doc/README.md

In richelbilderbeek/flechette: What If Speciation Takes Time?

raket

Folder structure

In raket_project, there are two folders:

• data: the simulated data
• results: the interpreted data, e.g. tables and figures

The data folder

In data, all files are put in a folder with a different number [this deviates from the razzo setup, but is easier to program now, and can be modified easier in the future].

In each of these folders, the files are:

Filename|Description|Created by -------------|---------------------------------------|-------------------------- parameters.RDa|the parameter file|create_parameter_files pbd.tree|the true PBD (species) tree|create_pbd_tree_file pbd.fasta|the true PBD alignment|pirouette bd.tree|the twin BD tree|pirouette bd.fasta|the twin BD alignment|pirouette pbd.trees|the posterior trees from pbd.tree|pirouette pbd.log|the posterior parameter estimates from pbd.tree|pirouette pbd_marg_lik.csv|the posterior's marginal likelihood from pbd.tree|pirouette bd.trees|the posterior trees from bd.tree|pirouette bd.log|the posterior parameter estimates from bd.tree|pirouette bd_marg_lik.csv|the posterior's marginal likelihood from bd.tree|pirouette pbd_nltts.csv|the nLTT statistic distribution between pbd.tree and pbd.trees|pirouette bd_nltts.csv|the nLTT statistic distribution between bd.tree and bd.trees|pirouette

See a raket_werper build log to see such a data folder.

The results folder

In results, there are only files:

Filename|Description|Created by -------------|---------------------------------------|-------------------------- esses.csv|all ESSes|create_esses_file marg_liks.csv|all marginal likelihoods|create_marg_liks_file nltt_stats.csv|all nLTT statistics, in short form|create_esses_file figure_1.png|figure 1|create_fig_1_file figure_2.png|figure 2|create_fig_2_file

See a raket_werper build log to see such a results folder.

Function overview

• Data creation: produces parameter files and output
• Results creation: creates figures and tables from the data

Data creation

Produces parameter files and output

File handling functions

All functions that end with _file or _files. These functions are friendly to scripted use and require only filenames as arguments.

Status|Description|Function name ---|---|--- ?|Create parameter files|create_parameters_files ?|Create PBD tree file|create_pbd_tree_file

Data handling functions

These functions do the actual work. They work on parsed data and are not intended to be called from a script

Status|Description|Function name ---|---|--- ?|1. Create parameters|create_parameters ?|2. Create PBD tree|create_pbd_tree

Results creation

Creates figures and tables from the data.

Data handling

All these functions take the project folder's name as an argument and return a tidy data frame or figure. They are not intended to be called from a script

Status|Description|Function name ---|---|--- ?|Collect marginal likelihoods|collect_marg_liks ?|Collect effective sample sizes|collect_esses ?|Collect nLTT statistics|collect_nltt_stats ?|Create figure 1|create_fig_1

File handling

All functions that end with _file or _files. These functions are friendly to scripted use and require only the project folder's name as an argument.

Status|Description|Function name ---|---|--- ?|Collect marginal likelihoods|create_marg_liks_file ?|Collect effective sample sizes|create_esses_file ?|Create nLTT statistics file|create_nltt_stats_file ?|Create figure 1|create_fig_1_file

How to create the dependency graph from the .dot file?

dot -Tps dependencies.dot -o dependencies.ps; convert dependencies.ps dependencies.png

richelbilderbeek/flechette documentation built on Dec. 30, 2019, 9:15 p.m.