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NEWS.md

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secuTrialR 1.3.2 and 1.3.3

  • clear some notes and warnings in preparation for CRAN submission (#265)

secuTrialR 1.3.1

  • build_secuTrial_url() now has optional parameter prefix with default "apps/WebObjects/". (#263)

secuTrialR 1.3.0

  • bug fix to read escaped enclosure characters in free text items, e.g. \" (#220, #261)
    • read_export_options() now also reads enclosure character from header
    • .print.secuTrialoptions() now also prints enclosure character. Quote and Tabulator are now printed as '\"' and '\t' rather than '"' and ' '.
    • read_export_table() now uses readr::read_delim() with options escape_backslash = TRUE and quote = export_options$quote
  • warning for ISO-8859 encoding moved from read_export_table() to read_secuTrial_raw() (one warning per export file instead of several warnings for each table)
  • read_export_options() now reads only the first 10 lines to find the encoding. Reading all lines would fail if the export options were ISO-8859 encoded and contained 'problematic' characaters, e.g. in center names.
  • Removed encoding option in plot_recruitment(): Not needed here, as centres are read with correct encoding in read_secuTrial_raw() and stored in the secuTrialR object.

secuTrialR 1.2.0

  • write_secuTrial() no longer allows format = "sas" due to deprecation of write_sas in haven (version 2.5.2).
  • read_secuTrial_raw now produces a more explicit warning when ISO-8859 encoding is used. Recent changes in R seem to have reduced compatibility with this encoding.

secuTrialR 1.1.1

  • fix CRAN notes - remove codecov badge, check class via inherits

secuTrialR 1.1.0

  • warning regarding overwritten pat_id variable

secuTrialR 1.0.12

  • adapt as.data.frame.secuTrialData() to allow named character vectors as option data.frames to specify custom names for data.frames (#250)

secuTrialR 1.0.11

  • recommendation to export with short names (#238)
  • addition of arguments in read_export_table etc allowing passing other options to read.table (#240)
  • addition of dictionary_secuTrial function for easy access a data dictionary (#241)
  • formtablename added to the output of visit_structure for better reference between the table names and labels (#242)
  • addition of export_date and export_datetime for easier access to the export date (and time) (#246)

secuTrialR 1.0.10

  • adapt read_export_options() to work with exports from new secuTrial version (6.1.2.5 - 6.3.2.5) (#245)

secuTrialR 1.0.9

  • transferred the Maintainer tag to Alan Haynes

secuTrialR 1.0.8

  • reverted factorize_secuTrial() back to 1.0.3 version due to problems with lookup table factorization (#224)
  • added citation (doi: 10.21105/joss.02816)

secuTrialR 1.0.7

  • moved tcltk and igraph dependency to suggested (#223)

secuTrialR 1.0.6

  • added skip parameter to read_validation_overview() (#212)

secuTrialR 1.0.5

  • fixed a bug where subset_secuTrial() would drop labels during the subsetting process (#203)

secuTrialR 1.0.4

  • improved import speed, specifically through changes in dates_secutrial() and factorize_secutrial() (#204)

secuTrialR 1.0.1, 1.0.2, 1.0.3

  • adjustments to handle review feedback from CRAN (#190)

secuTrialR 1.0.0

  • clarify correct options in read_secuTrial() failure message (#187)
  • check for project_setup in visit_structure() (#181)

secuTrialR 0.9.1

  • added "Form meta data: Structure" export option information to export_options (#182)
  • added error handling for missing structure data when running annual_recruitment() and return_random_participants() (#182)

secuTrialR 0.9.0

  • restructuring in preparation for a release on CRAN

secuTrialR 0.8.9

  • added suggestion to NOT export form data of hidden fields (#177)

secuTrialR 0.8.8

  • added check to make sure that specified centres are part of the export in return_random_participants() (#151)

secuTrialR 0.8.7

  • extended failure comment in read_secuTrial() to indicate that the problem could be a rectangular export file (#168)
  • added "Form data of hidden fields" export option information to export_options (#171)
  • added return_hidden_items() function (#172)

secuTrialR 0.8.6

  • bug fix: presence of the audit trail was incorrectly identified due to a comment in the source file of the export options (see #155, comments from @suvi-subra and @OliviaEbnerIAS)

secuTrialR 0.8.5

  • Added sorting option to visit_structure. (#152)

secuTrialR 0.8.4

  • adjusted warning message in label_secuTrial()
  • only allow unique labels in label_secuTrial()
  • added "Frequent warning messages" paragraph to the vignette (#156)

secuTrialR 0.8.3

  • added up-to-date vignette (#99)
  • path in print.secuTrialdata is now wrapped at 80 characters

secuTrialR 0.8.2

  • secutrialoptions class is now secuTrialoptions.

secuTrialR 0.8.1

  • add appveyor testing, pkgdown site
  • fix possible bug on windows due to regex in .prep_line_items (used in plot_recruitment) (#147)

secuTrialR 0.8.0

  • Changed license for the package from GPL-2 to MIT.

secuTrialR 0.7.9

  • The general nomenclature for a study subject will from now on be participant (pat). All variations of this (e.g. case, patient) have been adjusted in the code and the documentation.

secuTrialR 0.7.8

  • Removed generic plot() function for secuTrialdata objects. (#139)

secuTrialR 0.7.7

  • read_secuTrial() and read_secuTrial_raw() now check if the input file exists. (#137)

secuTrialR 0.7.6

  • factorize_secuTrial() warning messages have been adjusted to improve trouble shooting experience. (#134, #135)

secuTrialR 0.7.5

  • dates_secuTrial() incomplete date warnings are now concatenated and returned as one warning per form instead of many. (#124)

secuTrialR 0.7.4

  • Fixed issue #121 on GitHub. factorize_secuTrial() can now handle exports which have the reset option enabled in radio buttons.

secuTrialR 0.7.3

  • write_secuTrial() now allows xpt version 8 files to be written. (closes #57)

secuTrialR 0.7.2

  • check_export_options() function was added. It informs on deviations from suggested export options. (closes #17)
  • Removed tracking of obsolete export options (partial_date_string, partial_date_handling, unknown_date_string).
  • Added format_info (e.g. "CSV format for MS Excel") to export_options.

secuTrialR 0.7.1

  • Fixed issue #116 on GitHub.

secuTrialR 0.7.0

  • subset_secuTrial() function was added. It allows subsetting of secuTrialdata based on patient ID and/or study centre name.
  • get_participants() function was added. It allows easy extractions of participant info from a secuTrialdata object.

secuTrialR 0.6.5

  • return_random_cases() now returns a list. The first element are the cases and the second element is the output of RNGkind().

secuTrialR 0.6.4

  • New function diff_secuTrial() added to allow light weight comparison of the setup of two secuTrial exports.

secuTrialR 0.6.3

  • Metadata variables are now also transformed to date and datetime formats, whenever appropriate.

secuTrialR 0.6.2

  • factorize_secuTrial() now no longer triggers an unexpected warning when the name of a secuTrial lookuptable is equal to the name of the variable it is being used in. (PR #108)

secuTrialR 0.6.1

  • return_random_cases() has been added to the package. It allows to sample a random subset of cases from a secuTrial export in a reproducible fashion.

secuTrialR 0.6.0

  • read_secuTrial_raw() and read_secuTrial() no longer fail due to missing Add-ID, centre information or project setup in export data. Instead, adding of pat_id (no Add-ID), centre (no centre information) and visit_name (no project setup) to the data tables is now omitted if the relevant data for the operation is not available.

secuTrialR 0.5.5

  • read_secuTrial_raw() and read_secuTrial() no longer fail due to missing "Description" in export options.

secuTrialR 0.5.4

  • dates_secuTrial() now warns if not all dates were parsed (expected if there are incomplete dates).
  • factorize_secuTrial() now warns if there are issues with the factorization (not expected to trigger).

secuTrialR 0.5.2

  • New function build_secuTrial_url() has been added. It allows users to easily compose URLs to specific secuTrial forms.

secuTrialR 0.5.0

  • The function name of read_secuTrial_export() has been changed to read_secuTrial_raw() to avoid confusion with read_secuTrial().

secuTrialR 0.4.16

  • As of version 0.4.17, changes will be recorded in the NEWS file.