parse-SSE: Parse SSE results
In saviclab/savictools: Streamlined Data Manipulation for Pharmacometrics

etacorr_cat

R Documentation

Parse SSE results

Description

parse_sse() parses a single .csv file of SSE summary statistics.

parse_all_sse() recursively searches for SSE results csv files, parses them, and combines them into data frames summarizing parameter statistics and error rates.

Usage

etacorr_cat(runno, eta, ...)

parse_sse(
  file = "sse_results.csv",
  param_stats = c("relative_rmse", "bias"),
  ofv_cols = c(1, 4, 5, 6),
  ofv_colNames = c("effect", "pow.05", "pow.01", "pow.001"),
  sim_names = NULL,
  summary = FALSE
)

parse_all_sse(
  path = getwd(),
  exclude = NULL,
  file = "sse_results.csv",
  param_stats = c("relative_rmse", "bias"),
  ofv_cols = c(1, 4, 5, 6),
  ofv_colNames = c("effect", "pow.05", "pow.01", "pow.001"),
  sim_names = NULL,
  summary = FALSE
)

Arguments

`runno`	Either a xpose compliant run number, NONMEM data in the form of a data frame or data frame extension, or string representing the path to a NONMEM tablefile
`eta`	Which ETAs to plot, e.g. `eta = c(1, 2)`
`...`	Covariates to plot against ETAs.
`file`	Name of the SSE results file. Default is "sse_results.csv".
`param_stats`	Parameter statistics to summarize. Must be present in param_rows of the SSE results. Default is c("relative_rmse", "bias").
`ofv_cols`	Column numbers to include from the ofv statistics table.
`ofv_colNames`	OFV statistics column names. Must be the same length as ofv_cols.
`sim_names`	Optionally, descriptive names for each alternative model, in the same order as listed in the SSE results. For example, if there are 3 alternative models called "alt_efv.mod", "alt_wt.mod", and "alt_age.mod", in that order, then you could use `⁠simNames = c("efv", "wt, "age")⁠` or something similar.
`summary`	If TRUE, parse_sse creates a folder called "summary" within the current directory and writes two .csv files to it summarizing the results.
`path`	Path to the parent directory containing the SSE results. Defaults to the current working directory.
`exclude`	Optionally, a Perl-style regular expression matching file paths to exclude from the results.

Value

A named list of data frames. "params" is a data frame of parameter statistics. "type_I_error" and "type_II_error" are summaries of OFV statistics.

Author(s)

Alexander Floren

Sandy Floren

Examples


## Not run: 
setwd(~/Path/To/SSE/Results)

# Parse all "sse_results.csv" files in a directory
parse_all_sse()

# Parse all "sse_results.csv" files in a directory, except those with the
# pattern "induc" in their sub-directory
parse_all_sse(exclude = "induc")

# Generate summary .csv files
parse_all_sse(summary = TRUE)

## End(Not run)

saviclab/savictools documentation built on Dec. 7, 2023, 11:56 p.m.