R error in '[<-.data.frame 'C' *temp*',… replacement has # items, need # - r

Question

I have a function that I've executed many times but is now throwing an error, which I do not understand. I'm trying to apply the function over a list.
I did not write the function and I have limited experience with functions. So, I'm not sure how to troubleshoot the code.
function:
myfun<-function(Year, SampleID, Species, Abundance, resamps) {
library(vegan)
counter<-1
simbaseline<-data.frame(array(NA,dim=c(length(unique(Year)),5)))
names(simbaseline)<-c("Year", "Jaccard","Horn","Bray","Pearson")
simnext<-data.frame(array(NA,dim=c(length(unique(Year)),5)))
names(simnext)<-c("Year", "Jaccard","Horn","Bray","Pearson")
simhind<-data.frame(array(NA,dim=c(length(unique(Year)),5)))
names(simhind)<-c("Year", "Jaccard","Horn","Bray","Pearson")
counter2<-1
# getting vector with number of samples per year
nsamples<-c()
for(y in unique(Year)){
nsamples<-c(nsamples, length(unique(SampleID[Year==y])))
}
t<-1
minsample<-min(nsamples)
for(repeats in 1:resamps){
raref<-data.frame(array(NA,dim=c(1,3)))
names(raref)<-c("Year","Species","Abundance")
for(y in unique(Year)){
#getting samples for this year
samps<-unique(SampleID[Year==y])
# re-sampling samples to equalize number of samples
sam<-as.character(sample(samps,minsample,replace=T))
# getting data that belongs to bootstraped samples
rarefyear<-data.frame(SampleID[which(SampleID %in% sam & Year == y)],
Species[which(SampleID %in% sam & Year == y)],
Abundance[which(SampleID %in% sam & Year == y)])
names(rarefyear)<-c("SampleID", "Species", "Abundance")
# calculating pooled abundances of eahc species to store
spabun<-tapply(as.numeric(rarefyear[,3]),rarefyear[,2],sum)
spar<-data.frame(rep(y, length(spabun)),names(spabun),spabun, row.names=NULL)
names(spar)<-c("Year","Species","Abundance")
raref<-rbind(raref,spar)
counter<-counter+1
}
# calculating year by species table of abundance
rareftabtemp<-with(raref,tapply(Abundance,list(Year,Species),function(x)x))
rareftabtemp[is.na(rareftabtemp)]<-0
Pearsoncor<-cor(t(log(rareftabtemp+1)), method="pearson")
# calculating between year similarities (NOT DISTANCE!) with Jaccard, Morisita-Horn, Bray and Pearson correlations
Jacsim<-as.matrix(1-vegdist(rareftabtemp, method="jaccard"))
Hornsim<-as.matrix(1-vegdist(rareftabtemp, method="horn"))
Braysim<-as.matrix(1-vegdist(rareftabtemp, method="bray"))
n<-length(unique(Year))
simbaseline[counter2:(counter2+n-2),]<-
cbind(unique(Year)[2:n],Jacsim[2:n],Hornsim[2:n],Braysim[2:n],Pearsoncor[2:n])
simnext[counter2:(counter2+n-2),]<-
cbind(unique(Year)[2:n],Jacsim[row(Jacsim)-col(Jacsim)==1],
Hornsim[row(Hornsim)-col(Hornsim)==1],
Braysim[row(Braysim)-col(Braysim)==1],
Pearsoncor[row(Pearsoncor)-col(Pearsoncor)==1])
# added hindcasting
simhind[counter2:(counter2+n-2),]<-
cbind(unique(Year)[1:(n-1)],
Jacsim[row(Jacsim) %in% 1:(max(row(Jacsim))-1) &
col(Jacsim)==max(col(Jacsim))],
Hornsim[row(Hornsim)%in%1:(max(row(Hornsim))-1) &
col(Hornsim)==max(col(Hornsim))],
Braysim[row(Braysim)%in%1:(max(row(Braysim))-1) &
col(Braysim)==max(col(Braysim))],
Pearsoncor[row(Pearsoncor)%in%1:(max(row(Pearsoncor))-1) &
col(Pearsoncor)==max(col(Pearsoncor))])
counter2<-counter2+n
}
baselinesim<-data.frame(unique(Year)[2:n],
tapply(simbaseline$Jaccard,simbaseline$Year,mean),
tapply(simbaseline$Horn,simbaseline$Year,mean),
tapply(simbaseline$Bray,simbaseline$Year,mean),
tapply(simbaseline$Pearson,simbaseline$Year,mean))
names(baselinesim)<-c("Year", "Jaccard","Horn","Bray","Pearson")
nextsim<-data.frame(unique(Year)[2:n],
tapply(simnext$Jaccard,simnext$Year,mean),
tapply(simnext$Horn,simnext$Year,mean),
tapply(simnext$Bray,simnext$Year,mean),
tapply(simnext$Pearson,simnext$Year,mean))
names(nextsim)<-c("Year", "Jaccard","Horn","Bray","Pearson")
hindcastsim<-data.frame(unique(Year)[1:(n-1)],
tapply(simhind$Jaccard,simhind$Year,mean),
tapply(simhind$Horn,simhind$Year,mean),
tapply(simhind$Bray,simhind$Year,mean),
tapply(simhind$Pearson,simhind$Year,mean))
names(hindcastsim)<-c("Year", "Jaccard","Horn","Bray","Pearson")
a<-list(baselinesim,nextsim,hindcastsim)
return(a)
}
error:
Error in [<-.data.frame(*tmp*, counter2:(counter2 + n - 2), , value = c(NA, : replacement has 2 items, need 5
Traceback
6.
stop(sprintf(ngettext(m, "replacement has %d item, need %d",
"replacement has %d items, need %d"), m, n * p), domain = NA)
5.
`[<-.data.frame`(`*tmp*`, counter2:(counter2 + n - 2), , value = structure(c(NA,
2009), .Dim = 2:1))
4.
`[<-`(`*tmp*`, counter2:(counter2 + n - 2), , value = structure(c(NA,
2009), .Dim = 2:1))
3.
myfun(x$Year, x$Bay, x$Species, x$Abundance, 20)
2.
FUN(X[[i]], ...)
1.
lapply(summer.split, function(x) myfun(x$Year, x$Bay,
x$Species, x$Abundance, 20))
Again, the function worked
Someone seems to have asked a similar question before and was answered by #Marat Talipov but I'm not experienced enough to make sense of what the solution was.
The answer was:
This error pops up when you're unlucky and i <- runif(n) < 1/2 consists only of FALSE, i.e. no permutations happen. You need to add a check in the swap function to fix this problem.
R error in '[<-.data.frame'... replacement has # items, need #
A subset of my data can be found here:
https://fil.email/sI4Kyhaj
The data was split by "Bay" to generate the list
Note that the function may not throw an error on a different machine because it seems to occur periodically.

Answer 1

The problem is located at the peace of code below (and similar indexed reasignment of dataframe's expressions in your code):
simbaseline[counter2:(counter2+n-2),]<-
cbind(unique(Year)[2:n],Jacsim[2:n],Hornsim[2:n],Braysim[2:n],Pearsoncor[2:n])
What happend is that the amount of rows you are trying to assign in the left-hand experession is not equal to the right-hand one. To avoid it you can use intermediate dataframe filled-in with e.g. NAs then reassign temporary dataframe to your target data frame. Please see the simulated code below with explanations how it can be done:
# simulation
df <- data.frame(i = 1:10, l = letters[1:10], stringsAsFactors = FALSE)
head(df)
# i l
# 1 1 a
# 2 1 1
# 3 a a
# 4 4 d
# 5 5 e
# 6 6 f
# with error
df[1:5, ] <- cbind(1:3, c("a", "b", "c"))
# Error in `[<-.data.frame`(`*tmp*`, 1:5, , value = c("1", "2", "3", "a", :
# replacement has 6 items, need 10
# without error
dftemp_in <- cbind(1:3, c("a", "b", "c"))
dftemp_out <- df[1:5, ]
dftemp_out[] <- NA
dftemp_out[seq(nrow(dftemp_in)), ] <- dftemp_in
df[1:5, ] <- dftemp_out
df
# i l
# 1 1 a
# 2 2 b
# 3 3 c
# 4 <NA> <NA>
# 5 <NA> <NA>
# 6 6 f
# 7 7 g
# 8 8 h
# 9 9 i
# 10 10 j