Diagnostics for Nonlinear Mixed-Effect Models
![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
Documentation for package ‘xpose4’ version 4.7.3
Help Pages
A B C D E G I K L M N P R S T W X
| xpose4-package | The Xpose Package |
-- A --
| absval.cwres.vs.cov.bw | Absolute conditional weighted residuals vs covariates for Xpose 4 |
| absval.cwres.vs.pred | Absolute population conditional weighted residuals vs population predictions for Xpose 4 |
| absval.cwres.vs.pred.by.cov | Absolute value of the conditional weighted residuals vs. population predictions, conditioned on covariates, for Xpose 4 |
| absval.dcwres.vs.cov.model.comp | Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, for Xpose 4 |
| absval.dipred.vs.cov.model.comp | Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, for Xpose 4 |
| absval.diwres.vs.cov.model.comp | Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, for Xpose 4 |
| absval.dpred.vs.cov.model.comp | Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, for Xpose 4 |
| absval.dwres.vs.cov.model.comp | Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, for Xpose 4 |
| absval.iwres.cwres.vs.ipred.pred | Absolute population weighted residuals vs population predictions, and absolute individual weighted residuals vs individual predictions, for Xpose 4 |
| absval.iwres.vs.cov.bw | box and whisker plots of the absolute value of the individual weighted residuals vs. covariates |
| absval.iwres.vs.idv | absolute value of the individual weighted residuals vs. the independent variable |
| absval.iwres.vs.ipred | Absolute individual weighted residuals vs individual predictions for Xpose 4 |
| absval.iwres.vs.ipred.by.cov | Absolute individual weighted residuals vs individual predictions, conditioned on covariates, for Xpose 4 |
| absval.iwres.vs.pred | Absolute individual weighted residuals vs population predictions or independent variable for Xpose 4 |
| absval.iwres.wres.vs.ipred.pred | Absolute population weighted residuals vs population predictions, and absolute individual weighted residuals vs individual predictions, for Xpose 4 |
| absval.wres.vs.cov.bw | Absolute weighted residuals vs covariates for Xpose 4 |
| absval.wres.vs.idv | Absolute value of (C)WRES vs. independent variable plot in Xpose4. |
| absval.wres.vs.pred | Absolute population weighted residuals vs population predictions for Xpose 4 |
| absval.wres.vs.pred.by.cov | Absolute population weighted residuals vs population predictions, conditioned on covariates, for Xpose 4 |
| absval_delta_vs_cov_model_comp | Model comparison plots, of absolute differences in goodness-of-fit predictors against covariates, for Xpose 4 |
| add.absval | Column-transformation functions for Xpose 4 |
| add.dichot | Column-transformation functions for Xpose 4 |
| add.exp | Column-transformation functions for Xpose 4 |
| add.grid.table | Print tables or text in a grid object |
| add.grid.text | Print tables or text in a grid object |
| add.log | Column-transformation functions for Xpose 4 |
| add.model.comp | Additional model comparison plots, for Xpose 4 |
| add.tad | Column-transformation functions for Xpose 4 |
| addit.gof | Additional goodness-of-fit plots, for Xpose 4 |
| add_transformed_columns | Column-transformation functions for Xpose 4 |
| autocorr.cwres | Autocorrelation of conditional weighted residuals for Xpose 4 |
| autocorr.iwres | autocorrelation of the individual weighted residuals |
| autocorr.wres | Autocorrelation of weighted residuals for Xpose 4 |
-- B --
| basic.gof | Basic goodness-of-fit plots, for Xpose 4 |
| basic.model.comp | Basic model comparison plots, for Xpose 4 |
| boot.hist | Function to create histograms of results from the 'bootstrap' tool in PsN |
| bootgam.print | Print summary information for a bootgam or bootscm |
| bootscm.import | Import bootscm data into R/Xpose |
-- C --
| calc.npar | Read NONMEM output files into Xpose 4 |
| cat.dv.vs.idv.sb | Categorical observations vs. independent variable using stacked bars. |
| cat.pc | Categorical (visual) predictive check. |
| change.ab.graph.par | Functions changing variable definitions in Xpose 4 |
| change.bw.graph.par | Functions changing variable definitions in Xpose 4 |
| change.cat.cont | Functions changing miscellaneous parameter settings in Xpose 4 |
| change.cat.cont<- | Functions changing miscellaneous parameter settings in Xpose 4 |
| change.cat.levels | Functions changing miscellaneous parameter settings in Xpose 4 |
| change.cat.levels<- | Functions changing miscellaneous parameter settings in Xpose 4 |
| change.cond.graph.par | Functions changing variable definitions in Xpose 4 |
| change.dil.graph.par | Functions changing variable definitions in Xpose 4 |
| change.dv.cat.levels | Functions changing miscellaneous parameter settings in Xpose 4 |
| change.dv.cat.levels<- | Functions changing miscellaneous parameter settings in Xpose 4 |
| change.label.par | Functions changing variable definitions in Xpose 4 |
| change.lm.graph.par | Functions changing variable definitions in Xpose 4 |
| change.misc.graph.par | Functions changing variable definitions in Xpose 4 |
| change.miss | Functions changing miscellaneous parameter settings in Xpose 4 |
| change.parm | Change parameter scope. |
| change.pi.graph.par | Functions changing variable definitions in Xpose 4 |
| change.smooth.graph.par | Functions changing variable definitions in Xpose 4 |
| change.subset | Functions changing miscellaneous parameter settings in Xpose 4 |
| change.var.name | Changes the name of an Xpose data item |
| change.xlabel | Changes the label of an Xpose data item |
| change.xvardef | Change Xpose variable definitions. |
| change.xvardef<- | Change Xpose variable definitions. |
| change_graphical_parameters | Functions changing variable definitions in Xpose 4 |
| change_misc_parameters | Functions changing miscellaneous parameter settings in Xpose 4 |
| character_or_NULL-class | Class for creating multiple plots in xpose |
| character_or_numeric-class | Class "xpose.prefs" |
| compute.cwres | Compute the Conditional Weighted Residuals |
| cov.hist | Plot the parameter or covariate distributions using a histogram |
| cov.qq | Plot the parameter or covariate distributions using quantile-quantile (Q-Q) plots |
| cov.splom | Plot scatterplot matrices of parameters, random parameters or covariates |
| cov.summary | Summarize individual parameter values and covariates |
| create.parameter.list | Read NONMEM output files into Xpose 4 |
| create.xpose.plot.classes | Create xpose.multiple.plot class. |
| createXposeClasses | This function creates the Xpose data classes ("xpose.data" and "xpose.prefs") |
| cwres.dist.hist | Histogram of conditional weighted residuals (CWRES), for Xpose 4 |
| cwres.dist.qq | Quantile-quantile plot of conditional weighted residuals (CWRES), for Xpose 4 |
| cwres.vs.cov | Conditional Weighted residuals (CWRES) plotted against covariates, for Xpose 4 |
| cwres.vs.idv | Population conditional weighted residuals (CWRES) plotted against the independent variable (IDV) for Xpose 4 |
| cwres.vs.idv.bw | Box-and-whisker plot of conditional weighted residuals vs the independent variable for Xpose 4 |
| cwres.vs.pred | Population conditional weighted residuals (CWRES) plotted against population predictions (PRED) for Xpose 4 |
| cwres.vs.pred.bw | Box-and-whisker plot of conditional weighted residuals vs population predictions for Xpose 4 |
| cwres.wres.vs.idv | Weighted residuals (WRES) and conditional WRES (CWRES) plotted against the independent variable (IDV) |
| cwres.wres.vs.pred | Weighted residuals (WRES) and conditional WRES (CWRES) plotted against the population predictions (PRED) |
-- D --
| Data | Extract or assign data from an xpose.data object. |
| data.checkout | Check through the source dataset to detect problems |
| data.frame_or_NULL-class | Class xpose.data |
| Data<- | Extract or assign data from an xpose.data object. |
| data_extract_or_assign | Extract or assign data from an xpose.data object. |
| db.names | Prints the contents of an Xpose data object |
| dOFV.vs.cov | Change in individual objective function value vs. covariate value. |
| dOFV.vs.id | Change in Objective function value vs. removal of individuals. |
| dOFV1.vs.dOFV2 | Change in individual objective function value 1 vs. individual objective function value 2. |
| dv.preds.vs.idv | Observations (DV), individual predictions (IPRED) and population predictions (IPRED) plotted against the independent variable (IDV), for Xpose 4 |
| dv.vs.idv | Observations (DV) plotted against the independent variable (IDV) for Xpose 4 |
| dv.vs.ipred | Observations (DV) plotted against individual predictions (IPRED) for Xpose 4 |
| dv.vs.ipred.by.cov | Dependent variable vs individual predictions, conditioned on covariates, for Xpose 4 |
| dv.vs.ipred.by.idv | Dependent variable vs individual predictions, conditioned on independent variable, for Xpose 4 |
| dv.vs.pred | Observations (DV) plotted against population predictions (PRED) for Xpose 4 |
| dv.vs.pred.by.cov | Dependent variable vs population predictions, conditioned on covariates, for Xpose 4 |
| dv.vs.pred.by.idv | Dependent variable vs population predictions, conditioned on independent variable, for Xpose 4 |
| dv.vs.pred.ipred | Observations (DV) are plotted against individual predictions (IPRED) and population predictions (PRED), for Xpose 4 |
-- E --
| export.graph.par | Exports Xpose graphics settings to a file. |
| export.variable.definitions | Exports Xpose variable definitions to a file from an Xpose data object. |
-- G --
| GAM_summary_and_plot | GAM functions for Xpose 4 |
| get.doc | Functions changing miscellaneous parameter settings in Xpose 4 |
| gof | Structured goodness of fit diagnostics. |
| gofSetup | Structured goodness of fit diagnostics. |
-- I --
| import.graph.par | Imports Xpose graphics settings from a file to an Xpose data object. |
| import.variable.definitions | Imports Xpose variable definitions from a file to an Xpose data object. |
| ind.cwres | Compute the Conditional Weighted Residuals |
| ind.plots | 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.cwres.hist | Histograms of weighted residuals for each individual in an Xpose data object, for Xpose 4 |
| ind.plots.cwres.qq | Quantile-quantile plots of weighted residuals for each individual in an Xpose data object, for Xpose 4 |
| ind.plots.wres.hist | Histograms of weighted residuals for each individual in an Xpose data object, for Xpose 4 |
| ind.plots.wres.qq | Quantile-quantile plots of weighted residuals for each individual in an Xpose data object, for Xpose 4 |
| ipred.vs.idv | Individual predictions (IPRED) plotted against the independent variable (IDV) for Xpose 4 |
| is.cwres.readable.file | Compute the Conditional Weighted Residuals |
| iwres.dist.hist | Histogram of individual weighted residuals (IWRES), for Xpose 4 |
| iwres.dist.qq | Quantile-quantile plot of individual weighted residuals (IWRES), for Xpose 4 |
| iwres.vs.idv | Individual weighted residuals (IWRES) plotted against the independent variable (IDV) for Xpose 4 |
-- K --
| kaplan.plot | Kaplan-Meier plots of (repeated) time-to-event data |
-- L --
| list_or_NULL-class | Class for creating multiple plots in xpose |
| logical_or_numeric-class | Class for creating multiple plots in xpose |
-- M --
| make.sb.data | Make stacked bar data set. |
-- N --
| npc.coverage | Function to plot the coverage of the Numerical Predictive Check |
| nsim | Extract or set the value of the Nsim slot. |
| nsim<- | Extract or set the value of the Nsim slot. |
| numeric_or_NULL-class | Class xpose.data |
-- P --
| parm.hist | Plot the parameter or covariate distributions using a histogram |
| parm.qq | Plot the parameter or covariate distributions using quantile-quantile (Q-Q) plots |
| parm.splom | Plot scatterplot matrices of parameters, random parameters or covariates |
| parm.summary | Summarize individual parameter values and covariates |
| parm.vs.cov | Parameters plotted against covariates, for Xpose 4 |
| parm.vs.parm | Plot parameters vs other parameters |
| par_cov_hist | Plot the parameter or covariate distributions using a histogram |
| par_cov_qq | Plot the parameter or covariate distributions using quantile-quantile (Q-Q) plots |
| par_cov_splom | Plot scatterplot matrices of parameters, random parameters or covariates |
| par_cov_summary | Summarize individual parameter values and covariates |
| pred.vs.idv | Population predictions (PRED) plotted against the independent variable (IDV) for Xpose 4 |
| print-method | Create xpose.multiple.plot class. |
| print.xpose.multiple.plot | Print an Xpose multiple plot object. |
-- R --
| randtest.hist | Function to create a histogram of results from the randomization test tool ('randtest') in PsN |
| ranpar.hist | Plot the parameter or covariate distributions using a histogram |
| ranpar.qq | Plot the parameter or covariate distributions using quantile-quantile (Q-Q) plots |
| ranpar.splom | Plot scatterplot matrices of parameters, random parameters or covariates |
| ranpar.vs.cov | Random parameters plotted against covariates, for Xpose 4 |
| read.cwres.data | Compute the Conditional Weighted Residuals |
| read.lst | Read NONMEM output files into Xpose 4 |
| read.nm.tables | Reading NONMEM table files |
| read.npc.vpc.results | Read the results file from a Numerical or Visual Predictive Check run in PsN |
| read.TTE.sim.data | Read (repeated) time-to-event simulation data files. |
| read.vpctab | Read the vpctab file from PsN into Xpose |
| read_NM_output | Read NONMEM output files into Xpose 4 |
| read_nm_table | Read NONMEM table files produced from simulation. |
| reset.graph.par | Resets Xpose variable definitions to factory settings |
| runsum | Print run summary in Xpose 4 |
-- S --
| SData | Extract or assign data from an xpose.data object. |
| SData<- | Extract or assign data from an xpose.data object. |
| set.doc | Functions changing miscellaneous parameter settings in Xpose 4 |
| simpraz.xpdb | Simulated prazosin Xpose database. |
| simprazExample | Function to create files for the simulated prazosin example in Xpose |
| sqrtm | Compute the Conditional Weighted Residuals |
-- T --
| tabulate.parameters | Tabulate the population parameter estimates |
-- W --
| wres.dist.hist | Histogram of weighted residuals (WRES), for Xpose 4 |
| wres.dist.qq | Quantile-quantile plot of weighted residuals (WRES), for Xpose 4 |
| wres.vs.cov | Weighted residuals (WRES) plotted against covariates, for Xpose 4 |
| wres.vs.idv | Population weighted residuals (WRES) plotted against the independent variable (IDV) for Xpose 4 |
| wres.vs.idv.bw | Box-and-whisker plot of weighted residuals vs the independent variable for Xpose 4 |
| wres.vs.pred | Population weighted residuals (WRES) plotted against population predictions (PRED) for Xpose 4 |
| wres.vs.pred.bw | Box-and-whisker plot of weighted residuals vs population predictions for Xpose 4 |
-- X --
| xlabel | Extract and set labels for Xpose data items. |
| xlabel<- | Extract and set labels for Xpose data items. |
| xp.akaike.plot | GAM functions for Xpose 4 |
| xp.boot.par.est | Compare parameter estimates for covariate coefficients |
| xp.boot.par.est.corr | Correlations between covariate coefficients |
| xp.cook | GAM functions for Xpose 4 |
| xp.daic.npar.plot | Distribution of difference in AIC |
| xp.distr.mod.size | Plot of model size distribution for a bootgam or bootscm |
| xp.dofv.npar.plot | Distribution of difference in OFV |
| xp.dofv.plot | OFV difference (optimism) plot. |
| xp.get.disp | Default function for calculating dispersion in 'xpose.gam'. |
| xp.inc.cond.stab.cov | Trace plots for conditional indices |
| xp.inc.ind.cond.stab.cov | Trace plots for conditional indices rper replicate number |
| xp.inc.prob | Inclusion frequency plot |
| xp.inc.prob.comb.2 | Inclusion frequency plot for combination of covariates. |
| xp.inc.stab.cov | 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.incl.index.cov | Plot of inclusion index of covariates. |
| xp.incl.index.cov.comp | Inclusion index individuals, compare between covariates. |
| xp.incl.index.cov.ind | Individual inclusion index |
| xp.ind.inf.fit | GAM functions for Xpose 4 |
| xp.ind.inf.terms | GAM functions for Xpose 4 |
| xp.ind.stud.res | GAM functions for Xpose 4 |
| xp.plot | GAM functions for Xpose 4 |
| xp.scope3 | Define a scope for the gam. Used as default input to the 'scope' argument in 'xpose.gam' |
| xp.summary | GAM functions for Xpose 4 |
| xpose | The Xpose Package |
| xpose.bootgam | Title |
| xpose.calculate.cwres | Compute the Conditional Weighted Residuals |
| xpose.data | Create an Xpose data object |
| xpose.data-class | Class xpose.data |
| xpose.gam | Stepwise GAM search for covariates on a parameter (Xpose 4) |
| xpose.license.citation | Displays the Xpose license and citation information |
| xpose.logTicks | Functions to create nice looking axes when using Log scales. |
| xpose.multiple.plot | Create and object with class "xpose.multiple.plot". |
| xpose.multiple.plot-class | Class for creating multiple plots in xpose |
| xpose.multiple.plot.default | Xpose 4 generic function for plotting multiple lattice objects on one page |
| xpose.panel.bw | Default box-and-whisker panel function for Xpose 4 |
| xpose.panel.default | Default panel function for Xpose 4 |
| xpose.panel.histogram | Default histogram panel function for Xpose 4 |
| xpose.panel.qq | Default QQ panel function for Xpose 4 |
| xpose.panel.splom | Scatterplot matrix panel function for Xpose 4 |
| xpose.plot.bw | The generic Xpose functions for box-and-whisker plots |
| xpose.plot.default | The Xpose 4 generic functions for continuous y-variables. |
| xpose.plot.histogram | The Xpose 4 generic functions for continuous y-variables. |
| xpose.plot.qq | The generic Xpose functions for QQ plots |
| xpose.plot.splom | The Xpose 4 generic functions for scatterplot matrices. |
| xpose.prefs-class | Class "xpose.prefs" |
| xpose.print | Summarize an xpose database |
| xpose.read | Imports Xpose graphics settings from a file to an Xpose data object. |
| xpose.string.print | Print a pretty string. |
| xpose.VPC | Visual Predictive Check (VPC) using XPOSE |
| xpose.VPC.both | Xpose Visual Predictive Check (VPC) for both continuous and Limit of Quantification data. |
| xpose.VPC.categorical | Xpose visual predictive check for categorical data. |
| xpose.write | Exports Xpose graphics settings to a file. |
| xpose.xscale.components.log10 | Functions to create nice looking axes when using Log scales. |
| xpose.yscale.components.log10 | Functions to create nice looking axes when using Log scales. |
| xpose4 | Classic menu system for Xpose 4 |
| xpPage | Structured goodness of fit diagnostics. |
| xsubset | Extract or set the value of the Subset slot. |
| xsubset<- | Extract or set the value of the Subset slot. |
| xvardef | Extract and set Xpose variable definitions. |
| xvardef<- | Extract and set Xpose variable definitions. |