make_report_rmd: Generate report(s) with modeling stats and survival estimates...

In osofr/stremr: Streamlined Estimation for Static, Dynamic and Stochastic Treatment Regimes in Longitudinal Data

Description

Generate report(s) with modeling stats and survival estimates using pandoc.

Usage

make_report_rmd(
  OData,
  MSM,
  NPMSM,
  TMLE,
  GCOMP,
  WTtables,
  FUPtables,
  MSM.RDtables,
  TMLE.RDtables,
  plotKM = FALSE,
  printEstimateTables = FALSE,
  format = c("html", "pdf", "word"),
  skip.modelfits = FALSE,
  file.name = getOption("stremr.file.name"),
  file.path = getOption("stremr.file.path"),
  openFile = TRUE,
  serve_html_rmote = FALSE,
  keep_md = FALSE,
  keep_tex = FALSE,
  save_report_data = FALSE,
  use_ggplot = TRUE,
  ...
)

Arguments

OData	Input data object returned by the function importData.
MSM	The MSM object fits returned by the function survMSM.
NPMSM	Optional list of a resulting calls to survNPMSM or a result of a single call to survNPMSM.
TMLE	Optional list of a resulting calls to fit_TMLE or a result of a single call to fit_TMLE.
GCOMP	Optional list of a resulting calls to fit_GCOMP or a result of a single call to fit_GCOMP.
WTtables	Table(s) with distribution(s) of the IPTW weights, a result of calling the function get_wtsummary
FUPtables	Subject-specific data.table with maximum follow-up time saved for each subject in the column named max.t. See get_FUPtimes for additional details.
MSM.RDtables	List of tables with risk differences returned by the function get_MSM_RDs.
TMLE.RDtables	List of tables with risk differences returned by the function get_TMLE_RDs.
plotKM	Logical, set to TRUE to plot KM survival curves when NPMSM argument is specified. Default is FALSE.
printEstimateTables	...
format	Choose the Pandoc output format for the report file (html, pdf or word). Note that the html report file is always produced in addition to any other selected format.
skip.modelfits	Do not report any of the modeling stats.
file.name	File name for the report file without extension. Default file name is assigned based on the current date.
file.path	Directory path where the report file(s) should be written. Default is to use the system temporary directory.
openFile	Open the report file with OS default viewer?
serve_html_rmote	Serve the html report as a webpage via R package "rmote".
keep_md	Keep the source .md files?
keep_tex	Keep the source .tex files for pdf output?
save_report_data	Save the data needed for generating this report as a list in a separate 'report_name.Rd' file.
use_ggplot	Set to TRUE to enable plotting with ggplot.
...	Additional arguments may specify the report title (author), author (title). Specifying the logical flag only.coefs=TRUE disables printing of all h2o-specific model summaries. Additional set of arguments control the survival plotting, these are passed on to the function f_plot_survest: t_int_sel, y_lab, x_lab, miny, x_legend, y_legend.

Value

String specifying the path to the main report file.

osofr/stremr documentation built on Jan. 25, 2022, 8:07 a.m.