NEWS.md

In vigicaen: 'VigiBase' Pharmacovigilance Database Toolbox

vigicaen 0.15.6

New features

• vigi_routine() now plots details on drug liability and rechallenge when available (#119).

• desc_rch(), desc_dch() and desc_outcome() now handle out of memory arrow Table (#127).

• compute_dispro() now handles factors as x or y arguments, if levels are strictly equal to 0 and 1 (#134).

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

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.

```R # 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.

```R # 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

• Several documenting issues were adressed (#64, #77, #82, #106, #108, #109, #111)

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%.

pharmacocaen 0.12.0

New features

60 add table builders to arrow format (tb_* functions). This is supposed to overwrite the

current fst and dt_fst process, which is being deprecated as of this release.

New getting_started vignette shows the process.

dt_parquet function is to replace dt_fst in the workflow.

pharmacocaen 0.11.1

Minor

Sounds like minor but... Added tests to hit 100% test coverage for the package!

56 Had R CMD CHECK pass on 3 different OS! Test coverage also works.

58 Further anonymized datasets.

get_drecno now correctly inspects DrecNos identified from an mpi_list.

Fix a bug, get_drecno wasn't correctly returning DrecNos from mpi_list.

pharmacocaen 0.11.0

New features

55 add soc option to argument term_level of get_llt_soc.

15 compute_or_abcd is now internally vectorized on drugs and adrs.

53 get_atc_code now appropriately tolowers and trims names as it states,

even when argument vigilyze is set to FALSE.

39 added a d_names argument to add_drug.

Introducing tb_custom to pharmacocaen.

Minor

Improved description of add_drug and add_adr.

7 was fixed a long time ago. Internal improvement to get_llt_smq

pharmacocaen 0.10.0

New features

54 introduce the desc_outcome function to collect adr outcome. Help in the

descriptive vignette.

Minor

Fix add_adr data_type checker.

pharmacocaen 0.9.1

Patches:

47 get_drecno now handles correctly non lower-case names in d_sel.

43 improved documentation of add_drug

pharmacocaen 0.9.0

New features

50 Experimental screen_adr function to identify main adverse drug reactions in an adr dataset.

28 documentation of desc_* functions is now available in vignettes descriptive, template_main and template_dictionary.

Miscellaneous but very important

Vanquished the codetools::checkUsagePackage(pack = "pharmacocaen") note!

Patchs

52 fixed incorrect behavior of get_drecno with arg inspect set to TRUE

51 desc_facvar now shows appropriate big.marks for large numbers

46 desc_facvar and desc_cont now use a more reliable regex logic to display

results according to format argument.

44 columns names of desc_dch, desc_tto and desc_rch now consistently use drug_s and adr_s (instead of drug and adr for desc_rch in the past)

42 improved get_drecno documentation.

36 and #40 improved add_drug documentation.

45 removed argument tto_time_range from

desc_rch (formerly, the function also provided time to onset descriptives)

vigicaen documentation built on April 3, 2025, 8:55 p.m.