inst/notes.md

In benmarwick/pyrater: Estimate Speciation, Extinction, and Preservation Rates

laser package no longer on CRAN, so we can get it like this:

devtools::install_github("cran/laser")

input data looks like this:

head(car_models) make model first_year last_year 1 Allstate A-230 1952 1953 2 Allstate A-240 1952 1953 3 AM_General DJ5 1969 1974 4 AM_General FJ8 1973 1974 5 AM_General Hummer 1992 2001 6 American_Austin American_Austin 1930 1935

head(pottery_data) Ware most_recent_age..BP. oldest_age..BP. trait 1 Brown_Ware_A 66 265 1 2 Brown_Ware_A 66 265 5 3 Brown_Ware_A 66 265 3 4 Brown_Ware_A 1130 1265 5 5 Brown_Ware_A 1130 1265 1 6 Brown_Ware_A 1165 1365 2

edit the lineage_pyrate

- don't do global assignment

- don't write to csv

- don't use fixed paths

couldn't find preservation_pyrate_data_1BD_marginal.rates.log

couln't find PDF files for plots

output plotting functions have backslash problems

library(reticulate) use_python("C:/python27/") py_available(initialize = TRUE) py_available()

benmarwick/pyrater documentation built on May 7, 2019, 10:38 a.m.