Learn R Programming

spartan (version 3.0.2)

efast_run_Analysis: Runs the eFAST Analysis for the pre-generated summary file

Description

Produces a file summarising the analysis; partitioning the variance between parameters and providing relevant statistics. These include, for each parameter of interest, first-order sensitivity index (Si), total-order sensitivity index (STi), complementary parameters sensitivity index (SCi), and relevant p-values and error bar data calculated using a two-sample t-test and standard error respectively. For a more detailed examination of this analysis, see the references in the R Journal paper. For ease of representation, the method also produces a graph showing this data for each simulation output measure. These graphs and summaries can be produced for multiple timepoints.

Usage

efast_run_Analysis(FILEPATH, MEASURES, PARAMETERS, NUMCURVES, NUMSAMPLES,
  OUTPUTMEASURES_TO_TTEST, TTEST_CONF_INT, GRAPH_FLAG, EFASTRESULTFILENAME,
  TIMEPOINTS = NULL, TIMEPOINTSCALE = NULL, GRAPHTIME = NULL,
  check_done = FALSE, output_types = c("pdf"),
  csv_file_curve_summary = TRUE, write_csv_file_out = TRUE,
  CURVE_SUMMARY = NULL)

Arguments

FILEPATH

Directory where the simulation runs can be found, in folders or in CSV file format

MEASURES

Array containing the names of the output measures which are used to analyse the simulation

PARAMETERS

Array containing the names of the parameters of which parameter samples have been generated

NUMCURVES

The number of 'resamples' to perform (see eFAST documentation) - recommend using at least 3

NUMSAMPLES

The number of parameter subsets that were generated in the eFAST design

OUTPUTMEASURES_TO_TTEST

Which measures in the range should be tested to see if the result is statistically significant. To do all, and if there were 3 measures, this would be set to 1:3

TTEST_CONF_INT

The level of significance to use for the T-Test (e.g. 0.95)

GRAPH_FLAG

Whether graphs should be produced summarising the output - should be TRUE or FALSE

EFASTRESULTFILENAME

File name under which the full eFAST analysis should be stored. This will contain the partitioning of variance for each parameter.

TIMEPOINTS

mplemented so this method can be used when analysing multiple simulation timepoints. If only analysing one timepoint, this should be set to NULL. If not, this should be an array of timepoints, e.g. c(12,36,48,60)

TIMEPOINTSCALE

Sets the scale of the timepoints being analysed, e.g. "Hours"

GRAPHTIME

Value never needs stating, used internally to produce graphs when processing multiple timepoints

check_done

If using multiple timepoints, whether data entry has been checked

output_types

Files types of graph to produce (pdf,png,bmp etc)

csv_file_curve_summary

Whether curve summaries are provided in multiple CSV files (as in traditional spartan), or as an R object (as in spartanDB)

write_csv_file_out

Whether the analysis should output a CSV file (TRUE) or return an R object (FALSE)

CURVE_SUMMARY

If providing an R object (csv_file_curve_summary=FALSE), this is the R object containing those summaries

Value

Either NULL if a CSV file is returned, or an R object containing the results of this analysis