diff --git a/articles/effect_uncertainty_tips.html b/articles/effect_uncertainty_tips.html index 01a4659..ca15d42 100644 --- a/articles/effect_uncertainty_tips.html +++ b/articles/effect_uncertainty_tips.html @@ -109,14 +109,17 @@

Multistate-intersection

#> #> intersect, setdiff, setequal, union library(tidyr) -
-

Prepare data and tree -

+
+

Prepare data and tree +

 data('primate.tree')
 data('primate.data')
 tree <- primate.tree
 data <- primate.data
+data <- data[tree$tip.label,]
+rownames(data) <- paste0('taxon', 1:nrow(data))
+tree$tip.label <- paste0('taxon', 1:Ntip(tree))
 original <- data |>
     tibble::rownames_to_column(var = 'Taxa') |>
     select(Taxa, Activity_pattern) |>
@@ -140,61 +143,158 @@ 
Prepare data and tree}
-

99% uncertainty +

No uncertainty 

-set.seed(1234)
+fit <- fitMk(tree = tree, x = original,
+              model = "ARD", pi = "fitzjohn",
+              lik.func = "pruning", logscale = TRUE)
+ace <- ancr(fit, tips=TRUE)
+plot(ace, args.plotTree = list(direction="upwards"))
+title(main = '0% uncertain tips', line = -1)
+

+
+
+

Uncertaintity +

+
+

99% uncertainty +

+
+set.seed(123)
 m99 <- myFun(original, 0.99)
 m99 <- m99[tree$tip.label,]
-fit99 <- fitMk(tree = primate.tree, x = m99,
+fit99 <- fitMk(tree = tree, x = m99,
               model = "ARD", pi = "fitzjohn",
               lik.func = "pruning", logscale = TRUE)
 ace99 <- ancr(fit99, tips=TRUE)
 plot(ace99, args.plotTree = list(direction="upwards"))
 title(main = '99% uncertain tips', line = -1)
-

+

-
-

95% uncertainty -

-
-set.seed(1234)
+

+
95% uncertainty
+

+
+set.seed(123)
 m95 <- myFun(original, 0.95)
 m95 <- m95[tree$tip.label,]
-fit95 <- fitMk(tree = primate.tree, x = m95,
+fit95 <- fitMk(tree = tree, x = m95,
               model = "ARD", pi = "fitzjohn",
               lik.func = "pruning", logscale = TRUE)
 ace95 <- ancr(fit95, tips=TRUE)
 plot(ace95, args.plotTree = list(direction="upwards"))
 title(main = '95% uncertain tips', line = -1)

-

+

 

-

-
75% uncertainty
-

-
-set.seed(1234)
-m75 <- myFun(original, 0.75)
+

+
70% uncertainty
+

+
+set.seed(123)
+m75 <- myFun(original, 0.7)
 m75 <- m75[tree$tip.label,]
-fit75 <- fitMk(tree = primate.tree, x = m75,
+fit75 <- fitMk(tree = tree, x = m75,
               model = "ARD", pi = "fitzjohn",
               lik.func = "pruning", logscale = TRUE)
 ace75 <- ancr(fit75, tips=TRUE)
 plot(ace75, args.plotTree = list(direction="upwards"))
-title(main = '75% uncertain tips', line = -1)

-

+title(main = '70% uncertain tips', line = -1)

+

+
-

No uncertainty +

Session information

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

+
+sessioninfo::session_info()
+#> ─ Session info ───────────────────────────────────────────────────────────────
+#>  setting  value
+#>  version  R Under development (unstable) (2023-11-22 r85609)
+#>  os       Ubuntu 22.04.3 LTS
+#>  system   x86_64, linux-gnu
+#>  ui       X11
+#>  language en
+#>  collate  en_US.UTF-8
+#>  ctype    en_US.UTF-8
+#>  tz       Etc/UTC
+#>  date     2023-12-04
+#>  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
+#> 
+#> ─ Packages ───────────────────────────────────────────────────────────────────
+#>  package           * version    date (UTC) lib source
+#>  ape               * 5.7-1      2023-03-13 [1] CRAN (R 4.4.0)
+#>  bslib               0.6.1      2023-11-28 [1] CRAN (R 4.4.0)
+#>  cachem              1.0.8      2023-05-01 [1] CRAN (R 4.4.0)
+#>  cli                 3.6.1      2023-03-23 [1] CRAN (R 4.4.0)
+#>  clusterGeneration   1.3.8      2023-08-16 [1] CRAN (R 4.4.0)
+#>  coda                0.19-4     2020-09-30 [1] CRAN (R 4.4.0)
+#>  codetools           0.2-19     2023-02-01 [2] CRAN (R 4.4.0)
+#>  combinat            0.0-8      2012-10-29 [1] CRAN (R 4.4.0)
+#>  desc                1.4.2      2022-09-08 [1] CRAN (R 4.4.0)
+#>  digest              0.6.33     2023-07-07 [1] CRAN (R 4.4.0)
+#>  doParallel          1.0.17     2022-02-07 [1] CRAN (R 4.4.0)
+#>  dplyr             * 1.1.4      2023-11-17 [1] CRAN (R 4.4.0)
+#>  evaluate            0.23       2023-11-01 [1] CRAN (R 4.4.0)
+#>  expm                0.999-8    2023-11-29 [1] CRAN (R 4.4.0)
+#>  fansi               1.0.5      2023-10-08 [1] CRAN (R 4.4.0)
+#>  fastmap             1.1.1      2023-02-24 [1] CRAN (R 4.4.0)
+#>  fastmatch           1.1-4      2023-08-18 [1] CRAN (R 4.4.0)
+#>  foreach             1.5.2      2022-02-02 [1] CRAN (R 4.4.0)
+#>  fs                  1.6.3      2023-07-20 [1] CRAN (R 4.4.0)
+#>  generics            0.1.3      2022-07-05 [1] CRAN (R 4.4.0)
+#>  glue                1.6.2      2022-02-24 [1] CRAN (R 4.4.0)
+#>  highr               0.10       2022-12-22 [1] CRAN (R 4.4.0)
+#>  htmltools           0.5.7      2023-11-03 [1] CRAN (R 4.4.0)
+#>  igraph              1.5.1      2023-08-10 [1] CRAN (R 4.4.0)
+#>  iterators           1.0.14     2022-02-05 [1] CRAN (R 4.4.0)
+#>  jquerylib           0.1.4      2021-04-26 [1] CRAN (R 4.4.0)
+#>  jsonlite            1.8.7      2023-06-29 [1] CRAN (R 4.4.0)
+#>  knitr               1.45       2023-10-30 [1] CRAN (R 4.4.0)
+#>  lattice             0.22-5     2023-10-24 [2] CRAN (R 4.4.0)
+#>  lifecycle           1.0.4      2023-11-07 [1] CRAN (R 4.4.0)
+#>  magrittr            2.0.3      2022-03-30 [1] CRAN (R 4.4.0)
+#>  maps              * 3.4.1.1    2023-11-03 [1] CRAN (R 4.4.0)
+#>  MASS                7.3-60.1   2023-11-26 [2] local
+#>  Matrix              1.6-4      2023-11-30 [2] CRAN (R 4.4.0)
+#>  memoise             2.0.1      2021-11-26 [1] CRAN (R 4.4.0)
+#>  mnormt              2.1.1      2022-09-26 [1] CRAN (R 4.4.0)
+#>  nlme                3.1-164    2023-11-27 [2] CRAN (R 4.4.0)
+#>  numDeriv            2016.8-1.1 2019-06-06 [1] CRAN (R 4.4.0)
+#>  optimParallel       1.0-2      2021-02-11 [1] CRAN (R 4.4.0)
+#>  phangorn            2.11.1     2023-01-23 [1] CRAN (R 4.4.0)
+#>  phytools          * 2.0-3      2023-11-09 [1] CRAN (R 4.4.0)
+#>  pillar              1.9.0      2023-03-22 [1] CRAN (R 4.4.0)
+#>  pkgconfig           2.0.3      2019-09-22 [1] CRAN (R 4.4.0)
+#>  pkgdown             2.0.7      2022-12-14 [1] CRAN (R 4.4.0)
+#>  purrr               1.0.2      2023-08-10 [1] CRAN (R 4.4.0)
+#>  quadprog            1.5-8      2019-11-20 [1] CRAN (R 4.4.0)
+#>  R6                  2.5.1      2021-08-19 [1] CRAN (R 4.4.0)
+#>  ragg                1.2.6      2023-10-10 [1] CRAN (R 4.4.0)
+#>  Rcpp                1.0.11     2023-07-06 [1] CRAN (R 4.4.0)
+#>  rlang               1.1.2      2023-11-04 [1] CRAN (R 4.4.0)
+#>  rmarkdown           2.25       2023-09-18 [1] CRAN (R 4.4.0)
+#>  rprojroot           2.0.4      2023-11-05 [1] CRAN (R 4.4.0)
+#>  sass                0.4.7      2023-07-15 [1] CRAN (R 4.4.0)
+#>  scatterplot3d       0.3-44     2023-05-05 [1] CRAN (R 4.4.0)
+#>  sessioninfo         1.2.2      2021-12-06 [1] CRAN (R 4.4.0)
+#>  stringi             1.8.2      2023-11-23 [1] CRAN (R 4.4.0)
+#>  stringr             1.5.1      2023-11-14 [1] CRAN (R 4.4.0)
+#>  systemfonts         1.0.5      2023-10-09 [1] CRAN (R 4.4.0)
+#>  textshaping         0.3.7      2023-10-09 [1] CRAN (R 4.4.0)
+#>  tibble              3.2.1      2023-03-20 [1] CRAN (R 4.4.0)
+#>  tidyr             * 1.3.0      2023-01-24 [1] CRAN (R 4.4.0)
+#>  tidyselect          1.2.0      2022-10-10 [1] CRAN (R 4.4.0)
+#>  utf8                1.2.4      2023-10-22 [1] CRAN (R 4.4.0)
+#>  vctrs               0.6.5      2023-12-01 [1] CRAN (R 4.4.0)
+#>  withr               2.5.2      2023-10-30 [1] CRAN (R 4.4.0)
+#>  xfun                0.41       2023-11-01 [1] CRAN (R 4.4.0)
+#>  yaml                2.3.7      2023-01-23 [1] CRAN (R 4.4.0)
+#> 
+#>  [1] /usr/local/lib/R/site-library
+#>  [2] /usr/local/lib/R/library
+#> 
+#> ──────────────────────────────────────────────────────────────────────────────
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