vortexR (version 1.1.7)

SSMD_matrix: 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

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'

Details

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

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

# NOT RUN {
# 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)
# }