getal seems to require ordered population labels

[falseflattortuga]

Here is a simple example that illustrates the issue:

library(adegenet) library(hierfstat)

create genind object

df <- data.frame(locusA=c("11","11","12","12","22","12","21"), locusB=c(NA,"21","12","11","11","21","12"),locusC=c("22","22","21","22","11","22","12")) obj <- df2genind(df, ploidy=2, ncode=1) pop(obj) <- c(2,2,1,1,1,1,3) #assign individuals to populations obj #examine genind object /// GENIND OBJECT /////////

// 7 individuals; 3 loci; 6 alleles; size: 6.8 Kb

// Basic content @tab: 7 x 6 matrix of allele counts @loc.n.all: number of alleles per locus (range: 2-2) @loc.fac: locus factor for the 6 columns of @tab @all.names: list of allele names for each locus @ploidy: ploidy of each individual (range: 2-2) @type: codom @call: df2genind(X = df, ncode = 1, ploidy = 2)

// Optional content @pop: population of each individual (group size range: 1-4)

create hierfstat data frame

objh <- genind2hierfstat(obj) objh #examine hierfstat data frame pop locusA locusB locusC 1 1 11 NA 22 2 1 11 21 22 3 1 12 21 21 4 1 12 11 22 5 2 22 11 11 6 2 12 21 22 7 3 12 21 21

example 1

getal(objh) #produces error message Error in data.frame(pop = rep(data[, 1], 2), ind = ind, al = rbind(firstal, : arguments imply differing number of rows: 14, 10

example 2, with a different assignment of individuals to populations

objh[,1] <- c(1,2,2,1,1,1,3) getal(objh) # no error message, but individuals are incorrectly assigned to populations pop ind locusA locusB locusC 1 1 1 1 NA 2 2 2 2 1 2 2 3 2 3 1 2 2 4 1 4 1 1 2 5 1 1 2 1 1 6 1 2 1 2 2 7 3 1 1 2 2 11 1 1 1 NA 2 21 2 2 1 1 2 31 2 3 2 1 1 41 1 4 2 1 2 51 1 1 2 1 1 61 1 2 2 1 2 71 3 1 2 1 1

example 3, ordered population labels seem required to get correct results

objh[,1] <- c(1,1,1,1,2,2,3) getal(objh) pop ind locusA locusB locusC 1 1 1 1 NA 2 2 1 2 1 2 2 3 1 3 1 2 2 4 1 4 1 1 2 5 2 1 2 1 1 6 2 2 1 2 2 7 3 1 1 2 2 11 1 1 1 NA 2 21 1 2 1 1 2 31 1 3 2 1 1 41 1 4 2 1 2 51 2 1 2 1 1 61 2 2 2 1 2 71 3 1 2 1 1

looking at the code in the getal function, the issue seems to be in the following for loop (which, by the way, falls into the second circle of the R Inferno: growing objects):

for (i in sort(unique(data[, 1]))) { dum <- 1:sum(data[, 1] == i) if (i == 1) ind <- dum else ind <- c(ind, dum) }

if ordered population labels are assumed, then the loop above may be replaced by:

ind <- sequence(table(data[, 1]))

[jgx65]

Thanks for raising this issue. getal should not be accessible directly, it is an internal function called by others, where the sorting has be done. I'll fix this.

Cheers

[jgx65]

Issue fixed I believe:

library(adegenet)
library(hierfstat)

#create genind object
df <- data.frame(locusA=c("11","11","12","12","22","12","21"),
                 locusB=c(NA,"21","12","11","11","21","12"),locusC=c("22","22","21","22","11","22","12"))
obj <- df2genind(df, ploidy=2, ncode=1)
pop(obj) <- c(2,2,1,1,1,1,3) #assign individuals to populations
objh <- genind2hierfstat(obj)
> getal(objh)
   pop ind locusA locusB locusC
1    2   1      1     NA      2
2    2   2      1      2      2
3    1   1      1      2      2
4    1   2      1      1      2
5    1   3      2      1      1
6    1   4      1      2      2
7    3   1      1      2      2
11   2   1      1     NA      2
21   2   2      1      1      2
31   1   1      2      1      1
41   1   2      2      1      2
51   1   3      2      1      1
61   1   4      2      1      2
71   3   1      2      1      1

see https://github.com/jgx65/hierfstat/commit/f35069782833e4febd0466c5195f3f8107d8d8c8#diff-c68e163ba4719d8defe6ef01d9a88ee65f10532acf550009d1bcd81e4c823983

(note that you don't need to convert the genind object to ahierfstat one, getal(obj) works the same)

[jgx65]

@falseflattortuga is the issue solved and can I close it? many thanks