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A Command-Line Interface for mPTP - multi-rate Poisson Tree Processes

Source: R/mptp_tbl.R
mptp_tbl.Rd

mptp_tbl() returns species partition hypothesis estimated by mPTP software https://github.com/Pas-Kapli/mptp.

Usage

mptp_tbl(
  infile,
  exe = NULL,
  outfolder = NULL,
  method = c("multi", "single"),
  minbrlen = 1e-04,
  webserver = NULL,
  delimname = "mptp"
)

Source

Kapli T., Lutteropp S., Zhang J., Kobert K., Pavlidis P., Stamatakis A., Flouri T. 2016. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 33(11):1630-1638.

Arguments

infile

Path to tree file in Newick format. Should be dichotomous and rooted.

exe

Path to an mPTP executable.

outfolder

Path to output folder. Default to NULL. If not specified, a temporary location is used.

method

Which algorithm for Maximum Likelihood point-estimate to be used. Available options are:

  • single Single-rate PTP model. It assumes that every species evolved with the same rate.

  • multi Multi-rate mPTP model. It assumes that all species have different evolutionary rates.

minbrlen

Numeric. Branch lengths smaller or equal to the value provided are ignored from computations. Default to 0.0001. Use min_brlenfor fine tuning.

webserver

A .txt file containing mPTP results obtained from a webserver. Default to NULL.

delimname

Character. String to rename the delimitation method in the table. Default to 'mptp'.

Value

an object of class tbl_df

Details

mptp_tbl() relies on system to invoke mPTP software through a command-line interface. Hence, you must have the software available as an executable file on your system in order to use this function properly. mptp_tbl() saves all output files in outfolder and imports the results generated to Environment. If an outfolder is not provided by the user, then a temporary location is used. Alternatively, mptp_tbl() can parse a file obtained from webserver such as https://mptp.h-its.org/.

Author

Paschalia Kapli, Sarah Lutteropp, Jiajie Zhang, Kassian Kobert, Pavlos Pavlides, Alexandros Stamatakis, Tomáš Flouri.

Examples

# \donttest{

# get path to phylogram
path_to_file <- system.file("extdata/geophagus_raxml.nwk", package = "delimtools")

# run mPTP in single threshold mode (PTP)
ptp_df <- mptp_tbl(
  infile = path_to_file,
  exe = "/usr/local/bin/mptp",
  method = "single",
  minbrlen = 0.0001,
  delimname = "ptp",
  outfolder = NULL
)
#> mptp 0.2.5_linux_x86_64, 16GB RAM, 4 cores
#> https://github.com/Pas-Kapli/mptp
#> 
#> Parsing tree file...
#> Loaded rooted tree...
#> Number of edges greater than minimum branch length: 159 / 272
#> Score Null Model: 681.702507
#> Best score for single coalescent rate: 747.727196
#> LRT computed p-value: 0.000000
#> Writing delimitation file /tmp/RtmpRdWzeq/geophagus_raxml.nwk.mptp.single.txt ...
#> Number of delimited species: 17
#> Creating SVG delimitation file /tmp/RtmpRdWzeq/geophagus_raxml.nwk.mptp.single.svg ...
#> Done...
#> 
#> 
#> ℹ Warning: there are tip-to-tip distances smaller than the specified minimum branch length (0.0001).
#> Consider using `delimtools::min_brlen()` to explore branch lengths in your tree.
#> 
#> 
#> ℹ mPTP files are located in '/tmp/RtmpRdWzeq'.
#> 
#> 

# check
ptp_df
#> # A tibble: 137 × 2
#>    labels       ptp
#>    <chr>      <int>
#>  1 MZ051794.1     1
#>  2 MZ050845.1     1
#>  3 MZ051032.1     1
#>  4 MZ051706.1     1
#>  5 MZ504576.1     2
#>  6 MZ504578.1     2
#>  7 MZ504579.1     2
#>  8 MZ504588.1     2
#>  9 MZ504587.1     2
#> 10 MZ504592.1     2
#> # ℹ 127 more rows

# run mPTP in multi threshold mode (mPTP)

mptp_df <- mptp_tbl(
  infile = path_to_file,
  exe = "/usr/local/bin/mptp",
  method = "single",
  minbrlen = 0.0001,
  delimname = "mptp",
  outfolder = NULL
)
#> mptp 0.2.5_linux_x86_64, 16GB RAM, 4 cores
#> https://github.com/Pas-Kapli/mptp
#> 
#> Parsing tree file...
#> Loaded rooted tree...
#> Number of edges greater than minimum branch length: 159 / 272
#> Score Null Model: 681.702507
#> Best score for single coalescent rate: 747.727196
#> LRT computed p-value: 0.000000
#> Writing delimitation file /tmp/RtmpRdWzeq/geophagus_raxml.nwk.mptp.single.txt ...
#> Number of delimited species: 17
#> Creating SVG delimitation file /tmp/RtmpRdWzeq/geophagus_raxml.nwk.mptp.single.svg ...
#> Done...
#> 
#> 
#> ℹ Warning: there are tip-to-tip distances smaller than the specified minimum branch length (0.0001).
#> Consider using `delimtools::min_brlen()` to explore branch lengths in your tree.
#> 
#> 
#> ℹ mPTP files are located in '/tmp/RtmpRdWzeq'.
#> 
#> 

# check
mptp_df
#> # A tibble: 137 × 2
#>    labels      mptp
#>    <chr>      <int>
#>  1 MZ051794.1     1
#>  2 MZ050845.1     1
#>  3 MZ051032.1     1
#>  4 MZ051706.1     1
#>  5 MZ504576.1     2
#>  6 MZ504578.1     2
#>  7 MZ504579.1     2
#>  8 MZ504588.1     2
#>  9 MZ504587.1     2
#> 10 MZ504592.1     2
#> # ℹ 127 more rows
# }