knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) library(tidyverse)
The files included in folder /rubias/R-main/
allow the reproduction of all data,
statistics, and graphs presented in the publication ____. They also include
numerous graphs for further visualization of our model validation data, which were excluded
from the publication for brevity.
cross-validation.R
includes the first two methods of validation listed in the
publication: reproduction of the Leave-One-Out Cross-Validation in Hasselman et al. (2015) with and without parametric bootstrap correction, and the application of Monte Carlo
Cross-Validation to the same dataset. coalescent_sim.R
documents the third validation
method, the creation of simulated genotypes from the coalescent, followed by Leave-One-Out
Cross-Validation.
Sourcing these independent files will create (among other files from intermediate steps)
two data.frames for each validation method. One, ( )_rho_data
, contains true and
estimated reporting unit proportions (rho) created during the corresponding
cross-validation. The second, ( )_rho_dev
contains summary statistics describing the
deviation of each estimation method from its corresponding true rho value.
The validation is identified by the prefix, with coal
, Hass
, and mc
representing coalescent, Leave-One-Out, and Monte Carlo cross-validations, respectively.
For quick access, these output data are stored within the main rubias
folder as
cjfas_data.RData
.
Sourcing will also create a multitude of rough graphs which visualize this data. .lg
graphs plot the true vs. estimated rho value a la Figure 3, while .mse
,
.m.bias
, and .prop.bias
show mean squared error, mean bias, and mean proportional bias
for each reporting unit, with and without parametric bootstrapping. Prefixes c
, h
,
and mc
represent coalescent, Leave-One-Out, and Monte Carlo cross-validations.
The remaining two files of the R-main
folder use the data created by the
previous two; however, they begin by loading cjfas_data.RData
, and so can be run
independent of the original simulation scripts. proportion_sig_test
includes the
statistics and rough figures documenting the relationship between the residual for any
given simulation, $\tilde{\rho}_r - \rho^\mathrm{sim}_r$, and the structural metric
$\frac{N_C}{P} - \rho^\mathrm{sim}_r$. cjfas_graphs.R
contains the exact
scripts used to generate the ggplot2 figures found in
____.
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