similar to: reduce size of pdf

I have some square matrices with na values in corresponding rows and columns. M<-matrix(1:2,10,10) M[6,1:2]<-NA M[10,9]<-NA M<-as.matrix(as.dist(M)) print (M) 1 2 3 4 5 6 7 8 9 10 1 0 2 1 2 1 NA 1 2 1 2 2 2 0 1 2 1 NA 1 2 1 2 3 1 1 0 2 1 2 1 2 1 2 4 2 2 2 0 1 2 1 2 1 2 5 1 1 1 1 0 2 1 2 1 2 6 NA NA 2 2 2 0 1 2 1 2 7 1 1 1 1 1 1 0 2 1 2 8

I need to replace <NA> occurrences in multiple columns in a data.frame with "000/000" how do I achieve this? Thanks Nevil Amos

How do I remove a "$" character from a string sub() and gsub() with "$" or "\$" as pattern do not work. > sub("$","","ABC$DEF") [1] "ABC$DEF" > sub("\$","","ABC$DEF") Error: '\$' is an unrecognized escape in character string starting "\$" >

I am trying to replace "+" in a string with another character I am getting odd results using sub and gsub > X<-"one + two" > gsub("+","plus",X) [1] "plusoplusnpluseplus plus+plus plustpluswplusoplus" > sub("+","plus",X) [1] "plusone + two" > X<-"one ~ two" it seems to work fine with other

I would like to put confidence intervals on a mantel corellogram they are already calculated in the pmgram object but I am unsure how I get the x value in order to plot them? package(ecodist) X<-1:100 Y<-rnorm(1:100) Z<-rnorm(1:100) XY<-dist(data.frame(X,Y)) YX<-dist(data.frame(Y,X)) my.mgram<-mgram(XY,XZ) plot(my.mgram) print(my.mgram) > print(my.mgram) $mgram

Is there a fuction that will allow me to retrun the filename for a script from within that script. fir instance If I have a script "myscript.r": FileName<-unknown.fucntion() print(FileName) and run it source("myscript.r") will return "myscript.r" Thanks Nevil Amos [[alternative HTML version deleted]]

I am getting the following erro rmessage in ordistep. I have a number of similarly structured datasets using ordistep in a loop, and the message only occurs for some of the datasets. I cannot include a reproducible sample - the specific datasets where this is occur ing are fairly large and there are several pcnm's in the rhs of the formula. thanks for any pointers that may allow me to

Apologies, I cannot see how to make a rero for this issue. I have a function that uses levels(r) tor return the RAT of a raster "r" when the function is sourced from a script source(".\R\function.r") it works fine. when the function is built into a package and sourced from there library(mypackage) using the same script file to make the package levels(r)[[1]] the same line

[Env: OS: Win Xp; R 2.15.2; IDE: eclipse/StatET] Each time I update my heplots package, I get warnings from R CMD check on R-Forge, * checking sizes of PDF files under ?inst/doc? ... WARNING ?gs+qpdf? made some significant size reductions: compacted ?HE-examples.pdf? from 739Kb to 366Kb and upon submission to CRAN, a message from maintainers: On CRAN now: but again there were warnings

I have a spectrophotometric dataset with repeated measures of a value at 200 wavelengths for each of 150 individuals. I would like to use the repeated samples to at each wavelength to look at measurement/observer error, compared to difference between individuals error I have looked at doing this with icc{irr} or using an anova approach, but I am unclear how to acheive this given that there

I would like to perform partial mantel tests on only within group values, with "between group" values assigned to NA. This is possible in package ncf partial.mantel.test, however this sues a different permutation to that used in ecodist.ecodist will not accept data with NA values, returning a "matrix is not square error. is it possible to perform this test in ecodist? many thanks

Hey everyone, I have several RStudio (.rnw) files that I am using a script to assemble into a composite document. For this purpose, it would be helpful if the script could automatcially make a call to whatever is called when a user opens up one of these files and manually clicks "Compile PDF". Basically, this would allow me to refresh all of the reports before assimilating their

I am trying to use the cca/rda/capscale functions in vegan to analyse genetic distance data ( provided as a dist object calculated using dist.genpop in package adegenet) with geographic distance partialled out ( provided as a distance object using dist function in veganthis method is attempting to follow the method used by Geffen et al 2004 as suggested by Legendre and . FORTIN (2010). I

Hi, I don't know if I am the first one to report the problem: in 2.8.0 dev2bitmap gained aa support, but "extra" is null if neither taa nor naa is specified. > dev2bitmap("plot.pdf",type="pdfwrite") Error in paste(shQuote(gsexe), " -dNOPAUSE -dBATCH -q -sDEVICE=", type, : object "extra" not found >

How do I change the postion of the legend in s.value {ade4} from the defaul , bootom left? thanks Nevil Amos

I am trying to format data for the Geneland package I need to write a series of paired numbers and paired "000" to a plain ascii file without surrounding the numerals with quotes, the original data is in a matrix formatted paired strings, and written to file using write.table(x,"output filename",col.names=F,row.names=F) thus "77 79" "132 132" "000

A very basic query This code plots OK the axis values are in bold but the axis labels are not. how do I get them in bold too? thanks Nevil Amos plot(c(1,1),xlim=c(0,450),ylim=c(0.7,1.4),xlab="Distance (cells) from edge of grid",ylab="Resistance distance", type="l",col="white",lwd=2,font=2,family='sans')

Is it possible to print page numbers in pdf() with multiple pages? thanks Nevil Amos

I am trying to create a heap of boxplots, by looping though a series of factors and variables in a large data.frame suing paste to constrcut the facto and response names from the colnames I thought I could do this using get() however it is not working what am I doing wrong? thanks Nevil Amos > sp.codes=levels(data.all$CODE_LETTERS) > > for(spp in sp.codes) { > > >

Hi Vladimir, I have got 2.0.3 working on netBSD 3.0. To get it operational I needed to do the following (most of this is from memory...). 1). Recompile kernel with uhid removed. If uhid ataches to the device then libusb is not able to. Have to allow generic usb driver ugen to claim port. >From dmesg usb0 at uhci0: USB revision 1.0 uhub0 at usb0 uhub0: VIA Technologies UHCI root hub, class