https://github.com/dombennett/masters-project-pipeline
BIG MRes (2012-13, Silwood park) project code pipeline
https://github.com/dombennett/masters-project-pipeline
Last synced: about 1 year ago
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BIG MRes (2012-13, Silwood park) project code pipeline
- Host: GitHub
- URL: https://github.com/dombennett/masters-project-pipeline
- Owner: DomBennett
- Created: 2014-06-27T20:47:20.000Z (almost 12 years ago)
- Default Branch: master
- Last Pushed: 2014-06-27T20:47:24.000Z (almost 12 years ago)
- Last Synced: 2025-02-08T06:13:04.956Z (over 1 year ago)
- Language: R
- Homepage:
- Size: 125 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README
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README
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BIG MRes 2013 Project Code and Results
D.J. Bennett
05/09/2013
Testing for non-random phylogenetic responses to urbanisation using mass
phylogeny estimation (MPE)
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## Title
Analysis
## Required programs
R (v3+)
## Program packages
R: ape, reshape, picante, caper, lme4, stringr, RCurl, apTreeshape, phangorn,
stringdist, ggplot2, maps, mapdata, vioplot
## OS and system
Originally coded and run on:
Ubuntu 13.04 (Intel® Core™ i5-2540M CPU @ 2.60GHz × 4, 7.8 GiB)
## Folders
0_data --
files:
urban_data.csv (PREDICTS data) and name_modifiers.RData
published phylogenies and mass produced
folders:
pub_phylos (containing published phylogenies in Newick format
and a treecomp.csv specifying the comparisons to be performed),
mass_phylos (containing the distribution of trees for each study
in Newick format.)
1_results -- .csv and .RData files of the results
2_figures -- produced figures for thesis
functions -- EcoDataTools.R (functions for running ecological analysis) +
AP's plot fixed effects function.
## Description
These scripts are not for running automatively. Run 0_names.R first to generate
names for the taxa present across studies. Move these resultant files to the
0_names folder in the MPE pipeline. 0_names also produces a prem_taxadata.csv.
This contains information for each study to help speed up generation of a
taxadata.csv.
Once the MPE pipeline has run, move the name_modifiers.RData to the 0_data
folder here. And move all resultant trees (from 5_screen in MPE pipeline) to the
mass_phylos folder in 0_data.
To regenerate the results I produced for my thesis, re-run each script in the
order in which tehy are numbered.