# 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)
