In razzo_project
, there are two folders:
data
: the simulated dataresults
: the interpreted data, e.g. tables and figuresdata
folderIn data
, there are folders named after their parameters, e.g. 0.2-0.15-1-0.1
.
In each of these folders, there are folders named after their seeds, e.g. 1
.
In each of these folders, there are folders named after their site and clock models, e.g. strict-jc69
.
In each of these folders, there are:
Filename |Description
-----------------------------|----------------------------------------------------------------------------------------------------------------------
parameters.RDa
|the parameter file
mbd.tree
|the true MBD tree
mbd.fasta
|the true MBD alignment
mbd_gen.xml
|the BEAST2 input file, using the generative model
mbd_gen.trees
|the posterior trees from the true alignment, using the generative model
mbd_gen.log
|the posterior parameter estimates from the true tree, using the generative model
mbd_gen_evidence.trees
|the trees to estimate the marginal likelihood, using the generative model
mbd_gen_evidence.log
|the parameter estimates to estimate the marginal likelihood, using the generative model
mbd_gen.xml.state
|the final posterior state from the true tree, using the generative model
mbd_best.xml
|the BEAST2 input file, using the best candidate model
mbd_best.trees
|the posterior trees from the true tree, using best candidate model
mbd_best.log
|the posterior parameter estimates from the true tree, using the best candidate model
mbd_best.xml.state
|the final posterior state from the true tree, using the best candidate model
mbd_best_[x]_evidence.trees
|the trees to estimate the marginal likelihood, for the x
th candidate model (x == 1
for first model)
mbd_best_[x]_evidence.log
|the parameter estimates to estimate the marginal likelihood, for the x
th candidate model (x == 1
for first model)
mbd_marg_lik.csv
|the evidences (aka marginal likelihoods) all models have for the true alignment
mbd_nltts_gen.csv
|the error between true tree and its posterior for the generative model
mbd_nltts_best.csv
|the error between true tree and its posterior for the best candidate model
Filename |Description
-------------------------|---------------------------------------
mbd_twin.tree
|the twin MBD tree
mbd_twin.fasta
|the twin MBD alignment
mbd_gen_twin.trees
|the posterior trees from the twin alignment, using the generative model
mbd_gen_twin.log
|the posterior parameter estimates from the twin tree, using the generative model
mbd_best_twin.trees
|the posterior trees from the twin tree, using best candidate model
mbd_best_twin.log
|the posterior parameter estimates from the twin tree, using the best candidate model
mbd_marg_lik_twin.csv
|the evidences (aka marginal likelihoods) all models have for the twin alignment
mbd_nltts_gen_twin.csv
|the error between twin tree and its posterior for the generative model
mbd_nltts_best_twin.csv
|the error between twin tree and its posterior for the best candidate model
See a razzo_project build log
to see such a data
folder.
results
folderIn 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 razzo_project build log
to see such a results
folder.
Produces parameter files and output
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 all output files|run_razzo_from_file
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. Run the experiment|run_razzo
Creates figures and tables from the data.
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
?|12. Create figure 1|create_fig_1
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
.dot
file?dot -Tps dependencies.dot -o dependencies.ps; convert dependencies.ps dependencies.png
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