Rerunning the analyses

[caseywdunn]

First goal is to rerun the analyses. Readme notes that it runs ontop of our earlier repo, looking at the details.

Authors used absolute paths, these will need to be updated to relative paths that can run on any system.

From https://github.com/dunnlab/Testing_the_ortholog_conjecture/blob/master/Premanuscript_run_TM.R :

• setwd("/Users/admin/Desktop/nwork/simulation/")
• source( "/Users/admin/Desktop/nwork/Empirical/protein_trees.nhx/function_TM_new.R" )
• load("/Users/admin/Desktop/nwork/simulation/manuscript_dunn.RData")

There are several image dumps that are commented out. Likely need to uncomment one of those.

• #save.image("BM_trees_for_tau1.rda")
• #save.image("BM_trees_for_tau1.rda")
• #save.image("BM_trees_for_tau1.rda")
• #save.image("Data_TMRR.rda")

The following comment from the README suggests it is that last one that should be uncommented - "The outputs are generated and saved as "Data_TMRR.rda" available in https://doi.org/10.5281/zenodo.3354285."

Now a look at paths in https://github.com/dunnlab/Testing_the_ortholog_conjecture/blob/master/Manuscript.Rmd

• bibliography: /Users/admin/Desktop/nwork/simulation/TM.bib
• csl: /Users/admin/Desktop/nwork/simulation/styles-master/styles-master/plos.csl
• setwd("/Users/admin/Desktop/nwork/simulation/")
• source( "/Users/admin/Desktop/nwork/Empirical/protein_trees.nhx/function_TM_new.R" )
• load("/Users/admin/Desktop/nwork/simulation/manuscript_dunn.RData")
• load("/Users/admin/Desktop/nwork/simulation/Data_TMRR.rda")
• img <- png::readPNG("/Users/admin/Desktop/nwork/simulation/flowchart_S4_new.png")

[caseywdunn]

Will go with a model that assumes Testing_the_ortholog_conjecture (this repo) and comparative_expression_2017 (from https://github.com/caseywdunn/comparative_expression_2017) are sister directories, ie they both have the same parent directory.