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Changelog

Source: NEWS.md

pmxhelpr 0.3.5

  • Add option to pass the same dataset variable to TIME and NTIME attributes in time_vars for all functions
  • Add option to control default aesthetics (linewidth, linetype, size, shape, alpha) in plot_dvtime and plot_popgof
  • Fix bug in plot_popgof that was preventing upper error bars from inheriting the color mapped to “DV”

pmxhelpr 0.3.4

  • Fix bug in df_mrgsim_replicate that was precluding use of non-default time variable names

pmxhelpr 0.3.3

  • Fix bug in plot_dvtime and plot_popgof where variable for “DOSE” was being assessed when dosenorm = FALSE
  • Update breaks_time to accept abbreviations for time units

pmxhelpr 0.3.2

  • Add cent = "mean_sdl_upper" option to plot_dvtime and plot_popgof for plotting only the upper error bar
  • Add barwidth argument to plot_dvtime and plot_popgof to allow user to change error bar cap width.

pmxhelpr 0.3.1

  • Add plot_popgof to generate population overlay goodness-of-fit plots
  • Add data_sad_pkfit NONMEM PK model fit output dataset for data_sad based on model.
  • Fixed bug in plot_dvtime that was leading to plotting mean +/- 2*SD instead of mean +/- SD

pmxhelpr 0.3.0

  • Added new functionality for dose-proportionality assessment with df_doseprop and plot_doseprop, including helpers mod_loglog and df_loglog to perform and tabulate power law (log-log) regression of exposure versus dose

  • Added new internal package dataset data_sad_nca for use with dose-proportinality assessment functions

  • Added helper function dvtime_caption to generate the caption for plot_dvtime

  • Added helper function pmxhelpr_vpc_theme to capture default VPC plot aesthetics `

  • Revised vignettes to describe workflow with new default aesthetics

  • Remove use of log_y argument in VPC plot examples and added rationale to primary vignette for plot_vpc_exactbins

  • Add unit tests for all primary functions

pmxhelpr 0.2.4

  • Fix bug in plot_dvtime to ensure median + IQR error bars prints on both linear and log-scale axes when cent = "median_iqr"

pmxhelpr 0.2.3

  • Added cent = "median_iqr" option to plot_dvtime to plot median with inter-quartile range error bars
  • Updated the ind_dv logical argument in plot_dvtime to grp_dv to generalize use of grouping beyond connecting points within an individual subject
  • Added the grp_var argument to plot_dvtime to allow specification of the variable assigned to the group aesthetic by the user. Default is grp_var = "ID"

pmxhelpr 0.2.2

  • Corrected bug in plot_vpc_exactbins when ordered factor variables are pasted to the strat_var argument. Ordered factors cannot be passed to the underlying stratification function from the vpc package (add_stratification()); therefore, ordered factors will be coerced to unordered factors within plot_vpc_exactbins

pmxhelpr 0.2.1

  • Corrected bug in NA handling within breaks_time

pmxhelpr 0.2.0

  • Added plot_dvtime function for exploratory concentration-time plotting

  • Added breaks_time function to automatically determine x-axis breaks for time

  • Functionality from breaks_time added to plot_vpcexactbins

  • Exploratory Data Analysis vignette created to demonstrate functionality of new functions

  • Added dependency: labelling

pmxhelpr 0.1.4

  • Fixed bug leading to error when generating stratified vpcs using the strat_var argument

pmxhelpr 0.1.3

  • Vignette vpc plot axes updated to time unit breaks
  • Vignette bullet point lists updated to correct spacing
  • Coerce argument lloq argument of plot_legend() to character type

pmxhelpr 0.1.2

  • Vignettes copy edited

pmxhelpr 0.1.1

  • Added dependency: patchwork

pmxhelpr 0.1.0

  • Full VPC workflow now available in Version 0.1.0 with three vignettes to demonstrate this functionality!

  • VPC Plot Aeesthetics vignette demonstrating options for modifying plot aesthetics, creating a plot legend using plot_legend(), and adding the VPC plot and legend objects together into a single object using the patchwork package

pmxhelpr 0.0.3

  • Additional functionality for plot_vpc_exactbins

    • shown argument added to facilitate customization of which layers are shown in the plot and standardize with new function plot_legend. Passed to show argument of vpc::vpc()

  • plot_legend helper function to generate a legend for a VPC plot generated using plot_vpc_exactbins(), which can be combined with the VPC plot using the patchwork package

  • VPC Plots with BLQ Censoring vignette demonstrating appropriate handling of data missing due to assay sensitivity (below the lower limit of quantification) using plot_vpc_exactbins() and workflow leveraging df_mrgsim_replicate.

pmxhelpr 0.0.2

  • Additional functionality for plot_vpc_exactbins
    • loq argument added to facilitate incorporating BLQ censoring of observed data in summary quantiles
  • Bug fix to allow passing argument vpcdb = TRUE to vpc::vpc()

pmxhelpr 0.0.1

  • data_sad NONMEM and mrgsolve analysis-ready dataset for a hypothetical SAD study with assessment of food effect.

  • model mrgsolve model file (class mrgmod) in the internal pmxhelpr model library .

  • model_load function to load internal models from the pmxhelpr model library.

  • df_mrgsim_replicate mrgsim wrapper function to run a simulation that replicates the input dataset multiple times, intended for application to generating Visual Predictive Check (VPC) simulation-based model diagnostics.

  • plot_vpc_exactbins vpc wrapper function to using an exact time binning variable in the input dataset (e.g. nominal time) with plotting of observed data points using actual time.

  • VPC Plots with Exact Bins vignette demostrating use case for plot_vpc_exactbins() and workflow leveraging df_mrgsim_replicate.