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Changelog

Source: NEWS.md

vigicaen (development version)

New features

  • tb_vigibase() now accepts a new argument rm_suspdup (default TRUE) to automatically remove cases identified as suspected duplicates (from SUSPECTEDDUPLICATES.txt) when creating the main tables. You can disable this behavior by setting rm_suspdup = FALSE.

  • tb_vigibase() now supports a new argument overwrite_existing_tables (default FALSE). If set to FALSE, the function will skip the creation of any .parquet tables that already exist, allowing you to resume the process after a crash or interruption without rebuilding completed tables. Set to TRUE to force rebuilding all tables. This makes the table-building process more robust and efficient for large datasets or limited hardware.

  • vigi_routine() now supports two new arguments:

    • suspect_only (default FALSE): controls whether only suspected drug cases are included in IC analysis.
    • d_code_2 (optional): if provided, a single analysis is performed on cases exposed to both drugs in d_code and d_code_2. A CLI message is displayed when dual drug analysis is performed.

Bug fixes

  • vigi_routine() now has left/right justification of the patient label centered on 3 months (90 days) instead of the observed median. This resolves an issue where the label could be misplaced on the time to onset plot when the median did not match the visual center of the graph.(#145)

Documenting

  • The ‘smq’ argument in get_llt_smq() no longer requires length 1.(#126)

  • The example for get_atc_code() now uses explicit names for atc_sel.(#126)

  • The Value section of desc_tto() now clarifies the default descriptive format and how to change it.(#126)

  • Typos in routine pharmacovigilance vignette.(#126)

vigicaen 0.15.6

CRAN release: 2025-03-13

New features

Minor

  • Error and warnings all turned into cli syntax. Gathered redundant checkers internally (#133).

  • vigi_routine() now works with out of memory arrow Tables. Additional checkers to vigi_routine() for input data type.

  • compute_or_mod() now has an informative error message if either args estimate or std_er were not supplied (#123).

  • get_drecno() now handles non-WHO names matching a unique DrecNo that has several WHO names, and throws an error if matching multiple DrecNos (#139).

  • Adding dependency to glue.

vigicaen 0.15.5

CRAN release: 2025-02-21

Minor

  • Working on examples per CRAN query (#128).

  • create_ex_* family mostly aimed at example set up or internal use (#128).

vigicaen 0.15.4

Minor

  • Fixing typos in DESCRIPTION, per CRAN query.

vigicaen 0.15.3

Minor

  • Addressing CRAN queries on package DESCRIPTION.

  • Condensing examples and tb_vigibase() default output.

vigicaen 0.15.2

Minor

  • Clearing remaining temp files from tests

vigicaen 0.15.1

New features

  • tb_* family now has a cli style progress bar

  • get_llt_soc() output is reworked with cli features. The function also now correctly supports non-data.table data.frame.

  • vigi_routine() fails if there are no drug or adr cases found in demo_data.

vigicaen 0.15.0

Breaking changes

  • mp replaces mp_short throughout the package (#110). Users will have to change existing code to replace calls to mp_short with mp.

    # the old way
mp_short <- dt_parquet(path_who, "mp_short")
d_names <- list(drug1 = "paracetamol")
d_drecno <- get_drecno(d_names, mp_short = mp_short)

# the new way
mp <- dt_parquet(path_who, "mp")
d_names <- list(drug1 = "paracetamol")
d_drecno <- get_drecno(d_names, mp = mp)

  • In get_llt_smq(), smq_list and smq_content replace smq_list_content(#74). Users will have to change existing code to replace calls to smq_list_content with smq_list and smq_content. Example tables smq_list_ and smq_content_ are added to the package. This change was made to streamline the process of querying sub-SMQs.

    # the old way
smq_list_content <- dt_parquet(path_meddra, "smq_list_content")

smq_llt <- 
  get_llt_smq(
    list(ihd = "Ischaemic heart disease (SMQ)"),
    smq_list_content)

# the new way
smq_list <- dt_parquet(path_meddra, "smq_list")
smq_content <- dt_parquet(path_meddra, "smq_content")

smq_llt <- 
  get_llt_smq(
     list(ihd = "Ischaemic heart disease (SMQ)"),
     smq_list = smq_list,
     smq_content = smq_content)

  • compute_dispro() is the new name of compute_or_abcd(), to reflect that other disproportionality measures are available.

New features

  • Args inspect and show_all of get_drecno() are replaced by verbose (#102).

  • get_drecno() and get_llt_smq() messages are cleaner and written with the cli package.

  • New top_n argument added to screen_adr() (#86).

  • screen_drug() let you screen most reported drugs in drug (#103).

  • get_llt_smq() now queries sub-SMQs and return all relevant codes (#74).

  • Order of output columns in compute_dispro() has changed, to allow easier access to formatted values. Also new arguments min_n_obs and export_raw_values (#101).

  • tb_subset() handles ID code lists as input, instead of numeric vectors, to make workflow more consistent with other processes like add_*. (#112)

Minor and bug Fixes

  • screen_adr() now counts effects at the case level (#86).

  • arg data_type of add_* functions is now deprecated. Data_type is internally detected.

  • add_drug() and add_adr() have informative error if id code list is incorrect (#88).

Documenting

vigicaen 0.14.0

New features

#90 Introducing vigi_routine() to streamline the process for pharmacovigilance practitioners. This function is intended for non-expert users, to produce an Information Component and time to onset graph.

#94 The luda table no longer exists. It is replaced by an augmented version of link - built directly from tb_vigibase(), which is used downstream in place of luda.

Minor

#92 tb_main() and tb_sub() are fusionned into tb_vigibase().

#93 It is now possible to export raw data composing the value column of desc_facvar() and desc_cont(), with argument export_raw_values.

#83 vignette("descriptive") was translated in English.

Bug fixes

#89 and #87 the get_* family of functions now correctly handle out of memory tables (by pulling them into memory). The same is true for extract_tto().

#85 Useless default values to some arguments of extract_tto() were removed.

vigicaen 0.13.5

Patch

#91 tb_* family correctly handles different ways of providing paths, and check for the existence of the files before working on tables.

vigicaen 0.13.4

Patch

#78 compute_or_abcd() now correctly handles large amount of reports.

#80 hot fix on windows 1224 error

vigicaen 0.13.3

Patch

#75 clearer example for get_llt_soc()

#76 SizeUnit_Lx file in sub, which is encoded in an old format, is now appropriately treated as such.

vigicaen 0.13.2

Patch

Failed ubuntu latest oldrel-1 for licensing issue. Put license in license file.

vigicaen 0.13.1

Patch

Fixing Windows 1224, by using different temp sub folder for each test

vigicaen 0.13.0

New features

Changing the package’s name!! All set for a public release.

Improved documentation by adding tags, translating to english the basic_workflow vignette. #62, #67, and #69

Patchs

Increased code coverage back to 100%.