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.boot,
  ci = "cov",
  rse.cov = TRUE,
  label.pmtables
)

Arguments

pars: A parameter table as generated by `NMwork::createParameterTable()`.
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.

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"