SSMD_matrix: Generate a SSMD matrix with all possible pairwise comparisons

In carlopacioni/vortexR: Post Vortex Simulation Analysis

Generate a SSMD matrix with all possible pairwise comparisons

Description

SSMD_matrix conducts pairwise comparisons for all possible pairs using strictly standardised mean difference (SSDM, Zhang 2007).

Usage

SSMD_matrix(
  data,
  project,
  scenario,
  params = c("PExtinct", "Nextant", "Het", "Nalleles"),
  yrs = "max",
  ST = FALSE,
  save2disk = TRUE,
  dir_out = "DataAnalysis/SSMD_matrix"
)

Arguments

data	A data.frame generated by collate_dat
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
params	A character vector with the parameters to be compared, default: c('PExtinct', 'Nextant', 'Het', 'Nalleles')
yrs	The year(s) to be analysed, default: 'max'
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/SSMD_matrix

Details

When yrs='max' (default), VortexR automatically sets yrs to the last year of the simulation .

Value

A list where each element is a matrix of SSMD (belowe the diagonal) and related p-values (above the diagonal) for each combination of 'yrs', population and 'params'

References

Zhang, X. D. 2007. A pair of new statistical parameters for quality control in RNA interference high-throughput screening assays. Genomics 89:552-561.

Examples

# Using Campbell et al. and Pacioni et al. example data.
# See ?pacioni and ?campbell for more details on example data.
require(vortexRdata)

data("pac.clas")

SSMD_matrix(data=pac.clas, project="Pacioni_et_al",
scenario="ST_Classic",
params = c("PExtinct", "Nextant", "Het", "Nalleles"),
yrs = c(60, 120), ST = FALSE, save2disk = FALSE)

data(sta.main)
ssmd_mat <- SSMD_matrix(data=sta.main, project="test",
                       scenario="test",
                       params = c("PExtant", "Nextant"),
                       yrs = c(25, 50), ST = FALSE, save2disk = FALSE)

carlopacioni/vortexR documentation built on May 6, 2022, 12:07 p.m.