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)