cancerAcrossVertebrates

Before you start

Check your library

rscript checkLibrary.R
You can also run this in RStudio

Individual level data files are left out of the github. Some of these scripts require this data.

checkLibrary.R

Checks if user has libraries needed to run R scripts

Data

species-cancer-prevalence-data.xlsx

This is our species level life history data Contains data and data dictionary Minimum of 20 records per species min20-2022.05.16.xlsx is identical

species-cancer-prevalence-data.csv

Same life history species data as excel file, just as a csv

data-description-species-cancer-prevalence-data.txt

Data descrption for species-cancer-prevalence-data.csv

fastslow.csv

life history data sorted by slow and fast life history

min1.csv

All species level data

min20DOX.csv

Species level doxirubicin treatment data

min20RAD_UPDATE.csv

Species level radiation treatment data

Mutation_Data.csv

Species level mutation rate data

trophicData.csv

Trophic level data for each species

Statistical Method Script

min20all.R

Main PGLS analysis of all life history variables

min20mam.R

PGLS Analysis of life history variables for mammals

propMaligMin20.R

PGLS Analysis of list history relations with proportion of malignant neoplasms

min20aves.R

PGLS Analysis of life history variables for aves

min20amph.R

PGLS Analysis of life history variables for amphibians

min20Sauropsids.R

PGLS Analysis of life history variables for sauropsids

min20VertGroup.R

PGLS Analysis of life history variables for different vertebrate groups

min20AgeControl.Rmd

PGLS controlled for available individual age data

min20GEE.Rmd

Replication of Bull et al.'s phylogenetic life history statistical analysis

Mltv.AIC.Rmd

Multivariate pgls

mutationRegression.Rmd

PGLS for mutation data

pglsPagel.R and pglsPagel.Rmd

Run this code to use pgls in environment. This code is at beginning of all pgls script, so not necessary to run.

benignvmal.R

PGLS between benign and malignancy prevalence

bootstrap.R

Grabs a proportion of population's records and runs PGLS 100 times for both Neoplasia and Malignancy for each significant life history variable.

carnivorePgls.R

PGLS with Carnivore indicator added to models

doxfunc.R

PGLS for doxirubicin treatment data

kruskalwilcox.R

Perform Kruskal and Wilcox test between clades

speciesCut.Rmd

PGLS analysis with outlier species cut

tetrapodComp.R

PGLS analysis of same groups as Bull et al

arcsinMin20.Rmd || arcsinMin20.html

arcsine tranformation of significant dependent variables in pgls analysis

Results from Statistical Methods

bootstrapResult2.0.xlsx

Results of a run of bootstrap.R

geePglsComp.xlsx

Results of min20GEE.Rmd, min20All.R, and min20AgeControl.Rmd for model comparison

min20GEEOutput.xlsx

Results of Min20GEE.Rmd

Script for Visuals

superTree.R

script for large super tree

barTree.R

Creates phylo tree with bars above species name

CladeTree.R

Ancestral State Reconstruction with Clade bars

combined_distributions.R

Age of death distribution plots

violinsNeoMal.R

Script for violin plots

Experimentation

expExperiments.R

Simulation test of pglsPagelSey and compar.GEE. This is a large and and long-running script.