Error in if (n > 1) { : missing value where TRUE/FALSE needed when perform neutrality.stats

[xiekunwhy]

Hi,
PopGenome is a good software for population diversity analysis.
When I performed neutrality.stats sliding windows, I got following errors.
|===Error in if (n > 1) { : missing value where TRUE/FALSE needed
Calls: popgenome_diversity ... neutrality.stats -> neutrality.stats -> calc_freqstats -> init_coef
Execution halted
I think it was happened because no enough SNP to use in these windows.
I was wonder that if you can skip these windows or gives NAs back instead of stopping the program?

[xiekunwhy]

Hi,
I modified your R code, and it work through.
calc_freqstats, from 86 line

STATISTICS

####TAJIMA ##########
if(length(data)!=0){
n <- ceiling(data_length[xx]/data_total_length)
}else {
if(is.na(samplesize[xx])){
n <- 1
}else if(samplesize[xx] > 0){
n <- samplesize[xx]
}else {
n <- 1
}
}
coef <- init_coef(n)

[krystal915]

Hi, @xiekunwhy!

I have encountered the same problem with you. Thank you for posting your solution! But since I am new to R. I wonder where I can modifiy and refresh my package, for I loaded library(PopGenome) directly before I ran performed neutrality.stats sliding windows.

I may be a silly question, but I do need your help.

Best wishes!

[xiekunwhy]

@krystal915 ，here is the modified source code, extract it and install it using devtools:
devtools::install_local("/local/path/to/PopGenome_2.2.4/PopGenome", force = TRUE)
PopGenome_2.2.4.zip

[krystal915]

Hi, @xiekunwhy!

It is a wonderful thing to receive your prompt response. I did as you suggested and It works now! Thank you again! ;-)

cheers!