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).
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.
Working on examples per CRAN query (#128).
create_ex_* family mostly aimed at example set up or internal use (#128).
Addressing CRAN queries on package DESCRIPTION.
Condensing examples and tb_vigibase() default output.
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.
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.
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)
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).
#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.
#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.
#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.
#91 tb_* family correctly handles different ways of providing paths, and check for the existence of the files before working on tables.
#78 compute_or_abcd() now correctly handles large amount of reports.
#80 hot fix on windows 1224 error
#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.
Failed ubuntu latest oldrel-1 for licensing issue. Put license in license file.
Fixing Windows 1224, by using different temp sub folder for each test
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
Increased code coverage back to 100%.
#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.
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.
#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.
Improved description of add_drug and add_adr.
#7 was fixed a long time ago. Internal improvement to get_llt_smq
#54 introduce the desc_outcome function to collect adr outcome. Help in the
descriptive vignette.
Fix add_adr data_type checker.
Patches:
#47 get_drecno now handles correctly non lower-case names in d_sel.
#43 improved documentation of add_drug
#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.
Vanquished the codetools::checkUsagePackage(pack = "pharmacocaen") note!
#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)