When using csvToUMF to convert long data.frames (i.e., long = TRUE), the presence of a factor variable resulted in all other variables converting to factors. This is now fixed (with the caveat noted at the bottom). Additionally, the function now tries to automatically identify and extract site covariates and add them to the UnmarkedFrameOccu.
As a heads-up, though, the reshape::recast function used in many of these format... functions does not play well with factors, and it may be necessary to rethink this approach moving forward. For example, if the first variable recast encounters is a factor, bad things happen without an easy solution other than reorganizing your data.frame so that's not the case.
library(unmarked)
#> Loading required package: reshape
#> Loading required package: lattice
#> Loading required package: parallel
#> Loading required package: Rcpp
test <- expand.grid.df(expand.grid(site = LETTERS[1:4], julian = c(13, 20, 26)))
test <- test[with(test, order(site, julian)), ]
set.seed(42)
test <- within(test, {
ocov = round(rnorm(nrow(test)), 2)
scov = 2 * as.numeric(test$site)
obsfac = factor(sample(LETTERS[1:2], nrow(test), replace = TRUE))
sitefac = factor(round(as.numeric(site)/5))
y = rbinom(nrow(test), 1, 0.6)
})
str(unmarked:::formatLong(test, type = "unmarkedFrameOccu"))
#> Warning in `[<-.factor`(`*tmp*`, ri, value = c(2, 2, 2, 4, 4, 4, 6, 6, 6, :
#> invalid factor level, NA generated
#> Warning in `[<-.factor`(`*tmp*`, ri, value = c(2, 2, 2, 4, 4, 4, 6, 6, 6, :
#> invalid factor level, NA generated
#> Warning in `[<-.factor`(`*tmp*`, ri, value = c(2, 2, 2, 4, 4, 4, 6, 6, 6, :
#> invalid factor level, NA generated
#> Formal class 'unmarkedFrameOccu' [package "unmarked"] with 5 slots
#> ..@ y : 'matrix' int [1:4, 1:3] 1 0 1 0 1 1 0 0 0 1 ...
#> .. ..- attr(*, "dimnames")=List of 2
#> .. .. ..$ : NULL
#> .. .. ..$ : NULL
#> ..@ obsCovs :'data.frame': 12 obs. of 1 variable:
#> .. ..$ obsfac: Factor w/ 2 levels "A","B": 1 2 1 2 1 2 2 2 1 2 ...
#> ..@ siteCovs:'data.frame': 4 obs. of 4 variables:
#> .. ..$ sitefac : Factor w/ 2 levels "0","1": 1 1 2 2
#> .. ..$ scov : num [1:4] NA NA NA NA
#> .. ..$ ocov : num [1:4] NA NA NA NA
#> .. ..$ JulianDate: num [1:4] NA NA NA NA
#> ..@ mapInfo : NULL
#> ..@ obsToY : num [1:3, 1:3] 1 0 0 0 1 0 0 0 1
When using
csvToUMFto convert long data.frames (i.e.,long = TRUE), the presence of a factor variable resulted in all other variables converting to factors. This is now fixed (with the caveat noted at the bottom). Additionally, the function now tries to automatically identify and extract site covariates and add them to theUnmarkedFrameOccu.As a heads-up, though, the
reshape::recastfunction used in many of theseformat...functions does not play well with factors, and it may be necessary to rethink this approach moving forward. For example, if the first variablerecastencounters is a factor, bad things happen without an easy solution other than reorganizing yourdata.frameso that's not the case.