`add_asr_node_states` does not work with Mk model yet

From the Introduction section of the ASR vignette:

library(DAISIEprep)
set.seed(
  1,
  kind = "Mersenne-Twister",
  normal.kind = "Inversion",
  sample.kind = "Rejection"
)
phylo <- ape::rcoal(10)

phylo$tip.label <- c("bird_a", "bird_b", "bird_c", "bird_d", "bird_e", "bird_f",
                     "bird_g", "bird_h", "bird_i", "bird_j")

phylo <- phylobase::phylo4(phylo)

endemicity_status <- sample(
  x = c("not_present", "endemic", "nonendemic"),
  size = length(phylobase::tipLabels(phylo)),
  replace = TRUE,
  prob = c(0.6, 0.2, 0.2)
)

phylod <- phylobase::phylo4d(phylo, as.data.frame(endemicity_status))

# reconstruction using parsimony
phylod_parsimony <- add_asr_node_states(
  phylod = phylod,
  asr_method = "parsimony")

# reconstruction using Mk model
phylod_parsimony <- add_asr_node_states(
  phylod = phylod,
  asr_method = "Mk"
)
#> Error in ncol(asr$ancestral_likelihoods): object 'asr' not found

^{Created on 2022-07-28 by the reprex package (v2.0.1)}

Session info

``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.1.2 (2021-11-01) #> os macOS Catalina 10.15.6 #> system x86_64, darwin17.0 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Europe/Paris #> date 2022-07-28 #> pandoc 2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> ade4 1.7-19 2022-04-19 [1] CRAN (R 4.1.2) #> ape 5.6-2 2022-03-02 [1] CRAN (R 4.1.2) #> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) #> castor 1.7.2 2022-01-08 [1] CRAN (R 4.1.2) #> cli 3.3.0 2022-04-25 [1] CRAN (R 4.1.2) #> crayon 1.5.1 2022-03-26 [1] CRAN (R 4.1.2) #> DAISIEprep * 0.1.0 2022-07-26 [1] local #> DBI 1.1.2 2021-12-20 [1] CRAN (R 4.1.0) #> digest 0.6.29 2021-12-01 [1] CRAN (R 4.1.0) #> dplyr 1.0.9 2022-04-28 [1] CRAN (R 4.1.2) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0) #> evaluate 0.15 2022-02-18 [1] CRAN (R 4.1.2) #> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.1.2) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0) #> fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.1.2) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.2) #> highr 0.9 2021-04-16 [1] CRAN (R 4.1.0) #> hms 1.1.1 2021-09-26 [1] CRAN (R 4.1.0) #> htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.0) #> httr 1.4.3 2022-05-04 [1] CRAN (R 4.1.2) #> knitr 1.39 2022-04-26 [1] CRAN (R 4.1.2) #> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.1.2) #> lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0) #> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.2) #> MASS 7.3-54 2021-05-03 [1] CRAN (R 4.1.2) #> Matrix 1.4-0 2021-12-08 [1] CRAN (R 4.1.0) #> naturalsort 0.1.3 2016-08-30 [1] CRAN (R 4.1.0) #> nlme 3.1-153 2021-09-07 [1] CRAN (R 4.1.2) #> phylobase 0.8.10 2020-03-01 [1] CRAN (R 4.1.0) #> pillar 1.8.0 2022-07-18 [1] CRAN (R 4.1.2) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) #> plyr 1.8.7 2022-03-24 [1] CRAN (R 4.1.2) #> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0) #> progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.0) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0) #> R.cache 0.15.0 2021-04-30 [1] CRAN (R 4.1.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.1.2) #> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.1.2) #> R.utils 2.11.0 2021-09-26 [1] CRAN (R 4.1.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.0) #> Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.1.2) #> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.0) #> reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.1.0) #> rlang 1.0.4 2022-07-12 [1] CRAN (R 4.1.2) #> rmarkdown 2.14 2022-04-25 [1] CRAN (R 4.1.2) #> rncl 0.8.6 2022-03-18 [1] CRAN (R 4.1.2) #> RNeXML 2.4.7 2022-05-13 [1] CRAN (R 4.1.2) #> RSpectra 0.16-1 2022-04-24 [1] CRAN (R 4.1.2) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.0) #> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.1.2) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0) #> styler 1.7.0 2022-03-13 [1] CRAN (R 4.1.2) #> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.1.2) #> tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.1.2) #> tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.1.2) #> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0) #> uuid 1.1-0 2022-04-19 [1] CRAN (R 4.1.2) #> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.1.2) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.2) #> xfun 0.31 2022-05-10 [1] CRAN (R 4.1.2) #> XML 3.99-0.10 2022-06-09 [1] CRAN (R 4.1.2) #> xml2 1.3.3 2021-11-30 [1] CRAN (R 4.1.0) #> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.1.2) #> #> [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library #> #> ────────────────────────────────────────────────────────────────────────────── ```

joshwlambert / DAISIEprep

`add_asr_node_states` does not work with Mk model yet #11