v 0.5-9; fixed a bug in getal; some RD cleanup

CHANGES

@@ -1,3 +1,8 @@
+#version 0.5-9 15.02.2021
+-fs.dosage now also estimates pairwise fst
+-created alias pairwise.fst.dosage
+-fixed a bug in getal when pop is a factor, on pop id was 1 but not first level in factor
+
 #version 0.5-8 09.08.2020 
 -created class betas for objects generated by function betas
 -new function pairwise.betas for pairwise betas FST

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hierfstat
-Version: 0.5-8
-Date: 2020-08-09
+Version: 0.5-9
+Date: 2021-02-15
 Title: Estimation and Tests of Hierarchical F-Statistics
 Authors@R: c(person("Jerome","Goudet",role=c("aut","cre"),email="jerome.goudet@unil.ch"),
              person("Thibaut","Jombart",role="aut",email="t.jombart@imperial.ac.uk"),

NAMESPACE

@@ -43,6 +43,7 @@ export(ms2dos)
 export(nb.alleles)
 export(pairwise.WCfst)
 export(pairwise.betas)
+export(pairwise.fst.dosage)
 export(pairwise.neifst)
 export(pcoa)
 export(pop.freq)

R/fsdosage.R

@@ -5,7 +5,7 @@
 #' 
 #' Reports individual inbreeding coefficients, Population specific Fsts and Fiss from dosage data 
 #' 
-#' @aliases fst.dosage fis.dosage
+#' @aliases fst.dosage fis.dosage pairwise.fst.dosage
 #' @usage fs.dosage(dos, pop, matching = FALSE)
 #' 
 #' 

R/misc.R

@@ -36,11 +36,11 @@ if (min(data[,true.loci]%/%100,na.rm=TRUE)>=10 & max(data[,true.loci]%%100,na.rm
 if (max(data[,true.loci],na.rm=TRUE)<100) modulo<-10
 firstal<-data[,-1] %/% modulo
 secal<-data[,-1] %% modulo
-ind<-vector(length=0)
+ind<-NULL
 nbpop <- length(unique(data[,1]))
 for (i in sort(unique(data[,1]))) {
 dum<-1:sum(data[,1]==i)
-if (i==1) ind<-dum else ind<-c(ind,dum)
+ind<-c(ind,dum)
 }
 ind<-rep(ind,2)
 if (x[2]==2)  data.al<-data.frame(pop=rep(data[,1],2),ind=ind,al=c(firstal,secal))