replicateBE 1.1.3

Bug fixes

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

v1.1-1

Bug fixes

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

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 v1.1-0

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 Liège.
• 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.

Minor changes

• path.out in examples changed from "~/" to tempdir(). CRAN policy violation noted by B. 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 v1.0-15

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 v1.0-14

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 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 v1.0-13

On CRAN 2020-01-09.

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. Uses now 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) naïvely 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 v.1.0-12

On CRAN 2019-11-11 (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 v1.0-11

On CRAN 2019-08-25.

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 v1.0-10

On CRAN 2019-07-24.

Issue

• Corrupt LaTeX-Installation on CRAN. Therefore, in the PDF-manual URLs in references are converted to truncated (i.e., wrong) URLs in footnotes.

Bug fixes

• Stopped import when no missings according to the specifier na where found.

Minor changes

• README.md.
• NEWS.md instead of NEWS.
• Removed numbered references (see Issue above).
• Updated links to the EMA’s datasets in info.data().

replicateBE v1.0-9

On CRAN 2019-07-22.

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 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--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.
• stringsAsFactors = FALSE in res-list of all methods.
• Removed superfluous options(ow) after models.
• Updated man page of method.A() and the vignette.