[Basta-users] help with error in FUN(newX[,i], ...)

[Owen Jones]

Dear Caroline,

This is a possible bug in one of the sub-functions in basta that deals with the covariates. 

We're investigating and will get back to you shortly.

Best wishes,
Owen




On 1 Nov 2013, at 14:01, caroline <caroline.chong at anu.edu.au> wrote:

> Dear All,
> 
> I am running a simple Gompertz model with one categorical covariate, species (coded as species SPEC =  a, b, c.... ah for simplicity).
> After running DataCheck with autofix set to on, I encounter the following error "in FUN(newX[,i]...)" - would you have any experience with a similar situation, and could provide any help or suggestions on how to interpret and trouble-shoot the problem? I am unsure as to how to decipher where the error lies.
> N.b. this data set seems to run ok when I do not include the covariate matrix.
> 
> Very grateful for your help,
> best regards
> Caroline.
> 
> Caroline Chong
> Postdoctoral Fellow
> Research School of Biology
> Australian National University, Canberra ACT
> 
> speciesout <- basta(object = inputMat2$newData, studyStart = 1, studyEnd = 109, covarsStruct = "all.in.mort", nsim = 4, parallel = TRUE, ncpus = 4, updateJumps = TRUE, niter = 100000)
> No problems were detected with the data.
> 
> Error in FUN(newX[, i], ...) : invalid 'type' (character) of argument
> 
> #all commands below
> captHist <- read.csv("CaptHist.csv")
> source("CensusToCaptHist.R")
> 
> captHist$Date <- as.Date(captHist$ROBSDATES)
> captHist$julDay <- julian(captHist$Date)
> captHist$DayOfStudy <- (captHist$julDay - min(captHist$julDay))+1
> Y <- CensusToCaptHist(captHist$ID, captHist$DayOfStudy, timeInt="D")
> 
> #Y[,2:length(Y[1,])] <- sapply( Y[,2:length(Y[1,])], as.integer )
> y <- Y
> 
> y[,2:110] <- sapply(y[,2:110], as.character)
> y[,2:110] <- sapply(y[,2:110], as.numeric)
> y[y[,1]==2,]
> 
> birthDeath <- read.csv("penults_birthdeath.csv")
> birthDeath2 <- birthDeath
> 
> covarsRaw <- read.csv("specalphcode_covars.csv")
> df1 = data.frame(SPEC = covarsRaw$SPEC)
> 
> install.packages("BaSTA", repos="http://R-Forge.R-project.org",type="source")
> library("BaSTA")
> covars <- MakeCovMat(x = "SPEC", data = df1)
> 
> inputMat <- merge(birthDeath2, y, by.x = "ID", by.y = "ID")
> inputMat <- merge(inputMat, covars, by.x = "ID", by.y = "ID")
> inputMat2 <- DataCheck(inputMat, studyStart = 1, studyEnd = 109, autofix = rep(1, 7), silent = FALSE)
> 
> speciesout <- basta(object = inputMat2$newData, studyStart = 1, studyEnd = 109, nsim = 4, parallel = TRUE, ncpus = 4, updateJumps = TRUE, niter = 100000)
> 
> $newData
>     idnames birth death X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 X11 X12 X13 X14 X15 X16 X17 X18 X19 X20 X21 X22 X23 X24 X25 X26 X27 X28 X29
> 1          1     0    68  1  0  0  0  0  0  0  0  0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0
> 2          2     0    68  1  0  0  0  0  0  0  0  0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0
> 
> 
> 
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