NEWS.md

replicateBE 1.1.3.9000

Development version.

Bug fixes

• Fixed problems in the PDF manual created on CRAN.

Minor changes

• Cosmetics in man pages (HTML and LaTeX formatting) and vignette.
• Added doi of publication to DESCRIPTION (suggested by Uwe Ligges).

replicateBE 1.1.3

Published on GitHub 2022-05-02, on CRAN.

Bug fixes

• Fixed two more empty item{} discovered by CRAN pretest.

replicateBE 1.1.2

Published on GitHub 2022-05-02.

Bug fixes

• Corrected empty labels in man pages of datasets in item{} leading to notes on r-devel-linux.

replicateBE 1.1.1

Published on Github 2022-02-12, on CRAN.

Bug fixes

• Corrected example in the vignette (warning on r-devel-linux-x86_64-fedora-gcc and r-devel-linux-x86_64-fedora-gcc). THX to Brian D. Ripley.
• In the result data frame of method.B(..., print = FALSE, details = TRUE) falsely A instead of B was given.

Minor changes

• Updated GCC and WHO guideline (comparison of variabilities no more required); changed URL of EMA GL in man pages, README, and vignette.

replicateBE 1.1.0

Published on Github 2021-06-21, on CRAN.

Major changes

• If path.out is missing, R’s temporary folder will be used.
• Added regulator "HC" in method.B() to support Health Canada’s approach (upper cap of scaling ~57.4%). If alpha = 0.5 only the PE has to lie within 80.0--125.0% (highly variable C_max). However, both option = 1 (Satterthwaite) and option = 3 (Kenward-Roger) are only approximate because Health Canada prefers a mixed-effects model. THX to Philippe Liége.
• Added swT (full replicates), swR (and swR.rec if outlier(s) are detected) to the data frame of results (previously only in the result file). Referring to the columns in examples of man pages, vignette, and testthat.R adapted.
• In method.A() and ABE() changed the ANOVA from ‘Type I’ (default) to ‘Type III’ in order to get the correct test for carryover. Clarified in the vignette.
• Direct widening to 75.00--133.33% for C_max according to the conditions of the Gulf Cooperation Council. New argument regulator "EMA" (default) or "GCC" in method.A() and method.B(). Hence, at least version 1.5.3 of PowerTOST is required.

replicateBE 1.0.17

On CRAN 2021-05-14.

Minor changes

• path.out in examples changed from "~/" to tempdir(). CRAN policy violation noted by Brian D. Ripley.
• method.B.R: options(contrasts = c("contr.treatment", "contr.poly")) is the default. If a user has set other ones, restore them on exit.

replicateBE 1.0.15

Published on Github 2020-07-24, on CRAN.

Major changes

• Stops now if path.in or path.out (if print = TRUE | plot.bxp = TRUE) is not given. Previously the user’s home folder "~/" was automatically used. Man pages updated accordingly.

Minor changes

• Use normalizePath() in get.data.R and info.env.R for clarity (i.e., the OS-dependent full path is given in the result-file).
• Removed graphics.off() from the beginning of get.data.R. Caused the error in check() where a PDF is created.
• Checks whether the png-device is available on the system. If not, show a message and change to plot.bxp = FALSE.
• Cosmetic changes in vignette.

replicateBE 1.0.14

Published on Github 2020-04-08, on CRAN 2020-04-09.

Bug fixes

• Changed expected value of DF obtained by method.B(..., data = rds30, option = 1) from 17.86418 to 17.86417 and reduced tolerance in function expect_equivalent() of testthat from 5e-7 to 1e-6. Prevents errors with r-devel on Linux and r-patched on Solaris. Required due to changed default tolerance settings in v.1.1-23 of package lme4 of 2020-04-07. Not relevant because the CI passed the test already with the more strict tolerance and in practice only four to five significant digits (not seven) are required for the CI. Furthermore, all tests passed with the current release (R3.6.3) on all operating systems.

Minor changes

• Cosmetic changes in vignette, installation more detailed given in README.

replicateBE 1.0.13

Published on Github 2020-01-09, on CRAN.

Bug fixes

• Converts ext to lower-case. Mixed-case threw an error.
• Resolved issue 2 raised by MT. Results were correct but the message an annoyance. Now use as.data.frame(read_excel(..., col_names = FALSE, .name_repair = "minimal")) in get.data(). Since the file may contain a commentary header, we need col_names = FALSE and construct the names later (i.e., the default col_names = TRUE is not possible).

Minor changes

• If verbose = TRUE in all methods: print(anova(...), digits = 6, signif.stars = FALSE).
• Changed names of variables in the data frame of results. Updated man pages.
• Unified ANOVA-table and degrees of freedom if verbose = TRUE. Added response to verbose-output of method.B (automatically in method.A).
• Handles a case where a user exports one of the internal dataset as a CSV with row.names and quoted variables (i.e., instead of write.csv(rds01, 'rds01.csv', quote = FALSE, row.names = FALSE) naively uses just write.csv(rds01, 'rds01.csv')).
  Importing such a CSV-file was not possible so far. Resolved issue 3 raised by MT.
• Adapted tests for method.B(): rds29 and rds30 instead of rds18. Satterthwaite DF (..., option = 1) and Kenward-Roger (..., option = 3).
• Added two small imbalanced and incomplete datasets: rds29 (TRTR|TRTR, n=12), rds30 (TRR|RTR|RRT, n=14). Requested by a reviewer of the manuscript.

replicateBE 1.0.12

Published on Github 2019-11-11, on CRAN (carnival release).

Minor changes

• Updated CSS of vignette, fixes in README.
• Replaced TOC-links in vignette by CSS-div (fixed background image).
• Cosmetic fix. Treats the special case in verbose output of CV.calc.R when at least one studentized outlier is detected but no standarized outlier.
• Badges in README.
• Added Table of Contents in README.Rmd and vignette (THX to Yihui Xie on r-help for the latter).

replicateBE 1.0.11

Published on Github 2019-08-25, on CRAN.

Bug fixes

• Changed default path-variables from NULL to the user’s home folder "~/".

Minor changes

• print(..., , digits = 7) if verbose = TRUE. More significant digits not needed since given in the result data frame in full precision anyway.
• README.Rmd knitted to README.md.

replicateBE 1.0.10

Published on Github 2019-07-24, on CRAN.

Issues

• Seemingly the LaTeX-Installation on CRAN is corrupt (THX to Duncan Murdoch on r-package-devel). Either the file hyperref.sty is corrupt or missing (local rendering works on Windows and Linux). Therefore, on CRAN in the PDF-manual URLs in references are converted to truncated (i.e., wrong) URLs in footnotes. Notified Uwe Ligges.

Bug fixes

• Stopped import when no missings according to the specifier na where found (THX to Igor Rubets).

Minor changes

• README.md included.
• NEWS.md instead of NEWS.
• Removed numbered references since CRAN converts URLs to footnotes in the PDF manual.
• Updated links to the EMA’s datasets in info.data().

replicateBE 1.0.9

Published on Github 2019-07-22, on CRAN.

Bug fixes

• importFrom(pbkrtest, getKR) since error on win-builder.r-project.org
  'pbkrtest package required for Kenward-Roger's method' (not locally!)
• Forces logtrans = TRUE if a user asks for an internal dataset which does not have the column logPK.

Major changes

• Added Kenward-Roger degrees of freedom to method.B (..., option = 3).

Minor changes

• Updated links to the EMA’s documents (again...) in man pages. Numbered references.
• More informative warning in get.data() if na-specifier does not match the data in columns PK and/or logPK.
• Depends now on R >= 3.5.0 (since .rda saved with 3.6.0).
• Kept column logPK only in rds01 and rds02 because given by the EMA. Removed in rds06, rds12, rds14, rds18, rds19, rds20, rds21 (TRTR|RTRR) and rds03, rds17 (TRT|RTR). Man-pages corrected. Reduces the footprint of the library by 5%.
• If path.in and/or path.out not given or specified folder does not exist: Changed cat() to warning().
• Cosmetic changes in verbose output of method.A().
• suppressMessages() no more needed (vignette and testthat). Issue originating in rlang and ggplot2 resolved. Both packages don’t contain a NEWS file. THX Hadley for leaving us out in the dark!
• stringsAsFactors = FALSE in res-list of all methods.
• Removed superfluous options(ow) after models (THX to DL).
• Updated man page of method.A() and the vignette.

replicateBE 1.0.8

Published on Github 2019-06-14, on CRAN.

Bug fixes

• THX to Uwe Ligges @CRAN (adding on.exit(...) immediately after changing an option).

replicateBE 1.0.7

Published on Github 2019-06-14, on CRAN.

Bug fixes

• As suggested by [email protected]. Resubmitted to CRAN.

replicateBE 1.0.6

Published on Github 2019-06-12, submitted to CRAN (passed checks at R-release and R-devel).

Bug fixes

• LaTeX problems for the PDF-manual partly fixed (THX to Duncan Murdoch on r-help). Final solution: Text between \list{}{}. Note that this is discouraged acc. to the R-Extension Manual 2.1.1!
• Updated WHO-reference in man pages.

Major changes

• Added vignette.
• Added \tests for testthat().

Minor changes

• Simplified and reordered sources of man pages.
• Changed {\eqn{foo\textsubscript}{bar}} to the simple {\eqn{foo_{bar}} in two man pages.
• StartupWarnings seemingly unavoidable until rlang will be corrected.
• Small correction in text of box plot of CV.calc(). Studentized/standardized does not exactly agree with SAS (uses type = 2 by default).

replicateBE 1.0.5.9002

Published on GitHub 2019-05-30.

Issues

• Renaming S3 method doesn’t help.

Bug fixes

• Updated links in man pages to reflect changes in the FDA’s and the EMA’s sites.
• Updated links to reference data in info.data().
• Updated links in CSV-files.
• Import from XLS with a header.
• get.data() CSV-file: Issue with characters in the header which were == sep resolved. [MT]
• get.data() Sub/seq in data frame was empty for complete sequences.
• info.env() returned path.out as path.in.
• Mixed model was given in the result file of method.A().
• Adapt the number of subjects/sequence and number of missings/sequence to the reordered sequences in get.data(). Calculation was correct but output in result-files wrong.
• nTT was NA in get.data() for TRTR|RTRT. Now design (full/replicate) is obtained from info.design().
• In CV.calc(..., ole = TRUE) if an outlier is detected not in both methods (studentized, standardized).
• method.B(option = 1) output to file.
• In package PowerTOST T is always first. The order is only relevant in method.A(..., adjust = TRUE) and an unbalanced RTR|TRT-design. In this case the order of subjects/sequence is reversed by calling scABEL(..., n = rev(ret$Sub.Seq)). THX to DL for discovering this bug.

Minor changes

• Renamed S3 methods (prefixed with repBE) acc. to rlang issue 669. THX to MT.
• A warning in CHECK disappeared in R 3.6.0. Throws other ones in examples which change the working directory. Wrapped all examples in man pages in \dontrun{}.
• Rewrite of reading from file. [MT]
  • The header is automatically identified (removed as an argument from the calling functions).
  • The first column must no be more subject (any order is acceptable). Now the word ‘subject’ is allowed in the header.
• Argument set can be an empty string "" to support reading from CSV- files. Only required for XLS (the name of the sheet) now.
• Argument fence for box plots instead of the hard-coded 3 as a multiplier of IQR. The default 1.5 in most (all?) software packages detects a lot of outliers. 3 seems to be too liberal. The new default 2 is a compromise.
• Changed TRTR|TRRT|RTTR|RTRT to TRTR|RTRT|TRRT|RTTR. More logical (stacking sequences of the other full replicates). Adapted scripts and man pages accordingly.
• Changed the lexical order of sequences (T before R) in conformity with package PowerTOST and the EMA’s Q&A dataset II.
• Resolved issue 1: Introduced aliases in man pages for all data sets. Otherwise, warnings in CHECK about undocumented objects.
• Identify internal data sets based on their attribute. Uses now info.data(). THX to DL. Function which.data() removed.
• Man pages reworked. [DL]
• method.A(adjust = TRUE) assesses additionally the empiric Type I Error based on the recalculated CVwR (if applicable).
• Changed TRR.RTT to RTT.TRR for consistency (R always first).

Major changes

• Added dataset 27 for Balaam’s design (TR|RT|TT|RR) and dataset 28 (TTRR|RRTT); both simulated with homoscedasticy. The former only for completeness (poor power). The latter might be useful for steady state studies. Man pages for both.
• Balaam’s design implemented.
• Compare variabilites according to the FDA’s warfarin guidance, i.e., assess whether the upper confidence limit of σ_wT/σ_wR ≤2.5.
• Shows a ‘graphical’ presentation of the CI, PE, and BE-limits in the result file.
• Added datasets:
  • 26 (TRTR|RTRT). One of the few where we have results for comparison (regrettably only three significant digits).
  • 25 (TRTR|RTRT) simulated with heteroscedasticy.
  • 24 (TRRT|RTTR|TTRR|RRTT) from the FDA. Subject 16 completely missing. Adapted get.data() for such a case.
  • 23 as an example of a 4-period 4-sequence design (though not recommended by the FDA).
  • 22 for the extra-reference design (RTR|TRR).
• Calculate s_wT/s_wR (might be useful for the WHO’s scaling of AUC).
• ABE() has new arguments theta1 and theta2 (defaults 0.80 and 1.25). Useful for NTIDs (EMA) or wider limits of C_max (GCC).
• New function info.design(). Sorts sequences according to the preferred order (T first) and throws a message if the design is untested.
• Changed the names of result files reflecting the Method used rather the internals (lme/lmer).
• Lazy data: true in DESCRIPTION allows direct access of objects within data().

replicateBE 1.0.5

Released to collaborators 2017-06-24.

Issues

• CSV-files: Characters in the header which are equal to sep are lost.
• method.B(option = 1) cann’t print to file with internal data.

Minor changes

• Unified data sets, updated man pages, and changed which.data(): ref to rds. Warnings in CHECK: 'rdsXX' not found.

replicateBE 1.0.4

Released to collaborators 2017-06-23.

Issues

• If a user calls foo(path.in = path.in, ...) but the variable path.in is not defined before. Throws object 'path.in' not found in CV.calc().

Bug fixes

• If 'descr' was read from an external file and the code stopped for data not matching the id in which.data().
• Warning in man pages: Header must not contain the word 'subject'.
• If the specified file is not found in path.in the file browser opens on Windows (other operating systems?).
• If verbose=TRUE the anova was not shown in ABE().

Major changes

• New function which.data(): returns data frame 'id' of checksum (MD5), file "DS", set ("01", ... "XX"), ref ("refXX"), descr. Used in get.data() to obtain required variables of the currently attached internal data set based on its MD5-checksum.
• Changed the default variable separator from ";" to "," (more common). Suggested by DL.

Minor changes

• Removed CV.calc from NAMESPACE. Man-page not needed any more. THX to DL!
• Replaced subset() in get.data() and CV.calc() by direct assignment. No need for the hacks any more.
• Removed DS.xls and adapted man examples accordingly. CRAN policy: Data sets should not be larger than 1 MB. BTW, why is the zip so much larger than the tarball? Before removing DS.xls their sizes were similar.
• F.i. data(ref02) followed by print(ABE(details = TRUE, print = FALSE, data = data)) works. Problems: The descriptive header (variable descr) doesn’t exist in the internal data set as well as its name. Hence, the same with the default print = TRUE in all functions gives an error. Stupid: The data set must be chosen outside of the function call. foo(data = data(ref02)) gives an error.
• Added argument data = NULL (default NULL) to top-level functions.
• method.B(): Changed print(anova.lm(modB)) to print(anova(modB)). [DL]
• Modified imports in NAMESPACE. [DL]
• Working on \data and the documentation. All data sets observe the pattern refXX.rda in order to come last in the man page.

replicateBE 1.0.3

Released to collaborators and beta-testers 2016-06-19.

Major changes

• Renamed package from ABEL to replicateBE since ABE is now supported as well.
• Added function ABE() for conventional (unscaled) ABE.

Minor changes

• Added \data\ref01.rda (already factorized data frame) and man page.
• Changed enf.info(): If path(s) NULL, show the user’s home folder in the lines Input from and Output to.

replicateBE 1.0.2

Released to collaborators and beta-tester Mahmoud Teaima 2016-06-19.

Minor changes

• New argument plot.bxp. If FALSE (default) the boxplot will be shown in the default graphics device. If TRUE the boxplot will be saved in PNG format (720×720 px) to path.out. Argument ask is also observed.
• If path.in and/or path.out not given or not existing, the user’s home folder will be used. Updated the man pages accordingly.

replicateBE 1.0.1

Released to collaborators and beta-tester Mahmoud Teaima 2016-06-18.

Minor changes

• Argument ask (default FALSE). If TRUE and a result file already exists, the user is asked whether it should be overwritten.
• Removed lme4 from listed packages in env.inf(). lmer, summary, and anova obtained from lmerTest.
• Changed in get.data() name of file from "_results_" to "_ABEL_".
• Changed get.data(): path.out only required if print = TRUE. Default path.out in method.A() and method.B() set to NULL.
• Improved man pages. Added an example comparing Method B with Method A.

replicateBE 1.0.0

Released to collaborators and beta-tester Mahmoud Teaima 2016-06-16.

Major changes

• First version of package built.

Minor changes

• Simplified output in method.A() if adjust = TRUE.
• Housekeeping routine removed.
• The former variable path (used for in- and output) substituted by variables path.in and path.out.
• Functions env.info(), get.data(), CV.calc(), method.A(), method.B() stand-alone in order to support package-building.
• method.A(): Changed
  lm(foo ~ subject + period + treatment, data)
  to the subject decomposition acc. to the Q&A document
  lm(foo ~ sequence + subject%in%sequence + period + treatment, data)
  Note: PE, MSE, DF are identical to the simple model, but less confusing if the ANOVA is shown (verbose = TRUE). [suggested by Mahmoud Teaima]

replicateBE 0.95

Released to collaborators 2016-06-11.

Bug fixes

• print corrected. Line-endings CRLF (Windows), LF (UNIXes), CR (MacOS). Tested on Windows [HS] and on macOS Sierra 10.12.5 (THX to Mahmoud).
• Reading xls(x)-files corrected. Converts the tibble-object to a data frame.

Minor changes

• List in env.inf() only the packages which are used by the respective functions.
• y-axis in boxplot symmetrical around zero. I think that this is more informative than the default.
• Vector of na-strings supported since v1.0.0 of package readxl. Throws a message if the installed version is <1.0.0. Is there a method to automatically update a package?

replicateBE 0.94

Released to collaborators and beta-tester Mahmoud Teaima 2016-06-01.

Minor changes

• Outlier analysis to console if verbose = TRUE.
• Moved DF and alpha up after the number of subjects. More logical to me.
• If outlier(s) detected, CVwR is recalculated and BE is additionally assessed based on the new limits.
• Added optional outlier assessment (ola = TRUE) for the reference. Defaults to FALSE. Studentized and standardized residuals are calculated and shown in box plots. Note: Only standardized (a.k.a internally studentized) residual are available in Phoenix WinNonlin.

replicateBE 0.93

Released to collaborators and beta-tester Mahmoud Teaima 2016-12-16.

Minor changes

• Variable and decimal separators for reading CSV-files can be specified. Defaults ";" and "."
• Result-file UTF-8 encoded (important for OSX; THX to Mahmoud).
• Added license info and disclaimer (paranoia).
• Added a statement if nTR <12. Suggested by MT.
• Added a statement about ’uncertain’ CV_~wR if nRR <12 in one of the full replicate 3-period designs (acc. to the EMA’s Q&A Rev. 12).
• Added argument verbose (default FALSE) to method.A()/method.B() to support detailed information without debugging.
• Moved check for trailing '/' in the path-argument from method.A()/ method.B() to get.data().
• Restored the evaluation by lmer/lmerTest from v0.83 to support comparing the performance of packages. Wish of DL.

replicateBE 0.92

Released to collaborators and beta-tester Mahmoud Teaima (Faculty of Pharmacy, Cairo University) 2016-12-14.

Bug fixes

• Wrong Miss.per for data sets with NA = '.' fixed. [MT]

Minor changes

• If path does not exist, R’s working directory is used with a warning. [MT]

replicateBE 0.91

Released to collaborators 2016-12-14.

Minor changes

• The line names(Miss.per) is removed (not used in output). [MT]
• Vectorized Miss.seq and Miss.per in get.data(), unnecessary function complete() removed. [MT]

replicateBE 0.90

Released to collaborators 2016-12-14.

Minor changes

• Removed lmer/lmerTest (was called by option = 1 in previous versions), since Satterthwaite’s DF are not compliant with the EMA’s Q&A document (the SAS-code uses implicitely DDFM = CONTAIN).
• Added DF of the treatment difference to the output.

replicateBE 0.83

Released to collaborators 2016-12-11.

Major changes

• Added function complete() to construct a dataframe of complete data based on the subjects and design. Called by get.data() to calculate the number of missing values independent whether the DS contains this information (NA in PK) or not. Not vectorized yet.
• New variable Miss.seq: Missings / sequence.
• New variable Miss.per: Missings / period.

replicateBE 0.82

Released to collaborators 2016-12-10.

Bug fixes

• Added na.action = na.omit to lme() since its default (na.fail) stopped the model.

Major changes

• Changed the default in method.B() from option = 1 to option = 2. No DDFM applied. lme4/lmerTest (option = 1) - like Phoenix WinNonlin by default - uses Satterthwaite’s DF.
• Input checking:
  • Converts variable names (except PK and logPK) to lower case. Stops if variables are not coded as subject, period, sequence, and treatment.
  • Stops if treatments are not coded as R and T.
  • Stops if the number of sequences and/or periods does not match the specified design.

Minor changes

• Returns number of missings / sequence (currently only for NAs).

replicateBE 0.81

Released to collaborators 2016-12-09.

Bug fixes

• Checking packages fixed. [MT]

Minor changes

• (.) removed before names of variables. [MT]

replicateBE 0.8

Released to collaborators 2016-12-09.

Bug fixes

• Calculation of Nsub.seq fixed. [MT]

Minor changes

• / is added to the path if not present. [MT]
• The name of used package is added to the file name for method.B() (_lmer or _lme). [MT]
• lme4 is added to the list of packages (it was an implied subroutine call from lmerTest). [MT]

replicateBE 0.7

Released to collaborators and beta-tester Jiři Hofmann 2016-12-07.

Bug fixes

• Calculation of Nsub.seq in DA12 (with N=77) falsely gave 149 in both sequences.
• BE-assessment corrected (testing both res$CI and res$GMR instead of unique().

replicateBE 0.6

Released to collaborators 2016-12-02.

Major changes

• sequence+subject%in%sequence+period according to the EMA’s Q&A (setup in SAS) and the templates of Phoenix WinNonlin. Note that for unique coding of subjects the nested structure is superfluous / the model overspecified . The more simple model subject+period gives exactly the same residual error.

replicateBE 0.5

Released to collaborators 2016-11-28.

Major changes

• Added import format xls(x). Requires package readxl. Cave: If the sheet(s) contains a commentary header, in the argument skip the number of rows not to be used must be given.

replicateBE 0.4

Released to collaborators 2016-11-27.

Major changes

• New function CV.calc() as suggested by DL. Moved the calculations from get.data(). Adapted calls in method.A() and method.B().

Minor changes

• Vectorized Nsub.seq [MT].

replicateBE 0.3

Released to collaborators 2016-11-26.

Bug fixes

• Bug corrected in selecting subjects with RR [MT].

Minor changes

• Added number of subjects/sequence and check for balance (not vectorized yet).
• Results of iteratively adjusted alpha printed. Throws a warning if adjust = TRUE for an unsupported design.

replicateBE 0.2

Released to collaborators 2016-11-24.

Major changes

• Use package PowerTOST for assessment of the empiric Type I Error and (optionally) iteratively adjustment of α (only Method A). New argument adjust (default FALSE). Results only to the console. Changed hard-coded parts to the respective functions of PowerTOST.
• New argument logtrans (default TRUE). If TRUE, the raw data (column PK) are internally log-transformed. If FALSE the already log-transformed data (column logPK) are used.

Minor changes

• Data can now be provided without the column logPK. If erroneously a call is made with logtrans = FALSE (and the column logPK is missing), the code switches to internal log-transformation (as if logtrans = TRUE would have been called) and throws a warning.
• Added log half-width to the data frame res.

replicateBE 0.1

Released to collaborators 2016-11-23.

Major changes

• method.B() has a new argument option: 1 (default) evaluates by lmerTest() and 2 by nlme().
• New arguments print (default TRUE) and details (default FALSE).
  foo(..., print = FALSE, details = TRUE) returns a data frame of results in full precision.
• Using intervals() instead of a hard-coded confidence interval. [DL]
• Added coding for Method B by nlme. [MT]
• Unless stated otherwise all changes by [HS].

replicateBE 0.0

Released to collaborators 2016-11-22.

• New [HS].