options(rstudio.viewer.autorefresh = FALSE)
library(ape)
library(phytools)
#> Loading required package: maps
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following object is masked from 'package:ape':
#> 
#>     where
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(tidyr)

Prepare data and tree

## ARD with fitzjohn
## ER with fitzjohn
## ER with estimated
myMod <- 'ARD' # ARD*, ER
myPi <- 'fitzjohn' # fitzjohn*, equal, estimated
data('primate.tree')
data('primate.data')
tree <- primate.tree
data <- primate.data
data <- data[tree$tip.label,]
original <- data |>
    tibble::rownames_to_column(var = 'Taxa') |>
    select(Taxa, Activity_pattern) |>
    mutate(Presence = 1) |>
    pivot_wider(
        names_from = 'Activity_pattern', values_from = 'Presence',

                values_fill = 0
    ) |>
    arrange(Taxa) |>
    tibble::column_to_rownames(var = 'Taxa') |>
    as.matrix()
colnames(original) <- c(LETTERS[1:3])

myFun <- function(mat, per_uncertain = 0.1) {
    n_row <- nrow(mat)
    n <- round(n_row * per_uncertain)
    rows <- sample(x = 1:nrow(mat), size = n, replace = FALSE)
    mat[rows,] <- rep(1/ncol(mat), ncol(mat))
    mat
}

No uncertainty

fit <- fitMk(tree = tree, x = original,
              model = myMod, pi = myPi,
              lik.func = "pruning", logscale = TRUE)
ace <- ancr(fit, tips=TRUE)
plot(ace, args.plotTree = list(direction="upwards"))
title(main = '0% uncertain tips', line = -1)

Uncertainty about 12%

macaca <- grep('^Macaca_', rownames(original)) # A
galago <- grep('^Galago_', rownames(original)) # B
eulemur <- grep('^Eulemur', rownames(original)) # C
paste0(round((length(macaca) + length(galago) + length(eulemur)) / 90 * 100), '%')
#> [1] "12%"
m1 <- original
m1[] <- 1 / 3
m1[macaca, ] <- c(rep(1,3), rep(0, 6))
m1[galago, ] <- c(rep(0,4), rep(1, 4), rep(0, 4))
m1[eulemur, ] <- c(rep(0,8), rep(1, 4))

fit1 <- fitMk(tree = tree, x = m1,
              model = myMod, pi = myPi,
              lik.func = "pruning", logscale = TRUE)
ace1 <- ancr(fit1, tips=TRUE)
plot(ace1, args.plotTree = list(direction = "upwards"))
title(main = '12% uncertain tips', line = -1)

Let’s add some more taxa

cebus <- grep('^Cebus_', rownames(original)) # A
microcebus <- grep('^Microcebus', rownames(original)) # B
paste0(round((length(macaca) + length(galago) + length(eulemur) + length(cebus) + length(microcebus)) / 90 * 100), '%')
#> [1] "17%"
m2 <- original
m2[] <- 1 / 3
m2[macaca, ] <- c(rep(1,3), rep(0, 6))
m2[galago, ] <- c(rep(0,4), rep(1, 4), rep(0, 4))
m2[eulemur, ] <- c(rep(0,8), rep(1, 4))
m2[cebus, ] <- c(rep(1,2), rep(0, 4))
m2[microcebus, ] <- c(rep(0,2), rep(1, 2), rep(0, 2))

fit2 <- fitMk(tree = tree, x = m2,
              model = myMod, pi = myPi,
              lik.func = "pruning", logscale = TRUE)
ace2 <- ancr(fit2, tips=TRUE)
plot(ace2, args.plotTree = list(direction = "upwards"))
title(main = '17% uncertain tips', line = -1)

Session information

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.4.1 (2024-06-14)
#>  os       Ubuntu 22.04.4 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language en
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Etc/UTC
#>  date     2024-11-21
#>  pandoc   3.2 @ /usr/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package           * version    date (UTC) lib source
#>  ape               * 5.8        2024-04-11 [1] RSPM (R 4.4.0)
#>  bslib               0.8.0      2024-07-29 [1] RSPM (R 4.4.0)
#>  cachem              1.1.0      2024-05-16 [1] RSPM (R 4.4.0)
#>  cli                 3.6.3      2024-06-21 [1] RSPM (R 4.4.0)
#>  clusterGeneration   1.3.8      2023-08-16 [1] RSPM (R 4.4.0)
#>  coda                0.19-4.1   2024-01-31 [1] RSPM (R 4.4.0)
#>  codetools           0.2-20     2024-03-31 [2] CRAN (R 4.4.1)
#>  combinat            0.0-8      2012-10-29 [1] RSPM (R 4.4.0)
#>  DEoptim             2.2-8      2022-11-11 [1] RSPM (R 4.4.0)
#>  desc                1.4.3      2023-12-10 [1] RSPM (R 4.4.0)
#>  digest              0.6.37     2024-08-19 [1] RSPM (R 4.4.0)
#>  doParallel          1.0.17     2022-02-07 [1] RSPM (R 4.4.0)
#>  dplyr             * 1.1.4      2023-11-17 [1] RSPM (R 4.4.0)
#>  evaluate            1.0.1      2024-10-10 [1] RSPM (R 4.4.0)
#>  expm                1.0-0      2024-08-19 [1] RSPM (R 4.4.0)
#>  fansi               1.0.6      2023-12-08 [1] RSPM (R 4.4.0)
#>  fastmap             1.2.0      2024-05-15 [1] RSPM (R 4.4.0)
#>  fastmatch           1.1-4      2023-08-18 [1] RSPM (R 4.4.0)
#>  foreach             1.5.2      2022-02-02 [1] RSPM (R 4.4.0)
#>  fs                  1.6.5      2024-10-30 [1] RSPM (R 4.4.0)
#>  generics            0.1.3      2022-07-05 [1] RSPM (R 4.4.0)
#>  glue                1.8.0      2024-09-30 [1] RSPM (R 4.4.0)
#>  htmltools           0.5.8.1    2024-04-04 [1] RSPM (R 4.4.0)
#>  htmlwidgets         1.6.4      2023-12-06 [1] RSPM (R 4.4.0)
#>  igraph              2.1.1      2024-10-19 [1] RSPM (R 4.4.0)
#>  iterators           1.0.14     2022-02-05 [1] RSPM (R 4.4.0)
#>  jquerylib           0.1.4      2021-04-26 [1] RSPM (R 4.4.0)
#>  jsonlite            1.8.9      2024-09-20 [1] RSPM (R 4.4.0)
#>  knitr               1.49       2024-11-08 [1] RSPM (R 4.4.0)
#>  lattice             0.22-6     2024-03-20 [2] CRAN (R 4.4.1)
#>  lifecycle           1.0.4      2023-11-07 [1] RSPM (R 4.4.0)
#>  magrittr            2.0.3      2022-03-30 [1] RSPM (R 4.4.0)
#>  maps              * 3.4.2.1    2024-11-10 [1] RSPM (R 4.4.0)
#>  MASS                7.3-61     2024-06-13 [2] RSPM (R 4.4.0)
#>  Matrix              1.7-0      2024-04-26 [2] CRAN (R 4.4.1)
#>  mnormt              2.1.1      2022-09-26 [1] RSPM (R 4.4.0)
#>  nlme                3.1-165    2024-06-06 [2] RSPM (R 4.4.0)
#>  numDeriv            2016.8-1.1 2019-06-06 [1] RSPM (R 4.4.0)
#>  optimParallel       1.0-2      2021-02-11 [1] RSPM (R 4.4.0)
#>  phangorn            2.12.1     2024-09-17 [1] RSPM (R 4.4.0)
#>  phytools          * 2.3-0      2024-06-13 [1] RSPM (R 4.4.0)
#>  pillar              1.9.0      2023-03-22 [1] RSPM (R 4.4.0)
#>  pkgconfig           2.0.3      2019-09-22 [1] RSPM (R 4.4.0)
#>  pkgdown             2.1.1      2024-09-17 [1] RSPM (R 4.4.0)
#>  purrr               1.0.2      2023-08-10 [1] RSPM (R 4.4.0)
#>  quadprog            1.5-8      2019-11-20 [1] RSPM (R 4.4.0)
#>  R6                  2.5.1      2021-08-19 [1] RSPM (R 4.4.0)
#>  ragg                1.3.2      2024-05-15 [1] RSPM (R 4.4.0)
#>  Rcpp                1.0.13-1   2024-11-02 [1] RSPM (R 4.4.0)
#>  rlang               1.1.4      2024-06-04 [1] RSPM (R 4.4.0)
#>  rmarkdown           2.29       2024-11-04 [1] RSPM (R 4.4.0)
#>  sass                0.4.9      2024-03-15 [1] RSPM (R 4.4.0)
#>  scatterplot3d       0.3-44     2023-05-05 [1] RSPM (R 4.4.0)
#>  sessioninfo         1.2.2      2021-12-06 [1] RSPM (R 4.4.0)
#>  systemfonts         1.1.0      2024-05-15 [1] RSPM (R 4.4.0)
#>  textshaping         0.4.0      2024-05-24 [1] RSPM (R 4.4.0)
#>  tibble              3.2.1      2023-03-20 [1] RSPM (R 4.4.0)
#>  tidyr             * 1.3.1      2024-01-24 [1] RSPM (R 4.4.0)
#>  tidyselect          1.2.1      2024-03-11 [1] RSPM (R 4.4.0)
#>  utf8                1.2.4      2023-10-22 [1] RSPM (R 4.4.0)
#>  vctrs               0.6.5      2023-12-01 [1] RSPM (R 4.4.0)
#>  withr               3.0.2      2024-10-28 [1] RSPM (R 4.4.0)
#>  xfun                0.49       2024-10-31 [1] RSPM (R 4.4.0)
#>  yaml                2.3.10     2024-07-26 [1] RSPM (R 4.4.0)
#> 
#>  [1] /usr/local/lib/R/site-library
#>  [2] /usr/local/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────