Print parameter table to console, flextable, latex, or (latex) pdf file

Usage

printParameterTable(
  pars,
  engine = "kable",
  format,
  footnotes = NULL,
  script = NULL,
  file.mod,
  include,
  include.pattern,
  drop,
  drop.pattern,
  include.fix,
  caption,
  ci = "cov",
  rse.cov = TRUE,
  label.pmtables
)

Arguments

pars: A parameter table as generated by `NMwork::createParameterTable()`.
engine: "kable", "pmtables" or "flextable".
format: A format like "tex" or "pdf" for a preview or a file name for saving a file. What formats are available depends on `engine`.
footnotes: Additional footnotes to include. Footnotes about theta transformations, abbreviations, and source paths will automatically be included.
script: Path to source code to include in source code.
file.mod: Path to Nonmem control stream. Normally when `pars` was created with `createParameterTable()`, this is not needed because `pars` will contain this information already. If so, file.mod should only be used in cases where modifications to the original parameter table are being performed to generate new ones.
include: A character vector of symbol values to include. All else will be dropped.
include.pattern: A regular expression run on the `symbol` column. What matches will be kept.
drop: A character vector of symbol values to drop. All else will be kept.
drop.pattern: A regular expression run on the `symbol` column. What matches will be dropped.
include.fix: Either a logical or "NotZero". `TRUE` means fixed parameters are not filtered out, `FALSE` means they are filtered out, "NotZero" means they are only kept if not equal to zero.
caption: If supplied, this text will be added to a simple model naming string, based on the `file.mod` file name.
ci: The default ("cov") is to attempt to extract parameter estimation uncertainty from a succesful covariate step. To use a bootstrap estimate instead,
rse.cov: Include relative standard error estimate based on covariate step? Default is TRUE if source=="cov" and FALSE if not.
label.pmtables: If `engine=="pmtables"`, a latex label is needed. Like label.pmtables="tab:myfirsttable".

Details

kable: for rmd and rmd-latex: can't get longtable to work with footnotes. Currently not using footnotes.

pmtables is only available if the package called pmtables is installed. pmtables is not available on CRAN, at the time of writing this. It can be installed from MPN.

Examples

file.mod <- system.file("nonmem/xgxr134.mod",package="NMwork")
pars <- createParameterTable(file.lst=file.mod,
                  args.ParsText=list(format="%idx; %symbol ; %label [%unit] ; %trans",
                                     format.sigma="%symbol - %label "))
printParameterTable(pars=pars,format="R")
#> CI: Confidence Interval based on Nonmem Covariance step.
#> CV: Coefficient of Variation for log-normal distributed random effects.
#> Corr: Correlation.
#> RSE: Relative Standard Error on the scale where the parameter was estimated.
#> Model: /home/runner/work/_temp/Library/NMwork/nonmem/xgxr134.lst
#> 
#> 
#> |Parameter  |Label                                   |Est [CV% or Corr%] (RSE%) |95% CI        |Panel    |
#> |:----------|:---------------------------------------|:-------------------------|:-------------|:--------|
#> |THETA(1)   |log, Absorption rate [1/h]              |0.796 (8.0%)              |[0.67, 0.92]  |FixedEff |
#> |THETA(2)   |log, Central volume [L]                 |4.31 (1.4%)               |[4.2, 4.4]    |FixedEff |
#> |THETA(3)   |log, Clearance [L/h]                    |1.48 (7.9%)               |[1.3, 1.7]    |FixedEff |
#> |THETA(4)   |log, Peripheral volume [L]              |5.07 (4.8%)               |[4.6, 5.6]    |FixedEff |
#> |THETA(5)   |log, Intercomparmental clearance [L/h]  |2.13 (2.9%)               |[2, 2.3]      |FixedEff |
#> |THETA(6)   |log, Age effect on clearance []         |0.341 (42.2%)             |[0.059, 0.62] |FixedEff |
#> |THETA(7)   |log, Body-weight effect on clearance [] |0.188 (191.6%)            |[-0.52, 0.9]  |FixedEff |
#> |THETA(8)   |log, Male effect on clearance []        |1.17 (10.4%)              |[0.93, 1.4]   |FixedEff |
#> |OMEGA(1,1) |                                        |0 (fixed)                 |-             |IIV      |
#> |OMEGA(2,2) |                                        |0.178 [44%] (17.8%)       |[0.12, 0.24]  |IIV      |
#> |OMEGA(3,3) |                                        |0.24 [52%] (18.5%)        |[0.15, 0.33]  |IIV      |
#> |OMEGA(4,4) |                                        |0 (fixed)                 |-             |IIV      |
#> |OMEGA(5,5) |                                        |0 (fixed)                 |-             |IIV      |
#> |SIGMA(1,1) |Prop err                                |0.081 (6.7%)              |[0.07, 0.092] |resvar   |
#> |SIGMA(2,2) |Add err                                 |0 (fixed)                 |-             |resvar   |
printParameterTable(pars=pars,format="rmd")
#> Error in kable_rmd(x = structure(c("THETA(1)", "THETA(2)", "THETA(3)", "THETA(4)", "THETA(5)", "THETA(6)", "THETA(7)", "THETA(8)", "OMEGA(1,1)", "OMEGA(2,2)", "OMEGA(3,3)", "OMEGA(4,4)", "OMEGA(5,5)", "SIGMA(1,1)", "SIGMA(2,2)", "log, Absorption rate [1/h]", "log, Central volume [L]", "log, Clearance [L/h]", "log, Peripheral volume [L]", "log, Intercomparmental clearance [L/h]", "log, Age effect on clearance []", "log, Body-weight effect on clearance []", "log, Male effect on clearance []", "", "", "", "", "", "Prop err", "Add err", "0.796 (8.0%)", "4.31 (1.4%)", "1.48 (7.9%)", "5.07 (4.8%)", "2.13 (2.9%)", "0.341 (42.2%)", "0.188 (191.6%)", "1.17 (10.4%)", "0 (fixed)", "0.178 [44%] (17.8%)", "0.24 [52%] (18.5%)", "0 (fixed)", "0 (fixed)", "0.081 (6.7%)", "0 (fixed)", "[0.67, 0.92]", "[4.2, 4.4]", "[1.3, 1.7]", "[4.6, 5.6]", "[2, 2.3]", "[0.059, 0.62]", "[-0.52, 0.9]", "[0.93, 1.4]", "-", "[0.12, 0.24]", "[0.15, 0.33]", "-", "-", "[0.07, 0.092]", "-"), dim = c(15L, 4L), dimnames = list(NULL,     c("  ", " ", "Estimate (RSE%)\\newline[CV% or Corr%]", "95% Confidence Interval"    )), align = c("l", "l", "c", "c")), caption = "Model: xgxr134.",     escape = FALSE, booktabs = TRUE): could not find function "kable_rmd"