NEWS.md

xpose 0.4.19

• Fixed bug in condition number when eigen values outputted on multiple records in .lst file (@billdenney & @marianklose, #128)

xpose 0.4.18

• Compatibility fix for roxygen2 7.3.1
• Fix bug when reading a control stream and using $PROB instead of $PROBLEM (@AndreasCalvagone, #222)
• Introduced check_ext argument in xpose_data(), read_nm_model(), to bypass the strict NONMEM model format check if needed.
• xpose now recognizes PATAB, COTAB, CATAB table names as patab, cotab, and catab types respectively (@certara-mtomashevskiy, #221)
• Small documentation fixes and improvements

xpose 0.4.17

• Updated tests for ggplot2 (@hadley, #220)

xpose 0.4.16

• Updated tests for ggplot2 3.4.2

xpose 0.4.15

• Updated minimal requirements for readr (>= 2.1.0) (@sebastianueckert, #208)
• Updated minimal requirements for R (>= 3.5.0) because serialized objects in serialize/load version 3 cannot be read in older versions of R
• Don't summarize RANMETHOD as an estimation method (@vrognas, #213)
• Fix bug when a given estimation method is used several time in a single $PROBLEM. Sequential $ESTIMATION are now each attributed different subprob visible to the user using list_files(xpdb) (@vrognas, #213)
• Compatibility fix with ggplot2 3.4.0, all layers but geom_point and geom_text should now use linewidth instead of size for line width.
• Compatibility fix with dplyr 1.1.0
• Small fixes and improvements

xpose 0.4.14

• Compatibility fix with ggplot2 3.4.0
• Compatibility fix with stringr 1.5.0 (@hadley, #207)
• xpose will now give a warning on windows if options(readr.read_lazy = TRUE) (@AndreasCalvagone #198)
• Fixed errors in plots when calling function with xpose:: (@mattfidler #95)
• Updated continuous integration workflow
• Small fixes and improvements

xpose 0.4.13

• Compatibility fix with ggplot2 3.3.4
• Compatibility fix with readr 2.0.0 (@jimhester, #194)

xpose 0.4.12

• Compatibility fix for R 4.1.x

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

• Added wrapper around ronkeizer/vpc inside vpc_data().

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 %>%