Pextinct | R Documentation |
Calculates the cumulative probability of extinction and statistically compares each scenario
Pextinct( data, project, scenario, ST = FALSE, save2disk = TRUE, dir_out = "DataAnalysis/Pextinct" )
data |
The long format of run (lrun, the second element) of the output
from |
project |
The Vortex project name |
scenario |
The ST Vortex scenario name or the scenario that should be used as baseline if simulations were not conducted with the ST module |
ST |
Whether files are from sensitivity analysis (TRUE), or not (FALSE, default) |
save2disk |
Whether to save the output to disk, default: TRUE |
dir_out |
The local path to store the output. Default: DataAnalysis/Pairwise |
Pextinct
calculates the cumulative probability of extinction by
calculating the proportion of runs in which a population goes extinct for
each scenario.
Pextinct
then compares each scenario by calculating the strictly
standardised mean difference (SSMD, Zhang 2007) and reports this statistic
with its associated p values. Raw data are also reported.
A list with two elements, a table (data.table
) with the mean
Probability of extinction and its SD, the SSMD and its associated p-value
for each scenario and population, and a table (data.table
) with each
iteration where extinction is coded as one (and zero for no extinction)
Zhang, X. D. 2007. A pair of new statistical parameters for quality control in RNA interference high-throughput screening assays. Genomics 89:552-561.
# Using Pacioni et al. example data. See ?pac.run.lhs for more details. data(pac.run.lhs) Pext <- Pextinct(pac.run.lhs[[2]], project='Pacioni_et_al', scenario='ST_Classic', ST=TRUE, save2disk=FALSE, dir_out='DataAnalysis/Pextinct')
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