fit the following model with a sum of exponentials - y ~ Ae^(-md) + B e^(-nd) + c the model has 5 parameters A, b, m, n, c I am using nls to fit the data and I am using DEoptim package to pick the most optimal start values - fm4 - function(x) x[1] + x[2]*exp(x[3] * -dist) + x[4]*exp(x[5] * -dist) fm5 - function(x) sum((wcorr-fm4(x))^2) fm6 - DEoptim(fm5, lower=c(0,0.1,1,0.1,1), upper=c(10e7, 100, 300,100, 300 ), control=list(trace=FALSE)) par2 - fm6$optim$bestmem names(par2) - c(c, A, n1, B, n2) fit2 - nls(wcorr ~ (c + A*exp(n1 * -dist) + B*exp(n2 * -dist)), start=par2,control =list(maxiter=1000, warnOnly=TRUE)) However, I keep getting the following error - Error in numericDeriv(form[[3L]], names(ind), env) : Missing value or an infinity produced when evaluating the model OR In nls(wcorr ~ (c + A * exp(n1 * -dist) + B * exp(n2 * -dist)), : singular gradient Can anyone suggest how to resolve the problem? Thanks, Priya [[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] non-numeric argument to binary operator
Hello,
I wish to carry out the following:
factor_classes - as.factor(sample(c(BM, SM, F), 10, replace = TRUE))
C - 5
k - matrix(0, length(factor_classes), 1)
for (i in length(factor_classes)) {
k[i] - C*factor_classes[i]
}
I get the following error message:
non-numeric argument to binary operator
I wish to store the results of C*factor_classes[i] in matrix k.
Is there any way I can multiply the factor with the numeric variable?
Thanks for your help in advance.
Cheers,
sumaria
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Re: [R] non-numeric argument to binary operator
Hello,
Try
C*as.integer(factor_classes)
And note that you don't need the loop.
Hope this helps,
Rui Barradas
Em 16-12-2012 23:56, Shrupa Sumaria escreveu:
Hello,
I wish to carry out the following:
factor_classes - as.factor(sample(c(BM, SM, F), 10, replace = TRUE))
C - 5
k - matrix(0, length(factor_classes), 1)
for (i in length(factor_classes)) {
k[i] - C*factor_classes[i]
}
I get the following error message:
non-numeric argument to binary operator
I wish to store the results of C*factor_classes[i] in matrix k.
Is there any way I can multiply the factor with the numeric variable?
Thanks for your help in advance.
Cheers,
sumaria
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and provide commented, minimal, self-contained, reproducible code.
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Re: [R] non-numeric argument to binary operator
On 12-12-16 6:56 PM, Shrupa Sumaria wrote:
Hello,
I wish to carry out the following:
factor_classes - as.factor(sample(c(BM, SM, F), 10, replace = TRUE))
C - 5
k - matrix(0, length(factor_classes), 1)
for (i in length(factor_classes)) {
k[i] - C*factor_classes[i]
}
I get the following error message:
non-numeric argument to binary operator
I wish to store the results of C*factor_classes[i] in matrix k.
Is there any way I can multiply the factor with the numeric variable?
What do you expect to get from 5*BM?
Duncan Murdoch
Thanks for your help in advance.
Cheers,
sumaria
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and provide commented, minimal, self-contained, reproducible code.
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[R] Fw: simulate time data
- Forwarded Message -
From: Jichun Chan jic...@y7mail.com
To: David Winsemius dwinsem...@comcast.net
Sent: Friday, 14 December 2012 5:30 PM
Subject: Re: [R] simulate time data
Hi David,
Thank you for replying my email. I have to apology that I haven't been very
clear with my question.
I am actually trying to simulate a set of data with two correlated variables
(e.g. x1 and x2) , one of which (says x1) is associated with the outcome with a
predefined OR. Then, I want to calculate the HR of the other variable in
relation to the outcome using Cox's regression. But I don't know how to
simulate the time data as it is not normally distributed.
I tried to treat it like normally distributed and put it the covariance matrix,
it somehow produced the HR that is closely resembled that of real data. Am I
doing the right thing. The following is the Rcommond I used:
set.seed(12345)
for (i in 1:1000) {
sim - rmvnorm( n = 1000, mean = c(0.81,26.5,88.07), sigma = matrix(c(0.019,
0.41*sqrt(0.48), 1.27,
0.41*sqrt(0.48), 25.48, -23.82, 1.27, -23.82, 5297.64),3,3))
x1 - sim[,1]
x2 - sim[,2]
time- sim[,3]
L - log(1.89) * (x1/0.14) #0.14 is the SD and 1.89 is the preset OR
event - ifelse(runif(1000) plogis(L), 1, 0)
sdata- data.frame(x1, x2, event)
m1- coxph(Surv(time, event) ~ x2, data=sdata)
I also tried to simulate the time using Weibull distribution from the R help as
follows, but I don't quite understand what they are doing. And I don't know how
to combine it to the dataset so that the time variable is related to the
outcome. I hope you know what I mean.
n = 1000
beta1 =0.18 ; beta2 = -0.65
lambdaT = .007 # baseline hazard
lambdaC = .003 # hazard of censoring
T = rweibull(n, shape=1, scale=lambdaT*exp(-beta1*bmi-beta2*fnbmd))
C = rweibull(n, shape=1, scale=lambdaC) #censoring time
time = pmin(T,C) #observed time is minimum of censored and true
event = time==T # set to 1 if event is observed
Would you please kindly help me with this and forgive me if I ask silly
question as I am still new to statistics.
Regards
Scomet
From: David Winsemius dwinsem...@comcast.net
To: Jichun Chan jic...@y7mail.com
Cc: r-help@r-project.org r-help@r-project.org
Sent: Thursday, 13 December 2012 3:10 PM
Subject: Re: [R] simulate time data
On Dec 12, 2012, at 6:34 PM, Jichun Chan wrote:
Hi,
Does anyone know how to write a command to generate time-to-event data for
Cox's regression?
There are examples in the rms package for the cph function. I also see example
in the help pages for the survival package.
--David Winsemius, MD
Alameda, CA, USA
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Re: [R] interfacing with .Call
On Mon, Dec 17, 2012 at 8:02 AM, William Dunlap wdun...@tibco.com wrote:
The problem almost certainly lies in the parts of the code that you have
not shown, the R-language code including the .Call or, more likely in my
opinion, the C++ code for Projector.
I would have blamed the unPROTECTed coerceVector() result in the getDim
macro.
-thomas
You can get different values in
Projector's Lsum matrix if
(a) Projector doesn't assign values to all of them (allocMatrix
allocates memory
with random contents - you must fill it with values)
(b) Projector reads or writes memory that it doesn't own.
Using valgrind can help find both sorts of errors.
I am suspicious about your reversal of the dimensions of Lsum when
you allocate it, using dimG[1],dimG[0]. Does this mean you are doing
some odd pointer arithmetic in Projector that doesn't agree with R's
conventions?
I tried adding a simple Projector() and saw no problems aside from
the random numbers in the unassigned elements of Lsum and some
of the usual unassign values in the guts of Rprintf's formatting code.
extern C {
SEXP Projector5(SEXP L, SEXP G, SEXP W, SEXP xymod, SEXP modif);
}
//* the Projector part *//
void Projector(double *L, int *dimL, double *G, int *dimG, double *W, int
*dimW,
int *xymod, int *dimxy, double *modif, int *dimif, double *Lsum)
{
Rprintf(dimG=c(%d,%d)\n, dimG[0], dimG[1]);
double* pLsum = Lsum;
bool even = true ;
for(int j=0 ; j dimG[0] ; j++) {
for(int i=0 ; i dimG[1] ; i++) {
if (even) {
*pLsum = 1000 * (i+1) + (j+1);
} else {
// do not touch odd elements of pLsum
}
even = !even;
pLsum++;
}
}
}
called with
.Call(Projector5, matrix(1:6,2,3), matrix(701:720,4,5),
matrix(2^(1:12),2,6), 1:7, 1:10)
dimG=c(4,5)
[,1] [,2] [,3] [,4]
[1,] 1001 7.954e-322 1003 4.002e-322
[2,]0 2.002e+030 2.004e+03
[3,] 3001 0.000e+00 3003 0.000e+00
[4,]0 4.002e+030 4.004e+03
[5,] 5001 0.000e+00 5003 0.000e+00
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf
Of Shangru Li
Sent: Sunday, December 16, 2012 10:20 AM
To: r-help@r-project.org
Subject: [R] interfacing with .Call
Hi
My code is as following:
#include R.h
#include Rinternals.h
//* the Projector part *//
void Projector(double *L, int *dimL, double *G, int *dimG, double *W, int
*dimW, int *xymod, int *dimxy, double *modif, int *dimif, double *Lsum)
{ ...}
//* the interface part *//
#define getDim(A) INTEGER(coerceVector(getAttrib(A,R_DimSymbol), INTSXP))
SEXP Projector5(SEXP L, SEXP G, SEXP W, SEXP xymod, SEXP modif)
{
//* digest SEXPs from R *//
int *dimL, *dimG, *dimW, *dimxy, *dimif;
double *lptr, *gptr, *wptr, *ifptr;
int *xyptr;
dimL=getDim(L);
PROTECT(L=coerceVector(L, REALSXP));
lptr=REAL(L);
dimG=getDim(G);
PROTECT(G=coerceVector(G, REALSXP));
gptr=REAL(G);
dimW=getDim(W);
PROTECT(W=coerceVector(W, REALSXP));
wptr=REAL(W);
dimxy=getDim(xymod);
PROTECT(xymod=coerceVector(xymod, INTSXP));
xyptr=INTEGER(xymod);
dimif=getDim(modif);
PROTECT(modif=coerceVector(modif, REALSXP));
ifptr=REAL(modif);
//* create SEXP to hold the answer *//
SEXP ans;
double *ansptr;
PROTECT(ans=allocMatrix(REALSXP, dimG[1], dimG[0]));
ansptr=REAL(ans);
//* calculate the result *//
Projector(lptr, dimL, gptr, dimG, wptr, dimW, xyptr, dimxy, ifptr,
dimif, ansptr);
//* wrap up and return the result to R *//
UNPROTECT(6);
return(ans);
}
The function Projector works well and actually the interface with .C
works OK.
The question is that I can compile it in R, but .Call returns different
result each time with same inputs. Could anybody tell me why? Thanks!
Regards
Shangru
--
Department of Mathematics,
National University of Singapore,
Blk S17, 10 Lower Kent Ridge Road,
119076
--
Department of Mathematics,
National University of Singapore,
Blk S17, 10 Lower Kent Ridge Road,
119076
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and provide commented, minimal, self-contained, reproducible code.
__
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and provide commented, minimal, self-contained, reproducible code.
--
Thomas
Re: [R] averaging X of specific Y (latitude)
It is not necessary to rearrange the order. The aggregate function will do that. To get the mean Range for a latitude combining species within a latitude just remove Species: aggregate(Range~floor(Latitude), dta, mean) floor(Latitude) Range 1 9 616.440 2 10 714.360 3 12 851.550 4 16 690.770 5 18 766.155 --- David From: Elaine Kuo [mailto:elaine.kuo...@gmail.com] Sent: Sunday, December 16, 2012 5:17 PM To: dcarl...@tamu.edu; r-help@r-project.org; r-sig-...@stat.math.ethz.ch Subject: Re: [R] averaging X of specific Y (latitude) Thank you, David. Your answer reminded me of rearranging the order according to the latitude before running the calculation. One more question, please kindly help with the code to calculate the mean of the ranges of the same latitude? Or should any re-arrangement be noticed before the mean calculation? Thank you. Elaine - Original Message - From: David L Carlson dcarl...@tamu.edu To: 'Elaine Kuo' elaine.kuo...@gmail.com; r-help@r-project.org; 'r-sig-geo' r-sig-...@stat.math.ethz.ch Cc: Sent: Sunday, December 16, 2012 11:32 AM Subject: Re: [R] averaging X of specific Y (latitude) It is better to use dput() in R to create a text version of your data for us to work with. The aggregate command below gives you the mean ranges by butterfly species and latititude and saves the result as Bfly. The colnames() command simply renames the columns: dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L)) Bfly - aggregate(Range~Species+floor(Latitude), dta, mean) colnames(Bfly) - c(Species, Latitude, Mean) Bfly Species Latitude Mean 1 Butterfly A1 9 130.50 2 Butterfly A3 9 1102.38 3 Butterfly A2 10 450.68 4 Butterfly B1 10 820.20 5 Butterfly B2 10 872.20 6 Butterfly B5 12 982.78 7 Butterfly C1 12 720.32 8 Butterfly A4 16 893.34 9 Butterfly B3 16 488.20 10 Butterfly B4 18 620.11 11 Butterfly C2 18 912.20 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Elaine Kuo Sent: Saturday, December 15, 2012 10:15 PM To: r-help@r-project.org; r-sig-geo Subject: [R] averaging X of specific Y (latitude) Hello I have a table describing butterfly range traits. It is composed of three columns as below Species name range size (X) latitude of range midpoint (Y) There are 11 kinds of butterflies. Each has its range size, and the latitude of each range midpoint ranges from 9 to 19. I would like to have the average range size of every degree of latitude. For example, the average range size of latitude degree 10 (10.0-10.99: Butterfly A2, B1, B2) Please kindly help with R code to calculate the average values. Thank you. Elaine The details are as followed. Butterfly A1 130.5 9.45 Butterfly A2 450.68 10.2 Butterfly A3 1102.38 9.3 Butterfly A4 893.34 16.4 Butterfly B1 820.2 10.54 Butterfly B2 872.2 10.87 Butterfly B3 488.2 16.79 Butterfly B4 620.11 18.3 Butterfly B5 982.78 12.98 Butterfly C1 720.32 12.67 Butterfly C2 912.2 18.07 [[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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
[R] save to file
Hi, What's the equivalent of Save to File from the R console File menu on an R routine? Just trying to capture the whole R console into a text file when my code fails. Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx [[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] averaging X of specific Y (latitude)
HI, Not sure if this what you meant. ave(dta$Range,floor(dta$Latitude),FUN=mean) # [1] 616.440 714.360 616.440 690.770 714.360 714.360 690.770 766.155 851.550 #[10] 851.550 766.155 A.K. - Original Message - From: Elaine Kuo elaine.kuo...@gmail.com To: dcarl...@tamu.edu; r-help@r-project.org; r-sig-...@stat.math.ethz.ch Cc: Sent: Sunday, December 16, 2012 6:16 PM Subject: Re: [R] averaging X of specific Y (latitude) Thank you, David. Your answer reminded me of rearranging the order according to the latitude before running the calculation. One more question, please kindly help with the code to calculate the mean of the ranges of the same latitude? Or should any re-arrangement be noticed before the mean calculation? Thank you. Elaine - Original Message - From: David L Carlson dcarl...@tamu.edu To: 'Elaine Kuo' elaine.kuo...@gmail.com; r-help@r-project.org; 'r-sig-geo' r-sig-...@stat.math.ethz.ch Cc: Sent: Sunday, December 16, 2012 11:32 AM Subject: Re: [R] averaging X of specific Y (latitude) It is better to use dput() in R to create a text version of your data for us to work with. The aggregate command below gives you the mean ranges by butterfly species and latititude and saves the result as Bfly. The colnames() command simply renames the columns: dta - structure(list(Species = structure(1:11, .Label = c(Butterfly A1, + Butterfly A2, Butterfly A3, Butterfly A4, Butterfly B1, + Butterfly B2, Butterfly B3, Butterfly B4, Butterfly B5, + Butterfly C1, Butterfly C2), class = factor), Range = c(130.5, + 450.68, 1102.38, 893.34, 820.2, 872.2, 488.2, 620.11, 982.78, + 720.32, 912.2), Latitude = c(9.45, 10.2, 9.3, 16.4, 10.54, 10.87, + 16.79, 18.3, 12.98, 12.67, 18.07)), .Names = c(Species, Range, + Latitude), class = data.frame, row.names = c(NA, -11L)) Bfly - aggregate(Range~Species+floor(Latitude), dta, mean) colnames(Bfly) - c(Species, Latitude, Mean) Bfly Species Latitude Mean 1 Butterfly A1 9 130.50 2 Butterfly A3 9 1102.38 3 Butterfly A2 10 450.68 4 Butterfly B1 10 820.20 5 Butterfly B2 10 872.20 6 Butterfly B5 12 982.78 7 Butterfly C1 12 720.32 8 Butterfly A4 16 893.34 9 Butterfly B3 16 488.20 10 Butterfly B4 18 620.11 11 Butterfly C2 18 912.20 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Elaine Kuo Sent: Saturday, December 15, 2012 10:15 PM To: r-help@r-project.org; r-sig-geo Subject: [R] averaging X of specific Y (latitude) Hello I have a table describing butterfly range traits. It is composed of three columns as below Species name range size (X) latitude of range midpoint (Y) There are 11 kinds of butterflies. Each has its range size, and the latitude of each range midpoint ranges from 9 to 19. I would like to have the average range size of every degree of latitude. For example, the average range size of latitude degree 10 (10.0-10.99: Butterfly A2, B1, B2) Please kindly help with R code to calculate the average values. Thank you. Elaine The details are as followed. Butterfly A1 130.5 9.45 Butterfly A2 450.68 10.2 Butterfly A3 1102.38 9.3 Butterfly A4 893.34 16.4 Butterfly B1 820.2 10.54 Butterfly B2 872.2 10.87 Butterfly B3 488.2 16.79 Butterfly B4 620.11 18.3 Butterfly B5 982.78 12.98 Butterfly C1 720.32 12.67 Butterfly C2 912.2 18.07 [[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. [[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
Re: [R] save to file
I did check that link but it doesn't do what I want..thanks for trying though. Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Sent: Sunday, December 16, 2012 6:55 PM Subject: Re: [R] save to file Hi, sink() gives only the output to be saved in the foo.txt, but txtStart(), txtStop() gets the codes and the output. Sorry, I misunderstood your question. You can also check this link (if you haven't already seen) http://r.789695.n4.nabble.com/Capturing-R-console-output-into-a-file-sink-savehistory-td2227013.html A.K. From: Felipe Carrillo mazatlanmex...@yahoo.com To: arun smartpink...@yahoo.com Sent: Sunday, December 16, 2012 9:47 PM Subject: Re: [R] save to file What you did That's what sink() does but I mean the entire R console screen including the R statement below I just want to be able to capture everything during the R session R version 2.15.0 (2012-03-30) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i386-pc-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Sent: Sunday, December 16, 2012 6:37 PM Subject: Re: [R] save to file Hi, I am using Ubuntu 12.04. My sessionInfo() if that helps: sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TeachingDemos_2.8 stringr_0.6 reshape_0.8.4 plyr_1.7.1 loaded via a namespace (and not attached): [1] tcltk_2.15.0 tools_2.15.0 A.K. From: Felipe Carrillo mazatlanmex...@yahoo.com To: arun smartpink...@yahoo.com Sent: Sunday, December 16, 2012 9:28 PM Subject: Re: [R] save to file My text file is created but its empty. Did you start library(TeachingDemos) txtStart(foo.txt,commands=TRUE,results=TRUE,append=FALSE) on you R.profile to capture the R statement? Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Sent: Sunday, December 16, 2012 6:16 PM Subject: Re: [R] save to file Hi, If there are comments in your code, you need to ?txtComment() from library(TeachingDemos). I did a trial run and was able to get the snapshot in the output file. A.K. From: Felipe Carrillo mazatlanmex...@yahoo.com To: arun smartpink...@yahoo.com Sent: Sunday, December 16, 2012 9:13 PM Subject: Re: [R] save to file I know about sink() and capture.output() but these functions don't capture the entire console. I basically want a snapshot of all the text on the R console saved to a file. I am the users to send me the file so that I can see where the R crashed. I will check the Teaching Demos. Thanks Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: R help r-help@r-project.org Sent: Sunday, December 16, 2012 6:07 PM Subject: Re: [R] save to file HI, I guess ?sink() may not work for you as you need the whole R console. Have you tried library(TeachingDemos) ?txtStart(), ?txtStop() ? txtStart(foo.txt,commands=TRUE,results=TRUE,append=FALSE) codes txtStop() A.K. - Original Message - From: Felipe Carrillo mazatlanmex...@yahoo.com To: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch Cc: Sent: Sunday, December 16, 2012 8:30 PM Subject: [R] save to file Hi,
[R] forecasting accuracy problem in R
Hi, A few weeks back I used the following command: accuracy(train,test) where train and test are training and test data respectively. Last night I updated R and the forecast package and used the same command and I got error. After trying a little I used the following command accuracy(train,test[1:30]) and it worked. (I was checking the accuracy of 30 forecasted values). Is there some change in the forecast package or did I do something wrong? regards Leo __ 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] forecasting accuracy problem in R
Please read the posting guide. Packages have their own developers, as well as their own change logs [in this case http://cran.r-project.org/web/packages/forecast/ChangeLog]. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Leo spee...@gmail.com wrote: Hi, A few weeks back I used the following command: accuracy(train,test) where train and test are training and test data respectively. Last night I updated R and the forecast package and used the same command and I got error. After trying a little I used the following command accuracy(train,test[1:30]) and it worked. (I was checking the accuracy of 30 forecasted values). Is there some change in the forecast package or did I do something wrong? regards Leo __ 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] forecasting accuracy problem in R
Thanks. Could be the following reason given in the changelog. accuracy() can now figure out overlapping times for x and f. best regards Leo On Mon, Dec 17, 2012 at 10:11 AM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Please read the posting guide. Packages have their own developers, as well as their own change logs [in this case http://cran.r-project.org/web/packages/forecast/ChangeLog]. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Leo spee...@gmail.com wrote: Hi, A few weeks back I used the following command: accuracy(train,test) where train and test are training and test data respectively. Last night I updated R and the forecast package and used the same command and I got error. After trying a little I used the following command accuracy(train,test[1:30]) and it worked. (I was checking the accuracy of 30 forecasted values). Is there some change in the forecast package or did I do something wrong? regards Leo __ 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] save to file
HI, I guess ?sink() may not work for you as you need the whole R console. Have you tried library(TeachingDemos) ?txtStart(), ?txtStop() ? txtStart(foo.txt,commands=TRUE,results=TRUE,append=FALSE) codes txtStop() A.K. - Original Message - From: Felipe Carrillo mazatlanmex...@yahoo.com To: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch Cc: Sent: Sunday, December 16, 2012 8:30 PM Subject: [R] save to file Hi, What's the equivalent of Save to File from the R console File menu on an R routine? Just trying to capture the whole R console into a text file when my code fails. Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx [[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] save to file
On 17/12/2012 11:03, Felipe Carrillo wrote: I did check that link but it doesn't do what I want..thanks for trying though. Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Sent: Sunday, December 16, 2012 6:55 PM Subject: Re: [R] save to file Hi, sink() gives only the output to be saved in the foo.txt, but txtStart(), txtStop() gets the codes and the output. Sorry, I misunderstood your question. You can also check this link (if you haven't already seen) http://r.789695.n4.nabble.com/Capturing-R-console-output-into-a-file-sink-savehistory-td2227013.html A.K. From: Felipe Carrillo mazatlanmex...@yahoo.com To: arun smartpink...@yahoo.com Sent: Sunday, December 16, 2012 9:47 PM Subject: Re: [R] save to file What you did That's what sink() does but I mean the entire R console screen including the R statement below I just want to be able to capture everything during the R session R version 2.15.0 (2012-03-30) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i386-pc-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Sent: Sunday, December 16, 2012 6:37 PM Subject: Re: [R] save to file Hi, I am using Ubuntu 12.04. My sessionInfo() if that helps: sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TeachingDemos_2.8 stringr_0.6 reshape_0.8.4 plyr_1.7.1 loaded via a namespace (and not attached): [1] tcltk_2.15.0 tools_2.15.0 A.K. From: Felipe Carrillo mazatlanmex...@yahoo.com To: arun smartpink...@yahoo.com Sent: Sunday, December 16, 2012 9:28 PM Subject: Re: [R] save to file My text file is created but its empty. Did you start library(TeachingDemos) txtStart(foo.txt,commands=TRUE,results=TRUE,append=FALSE) on you R.profile to capture the R statement? Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Sent: Sunday, December 16, 2012 6:16 PM Subject: Re: [R] save to file Hi, If there are comments in your code, you need to ?txtComment() from library(TeachingDemos). I did a trial run and was able to get the snapshot in the output file. A.K. From: Felipe Carrillo mazatlanmex...@yahoo.com To: arun smartpink...@yahoo.com Sent: Sunday, December 16, 2012 9:13 PM Subject: Re: [R] save to file I know about sink() and capture.output() but these functions don't capture the entire console. I basically want a snapshot of all the text on the R console saved to a file. I am the users to send me the file so that I can see where the R crashed. I will check the Teaching Demos. Thanks Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: R help r-help@r-project.org Sent: Sunday, December 16, 2012 6:07 PM Subject: Re: [R] save to file HI, I guess ?sink() may not work for you as you need the whole R console. Have you tried library(TeachingDemos) ?txtStart(), ?txtStop() ? txtStart(foo.txt,commands=TRUE,results=TRUE,append=FALSE) codes txtStop() A.K. - Original Message - From: Felipe Carrillo mazatlanmex...@yahoo.com To: r-h...@stat.math.ethz.ch
Re: [R] save to file
Hi, This is what I did: library(TeachingDemos) txtStart(foo1.txt,commands=TRUE,results=TRUE,append=FALSE) Output being copied to text file, use txtStop to end txt ave(dta$Range,dta$Lat1,FUN=mean) [1] 616.440 714.360 616.440 690.770 714.360 714.360 690.770 766.155 851.550 [10] 851.550 766.155 txt txtStop() #Output in foo1.txt ave(dta$Range, dta$Lat1, FUN = mean) [1] 616.440 714.360 616.440 690.770 714.360 714.360 690.770 766.155 851.550 [10] 851.550 766.155 A.K. From: Felipe Carrillo mazatlanmex...@yahoo.com To: arun smartpink...@yahoo.com Sent: Sunday, December 16, 2012 9:28 PM Subject: Re: [R] save to file My text file is created but its empty. Did you start library(TeachingDemos) txtStart(foo.txt,commands=TRUE,results=TRUE,append=FALSE) on you R.profile to capture the R statement? Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Sent: Sunday, December 16, 2012 6:16 PM Subject: Re: [R] save to file Hi, If there are comments in your code, you need to ?txtComment() from library(TeachingDemos). I did a trial run and was able to get the snapshot in the output file. A.K. From: Felipe Carrillo mazatlanmex...@yahoo.com To: arun smartpink...@yahoo.com Sent: Sunday, December 16, 2012 9:13 PM Subject: Re: [R] save to file I know about sink() and capture.output() but these functions don't capture the entire console. I basically want a snapshot of all the text on the R console saved to a file. I am the users to send me the file so that I can see where the R crashed. I will check the Teaching Demos. Thanks Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: R help r-help@r-project.org Sent: Sunday, December 16, 2012 6:07 PM Subject: Re: [R] save to file HI, I guess ?sink() may not work for you as you need the whole R console. Have you tried library(TeachingDemos) ?txtStart(), ?txtStop() ? txtStart(foo.txt,commands=TRUE,results=TRUE,append=FALSE) codes txtStop() A.K. - Original Message - From: Felipe Carrillo mazatlanmex...@yahoo.com To: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch Cc: Sent: Sunday, December 16, 2012 8:30 PM Subject: [R] save to file Hi, What's the equivalent of Save to File from the R console File menu on an R routine? Just trying to capture the whole R console into a text file when my code fails. Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx [[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] Mixed Anova
I am new to R and have been doing my utmost to learn it in order to teach my students how to use it as an alternative to programs you have to purchase and I am very grateful for the program and what it can do.but I am having a slight problem as I also am not very much into programming though willing to learn. I have been trying to apply a mixed model ANOVA to some data I have. In short one repeated measure (behavior being observed with 8 levels), one independent measure (Age with 2 levels - classified as 21 or =21) and then the dependent variable is the score that the subjects obtained for the specific behavior (Frequency). I have been trying to use the aov model set up in the following way based on what I have searched online: aov(Frequency~Behavior*Age+Error(Subject/Behavior)+Age, dataframe). My data is organized such that I have the data in the long format Subject, Age, Behavior, Frequency. All this gives me the following error: Warning message: In aov(Frequency~Behavior*Age+Error(Subject/Behavior)+Age, : Error() model is singular If you would kindly excuse my ignorance, would someone please guide me as to what I am doing wrong. Thank you in advance. Stephen [[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] save to file
Well, I am going to give copies of an application to different offices and want to be able to generate an output file in the event that an error would ocurr while running the different R routines. By saving the entire R console along with the R version, I should be able to see where the error ocurred. I've seen text files with every single text from the R console but can't find the way to capture that. Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Sent: Sunday, December 16, 2012 7:13 PM Subject: Re: [R] save to file As a workaround, you could copy manually the R statements R version 2.15.0 (2012-03-30)--- Type 'q()' to quit R. and then use txtStart()..txtStop(). Would it work? The reason I am saying is that with 1000s of lines of code, this will be still easier. A.K. From: Felipe Carrillo mazatlanmex...@yahoo.com To: arun smartpink...@yahoo.com; r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch Sent: Sunday, December 16, 2012 10:03 PM Subject: Re: [R] save to file I did check that link but it doesn't do what I want..thanks for trying though. Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Sent: Sunday, December 16, 2012 6:55 PM Subject: Re: [R] save to file Hi, sink() gives only the output to be saved in the foo.txt, but txtStart(), txtStop() gets the codes and the output. Sorry, I misunderstood your question. You can also check this link (if you haven't already seen) http://r.789695.n4.nabble.com/Capturing-R-console-output-into-a-file-sink-savehistory-td2227013.html A.K. From: Felipe Carrillo mazatlanmex...@yahoo.com To: arun smartpink...@yahoo.com Sent: Sunday, December 16, 2012 9:47 PM Subject: Re: [R] save to file What you did That's what sink() does but I mean the entire R console screen including the R statement below I just want to be able to capture everything during the R session R version 2.15.0 (2012-03-30) Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: i386-pc-mingw32/i386 (32-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Sent: Sunday, December 16, 2012 6:37 PM Subject: Re: [R] save to file Hi, I am using Ubuntu 12.04. My sessionInfo() if that helps: sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TeachingDemos_2.8 stringr_0.6 reshape_0.8.4 plyr_1.7.1 loaded via a namespace (and not attached): [1] tcltk_2.15.0 tools_2.15.0 A.K. From: Felipe Carrillo mazatlanmex...@yahoo.com To: arun smartpink...@yahoo.com Sent: Sunday, December 16, 2012 9:28 PM Subject: Re: [R] save to file My text file is created but its empty. Did you start library(TeachingDemos) txtStart(foo.txt,commands=TRUE,results=TRUE,append=FALSE) on you R.profile to capture the R statement? Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Sent: Sunday, December 16, 2012 6:16 PM Subject: Re: [R] save to file Hi, If there are comments in your code, you need to ?txtComment() from library(TeachingDemos). I did a trial run and was able to get the snapshot in the output file. A.K.
[R] User defined functions error - where is it ?
Hello, I have a written a couple of functions (states.trends(.) and
trend.generator(.))
to create monthly aggregated time series from disaggregated data. They seem
to work pretty
fine with all the data I provide, but they give me the following error in
one the case I use
a particular table (per.after.sub):
states.trends(per.after.sub,'CUST_SINCE')
Error in if (d.length%%d.length2 != 0) { :
missing value where TRUE/FALSE needed
traceback()
5: update.POSIXct(x, mdays = 1, hours = 0, minutes = 0, seconds = 0)
4: update(x, mdays = 1, hours = 0, minutes = 0, seconds = 0)
3: floor_date(x[[w]], month) at #15
2: trend.generator(x, STATE, vec.states[i, 1], y) at #4
1: states.trends(per.after.sub, CUST_SINCE)
I use several tables:
1) full1, which contains data from 2009 to 2012
2) per2012.sub, which is a subset of full1 based on the criterion:
{ date_per = '2012-01-01'
date_per = as.POSIXct(date_per,tz='', %Y-%m-%d)
per2012.sub = subset(full1, CUST_SINCE = date_per)}
3) per.after.sub, which is a subset of full1 based on the criterion:
{ date_per1 = '2012-08-01'
date_per1 = as.POSIXct(date_per1,tz='',%Y-%m-%d)
per.after.sub = subset(full1, CUST_SINCE = date_per1) }
All the procedures works fine with the tables 'full1' and 'per2012.sub' but
it gives me the
error when using the table 'per.after.sub'. What has this data set
different from the other two ?
Can you help me ? Where can the error be ?
Thank you
Edoardo
[[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.
Re: [R] nls for sum of exponentials
1. Fit a simpler model -- you're probably overfitting. 2. Consult your local statistician. 3. Post to stats.stackexchange.com, as this appears to be primarily a statistical issue, not an R issue. But 2) would probably be better. Cheers, Bert On Sun, Dec 16, 2012 at 3:57 PM, Diviya Smith diviya.sm...@gmail.comwrote: Hi there, I am trying to fit the following model with a sum of exponentials - y ~ Ae^(-md) + B e^(-nd) + c the model has 5 parameters A, b, m, n, c I am using nls to fit the data and I am using DEoptim package to pick the most optimal start values - fm4 - function(x) x[1] + x[2]*exp(x[3] * -dist) + x[4]*exp(x[5] * -dist) fm5 - function(x) sum((wcorr-fm4(x))^2) fm6 - DEoptim(fm5, lower=c(0,0.1,1,0.1,1), upper=c(10e7, 100, 300,100, 300 ), control=list(trace=FALSE)) par2 - fm6$optim$bestmem names(par2) - c(c, A, n1, B, n2) fit2 - nls(wcorr ~ (c + A*exp(n1 * -dist) + B*exp(n2 * -dist)), start=par2,control =list(maxiter=1000, warnOnly=TRUE)) However, I keep getting the following error - Error in numericDeriv(form[[3L]], names(ind), env) : Missing value or an infinity produced when evaluating the model OR In nls(wcorr ~ (c + A * exp(n1 * -dist) + B * exp(n2 * -dist)), : singular gradient Can anyone suggest how to resolve the problem? Thanks, Priya [[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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[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] Mixed Anova
please check this: http://stats.stackexchange.com/questions/11079/problem-with-anova-repeated-measures-error-model-is-singular On Mon, Dec 17, 2012 at 12:11 PM, Stephen Sammut ssam...@gmail.com wrote: model is singular -- Thanks and Regards, Vivek Kumar Singh Alcatel-Lucent, Bangalore (91)9886317184, 8123951698 [[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] Mixed Anova
What you are doing wrong: 1. You haven't read the posting guide, and so have not posted with sufficient clarity for people to help (at least I can't -- what's your data look like?); 2. You've posted to the wrong list: mixed models posts are better answered on the r-sig-mixed-models list. 3. I am not even sure that this is an R question, and not just a statistical question. But I'll leave that for the experts on the mixed models list. -- Bert On Sun, Dec 16, 2012 at 8:11 PM, Stephen Sammut ssam...@gmail.com wrote: I am new to R and have been doing my utmost to learn it in order to teach my students how to use it as an alternative to programs you have to purchase  and I am very grateful for the program and what it can doŠ.but I am having a slight problem as I also am not very much into programming  though willing to learn. I have been trying to apply a mixed model ANOVA to some data I have. In short  one repeated measure (behavior being observed with 8 levels), one independent measure (Age with 2 levels - classified as 21 or =21) and then the dependent variable is the score that the subjects obtained for the specific behavior (Frequency). I have been trying to use the aov model set up in the following way based on what I have searched online: aov(Frequency~Behavior*Age+Error(Subject/Behavior)+Age, dataframe). My data is organized such that I have the data in the long format  Subject, Age, Behavior, Frequency. All this gives me the following error: Warning message: In aov(Frequency~Behavior*Age+Error(Subject/Behavior)+Age, : Error() model is singular If you would kindly excuse my ignorance, would someone please guide me as to what I am doing wrong. Thank you in advance. Stephen [[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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[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] kruskalmc, significant differences while median values are the same
Thank for help! My ''problem'' is a little bit complicated. I have a dataset of trees (five tree species) and I need to calculate if there are the significant differences in the period of suppressed growth among tree species (length in years, e.g. 1, 2, 3, 6, 10, 50, 80, etc.). Because data are not normally distributed (Levene test), my idea was to use kruskalmc test. So, my question is, how to evaluate the differences in the duration of suppressed growth among groups? Is ''bootstrap confidence interval'' for each tree species right solution? thanks, OV From: Thomas Lumley tlum...@uw.edu To: Omphalodes Verna omphalodes.ve...@yahoo.com Cc: R Help r-help@r-project.org Sent: Sunday, December 16, 2012 11:59 PM Subject: Re: [R] kruskalmc, significant differences while median values are the same On Sat, Dec 15, 2012 at 10:04 PM, Omphalodes Verna omphalodes.ve...@yahoo.com wrote: Dear list! I work with multiple Kruskal-Wallis test (kruskalmc, package pgirmess), which evaluates differences in medians among groups (5 groups). A result of a test is significant differences among some groups, while median values are the same for 4 groups (using tapply). Why? The Kruskal-Wallis test *doesn't* evaluate differences in medians, so there is quite likely nothing wrong in a formal sense. However, this does suggest that your groups may not be stochastically ordered, which means the results of the Kruskal-Wallis test could be quite misleading. I'd suggest that you at least look at pairwise Wilcoxon tests to make sure the direction agrees with what the Kruskal-Wallis test implies. Box plots might also be a good idea. Or, if you really want differences in medians, look at differences in medians. A permutation test or a bootstrap confidence interval is probably the best way to do this. -thomas -- Thomas Lumley Professor of Biostatistics University of Auckland __ 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] looping through spatial points and getting counts of spatial points in spatial grid in R
Hi, I am stuck in a looping problem. It might be an easy problem for experienced R users but I have been unable to do it. Any kind of help or advice will be great appreciated. I am creating a spatial grid and have a list of spatial points in a folder. I can read the spatial points separately and get a count of the points in the spatial grid in R. The output should be a table showing the counts of points in the spatial grid. However, since there are many of these spatial points, I want this process to be automated. Can someone help me with this? All my spatial points are in one folder. # Creating spatial points in R - reading the POI shapefiles as SpatialPointsDataFrame in R autopts.rg - readOGR(., AutoSvc)class (autopts.rg) # Getting a count of the Spatial Points in the Spatial Data Frame in.cell - overlay(SpatialGrid_LS,FinInstq2) newdata - data.frame(table(in.cell))View(newdata) SpatialGrid_LS is the spatial grid that I had created in R. I guess a For loop would help, but although I tried several things, I haven't been successful yet. Thanks! Tilo [[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] save to file
On Dec 16, 2012, at 7:35 PM, Felipe Carrillo wrote: Well, I am going to give copies of an application to different offices and want to be able to generate an output file in the event that an error would ocurr while running the different R routines. By saving the entire R console along with the R version, I should be able to see where the error ocurred. I've seen text files with every single text from the R console but can't find the way to capture that. Most consoles will accept cmd-A or similar to select all text in a console session. Figure out what that keystroke combo is for your OS and then ctl- or cmd-C and paste into text editor. -- David Winsemius Alameda, CA, USA __ 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] save to file
try the following. it works for linux: $ R|tee log.txt I stored the log for a small period. *R version 2.15.1 (2012-06-22) -- Roasted Marshmallows Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. q() Save workspace image? [y/n/c]: n* On Mon, Dec 17, 2012 at 3:23 PM, David Winsemius dwinsem...@comcast.netwrote: On Dec 16, 2012, at 7:35 PM, Felipe Carrillo wrote: Well, I am going to give copies of an application to different offices and want to be able to generate an output file in the event that an error would ocurr while running the different R routines. By saving the entire R console along with the R version, I should be able to see where the error ocurred. I've seen text files with every single text from the R console but can't find the way to capture that. Most consoles will accept cmd-A or similar to select all text in a console session. Figure out what that keystroke combo is for your OS and then ctl- or cmd-C and paste into text editor. -- David Winsemius Alameda, CA, USA __ 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. -- Thanks and Regards, Vivek Kumar Singh Alcatel-Lucent, Bangalore (91)9886317184, 8123951698 [[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.
