| The Xpose Package | xpose4-package xpose |
| Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, for Xpose 4 | absval.dcwres.vs.cov.model.comp absval.dipred.vs.cov.model.comp absval.diwres.vs.cov.model.comp absval.dpred.vs.cov.model.comp absval.dwres.vs.cov.model.comp absval_delta_vs_cov_model_comp |
| Absolute conditional weighted residuals vs covariates for Xpose 4 | absval.cwres.vs.cov.bw |
| Absolute population conditional weighted residuals vs population predictions for Xpose 4 | absval.cwres.vs.pred |
| Absolute value of the conditional weighted residuals vs. population predictions, conditioned on covariates, for Xpose 4 | absval.cwres.vs.pred.by.cov |
| Absolute population weighted residuals vs population predictions, and absolute individual weighted residuals vs individual predictions, for Xpose 4 | absval.iwres.cwres.vs.ipred.pred absval.iwres.wres.vs.ipred.pred |
| box and whisker plots of the absolute value of the individual weighted residuals vs. covariates | absval.iwres.vs.cov.bw |
| absolute value of the individual weighted residuals vs. the independent variable | absval.iwres.vs.idv |
| Absolute individual weighted residuals vs individual predictions for Xpose 4 | absval.iwres.vs.ipred |
| Absolute individual weighted residuals vs individual predictions, conditioned on covariates, for Xpose 4 | absval.iwres.vs.ipred.by.cov |
| Absolute individual weighted residuals vs population predictions or independent variable for Xpose 4 | absval.iwres.vs.pred |
| Absolute weighted residuals vs covariates for Xpose 4 | absval.wres.vs.cov.bw |
| Absolute value of (C)WRES vs. independent variable plot in Xpose4. | absval.wres.vs.idv |
| Absolute population weighted residuals vs population predictions for Xpose 4 | absval.wres.vs.pred |
| Absolute population weighted residuals vs population predictions, conditioned on covariates, for Xpose 4 | absval.wres.vs.pred.by.cov |
| Column-transformation functions for Xpose 4 | add.absval add.dichot add.exp add.log add.tad add_transformed_columns |
| Print tables or text in a grid object | add.grid.table add.grid.text |
| Additional model comparison plots, for Xpose 4 | add.model.comp |
| Additional goodness-of-fit plots, for Xpose 4 | addit.gof |
| Autocorrelation of conditional weighted residuals for Xpose 4 | autocorr.cwres |
| autocorrelation of the individual weighted residuals | autocorr.iwres |
| Autocorrelation of weighted residuals for Xpose 4 | autocorr.wres |
| Basic goodness-of-fit plots, for Xpose 4 | basic.gof |
| Basic model comparison plots, for Xpose 4 | basic.model.comp |
| Function to create histograms of results from the 'bootstrap' tool in PsN | boot.hist |
| Print summary information for a bootgam or bootscm | bootgam.print |
| Import bootscm data into R/Xpose | bootscm.import |
| Categorical observations vs. independent variable using stacked bars. | cat.dv.vs.idv.sb |
| Categorical (visual) predictive check. | cat.pc |
| Functions changing variable definitions in Xpose 4 | change.ab.graph.par change.bw.graph.par change.cond.graph.par change.dil.graph.par change.label.par change.lm.graph.par change.misc.graph.par change.pi.graph.par change.smooth.graph.par change_graphical_parameters |
| Functions changing miscellaneous parameter settings in Xpose 4 | change.cat.cont change.cat.cont<- change.cat.levels change.cat.levels<- change.dv.cat.levels change.dv.cat.levels<- change.miss change.subset change_misc_parameters get.doc set.doc |
| Change parameter scope. | change.parm |
| Changes the name of an Xpose data item | change.var.name |
| Changes the label of an Xpose data item | change.xlabel |
| Change Xpose variable definitions. | change.xvardef change.xvardef<- |
| Compute the Conditional Weighted Residuals | compute.cwres ind.cwres is.cwres.readable.file read.cwres.data sqrtm xpose.calculate.cwres |
| Plot scatterplot matrices of parameters, random parameters or covariates | cov.splom parm.splom par_cov_splom ranpar.splom |
| Create xpose.multiple.plot class. | create.xpose.plot.classes print,xpose.multiple.plot-method |
| This function creates the Xpose data classes ("xpose.data" and "xpose.prefs") | createXposeClasses |
| Histogram of conditional weighted residuals (CWRES), for Xpose 4 | cwres.dist.hist |
| Quantile-quantile plot of conditional weighted residuals (CWRES), for Xpose 4 | cwres.dist.qq |
| Conditional Weighted residuals (CWRES) plotted against covariates, for Xpose 4 | cwres.vs.cov |
| Population conditional weighted residuals (CWRES) plotted against the independent variable (IDV) for Xpose 4 | cwres.vs.idv |
| Box-and-whisker plot of conditional weighted residuals vs the independent variable for Xpose 4 | cwres.vs.idv.bw |
| Population conditional weighted residuals (CWRES) plotted against population predictions (PRED) for Xpose 4 | cwres.vs.pred |
| Box-and-whisker plot of conditional weighted residuals vs population predictions for Xpose 4 | cwres.vs.pred.bw |
| Weighted residuals (WRES) and conditional WRES (CWRES) plotted against the independent variable (IDV) | cwres.wres.vs.idv |
| Weighted residuals (WRES) and conditional WRES (CWRES) plotted against the population predictions (PRED) | cwres.wres.vs.pred |
| Extract or assign data from an xpose.data object. | Data Data<- data_extract_or_assign SData SData<- |
| Check through the source dataset to detect problems | data.checkout |
| Prints the contents of an Xpose data object | db.names |
| Change in individual objective function value vs. covariate value. | dOFV.vs.cov |
| Change in Objective function value vs. removal of individuals. | dOFV.vs.id |
| Change in individual objective function value 1 vs. individual objective function value 2. | dOFV1.vs.dOFV2 |
| Observations (DV), individual predictions (IPRED) and population predictions (IPRED) plotted against the independent variable (IDV), for Xpose 4 | dv.preds.vs.idv |
| Observations (DV) plotted against the independent variable (IDV) for Xpose 4 | dv.vs.idv |
| Observations (DV) plotted against individual predictions (IPRED) for Xpose 4 | dv.vs.ipred |
| Dependent variable vs individual predictions, conditioned on covariates, for Xpose 4 | dv.vs.ipred.by.cov |
| Dependent variable vs individual predictions, conditioned on independent variable, for Xpose 4 | dv.vs.ipred.by.idv |
| Observations (DV) plotted against population predictions (PRED) for Xpose 4 | dv.vs.pred |
| Dependent variable vs population predictions, conditioned on covariates, for Xpose 4 | dv.vs.pred.by.cov |
| Dependent variable vs population predictions, conditioned on independent variable, for Xpose 4 | dv.vs.pred.by.idv |
| Observations (DV) are plotted against individual predictions (IPRED) and population predictions (PRED), for Xpose 4 | dv.vs.pred.ipred |
| Exports Xpose graphics settings to a file. | export.graph.par xpose.write |
| Exports Xpose variable definitions to a file from an Xpose data object. | export.variable.definitions |
| GAM functions for Xpose 4 | GAM_summary_and_plot xp.akaike.plot xp.cook xp.ind.inf.fit xp.ind.inf.terms xp.ind.stud.res xp.plot xp.summary |
| Structured goodness of fit diagnostics. | gof gofSetup xpPage |
| Imports Xpose graphics settings from a file to an Xpose data object. | import.graph.par xpose.read |
| Imports Xpose variable definitions from a file to an Xpose data object. | import.variable.definitions |
| Observations (DV), individual predictions (IPRED) and population predictions (PRED) are plotted against the independent variable for every individual in the dataset, for Xpose 4 | ind.plots |
| Histograms of weighted residuals for each individual in an Xpose data object, for Xpose 4 | ind.plots.cwres.hist ind.plots.wres.hist |
| Quantile-quantile plots of weighted residuals for each individual in an Xpose data object, for Xpose 4 | ind.plots.cwres.qq ind.plots.wres.qq |
| Individual predictions (IPRED) plotted against the independent variable (IDV) for Xpose 4 | ipred.vs.idv |
| Histogram of individual weighted residuals (IWRES), for Xpose 4 | iwres.dist.hist |
| Quantile-quantile plot of individual weighted residuals (IWRES), for Xpose 4 | iwres.dist.qq |
| Individual weighted residuals (IWRES) plotted against the independent variable (IDV) for Xpose 4 | iwres.vs.idv |
| Kaplan-Meier plots of (repeated) time-to-event data | kaplan.plot |
| Make stacked bar data set. | make.sb.data |
| Function to plot the coverage of the Numerical Predictive Check | npc.coverage |
| Extract or set the value of the Nsim slot. | nsim nsim<- |
| Plot the parameter or covariate distributions using a histogram | cov.hist parm.hist par_cov_hist ranpar.hist |
| Plot the parameter or covariate distributions using quantile-quantile (Q-Q) plots | cov.qq parm.qq par_cov_qq ranpar.qq |
| Summarize individual parameter values and covariates | cov.summary parm.summary par_cov_summary |
| Parameters plotted against covariates, for Xpose 4 | parm.vs.cov |
| Plot parameters vs other parameters | parm.vs.parm |
| Population predictions (PRED) plotted against the independent variable (IDV) for Xpose 4 | pred.vs.idv |
| Print an Xpose multiple plot object. | print.xpose.multiple.plot |
| Function to create a histogram of results from the randomization test tool ('randtest') in PsN | randtest.hist |
| Random parameters plotted against covariates, for Xpose 4 | ranpar.vs.cov |
| Read NONMEM output files into Xpose 4 | calc.npar create.parameter.list read.lst read_NM_output |
| Read NONMEM table files produced from simulation. | read_nm_table |
| Reading NONMEM table files | read.nm.tables |
| Read the results file from a Numerical or Visual Predictive Check run in PsN | read.npc.vpc.results |
| Read (repeated) time-to-event simulation data files. | read.TTE.sim.data |
| Read the vpctab file from PsN into Xpose | read.vpctab |
| Resets Xpose variable definitions to factory settings | reset.graph.par |
| Print run summary in Xpose 4 | runsum |
| Simulated prazosin Xpose database. | simpraz.xpdb |
| Function to create files for the simulated prazosin example in Xpose | simprazExample |
| Tabulate the population parameter estimates | tabulate.parameters |
| Histogram of weighted residuals (WRES), for Xpose 4 | wres.dist.hist |
| Quantile-quantile plot of weighted residuals (WRES), for Xpose 4 | wres.dist.qq |
| Weighted residuals (WRES) plotted against covariates, for Xpose 4 | wres.vs.cov |
| Population weighted residuals (WRES) plotted against the independent variable (IDV) for Xpose 4 | wres.vs.idv |
| Box-and-whisker plot of weighted residuals vs the independent variable for Xpose 4 | wres.vs.idv.bw |
| Population weighted residuals (WRES) plotted against population predictions (PRED) for Xpose 4 | wres.vs.pred |
| Box-and-whisker plot of weighted residuals vs population predictions for Xpose 4 | wres.vs.pred.bw |
| Extract and set labels for Xpose data items. | xlabel xlabel<- |
| Compare parameter estimates for covariate coefficients | xp.boot.par.est |
| Correlations between covariate coefficients | xp.boot.par.est.corr |
| Distribution of difference in AIC | xp.daic.npar.plot |
| Plot of model size distribution for a bootgam or bootscm | xp.distr.mod.size |
| Distribution of difference in OFV | xp.dofv.npar.plot |
| OFV difference (optimism) plot. | xp.dofv.plot |
| Default function for calculating dispersion in 'xpose.gam'. | xp.get.disp |
| Trace plots for conditional indices | xp.inc.cond.stab.cov |
| Trace plots for conditional indices rper replicate number | xp.inc.ind.cond.stab.cov |
| Inclusion frequency plot | xp.inc.prob |
| Inclusion frequency plot for combination of covariates. | xp.inc.prob.comb.2 |
| Inclusion stability plot A plot of the inclusion frequency of covariates vs bootgam/bootscm iteration number. This plot can be used to evaluate whether sufficient iterations have been performed. | xp.inc.stab.cov |
| Plot of inclusion index of covariates. | xp.incl.index.cov |
| Inclusion index individuals, compare between covariates. | xp.incl.index.cov.comp |
| Individual inclusion index | xp.incl.index.cov.ind |
| Define a scope for the gam. Used as default input to the 'scope' argument in 'xpose.gam' | xp.scope3 |
| Title | xpose.bootgam |
| Create an Xpose data object | xpose.data |
| Class xpose.data | data.frame_or_NULL-class numeric_or_NULL-class xpose.data-class |
| Stepwise GAM search for covariates on a parameter (Xpose 4) | xpose.gam |
| Displays the Xpose license and citation information | xpose.license.citation |
| Functions to create nice looking axes when using Log scales. | xpose.logTicks xpose.xscale.components.log10 xpose.yscale.components.log10 |
| Create and object with class "xpose.multiple.plot". | xpose.multiple.plot |
| Class for creating multiple plots in xpose | character_or_NULL-class list_or_NULL-class logical_or_numeric-class xpose.multiple.plot-class |
| Xpose 4 generic function for plotting multiple lattice objects on one page | xpose.multiple.plot.default |
| Default box-and-whisker panel function for Xpose 4 | xpose.panel.bw |
| Default panel function for Xpose 4 | xpose.panel.default |
| Default histogram panel function for Xpose 4 | xpose.panel.histogram |
| Default QQ panel function for Xpose 4 | xpose.panel.qq |
| Scatterplot matrix panel function for Xpose 4 | xpose.panel.splom |
| The generic Xpose functions for box-and-whisker plots | xpose.plot.bw |
| The Xpose 4 generic functions for continuous y-variables. | xpose.plot.default |
| The Xpose 4 generic functions for continuous y-variables. | xpose.plot.histogram |
| The generic Xpose functions for QQ plots | xpose.plot.qq |
| The Xpose 4 generic functions for scatterplot matrices. | xpose.plot.splom |
| Class "xpose.prefs" | character_or_numeric-class xpose.prefs-class |
| Summarize an xpose database | xpose.print |
| Print a pretty string. | xpose.string.print |
| Visual Predictive Check (VPC) using XPOSE | xpose.VPC |
| Xpose Visual Predictive Check (VPC) for both continuous and Limit of Quantification data. | xpose.VPC.both |
| Xpose visual predictive check for categorical data. | xpose.VPC.categorical |
| Classic menu system for Xpose 4 | xpose4 |
| Extract or set the value of the Subset slot. | xsubset xsubset<- |
| Extract and set Xpose variable definitions. | xvardef xvardef<- |
