NEWS.md

In cturbelin/ifnBase: InfluenzaNet Data Analysis Base

ifnBase 0.6.5

• Handling new response mapping for gender (other)
• Improve error message when mapping key is missing (show keys besides the missing one to make easier to locate the problem)

ifnBase 0.6.4

• Fix episode last & first strategy for factors, add unit test

ifnBase 0.6.3

• Fix rlang::with_abort() for rlang >= 1.0

ifnBase 0.6.2

• Improve error message from survey definition (platform file parsing)
• enable to create a virtual row id
• add template for vaccination survey 'eu:vaccination'
• Update docs & add families

ifnBase 0.6.1

• fix vomiting constant SYMPT_VOMITING
• add constant SYMPTOMS_TOPIC with symptoms names by topics
• add Upset graph functions and binary grouping

ifnBase 0.6

• Add common variables in eu templates
• Allow to check mapping completeness
• Migrate to github actions instead of travis
• add helper var_labels()

ifnBase 0.5.3

• fix tests for R 4
• check variable_available quosure to ensure result is a single logical

ifnBase 0.5.2

• Add new symptom as standard (was handled locally now all platforms have them)

ifnBase 0.5.1

• fix x_vertical direction
• freq_bool_by() accepts design as data argument

ifnBase 0.5

• dplyr 1.0 as import dependency
• Add strata functions to manage participant weight and adjusted frequency computation
• fix IncidenceRS2014 error when there is no participant for a week

ifnBase 0.4.11

• SyndromeProviderCovid added to compute covid-like syndrome definitions

ifnBase 0.4.10

• SyndromeProviderRS2019 rename 'ili' to 'ili.rs' and revert fever level, 'ari.ecdc' will now 'ili.ecdc'

ifnBase 0.4.9

• SyndromeProviderRS2019 fix fever level for 'ili' syndrome
• episode_fusion_strategy fix parameter episode.column

ifnBase 0.4.8

• design_incidence() now accept use.gender argument
• calc_adjusted_incidence() handles use.gender in strata design

infBase 0.4.7

• IncidenceRS2014 can now extract active participants for each week (with 'participant' in output)
• add i18n_set() to define translation directly
• add NO_SYMPTOM constant for question weekly::Q1
• add geographic code normalizer (mishandled by some db provider)
• add create_path()function to create path without changing the current
• survey_variable_available()handles country parameter
• RSQLite as suggested package (not tested yet)
• sympt.cause is now loaded for incidence (needed to compute syndromic ifn)
• add SyndromeProviderIfn class
• SyndromeProviderRS2019 now expect parameters in constructor instead of compute()
• fix graph_colors() to handle color brewer correctly, add rainbow failback and dark parameter

ifnBase 0.4.6

• health.status options was not handled correctly
• calc_age() fixed to correctly handle month
• load_results_for_incidence() rename ifn syndrome name if duplicate with a provider
• SyndromeProviderRS2019 can relax "sudden" criteria

ifnBase 0.4.5

• dbConnect() now accepts port entry in dsn
• new function survey_rename_columns() to rename columns from external source (csv)

ifnBase 0.4.4

infBase 0.4.3

• add survey_recode_all()
• recode_weekly() can recode all variables, and check for already recoded highest.temp
• add test for episodes & syndrome

ifnBase 0.4.2

• add variable_available() helper to define by season availability of variables
• platform_define_survey() now preserves inherited attributes of variables
• add file based age group population loader & config in platform_options()
• i18n_file now handles both .r and .R files
• add ggplot2 theme_with() helper function
• fix complete_intake() if not intake is available
• Refactor survey_participant_previous_season() to better handler single table model
• Internal: add db helpers function db_quote_str(), db_quote_var(), db_equal()
• improve documentation, add several vignettes surveys,
• fix recode_alias()
• add print S3 methods for survey_definition
• add episode fusion strategies
• add functions to manage paths : get_current_paths(), add_path_prefix()

ifnBase 0.4.1

• use roxygen 7
• fix recoding name for main.activity variable
• recoding are now S3 class survey_recode allowing pretty print
• recode_intake now recode all available variables
• remove function coalesce()
• fix season censoring using get_season_censoring() in platform env
• censoring can be parametrized passing list() in first.season in load_incidence_results()
• episode function now handle fusion strategies and end date of episode computation
• 'ari*' definitions provided by SyndromeProviderRS2019 dont anymore consider pain and headache for child under age defined by pain.age.limit
• recode_weekly check if data was already recoded and dont recode it, added flags
• added constants objects in uppercase YES, NO, DONTKNOW, see ?constants
• added concepts page ?concepts

ifnBase 0.4.0

• introduce episodes computation functions
• extract onset computation from incidence IncidenceRS2014 & IncidenceDailyRS2014 now done in load_incidence_results, remove onset.columns parameter, date recoding are extracted (done in recode_weekly).
• onset is computed using a quosure by compute_onset()
• add episode_onset_design() returning expression to compute onset date used for episodes
• add base_onset_design() returning expression to compute onset date used for incidence
• load_incidence_results() get a parameter 'onset' to get the onset expression, returns now a class "incidence_loader"
• date recoding are in recode_weekly_date
• recode_weekly() now recodes dates using recode_weekly_date adds an attribute "recode_weekly" to flag the weekly as recoded

ifnBase 0.3.2

• Fix namespace imports
• Fix function name

ifnBase 0.3.1

• add compute_weekly_syndromes to create syndrome columns in weekly using several kind of strategies
• add complete_intake_strategy() and complete_intake() for intake survey completion accross seasons
• add load_results_for_incidence to load & prepare data in order to compute incidence
• add SyndromeProviderCountry R6 class to compute by country definition (draft)
• add SyndromeProviderClass as base R6 class for syndrome provider classes

ifnBase 0.3

• SyndromeProviderRS2019 R6 class compute 2019 revised syndrom definition
• adding incidence functions as R6 classes IncidenceRS2014 and IncidenceDailyRS2014
• fix plot_age_pyramid() scale
• add theme_with() for ggplot receipes
• syndromes_rs_2018() embeds all function related to syndromes definitions for Guerrisi,Euro Surv., 2018
• stats function multitple_freq(), multiple_xfreq()
• new function get_db_handle() to get the db connexion
• rename cut.age() function cut_age()
• add country in platform_geographic_levels()

ifnBase 0.2

• adding swMisc package as Import dependency https://github.com/sentiweb/swMisc
• Move merge_list(), ending_slash(), get_r_file() and misc functions (not used directly in the package) to swMisc
• rename merge.list() to merge_list(), keep.last.survey() to keep_last_survey(), calc.age() to calc_age()
• recode_weekly: weekly date is computed using truncated POSIXct value to day
• Added a NEWS.md file to track changes to the package.
• adding ggplot2 related functions, ggplot is now an Import dependency
• ISOYearWeek() renamed to iso_yearweek()
• makeWeekIndex() renamed to make_week_index()
• mondayOfDate() renamed to monday_of_date()
• WeekStart() renamed to monday_of_week()
• YearStart() renamed to monday_of_year()
• weesbydates() renamed to weeks_of_date()
• WeekStamp() renamed to week_stamp()
• fixing documentation

cturbelin/ifnBase documentation built on Nov. 5, 2023, 12:54 p.m.