This software is under active development, and as such cannot be
assumed to be free of bugs or poor functionality. Always inspect results
carefully. If you find a problem, please report it with as much detail
as possible in Issues.
Unfortunately in it’s current form, some of the functions
(abgd_tbl()
, asap_tbl()
and
mptp_tbl()
) will not work on Windows operating systems,
only on Unix (MacOS, Linux). This is because third party binaries
(executable programs) are required. We are working to implement
importing results from the webservers that are commonly used to run
these analyses. There are also difficulties with installing R required
package dependancies to run gmyc_tbl()
and
bgmyc_tbl()
because these are no longer under development
and available on CRAN, and must be installed from archived sources.
Please refer to https://legallab.github.io/delimtools/articles/install.html
for instructions on how to install.
The official GitHub repository for the R package
delimtools
(Bittencourt et al., in prep.).
delimtools
provides helper functions for the analysis of
single-locus species delimitation methods such as GMYC (Monaghan et al., 2009),
bGMYC (Reid &
Carstens, 2012), mPTP (Kapli et al.,
2017) and ASAP (Puillandre et al.,
2020). These software run multiple different platforms (e.g. R,
Unix, webservers), and also do not output their results in a consistent
format to allow easy comparison. To address these shortcomings we have
developed a suite of functions to standardise and simplify generating
single-locus species delimitations.
Delimtools mainly depends on the tidyverse and ggtree packages. To install these, run the command lines below:
Install tidyverse
:
install.packages("tidyverse")
Install ggtree
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
::install("ggtree") BiocManager
To install delimtools
you may execute the following
commands. We recommend the usage of the latest CRAN release always.
Latest stable version from CRAN
install.packages("delimtools")
Development version from GitHub:
::install_github("LegalLab/delimtools") devtools
Or a specific version via renv:
::install("LegalLab/delimtools@v0.1.0") renv
Here, we will demonstrate a single-locus species delimitation analysis on a Geophagus eartheater cichlid dataset (Ximenes et al., 2021) using a variety of methods. For full details please see the GitHub repository accompanying this R package at github.com/boopsboops/delimtools-testing.
library(delimtools)
library(dplyr)
# make tip label table
<- geophagus_info |>
tip.tab filter(gbAccession %in% geophagus_beast@phylo$tip.label) |>
mutate(labs= glue::glue("{gbAccession} | {scientificName}")) |>
select(gbAccession, labs, scientificName)
# get cols
<- delim_brewer(delim= geophagus_delims, package="randomcoloR", seed=42)
cols
# plot
delim_autoplot(delim = geophagus_delims,
tr = geophagus_beast,
consensus = TRUE,
n_match = 4,
delim_order = c("asap","abgd","locmin","gmyc","bgmyc","ptp", "mptp","morph"),
tbl_labs = tip.tab,
col_vec = cols,
hexpand = 0.7,
widths = c(0.5, 0.5))
#> Warning: `aes_()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`
#> ℹ The deprecated feature was likely used in the ggtree package.
#> Please report the issue at <https://github.com/YuLab-SMU/ggtree/issues>.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Warning in fortify(data, ...): Arguments in `...` must be used.
#> ✖ Problematic arguments:
#> • as.Date = as.Date
#> • yscale_mapping = yscale_mapping
#> • hang = hang
#> • color = "grey50"
#> • size = 1
#> ℹ Did you misspell an argument name?
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the ggtree package.
#> Please report the issue at <https://github.com/YuLab-SMU/ggtree/issues>.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
#> Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
#> ℹ Please use tidy evaluation idioms with `aes()`.
#> ℹ See also `vignette("ggplot2-in-packages")` for more information.
#> ℹ The deprecated feature was likely used in the ggtree package.
#> Please report the issue at <https://github.com/YuLab-SMU/ggtree/issues>.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
#> generated.
delimtools
in R by running
citation(package='delimtools')
.