* using log directory 'd:/Rcompile/CRANpkg/local/4.4/gaiah.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'gaiah/DESCRIPTION' ... OK
* this is package 'gaiah' version '0.0.5'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
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* checking whether package 'gaiah' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
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* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s] OK
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* checking R code for possible problems ... [4s] OK
* checking Rd files ... [1s] NOTE
checkRd: (-1) min_hpd_inc_area_df.Rd:20: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) min_hpd_inc_area_df.Rd:21-22: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) min_hpd_inc_area_df.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces
    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                ^
checkRd: (-1) vza_mean_and_var_rasters.Rd:20: Lost braces; missing escapes or markup?
    20 | of the paper on Wilson's warbler, this function computes $tilde{T}^{(mu)}$ (returned as
       |                                                                    ^
checkRd: (-1) vza_mean_and_var_rasters.Rd:21: Lost braces; missing escapes or markup?
    21 | list component \code{mean.raster}) and $R^{(sigma^2)}$ (returned as list component
       |                                           ^
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* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... [12s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [16s] ERROR
Running examples in 'gaiah-Ex.R' failed
The error most likely occurred in:

> ### Name: comboize_and_fortify
> ### Title: prepare fortified output for multipanel plot
> ### Aliases: comboize_and_fortify
> 
> ### ** Examples
> 
> # run through the example for comboize to get the variables
> # mgen, miso, and mhab that we will use.
> example(comboize)

comboz> # first, run through the example for isotope_posterior_probs() to get
comboz> # the rasters for two migrant birds. This gives us the list "birds2"
comboz> example(isotope_posterior_probs)

istp__> # obtain posterior probability rasters for the first 2 birds in the migrant_wiwa_isotopes
istp__> # data set.  This takes about 15 seconds on my laptop (most of that time is preparatory---once
istp__> # that is done, each bird goes much faster). So we don't run it here.
istp__> ## Not run: 
istp__> ##D birds2 <- isotope_posterior_probs(isoscape = isomap_job54152_prediction,
istp__> ##D                         ref_birds = breeding_wiwa_isotopes,
istp__> ##D                         assign_birds = migrant_wiwa_isotopes[1:2,]
istp__> ##D                         )
istp__> ## End(Not run)
istp__> 
istp__> # However, you can load the results as a saved data object to see what they look like:
istp__> birds2 <- example_isotope_posteriors

istp__> # Since the ref_birds above were separate from the migrant birds, no leave-one-out was
istp__> # performed.  Hence birds2$loo_results is NULL, and all the results are in
istp__> # birds2$regular.
istp__> 
istp__> # Look at the names of the resulting output for the first bird:
istp__> names(birds2$regular[[1]])
[1] "posterior_probs"       "assignment_parameters"

istp__> names(birds2$regular[[1]]$assignment_parameters)
[1] "Tilde_T_mu"      "R_sigma_squared" "a_bar"           "b_bar"          
[5] "sd_indiv"       

istp__> # If you want to do self-assignment for a whole bunch of reference birds, it takes much longer.
istp__> # It looks like this:
istp__> ## Not run: 
istp__> ##D self_ass <- isotope_posterior_probs(isoscape = isomap_job54152_prediction,
istp__> ##D                                     ref_birds = breeding_wiwa_isotopes,
istp__> ##D                                     self_assign = TRUE)
istp__> ## End(Not run)
istp__> 
istp__> 
istp__> 

comboz> # extract the posterior probs rasters from  that output into a raster stack
comboz> miso <- lapply(birds2$regular, function(x) x$posterior_probs) %>%
comboz+   raster::stack()

comboz> # see the names of the birds we are dealing with:
comboz> names(miso)
[1] "WIWA02" "WIWA03"

comboz> # get the genetic posteriors for those two birds
comboz> mig_gen2 <- migrant_wiwa_genetic_posteriors %>%
comboz+   dplyr::filter(ID %in% c(names(miso)))

comboz> # make genetic posterior rasters for those two birds, make sure they are
comboz> # sorted in the same order as miso, and make a raster stack of it
comboz> mgen <- genetic_posteriors2rasters(G = mig_gen2, R = genetic_regions)[names(miso)] %>%
comboz+   raster::stack()

comboz> # make a normalized prior from habitat quality that is zeros everywhere
comboz> # outside of the "known" range.
comboz> tmp <- wiwa_habitat_unclipped * wiwa_breed

comboz> mhab <- tmp / raster::cellStats(tmp, sum)

comboz> # combine genetics, isotopes and habitat with exponents of 1 on each
comboz> mcombo <- comboize(mgen, miso, mhab, 1, 1, 1)
> 
> # then run that on the first bird to get a data frame
> # that you can use with ggplot
> ff <- comboize_and_fortify(mgen[[1]], miso[[1]], mhab)
Error:
! `tbl_df()` was deprecated in dplyr 1.0.0 and is now defunct.
ℹ Please use `tibble::as_tibble()` instead.
Backtrace:
     ▆
  1. ├─gaiah::comboize_and_fortify(mgen[[1]], miso[[1]], mhab)
  2. │ ├─... %>% dplyr::bind_rows(.id = "genetics_beta")
  3. │ └─base::lapply(...)
  4. │   └─gaiah (local) FUN(X[[i]], ...)
  5. │     ├─... %>% dplyr::bind_rows(.id = "isotope_beta")
  6. │     └─base::lapply(...)
  7. │       └─gaiah (local) FUN(X[[i]], ...)
  8. │         ├─... %>% dplyr::bind_rows(.id = "habitat_beta")
  9. │         └─base::lapply(...)
 10. │           └─gaiah (local) FUN(X[[i]], ...)
 11. │             └─... %>% dplyr::tbl_df()
 12. ├─dplyr::bind_rows(., .id = "genetics_beta")
 13. │ └─rlang::list2(...)
 14. ├─dplyr::bind_rows(., .id = "isotope_beta")
 15. │ └─rlang::list2(...)
 16. ├─dplyr::bind_rows(., .id = "habitat_beta")
 17. │ └─rlang::list2(...)
 18. └─dplyr::tbl_df(.)
 19.   └─lifecycle::deprecate_stop("1.0.0", "tbl_df()", "tibble::as_tibble()")
 20.     └─lifecycle:::deprecate_stop0(msg)
 21.       └─rlang::cnd_signal(...)
Execution halted
* checking PDF version of manual ... [18s] OK
* checking HTML version of manual ... [5s] OK
* DONE
Status: 1 ERROR, 1 NOTE