Last updated on 2026-02-03 14:51:27 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.0.5 | 4.51 | 79.05 | 83.56 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 0.0.5 | 3.17 | 55.56 | 58.73 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 0.0.5 | 8.00 | 123.58 | 131.58 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.0.5 | 8.00 | 120.82 | 128.82 | ERROR | |
| r-devel-windows-x86_64 | 0.0.5 | 8.00 | 89.00 | 97.00 | NOTE | |
| r-patched-linux-x86_64 | 0.0.5 | 4.55 | 72.40 | 76.95 | NOTE | |
| r-release-linux-x86_64 | 0.0.5 | 4.47 | 72.74 | 77.21 | NOTE | |
| r-release-macos-arm64 | 0.0.5 | NOTE | ||||
| r-release-macos-x86_64 | 0.0.5 | 3.00 | 67.00 | 70.00 | NOTE | |
| r-release-windows-x86_64 | 0.0.5 | 6.00 | 87.00 | 93.00 | NOTE | |
| r-oldrel-macos-arm64 | 0.0.5 | NOTE | ||||
| r-oldrel-macos-x86_64 | 0.0.5 | 3.00 | 55.00 | 58.00 | NOTE | |
| r-oldrel-windows-x86_64 | 0.0.5 | 8.00 | 112.00 | 120.00 | NOTE |
Version: 0.0.5
Check: Rd files
Result: 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
| ^
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.0.5
Check: examples
Result: 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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc