NEWS
xpose 0.4.19
xpose 0.4.18 (2024-02-01)
- 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 (2023-06-29)
xpose 0.4.16 (2023-04-18)
- Updated tests for
ggplot2 3.4.2
xpose 0.4.15 (2023-02-25)
- 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 (2022-11-07)
- 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 (2021-06-30)
- Compatibility fix with
ggplot2 3.3.4
- Compatibility fix with
readr 2.0.0 (@jimhester, #194)
xpose 0.4.12 (2021-01-12)
- Compatibility fix for R 4.1.x
xpose 0.4.11 (2020-07-22)
xpose 0.4.10 (2020-06-08)
- Compatibility fix for
vpc 1.2.1
xpose 0.4.9 (2020-05-25)
- Compatibility fix for
dplyr 1.0.0 and vpc 1.2.0
xpose 0.4.8 (2020-03-17)
- Compatibility fix for
ggplot 3.3.0 and tibble 3.0.0
xpose 0.4.7 (2020-02-04)
- Fixed error in documentation check fail in R 4.0.0
xpose 0.4.6 (2020-01-12)
- Updated tests for compatibility with R 4.0.0
- Shortened title of
dv_preds_vs_idv
xpose 0.4.5 (2019-10-07)
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 (2019-03-21)
General
xpose 0.4.3 (2018-07-28)
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 (2018-01-30)
General
- Address CRAN requests
- Improved internal structure of VPC
- Fixed bug with
vpc 1.0.1
xpose 0.4.1 (2018-01-09)
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 (2017-11-17)
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
xpose 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 %>%