adds transcluster

[Kincekara]

I am attempting to add a useful R package for identifying outbreak clusters. It was also mentioned in the NE BRR meeting. There is no release, so I use the latest commit.

paper: https://academic.oup.com/mbe/article/36/3/587/5300248
github: https://github.com/JamesStimson/transcluster

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/build-files/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number in build-files (i.e. docker-builds/build-files/spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. build-files/shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. docker-builds/build-files/spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[erinyoung]

It looks like the tests worked

#12 [test 3/3] RUN mkdir test1 test2 &&    cd test1 &&    R < ../test1.R --vanilla &&    cd ../test2 &&    R < ../test2.R --vanilla
#12 0.098 
#12 0.098 R version 4.1.2 (2021-11-01) -- "Bird Hippie"
#12 0.098 Copyright (C) 2021 The R Foundation for Statistical Computing
#12 0.098 Platform: x86_64-pc-linux-gnu (64-bit)
#12 0.098 
#12 0.098 R is free software and comes with ABSOLUTELY NO WARRANTY.
#12 0.098 You are welcome to redistribute it under certain conditions.
#12 0.098 Type 'license()' or 'licence()' for distribution details.
#12 0.098 
#12 0.098 R is a collaborative project with many contributors.
#12 0.098 Type 'contributors()' for more information and
#12 0.098 'citation()' on how to cite R or R packages in publications.
#12 0.098 
#12 0.098 Type 'demo()' for some demos, 'help()' for on-line help, or
#12 0.098 'help.start()' for an HTML browser interface to help.
#12 0.098 Type 'q()' to quit R.
#12 0.098 
#12 0.164 > #!/usr/bin/R
#12 0.164 > 
#12 0.164 > # Adapted from https://github.com/JamesStimson/transcluster/blob/master/vignettes/how-to-guide.Rmd
#12 0.164 > 
#12 0.164 > # Start by loading the libraries:
#12 0.164 > library(transcluster)
#12 0.169 > library(stats)
#12 0.169 > library(clue)
#12 0.184 > library(igraph)
#12 0.218 
#12 0.218 Attaching package: 'igraph'
#12 0.218 
#12 0.219 The following objects are masked from 'package:stats':
#12 0.219 
#12 0.219     decompose, spectrum
#12 0.219 
#12 0.219 The following object is masked from 'package:base':
#12 0.219 
#12 0.219     union
#12 0.219 
#12 0.220 > 
#12 0.220 > # Then create some data. This is the same as the first example in the paper.
#12 0.220 > ids <- c('A', 'B', 'C', 'D')
#12 14.78 + attr: name (v/c), weight (e/n)
#12 14.78 + edges from cb13b0c (vertex names):
#12 14.78  [1] 11s006--A9s250 11s006--A9s287 11s006--A9s305 11s006--A9s391 11s149--11s341
#12 14.78  [6] 11s149--13s046 11s149--13s158 11s149--A9s194 11s149--A9s216 11s149--A9s249
#12 14.78 [11] 11s149--A9s320 11s149--A9s349 11s341--13s046 11s341--13s158 11s341--A9s349
#12 14.78 [16] 13s046--13s158 13s046--14s256 13s158--14s256 A5s071--A5s271 A5s071--A6s118
#12 14.78 [21] A5s071--A7s017 A5s254--A6s270 A5s254--A6s329 A5s271--A6s118 A5s271--A7s017
#12 14.78 [26] A5s271--A7s238 A5s271--A7s312 A6s118--A7s017 A6s118--A7s238 A6s118--A7s312
#12 14.78 [31] A6s118--A8s058 A6s270--A6s329 A7s017--A7s238 A7s017--A7s312 A7s017--A8s058
#12 14.78 [36] A7s017--A8s136 A7s017--A8s170 A7s155--A7s168 A7s238--A7s312 A7s238--A8s058
#12 14.78 + ... omitted several edges
#12 14.78 > 
#12 14.78 There were 50 or more warnings (use warnings() to see the first 50)
#12 DONE 14.8s

[erinyoung]

Do we need to worry about the warnings?

There were 50 or more warnings (use warnings() to see the first 50)