search for: ploidy

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 package: spam Package 'spam'...

..., 0, 0, 0, 1, 0, 0, 0, 0, 0), nrow = 5, byrow = T) rland <- new.local.demo(rland,SZ,RZ,M) rland <- new.epoch.island(rland,0,c(0,0,0,0,0),c(0,0,0,0,0),0,c(0,0,0,0,0),c(0,0,0,0,0), 0,c(0,0,0,0,0),c(0,0,0,0,0), carry = rep(carrycap,habitats)) rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0, numalleles = 1, mutationrate = 0.001) rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0, numalleles = 1, mutationrate = 0.001) rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0, numalleles = 1, mutationrate = 0.001) rland <- new.locus...

...; rland <- new.local.demo(rland,SZ,RZ,M) >> >> rland <- >> new.epoch.island(rland,0,c(0,0,0,0,0),c(0,0,0,0,0),0,c(0,0,0,0,0),c(0,0,0, >> 0,0), >> 0,c(0,0,0,0,0),c(0,0,0,0,0), carry = rep(carrycap,habitats)) >> >> rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0, >> numalleles = 1, mutationrate = 0.001) >> rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0, >> numalleles = 1, mutationrate = 0.001) >> rland <- new.locus(rland, type = 1, ploidy = 2, transmission = 0, >> numalleles = 1, m...

Dear prof. Harrell, I'm not able to use the force option with fastbw, here an example of the error I've got (dataset stagec rpart package): > fitstc <- cph(Surv(stagec$pgtime,stagec$pgstat) ~ age + eet + g2 + grade + gleason + ploidy, data=stagec) > fbwstc <- fastbw(fitstc,rule="aic",type="individual") > fbwstc Deleted Chi-Sq d.f. P Residual d.f. P AIC eet 0.19 1 0.6610 0.19 1 0.6610 -1.81 age 0.74 1 0.3889 0.93 2 0.6266 -3.07 gleason 1.91 1 0.1673...

...te?. Here is an example of what I do: > stagec <- > read.table("http://www.stanford.edu/class/stats202/DATA/stagec.data", > col.names=c("pgtime", "pgstat", "age","eet", "g2", "grade", "gleason", > "ploidy")) > fit <- rpart(Surv(pgtime, pgstat) ~ age + eet + g2 + grade + gleason + > ploidy, data=stagec) Result: 1) root 146 195.411600 1.0000000 2) grade< 2.5 61 45.021520 0.3624701 4) g2< 11.36 33 9.120116 0.1225562 * 5) g2>=11.36 28 27.804100 0.7335298...

...p(0,6))) CoxG0 <- coxph(Surv(time,Dth) ~ Gp, Gastric) srvGastA <- survfit(Surv(Gastric$time,Gastric$Dth)~1) ## 88 distinct times #Gastric$time is all the time points either death or largest obervation time. #srvGastA$time is all the unique times newGas <- data.frame(start=0, stop=1, Dth=1, Ploidy=1, tim=0) #newGas <- r(0,1,1,1,0) for (i in 2:90) { timind <- match(Gastric$time[i],srvGastA$time) tmpmat <- array(0, dim=c(timind,5))#build an array with dim('index',5) tmpmat[,4] <- rep(Gastric[i,1], timind)#fourth column, return i's group tmpmat[timind,3]...

I do the these passages: library(Geneland) set.seed(1) data <- simdata(nindiv=200, coord.lim=c(0,1,0,1) , number.nuclei=5 , allele.numbers=rep(10,20), IBD=FALSE, npop=2, give.tess.grid=FALSE) geno <- data$genotypes coord <- t(data$coord.indiv) path.mcmc <-

...Locus1 Locus2 Locus3 # Samp1 GG <NA> GG # Samp2 AG CA GA # Samp3 AG CA GG # converts geno matrix to genind object (adegenet) Mydata1 <- df2genind(locus, ploidy = 2, ind.names = ind[1:SAMPS], pop = population[1:SAMPS], sep="") Mydata1$tab # get stats on newly created genind object # Locus1.G Locus1.A Locus2.C Locus2.A Locus3.G Locus3.A # Samp1 2 0 NA...

...mory raw vectors. * poistweedie (1.0) David Pechel Cactcha http://crantastic.org/packages/poistweedie Simulation of models Poisson-Tweedie. * polysat (0.1) Lindsay V. Clark http://crantastic.org/packages/polysat polysat is a collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes. It can import and export data in ABI GeneMapper, Structure, ATetra, Tetrasat/Tetra, GenoDive, SPAGeDi, and binary presence/absence formats. It can calculate pairwise differences between...