pmxpartab (version 0.5.0)

pmxpartab: Generate an formatted HTML table of parameter estimates

Description

Generate an formatted HTML table of parameter estimates

Usage

pmxpartab(
  parframe,
  columns = c(est = "Estimate", rse = "RSE%", ci95 = "95% CI", shrinkage =
    "Shrinkage"),
  sections = !is.null(parframe$type),
  section.labels = c(Structural = "Typical Values", CovariateEffect =
    "Covariate Effects", RUV = "Residual Error", IIV = "Between Subject Variability", IOV
    = "Inter-Occasion Variability"),
  footnote = NULL,
  show.fixed.to.zero = FALSE,
  merge.units = TRUE,
  na = "-",
  digits = 3
)

Arguments

parframe

A data.frame such as returned by pmxparframe.

columns

A named character vector of columns to include in the table (and in what order). The names correspond to column names in parframe and the value to the column labels that appear in the formatted table.

sections

A logical indicating whether or not the table should be formatted into sections according the the type column of parframe.

section.labels

A named character vector. The names correspond to values in the type column of parframe, and the values to labels that appear in the formatted table.

footnote

A character vector of footnotes to place underneath the formatted table (may contain HTML codes).

show.fixed.to.zero

A logical indicating whether parameters that are fixed to zero should appear in the formatted table (by default, parameters that are formatted to values other than zero do appear in the table, but those that are fixed to zero are ignored).

merge.units

A logical indicating whether or not units (if present) should be merged into the parameter label (i.e., in parentheses following the name/label).

na

A character string to use in the formatted table to indicate missing or non-applicable values.

digits

Number of significant digits to include in the formatted table.

Value

An object of class "pmxpartab". This is essentially just an HTML character string that displays in the default web browser or viewer when printed (as per htmltools::print.html()).

See Also

pmxparframe

Examples

# NOT RUN {
outputs <- list(
  est = list(
    th = list(CL = 0.482334, VC = 0.0592686),
    om = list(nCL = 0.315414, nVC = 0.536025),
    sg = list(ERRP = 0.0508497)),
  se = list(
    th = list(CL = 0.0138646, VC = 0.00555121),
    om = list(nCL = 0.0188891, nVC = 0.0900352),
    sg = list(ERRP = 0.00182851)),
  fixed = list(
    th = list(CL = FALSE, VC = FALSE),
    om = list(nCL = FALSE, nVC = FALSE),
    sg = list(ERRP = FALSE)),
  shrinkage = list(nCL = 9.54556, nVC = 47.8771))

meta <- list(
  parameters = list(
    list(name="CL", label="Clearance", units="L/h", type="Structural"),
    list(name="VC", label="Volume", units="L", type="Structural", trans="exp"),
    list(name="nCL", label="On Clearance", type="IIV", trans="SD (CV%)"),
    list(name="nVC", label="On Volume", type="IIV"),
    list(name="ERRP", label="Proportional Error", units="%", type="RUV", trans="%")))

pmxpartab(pmxparframe(outputs, meta),
    columns=c(est="Estimate", rse="RSE%", ci95="95% CI", shrinkage="Shrinkage"),
    footnote="CI=confidence interval; RSE=relative standard error.")


# An example using a Cox model, where we construct the parframe manually:
library(survival)
cph.fit <- coxph(Surv(time, status) ~ ph.ecog + age, data=lung)
parframe <- with(summary(cph.fit), data.frame(
    name  = c("ph.ecog", "age"),
    label = c("ECOG performance score", "Age"),
    est   = coefficients[,"exp(coef)"],
    pval  = coefficients[,"Pr(>|z|)"],
    lci95 = conf.int[,"lower .95"],
    uci95 = conf.int[,"upper .95"]
))
pmxpartab(parframe=parframe,
    columns=c(est="HR", ci95="95% CI", pval="P-Value"))
# }