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NEWS.md

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xpose 0.4.11

  • Improve noLD in tests

xpose 0.4.10

  • Compatibility fix for vpc 1.2.1

xpose 0.4.9

  • Compatibility fix for dplyr 1.0.0 and vpc 1.2.0

xpose 0.4.8

  • Compatibility fix for ggplot 3.3.0 and tibble 3.0.0

xpose 0.4.7

  • Fixed error in documentation check fail in R 4.0.0

xpose 0.4.6

  • Updated tests for compatibility with R 4.0.0
  • Shortened title of dv_preds_vs_idv

xpose 0.4.5

General

  • The gg_theme argument in xpose_data, update_themes or plots now accepts a function returning a complete ggplot2 theme. In addition theme gg_theme can now accept theme elements in update_themes and plots. (#157)
  • Added compatibility with tidyr 1.0.0 (#166)
  • Small fixes to vignettes, documentations and website

xpose 0.4.4

General

  • Improved documentation for xpose_data (@billdenney #99)
  • Fixed VPC error in the documentation (@callistosp #130)
  • Fixed bug leading to errors when plotting poorly formatted ETA name (@romainfrancois #127)
  • Compatibility improvements

xpose 0.4.3

General

  • Fixed bug in get_prm()/prm_table() where off diagonal correlations were improperly computed.
  • Fixed bug in print.xpose_data()where a warning from stringi was returned.
  • Fixed multiple bugs introduced by the new versions of tidyverse packages
  • Added compatibility to ggplot2 v3.0.0

xpose 0.4.2

General

  • Address CRAN requests
  • Improved internal structure of VPC
  • Fixed bug with vpc 1.0.1

xpose 0.4.1

General

  • Improved integration of the xpose.nlmixr package
  • Prevented a problem in the print() function with the upcoming ggplot2 version
  • Fixed bug in summary() where missing estimation method was reported if NM code written as METH=... instead of METHOD=...
  • Fixed bug where labels in prm_table(), get_prm() were missing with a commented row in $THETA, $OMEGA or $SIGMA
  • Fixed bug in prm_table(), get_prm() where only NA would be reported when missing the -1000000006 record in the .ext file (i.e. NM <7.3)
  • Prevented negative RSE in prm_table() and get_prm()
  • Improved description of the prm_table() output
  • Fixed bug in summary() with non numeric covariance step time
  • Fixed bug in ind_plots() where the aesthetics would get mixed up if the variable names were changed
  • Small fixes to vignettes, documentations and website

xpose 0.4.0

General

  • Added xpdb memory usage to print.xpose_data()
  • Replaced print.prm.data() to prm_table()
  • Fixed documentation

Data import/edit

  • Added compatibility with dplyr::n() when editing xpdb #51
  • Added get_special() to access special data
  • Improved get_prm() labeller parsing with OMEGA and SIGMA BLOCKS
  • get_prm() and prm_table():
    • Both gained a transform argument to disable parameter transformation
    • RSE is now always reported (also for untransformed)
    • Corrected RSE for off-diagonal elements from OMEGA and SIGMA when output as correlation and SE when output as standard deviation
  • Added list_data(), list_files() and list_special() to get info on the data structure in the xpdb
  • Renamed the arguments problem, subprob, method and source to .problem, .subprob, etc. for consistency with dplyr functions.
  • Improved error checking for themes in xpose_data
  • Improved error checking in get_prm()

Plots

  • print.xpose_plot() now displays a message when the number of facets is > 20, informing that many panels are being printed and that it may take a while to render the plot
  • Improved .problem, .subprob and .method error checking

xpose 0.3.0

General

  • Improved documentation and testing
  • Improved compatibility with NONMEM 7.4.1
  • Improved website look, and content with new 'FAQ' and 'Plot' sections and a cheat-sheet
  • Multiple bug small bug fixes and code improvements
  • Added multiple page functionality to all plots and xpose_save()
  • Added get_prm() function

Data import/edit

  • Improved dir and file arguments usage
  • Improved error robustness of xpose_data()
  • Added new dplyr verbs for xpdb editing: slice(), select(), rename(), distinct(), summarize(), group_by() and ungroup()
  • dplyr verbs can now also be used to edit vpc data
  • Added irep() function to add simulation counter to any dataset
  • Bug fix in read_nm_files() not properly reporting FO method
  • Bug fix in read_nm_tables() not properly parsing data (missing minus signs) in some very specific cases

Plots

  • Small modifications to xp_theme() defaults
  • Faceting options can now be defined globally in the xp_theme
  • Added amt_vs_idv() plot
  • Improved faceting of minimization plots
  • Multiples improvements to the vpc_data() and vpc() functions.
  • More keywords added to template_titles

xpose 0.2.0

General

  • Renamed package xpose
  • Added example dataset xpdb_ex_pk
  • New internal data structure using nested tibbles
  • Improvement of documentation, and testing

Data import

read_nm_tables()

  • Handles NONMEM tables in .csv, .zip format
  • Handles multiple $PROB and tables with FIRSTONLY option
  • Added option to import data manually as in xpose4 with manual_nm_import()
  • Added indexing of variable and convenience functions to edit it: set_vars_type(), set_vars_label(), set_vars_units()

read_nm_files()

  • Now imports multiple $PROB and sub-problems

Summary

  • Added print() and summary() methods for xpdb
  • Added list_vars() function to list available variables
  • Added many new keywords to template_titles

Access xpdb

  • Added convenience functions to access data from xpdb get_code(), get_data(), get_file(), get_summary().
  • Added a method for xpdb to dplyr::filter()

Plots

  • Changed cwres_vs_idv, type residual functions to more general res_vs_idv(res = 'CWRES') functions
  • Implemented/improved general plotting functions: xplot_distrib(), xplot_qq(), xplot_scatter(), with convenience function to fetch data in xpdb data_opt_set().
  • Implemented: dv_vs_idv(), ipred_vs_idv(), pred_vs_idv(), dv_preds_vs_idv(), ind_plots(), vpc(), prm_distrib(), eta_distrib(), res_distrib(), cov_distrib(), prm_qq(), eta_qq(), res_qq(), cov_qq(), prm_vs_iteration(), grd_vs_iteration().
  • Updated/renamed: theme_bw2(), theme_readable(), theme_xp_default(), theme_xp_xpose4().

VPC

ggxpose 0.1.0

First commit

  • Proof of concept pre-release around simple goodness-of-fit functions like dv_vs_ipred()

Definition of core functions and workflow

  • Defined the xpose_geom() core function to specifically direct arguments to ggplot2 layers
  • Defined the concept of template titles
  • Define the templates for xpose_theme()
  • Makes use of the tidyverse and pipes %>%