similar to: How to remove $ (Dollar sign) from string

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 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

I am receiving the above error ( full r session output below) the script runs OK in windows. and "genotypes" and "ploidy" are both correct arguments any suggestions would be most welcome Nevil Amos MERG/ACB Monash University School of Biological Sciences > library(Geneland) Loading required package: RandomFields Loading required package: fields Loading required

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

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

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

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]]

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

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

is there a way to reduce the size of pdf files in R: ? compression? lower dpi ? or some other option?

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) { > > >

What is the size of the boostrapped subsample in ecodist mantel() thanks [[alternative HTML version deleted]]

Dear all, let's assume I have a vector of character strings: x <- c("abcdef", "defabc", "qwerty") What I would like to find is the following: all elements where the word 'abc' does not appear (i.e. 3 in this case of 'x'). Since I am not really experienced with regular expressions, I started slowly and thought I find all word were

I am getting the above warning following loading of Geneland 3.1.5 on unix , while a simple plot sends output to the pdf file ( see attached code) no output results from Geneland functions, resulting in empty pdf files > library (Geneland) Loading required package: RandomFields Loading required package: fields Loading required package: spam Package 'spam' is loaded. Spam version