nmDocx: Create a run summary word document

In nlmixr: Nonlinear Mixed Effects Models in Population PK/PD

Create a run summary word document

Description

Create a run summary word document

Usage

nmDocx(
  x,
  docxOut = NULL,
  docxTemplate = NULL,
  plot = TRUE,
  titleStyle = getOption("nlmixr.docx.title", "Title"),
  subtitleStyle = getOption("nlmixr.docx.subtitle", "Subtitle"),
  normalStyle = getOption("nlmixr.docx.normal", "Normal"),
  headerStyle = getOption("nlmixr.docx.heading1", "Heading 1"),
  centeredStyle = getOption("nlmixr.docx.centered", "centered"),
  preformattedStyle = getOption("nlmixr.docx.preformatted", "HTML Preformatted"),
  width = getOption("nlmixr.docx.width", 69),
  save = FALSE
)

nmSave(x, ..., save = TRUE)

Arguments

x	nlmixr fit object.
docxOut	Output file for run information document. If not specified it is the name of R object where the fit is located with the -YEAR-MONTH-DAY.docx appended. If it is NULL the document is not saved, but the officer object is returned.
docxTemplate	This is the document template. If not specified it defaults to option("nlmixr.docx.template"). If option("nlmixr.docx.template") is not specified it uses the included nlmixr document template. When docxTemplate=NULL it uses the officer blank document.
plot	Boolean indicating if the default goodness of fit plots are added to the document. By default TRUE
titleStyle	This is the word style name for the nlmixr title; Usually this is nlmixr version (R object). Defaults to option("nlmixr.docx.title") or Title
subtitleStyle	This is the word style for the subtitle which is nlmixr model name and date. Defaults to option("nlmixr.docx.subtitle") or Subtitle
normalStyle	This is the word style for normal text. Defaults to option("nlmixr.docx.normal") or Normal
headerStyle	This is the word style for heading text. Defaults to option("nlmixr.docx.heading1") or Heading 1
centeredStyle	This is the word style for centered text which is used for the figures. Defaults to option("nlmixr.docx.centered") or centered
preformattedStyle	This is the preformatted text style for R output lines. Defaults to option("nlmixr.docx.preformatted") or HTML Preformatted
width	Is an integer representing the number of characters your preformatted style supports. By default this is option("nlmixr.docx.width") or 69
save	Should the docx be saved in a zip file with the R rds data object for the fit? By default this is FALSE with nmDocx and TRUE with nmSave
...	when using 'nmSave' these arguments are passed to 'nmDocx'

Value

An officer docx object

Author(s)

Matthew Fidler

Examples

 library(nlmixr)
pheno <- function() {
    # Pheno with covariance
  ini({
    tcl <- log(0.008) # typical value of clearance
    tv <-  log(0.6)   # typical value of volume
    ## var(eta.cl)
    eta.cl + eta.v ~ c(1,
                       0.01, 1) ## cov(eta.cl, eta.v), var(eta.v)
                      # interindividual variability on clearance and volume
    add.err <- 0.1    # residual variability
  })
  model({
    cl <- exp(tcl + eta.cl) # individual value of clearance
    v <- exp(tv + eta.v)    # individual value of volume
    ke <- cl / v            # elimination rate constant
    d/dt(A1) = - ke * A1    # model differential equation
    cp = A1 / v             # concentration in plasma
    cp ~ add(add.err)       # define error model
  })
}

fit.s <- nlmixr(pheno, pheno_sd, "saem")

## Save output information into a word document
RxODE::.rxWithWd(tempdir(), # Put document in temporary directory
  nmDocx(fit.s)
)

nlmixr documentation built on March 27, 2022, 5:05 p.m.