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Phylogenetic tree: mammaltree
Number of tips: 5987
Number of nodes: 5986
Branch lengths:
mean: 2.680715
variance: 24.17565
distribution summary:
Min. 1st Qu. Median 3rd Qu. Max.
0.0000000 0.5284341 1.3073255 2.9454665 106.6007500
No root edge.
First ten tip labels: X_Shuotherium
X_Pseudotribos
X_Asfaltomylos
X_Obdurodon
Zaglossus_bartoni
Zaglossus_bruijnii
Zaglossus_attenboroughi
Tachyglossus_aculeatus
Ornithorhynchus_anatinus
X_Teinolophos
No node labels.#read in the data
Binary_traits <- read_csv("data/Phylo_Project_Data/Masters_Binary_Traits.csv")Rows: 244 Columns: 13
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (4): Family, Genus_names, species_name, subspecies
dbl (9): Size_Dimorphism, Sexual_Dimorphism, DM_Head, Natal_Coat, ConD, ConM...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.head(Binary_traits)# A tibble: 6 × 13
Family Genus…¹ speci…² subsp…³ Size_…⁴ Sexua…⁵ DM_Head Natal…⁶ ConD ConM
<chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 cercopith… alleno… nigrov… <NA> 1 0 0 1 0 0
2 cheirogal… alloce… tricho… <NA> 1 0 0 0 0 0
3 cebidae alouat… caraya <NA> 1 1 1 1 1 0
4 cebidae alouat… guariba <NA> 1 1 1 1 0 0
5 cebidae alouat… pallia… pallia… 1 1 0 1 0 0
6 cebidae alouat… pigra <NA> 1 0 0 1 0 0
# … with 3 more variables: ConB <dbl>, Sexual_Dichromatism <dbl>,
# DC_Head <dbl>, and abbreviated variable names ¹Genus_names, ²species_name,
# ³subspecies, ⁴Size_Dimorphism, ⁵Sexual_Dimorphism, ⁶Natal_Coat#combine genus and species names and capitalize first letter
Binary_traits_combined = Binary_traits %>% unite("species",`Genus_names`, `species_name`) %>% mutate(species = str_to_title(species))
head(Binary_traits_combined)# A tibble: 6 × 12
Family species subsp…¹ Size_…² Sexua…³ DM_Head Natal…⁴ ConD ConM ConB
<chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 cercopithec… Alleno… <NA> 1 0 0 1 0 0 0
2 cheirogalei… Alloce… <NA> 1 0 0 0 0 0 0
3 cebidae Alouat… <NA> 1 1 1 1 1 0 0
4 cebidae Alouat… <NA> 1 1 1 1 0 0 0
5 cebidae Alouat… pallia… 1 1 0 1 0 0 0
6 cebidae Alouat… <NA> 1 0 0 1 0 0 0
# … with 2 more variables: Sexual_Dichromatism <dbl>, DC_Head <dbl>, and
# abbreviated variable names ¹subspecies, ²Size_Dimorphism,
# ³Sexual_Dimorphism, ⁴Natal_Coat# prune tree for species in data
species_not_in_tree=setdiff(mammaltree$tip.label, Binary_traits_combined$species)
pruned.tree<-drop.tip(mammaltree,species_not_in_tree)
summary(pruned.tree)
Phylogenetic tree: pruned.tree
Number of tips: 236
Number of nodes: 235
Branch lengths:
mean: 2.860618
variance: 17.84922
distribution summary:
Min. 1st Qu. Median 3rd Qu. Max.
0.04705822 0.88148050 1.69536613 3.05531386 49.61463191
No root edge.
First ten tip labels: Nycticebus_pygmaeus
Nycticebus_coucang
Loris_tardigradus
Galagoides_thomasi
Galago_matschiei
Galago_moholi
Galago_senegalensis
Galago_gallarum
Otolemur_garnettii
Otolemur_crassicaudatus
No node labels.#prune data for species in tree
data_pruned = Binary_traits_combined %>% filter(species %in% pruned.tree$tip.label)
head(data_pruned)# A tibble: 6 × 12
Family species subsp…¹ Size_…² Sexua…³ DM_Head Natal…⁴ ConD ConM ConB
<chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 cercopithec… Alleno… <NA> 1 0 0 1 0 0 0
2 cheirogalei… Alloce… <NA> 1 0 0 0 0 0 0
3 cebidae Alouat… <NA> 1 1 1 1 1 0 0
4 cebidae Alouat… <NA> 1 1 1 1 0 0 0
5 cebidae Alouat… pallia… 1 1 0 1 0 0 0
6 cebidae Alouat… <NA> 1 0 0 1 0 0 0
# … with 2 more variables: Sexual_Dichromatism <dbl>, DC_Head <dbl>, and
# abbreviated variable names ¹subspecies, ²Size_Dimorphism,
# ³Sexual_Dimorphism, ⁴Natal_Coat#put data into useful form for phylolm
colnames(data_pruned) = gsub(" ", "_", colnames(data_pruned))
data_pruned_rownames = column_to_rownames(data_pruned, var = "species")
head(data_pruned_rownames) Family subspecies Size_Dimorphism
Allenopithecus_nigroviridis cercopithecidae <NA> 1
Allocebus_trichotis cheirogaleidae <NA> 1
Alouatta_caraya cebidae <NA> 1
Alouatta_guariba cebidae <NA> 1
Alouatta_palliata cebidae palliata 1
Alouatta_pigra cebidae <NA> 1
Sexual_Dimorphism DM_Head Natal_Coat ConD ConM ConB
Allenopithecus_nigroviridis 0 0 1 0 0 0
Allocebus_trichotis 0 0 0 0 0 0
Alouatta_caraya 1 1 1 1 0 0
Alouatta_guariba 1 1 1 0 0 0
Alouatta_palliata 1 0 1 0 0 0
Alouatta_pigra 0 0 1 0 0 0
Sexual_Dichromatism DC_Head
Allenopithecus_nigroviridis 0 0
Allocebus_trichotis 0 0
Alouatta_caraya 1 0
Alouatta_guariba 1 0
Alouatta_palliata 0 0
Alouatta_pigra 0 0# run phylolm and get summary
SizeSDC <- phyloglm(Sexual_Dichromatism ~ Size_Dimorphism, data_pruned_rownames, phy = pruned.tree,method="logistic_MPLE")
summary(SizeSDC)
Call:
phyloglm(formula = Sexual_Dichromatism ~ Size_Dimorphism, data = data_pruned_rownames,
phy = pruned.tree, method = "logistic_MPLE")
AIC logLik Pen.logLik
282.5 -138.3 -135.4
Method: logistic_MPLE
Mean tip height: 66.17414
Parameter estimate(s):
alpha: 0.2594769
Coefficients:
Estimate StdErr z.value p.value
(Intercept) -1.40978 0.28342 -4.9742 6.551e-07 ***
Size_Dimorphism 1.02511 0.31459 3.2585 0.00112 **
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Note: Wald-type p-values for coefficients, conditional on alpha=0.2594769
sessionInfo()R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.0
[5] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.1.8
[9] ggplot2_3.4.1 tidyverse_2.0.0 phylolm_2.6.2 ape_5.7
[13] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.11 lattice_0.20-45 listenv_0.9.0
[4] getPass_0.2-2 ps_1.7.2 rprojroot_2.0.4
[7] digest_0.6.30 utf8_1.2.2 parallelly_1.36.0
[10] R6_2.5.1 evaluate_0.20 httr_1.4.4
[13] pillar_1.8.1 rlang_1.0.6 rstudioapi_0.14
[16] whisker_0.4.1 callr_3.7.3 jquerylib_0.1.4
[19] rmarkdown_2.20 bit_4.0.5 munsell_0.5.0
[22] compiler_4.2.1 httpuv_1.6.11 xfun_0.41
[25] pkgconfig_2.0.3 globals_0.16.2 htmltools_0.5.4
[28] tidyselect_1.2.0 codetools_0.2-18 fansi_1.0.3
[31] future_1.33.0 crayon_1.5.2 tzdb_0.3.0
[34] withr_2.5.0 later_1.3.1 grid_4.2.1
[37] nlme_3.1-160 jsonlite_1.8.4 gtable_0.3.1
[40] lifecycle_1.0.3 git2r_0.32.0 magrittr_2.0.3
[43] scales_1.2.1 vroom_1.6.1 future.apply_1.11.0
[46] cli_3.6.0 stringi_1.7.8 cachem_1.0.6
[49] fs_1.6.1 promises_1.2.1 bslib_0.4.2
[52] ellipsis_0.3.2 vctrs_0.5.2 generics_0.1.3
[55] tools_4.2.1 bit64_4.0.5 glue_1.6.2
[58] hms_1.1.2 processx_3.8.0 parallel_4.2.1
[61] fastmap_1.1.0 yaml_2.3.7 timechange_0.2.0
[64] colorspace_2.0-3 knitr_1.42 sass_0.4.5