Package index • NMwork

All functions

EtaPairsLowerTriangle(): Gets pairwise data between all columns of data, then provide organizing columns to allow the data to be plotted in a pairwise way in a matrix plot. This function returns the dataset in a format that will be directly used to plot the scatterplot in the lower triangle of the pairs plot. . The output of this function gets sent to NMwork:::EtaPairsScatMat.R (slightly modified version of GGally::scatmat), and then to NMwork::PlotEtaPairs(). Taken with minimal modifications from GGally:::lowertriangle().
EtaPairsScatMat(): Eta pairs scatterplot matrix lower triangle and diagonal elements. This function takes (1) the time-constant etas dataset, and (2) the output of NMwork:::EtaPairsLowerTriangle() to create the lower triangle and diagonal of the eta pairs plot. The output of this function gets sent to NMwork::PlotEtaPairs(). Taken with minimal modifications from GGally::scatmat().
EtaPairsUpperTriangle(): Gets pairwise data between all columns of data, then calculates correlation and p value of correlation to plot in upper triangle of eta pairs plot.. This function returns the dataset in a format that will be directly used to plot the correlation statistics in the upper triangle of the pairs plot. The output of this function gets sent to NMwork::PlotEtaPairs(). This function is taken with minimal modifications from GGally:::uppertriangle().
NMplotBSV(): Generate distribution plots of between-occasion variability terms from Nonmem
NMscript(): Run script on models using Rscript, optionally using sge
PlotEtaPairs(): Plots Eta pairs scatterplot matrix with lower triangle being a scatterplot, diagonal being a density plot, and upper triangle being text of the correlation and p-value. This function takes (1) the time-constant etas dataset, and (2) the output of NMwork:::EtaPairsUpperTriangle(), (3) the output of NMwork:::EtaPairsScatMat() (and NMwork::EtaPairsLowerTriangle), to plot a full eta pairs matrix plot. Taken with minimal modifications from GGally::ggscatmat().
createParameterTable(): Create parameter table data.frame using `NMreadExt()` and `NMreadParsText()`
findModels(): find model paths winin a directory
formatParameterTable(): Deprecated: Quickly format a parameter table into flextable objects
getSource(): Get and source an R script.
mergeLabel(): Add parameter labels from a parameter table
modelPaths(): Create a convenient set of file paths and other info related to a model.
newModel(): Create new control stream based on an existing model
plotCorrelationHeatmap(): Plot correlation matrix heatmap from completed NONMEM run This function differs from `plotEstCorr` in that it will plot a full matrix with diagonals representing standard error (rather than half matrix with no diagonals). Requires successful covariance step in NONMEM.
plotDVpredIpred(): Plot DV vs PRED or IPRED
plotEstCor(): Plot correlation matrix heatmap from completed NONMEM run
plotIndivProfilesDvPredIpred(): Plot Inidividual profiles observed (DV) and predicted (PRED and IPRED)
plotResPred(): Plot CWRES/IWRES vs population predictions (PRED)
plotResTime(): Plot CWRES/IWRES vs time (after dose, after first dose)
plotTrace(): Plot parameter estimation iterations
plot_vpc(): Plot VPC data generated by tidyvpc using custom function
printParameterTable(): Print parameter table to console, flextable, latex, or (latex) pdf file
scriptPaths(): Create list of script paths and other info related to a script
wrapTextToLength(): Does a script fit on a single page?