NEWS.md

In xpose4: Diagnostics for Nonlinear Mixed-Effect Models

xpose 4.7.2

• Changed default method of reading table files to the "slow" method, so that xpose.data(..other arguments.., method="slow") is default. For other methods see ?read_nm_table

• Other small changes

xpose4 4.7.1

• Fix a bug where the filtering of "-99" rows of table files would not filter on all plotting variables.

• Fix a bug where items in the catab and cotab files were not added to the list of covariates in the xpose database (#16).

• Fix a bug where csv files were improperly read into the database in some situations (#16).

• Updated code that was using depreciated dplyr and tibble functions.

xpose4 4.7.0

• allow changes in the relative length of the censored lines in kaplan.plot().

• Handle directory without trailing slash for xpose.data() (#14, @rikardn).

• fix bug in classic menu system not allowing change of variable definitions.

• Various small spelling and bug fixes (#13, @vrognas).

xpose4 4.6.1

• Updates to comply with changes in the readr and gam packages.

xpose4 4.6.0

• Update to xpose.VPC() so that outliers can be identified and plotted.

• Update to xpose.VPC() so that for any lines in the VPC they are plotted at the median of the observed values of the X axis for all bins by default.

• Update to xpose.VPC() to allow a rug at the bottom of the plot showing where the bins are located.

• Update to the namespace so that only lattice is loaded when loading xpose.

• All documentation now written in roxygen

• Updates to boot GAM and boot SCM plots and documentation.

• Various small bug fixes.

xpose4 4.5.3

• Update to ind.plots() to allow subsets on a per-y-variable basis. Useful to show IPRED and PRED in a finer grid than DV. See option “y.vals.subset”.

• Update to how axes limits are computed with xpose.plot.default.

• Fix for using expression() in the ylb argument of xpose.VPC.

• Various small bug fixes.

xpose4 4.5.2

• Internal release

• Updates to read.bootscm.par.est()

xpose4 4.5.1

• Internal release

• Updated xpose.gam to work with the latest version of the gam package

• Updated kaplan.plot to allow for ylim specification when "cov" argument is used.

• Updated compute.cwres and associated functions to work with NONMEM 7.

• Fixed warnings created in xpose.VPC.categorical when creating personalized x and y axis labels.

xpose4 4.5.0

• External release with just one package instead of five.

• Added to ind.plots so that when there is only one data point for an individual, the PRED and IPRED show up in the plot.

xpose4 4.4.3

• Internal release

• Added functionality for plotting the delta mean output from the vpc tool in PsN. Option is for xpose.VPC() and can be turned on using PI.delta.mean=T. See ?xpose.panel.default for more information.

xpose4 4.4.2

• Internal release

• Removed some default messages that were print to the screen when running xpose.VPC(). can change back to previous behavior with option verbose=TRUE.

• Combined the five packages of xpose into one package.

• Updated the Histogram functionality.

• New plots randtest.hist() and boot.hist() for creating histograms of results from PsN's 'randtest' and 'bootstrap' tools.

• Updated the xpose.VPC() function to handle plotting of mean values from simulations.

xpose4 4.4.1

• Updates to kaplan.plot.R (thanks to Leonid Gibiansky for reporting the problems)

• kaplan.plot.R: Removed debugging command that was mistakenly left in function

• kaplan.plot.R: "ylab" argument is now passed to the plot when cov option is used.

• kaplan.plot.R: Using the cov option with repeated censoring and no observations to break up the chain then the mean value calculation was wrong (only used the surviving IDs and the last censored ID). Fixed now.

• Changed the "aspect" argument for all plots to default to "fill". Previously it was "1".

xpose4 4.4.0

• Added bootstrap of the GAM and diagnostics for the boostrap of the PsN function boot_scm.

xpose4 4.3.6

• fixed the plot in the classic menu system "Weighted residuals vs covariates".

xpose4 4.3.5

• Updated help files with workable examples, and an example dataset. Look at data(simpraz.xpdb), simprazExample() and example(xpose.data) for dataset examples and example(basic.gof) and example(cwres.vs.idv) for plot examples. Most of the xpose4specific functions now have examples that can be run with example().

• Updated kaplan.plot() so that the kaplan-Meier mean covariate (KMMC) plot can be created. Also added more options for adjusting plot properties.

• New gofSetup() command to create your own customized series of GOF plots.

• fixed how RSE values were reported on runsum() when the parameter was fixed.

• Fixed argument to xpose.VPC.categorical(max.plots.per.page=1), so that only one plot per page was possible.

• Fixed xpose.VPC() so that the psn option for vpc "confidence_interval=X" works.

• Fixed compute.cwres() function that wasn't computing anything (and returning an error).

xpose4 4.3.2

• Fixed bug in xpose.VPC when asking for logx=T (didn't work previously).

• Fixed dOFV.vs.id for when there are ties in individual dOFV drops.

xpose4 4.3.0

• Updated read.nm.tables so that comma separated NONMEM 7 files can be read into Xpose.

• Changing the behavior of xpose.multiple.plot.default. Now multiple plots are returned as objects just like single plots are (no automatic printing from the function that created the plot list). This is accomplished by defining a new class - xpose.multiple.plots - and corresponding print and show methods for that class.

• Updated xpose.VPC, xpose.VPC.categorical and xpose.VPC.both to handle the new format of PsN vpc_results.csv files.

• xpose.VPC.categorical now has a new option: censored (T or F) which will create BLOQ VPC plots when TRUE.

• xpose.VPC.both tries to combine continuous and categorical BLOQ plots.

• page numbers can be turned off in multiple page plots using the page.numbers option (T or F).

xpose4 4.1.0

• Updated ind.plots(), the function is much more flexible now.
• Added graphical options to xpose.VPC.categorical()
• Fixed logy=T option for xpose.VPC(Pi.ci=T,logy=T).
• Fixed logy=T and logx=T option (bug resulting in error).
• VPC changed to require that y-axis be continuous as default.
• Fixed classic version of parm.vs.parm() plot.
• Fixed runsum(). Previous version had a line between each line in model file.
• Added a new function change.xvardef(), which replaces much of the previous change functions. Thanks to Sebastien Bihorel for input which helped create this function.
• Added the ability to apply functions to the x-axis of plots. The function options are now called funx and funy.
• Added support for reading NONMEM 7 table and output files.
• Added functions for odd type (categorical, TTE, count) plots including VPCs.
• Updated handling of PsN vpc output file
• Updated interpretation of categories in xpose.VPC.categorical()

xpose4 4.0.4

• cwres.vs.pred.bw() was fixed. Previously cwres.vs.pred.bw() gave the same result as cwres.vs.idv.bw().
• Fixed xpose.VPC() bug causing plots to not be created in some situations.
• Added functionality to xpose.VPC() so that users can define their own titles for each subplot if stratification is used in the VPC. see ?xpose.VPC for more info.
• Updated method for opening graphical devices in windows to be consistent with the new methods used in R version 2.8.0.
• Added functionality to allow the user to plot vertical and horizontal lines in histograms. See ?xpose.panel.histogram for more information.
• Fixed small bug with xpose.panel.splom().

xpose4 4.0.3

• in compute.cwres() a debugging flag had been left in the file resulting in R going into debugging mode when this function was called. This has been fixed.

xpose4 4.0.2

• Added ability to smooth the PI.ci "area" plots so that they match the "line" plots. See 'PI.ci.area.smooth' in xpose.panel.default()
• Added 'logx' and 'logy' functionality to the PI plots.
• Changed the par.summary and cov.summary routines and removed functions doing almost the same thing (adding that functionality to the current functions).
• fixed GAM plot problems in xp.plot() and added more support for GAM from the command line.
• Fixed a problem with ind.plots() when the ID variable is not called ID.
• Changed all functions in xpose4specific that began with "abs." to begin with "absval." to be consistent with the rules for generic function definitions in R.
• Changed name of add.abs() to add.absval().
• Changed name of par.summary() to parm.summary().
• Changed name of param.vs.cov() to parm.vs.cov().
• Changed name of param.vs.param() to parm.vs.parm().

xpose4 4.0.1

• Added functionality for visual predictive checks
• Added functionality for numerical predictive checks

xpose4 4.0.0.3.7

• Added generic functions xpose.draw.table, xpose.draw.cell, xpose.get.c and xpose.get.r for drawing tables using the graphics device (JW)
• Added specific function param.table to display parameter estimates using the graphics device (e.g. in a PDF file) (JW)
• Added additional specific functions for:
• Added additional specific functions: IWRES distribution (histogram) (iwres.dist.hist)
• Added additional specific functions: IWRES distribution (QQ) (iwres.dist.qq)
• Added additional specific functions: ETA distribution (histogram) (ranpar.dist.hist)
• Added additional specific functions: ETA scatter-plot matrices (ranpar.splom)
• Added additional specific functions: ETAs vs covariates (ranpar.vs.cov)
• Added additional specific functions: Parameter tables on the graphics device (param.table)
• Updated compute.cwres function so that it would work without xpose 4 Just 'source' the file (compute.cwres.R) and it should work (AH)
• fixed problems with the run summary function (AH)
• added new general class of printing multiple plot objects on the same page (AH)
• Fixed bug with plotting results of GAM (AH)

xpose4 4.0.0.3.5

• Bugs in 'groups' argument fixed in xpose.plot.default, dv.vs.pred.ipred, dv.preds.vs.idv (multiple values of x or y not properly handled) (JW)
• File devices (e.g. pdf, postscript, etc) now work correctly in all functions (JW)
• Bug in multiple-page covariate plots fixed (only the first page would display) (JW)
• Bug in reading table files could sometimes leave file debris, which could interfere with reading subsequent data - fixed (JW)
• Bug in covariate checking could sometimes cause plot functions to fail (e.g. abs.wres.vs.pred.by.cov) - fixed (JW)
• Bug in the classic menu system prevented display of some plots - fixed (JW)
• Bug in the classic menu system prevented display of some plots - fixed (JW)
• Bug in CWRES calculation fixed (AH)
• Bug in parameter histogram display fixed (JW)
• Missing values (defaults to -99) now handled correctly (JW)
• QQ plots no longer display categorical variables (JW)

xpose4 4.0.0.3.3

• Bug in 'subset' argument to individual plots corrected (JW)

xpose4 4.0.0.3.2

• Online documentation cleaned up (JW)
• Numerous small bugs fixed (JW)
• *nix support added (JW)
• Multipage plots now create stacks of display windows, rather than stacks of plots in a single window (JW)
• Scatter-plot matrices added (JW)
• QQ plots for parameters and covariates added (JW)
• Generic functions renamed for consistency (JW)

xpose4 4.0.0.3.1

• Bugs in CWRES application and documentation fixed (AH)
• Bugs in histogram functions fixed
  • lack of defined covariates no longer causes crash
  • customization options now work

xpose4 4.0.0.3

• GAM added (AH)
• CWRES plots and functions added (AH)
• gam package now required
• Known bugs corrected

xpose4 4.0.0.2

• SUBSET functionality fixed for all procedures
• Preferences, summaries and data checkout implemented
• Box and whisker plots now do what their preferences tell them to
• 'label' function renamed to 'xlabel' for compatibility
• Hmisc package now required
• Many small additions and tweaks
• R package functionality fixed

xpose4 4.0.0.2.1

• Ind.plots.R updated (AH)

xpose4 4.0.0.1

• Xpose 4 is a completely rewritten version of Xpose 3.1, and so everything has changed.

xpose4 documentation built on May 31, 2022, 5:07 p.m.