Names of ostat output

[Quentin Read]

Comment from Pat in email:

I like the output structure from Ostats. What do you think about adding column names for these to matrices ( "$overlap_norm" and "$overlap_unorm" )?

[Quentin Read]

Actually, I'm not sure what Pat meant here because the matrices in the output of Ostats() are already named. See line 130 of Ostats.R:

  # Name rows and columns of the outputs.
  dimnames(overlaps_norm) <- list(levels(plots), dimnames(traits)[[2]])
  dimnames(overlaps_unnorm) <- list(levels(plots), dimnames(traits)[[2]])

@billspat Can you please clarify what you meant?

[Pat Bills]

Really possible I am mistaken, or I missed something or maybe it was from my non-dplyr filtering, but I get null column names. The row names work great.

library(Ostats)

dat <- read.csv('https://ndownloader.figshare.com/files/9167548', stringsAsFactors =FALSE)
dat <- dat[!is.na(dat$logweight) & dat$siteID %in% c('HARV','JORN'),
       c('siteID', 'taxonID', 'weight', "logweight") ]
names(dat)
# [1] "siteID"    "taxonID"   "weight"    "logweight"

Ostats_example2 <- Ostats(traits = as.matrix(dat[,'logweight']),
   sp = factor(dat$taxonID),
   plots = factor(dat$siteID),
   density_args=list(bw = 'nrd0', adjust = 2, n=200))

Ostats_example2 <- Ostats(traits = as.matrix(dat[,'logweight']),
   sp = factor(dat$taxonID),
   plots = factor(dat$siteID),
   density_args=list(bw = 'nrd0', adjust = 2, n=200))

mat = Ostats_example2$overlaps_norm
mat
# [,1]
# HARV 0.89454559
# JORN 0.01820969
names(mat)
 # NULL

[Quentin Read]

@billspat thanks for the reprex! I determined this was a result of R's "helpful" default behavior of converting a matrix to a vector if only a single column is selected with the indexing operator [, which strips the names. I pushed a commit 1fe07d6 which adds drop = FALSE to all the indexing of single columns done in the vignette, which should result in the names being preserved. For example as.matrix(dat[,'logweight', drop = FALSE]