| add_path_prefix | Register a path prefix |
| apply_binary_mask | Create a binary group value from a set of logical columns. |
| as_mapping | Create a mapping to recode variable value to labels |
| axis_week | Axis for yearweek data |
| base_onset_design | Base onset design, used for incidence computation |
| calc_adjusted_incidence | Compute crude & adjusted incidence from a count data |
| calc_age | Age of participants from a Year-month birth date |
| calc.conf.int | Compute confidence interval for rate using poisson... |
| calc_season | Return the season number of a yearweek or a Date |
| calc_season_fixed | Compute a season index of each year week |
| calc_weekly_delay | Compute delay between 2 surveys for each participant |
| calc_weekly_order | Compute order of weekly response |
| can_use_country | Check if the platform is allowed to use "country" value |
| check_list_mapping | Check if two named list are compatible to merge |
| check_season_dates | Check if provided date bounds are compatible with a season |
| check_survey_template | Check if a survey definition is compatible with a survey... |
| check_unique | Check if list values are unique |
| complete_intake | Complete intake for a survey using intake from the past... |
| complete_intake_strategy | Complete intake according to platform's strategy |
| compute_onset | Compute the onset date from a design object |
| compute_weekly_syndromes | Create syndrome columns in the weekly data |
| concepts | Package concepts |
| constants | Constants values |
| create_binary_groups | Create new groups from a set of columns |
| create_binary_mask | Create a binary mask for each value |
| create_participant_weight | Define participants weight from general population to compute... |
| create_path | Generate a path with path components. |
| create_step_tracker | Create a step counter |
| create_survey_definition | Create a survey definition |
| create_syndrome_columns | Create syndrom columns from factor encoded column |
| cut_age | Cut age values into categories using breaks and defining... |
| dbConnect | Connect or Reconnect to DB |
| db_equal | Create an equal criteria |
| dbQuery | Run a query |
| design_incidence | Describe the stratification to use for incidence computation... |
| design_weight | Create a design for adjustment computation |
| episode_build | Build Episodes data from survey data |
| episode_compute | Compute episodes in weekly data |
| episode_compute_ariza | Compute episodes using M Ariza's algorithm The onset date is... |
| episode_compute_ecollan | Compute Episodes using Marie Ecollan's strategy |
| episode_compute_souty | Compute Episodes using Cecile Souty's strategy |
| episode_design | Create a design definition for episodes computation |
| episode_fusion | Apply function strategy |
| episode_fusion.simple_strategy | Merge episodes using a simple function as merge strategy |
| episode_fusion_strategy | Compute episode dataset |
| episode_fusion.worst_strategy | Apply 'worst' fusion strategy |
| episode_onset_design | Onset definition used for episodes |
| episode_prepare_data | Prepare data and select participants using given rules |
| episode_select_participants | Select participants based on a list of rules |
| episode_strategy | Define a strategy to merge data of the same episode of a... |
| FEVER.CODES | List of coded values for fever names are pretty labels,... |
| format_week | Format a yearweek value to a human readable format |
| freq_bool_by | Compute frequency of a set of logical variables by group... |
| freq_var_by | Compute frequency by group of a qualitative variable of a... |
| freq_vars_by | Frequency of several variables by group |
| geo_base_level | Get base level of geographic tables (lowest level) |
| geo_base_table | Get Base geographic tables It should contains all levels,... |
| geo_check_level | Check if level exists |
| geo_column | Get geographic column name for a given level |
| geo_definition | Get geographic structure description |
| geo_hierarchy | Get a hierarchy path of geographic levels |
| geo_is_type | Allow to define "type" of geographic levels & area |
| geo_level | Create a geographic level object |
| geo_level_nav | Navigate through geographic levels (get the upper level, the... |
| geo_level_table | Get geographic table definition for a given geographic level |
| geo_normalize | Normalize with geographic codes for a level after it has been... |
| geo_normalize.data.frame | Normalize with geographic codes for a level after it has been... |
| geo_normalize.default | Normalize with geographic codes for a level after it has been... |
| get_columns_for_incidence | Returns list of columns needed of weekly survey to compute... |
| get_current_paths | Get the current paths defined by 'init.path()' or... |
| get_db_handle | get database connexion handle |
| get_default_color | Get default color |
| get_geo_join | Get information needed to make a join with geo tables from... |
| get_historical_seasons | Get list of available season names |
| get_historical_tables | Get Historical tables |
| get_labels_from_binary | Get corresponding label from a binary group value |
| get_option | Get package option from name From 'ifn' options() entry |
| get_season_dates | Get dates of the season |
| get_symptoms_aliases | Aliases for symptom columns |
| gg_barplot_percent | Percentage barplot |
| graph.close | End a graphic export to a file. Use it instead of dev.off().... |
| graph_colors | Return a list of n colors by the "best" color generator... |
| graph_get_last | get last output graph |
| graph.hook | Declare a hook function called when graph.close() is called |
| graph.open | Open a graph using standard library |
| graph.save | Export a ggplot2 and run graph hooks. To be used with ggplot2... |
| i18n | Translate a string |
| i18n_inflect | Inflexion for a count |
| i18n_load | Load i18n translations from a list of files |
| i18n_names | translate names attribute |
| ifnBase-package | InfluenzaNet Data Analysis Base Package |
| IncidenceDailyRS2014 | Incidence estimator using rs2014 method implemented using... |
| IncidenceRS2014 | Compute Incidence using rs2014 method Active participants are... |
| init.path | Define an path for files, usable by my.path() |
| iso_yearweek | iso_yearweek(dates) |
| is_syndrome_provider | Test if object is a syndrome provider object |
| join_surveyuser | Create join clause to survey_surveyuser table for a survey |
| keep_last_survey | Keep the last survey for each participant |
| load_geo_zone | Load areas defined at a given geographic level |
| load_platform | Load platform file containing definitions and specific... |
| load_population | Load global population for a geographic level and a census... |
| load_population_age | Load popuplation by age-group & sex |
| load_population_age.impl | Load Population by age |
| load_results_for_incidence | Load data for incidence computation |
| make_week_index | Make an index data.frame associating week index (wid) to a... |
| merge_by_value | Merge two named lists by their values (survey recoding) |
| monday_of_date | Monday of the week of the date |
| monday_of_week | Date of the monday of a yearweek |
| monday_of_year | Date of the first monday of the year |
| multiple_freq | Compute frequency table for multiple options matrix |
| multiple_xfreq | Frequency for multiple options by group |
| my.path | Return the path of a file in the current ouput path |
| NO_SYMPTOM | No symptome variable name |
| output_incidence | Define structure containing incidence results output and some... |
| override | Allow override of mapping or recoding from template |
| parse_season | Check if input is a season number |
| platform_define_survey | Describe a survey of a platform and register it |
| platform_env | Get the platform env |
| platform_geographic_levels | Create structure defining an geographic table system. |
| platform_geographic_tables | Create geographic tables description |
| platform_import | Import a file in the platform environment |
| platform_options | Define platform options |
| platform_path | Path to platform definition files |
| platform_season_history | Define historical data |
| plot_age_pyramid | Plot Age Pyramid |
| polygon_ic | Draw confidence interval with polygon |
| print.fusion_strategy | Print fusion strategy |
| print.fusion_strategy_dict | Print fusion strategy |
| print.paths_definition | Print path definition |
| print.survey_definition | print survey definition |
| print.survey_error | Print checks results |
| print.survey_labels | print survey labels mapping |
| print.survey_mapping | print survey variable mapping |
| print.survey_recode | print survey recoding |
| prop_by_weighted | Compute weighted proportion by group for a logical variable |
| PROTECTED_QUESTIONS | List of not usable for data variable names in survey mapping |
| raw_value | Create a list of values marked as "raw" |
| recode_alias | create a recoding alias |
| recode_intake | Recode Intake variables to more error-proof labels Value to... |
| recode_var | Recode values with a given mapping |
| recode_weekly | Apply common recoding for weekly data |
| recode_weekly_date | Recode weekly dates Recode weekly dates |
| recode_ynp | recode Y/N/DNK where Y=0 to boolean (wow!) Used to recode... |
| regroup.syndrome | Regroup mixed syndromes to non-specific for the 2012's... |
| relative_seasons | Get relative season numbers to a reference season number |
| scale_x_wid | Scale from wid to Yearweek values |
| season_definition | Get historical season definition |
| share.cache.path | return the path of a file in cache files |
| share.data.path | path of a file in data |
| share.lib | Load a share library |
| share.lib.path | Get file in lib path |
| share.option | get options for the ifn environment |
| share_path | path of a file in share/ directory |
| strategy_create_coding | Create a encoding dictionnary for each variable used in a... |
| survey_aliases | Convert DB column name from and to question variable name... |
| survey_default_language | Get the default language used for survey Uses... |
| survey_definition | Get survey definition |
| survey_labeller | Get a labeller object for a given name in the survey Will to... |
| SurveyLabeller | Survey Labeller Class |
| survey_labels | Return the "labels" for a given question variable name |
| survey_load_all | Load all definition data about a survey |
| survey_load_health_status | Load health status for each weekly responses |
| survey_load_options | load options of a question from the database, identified by... |
| survey_load_participants | Load participants data |
| survey_load_participations | Load last participation date for intake & weekly survey for... |
| survey_load_questions | load questions of a survey from the database |
| survey_load_results | load a survey results set |
| survey_load_results_historic | Load historical data for a set of users |
| survey_load_translation | load a translation for a survey for a given language |
| survey_options_for | Get the options for a survey's varname This is not the... |
| survey_participant_previous_season | List of participants registered in weekly at least once in... |
| survey_participant_season | Get list of participant id (person_id = survey_user_id) List... |
| survey_question_id | get the question_id (id in the question table in the... |
| survey_recode | Recode data from the DB storage code to the R labels (or to... |
| survey_recode_all | Recode all known variables in survey data |
| survey_recodings | Get all the recodings defined in a survey |
| survey_rename_columns | Rename columns to the survey variable names |
| survey_single_table | Returns TRUE if the survey's data are store using a single... |
| survey_template | Survey Template definitions |
| survey_variable_available | Check if variables are available for a given season |
| survey_variable_recoding | Get the recoding mapping of a variable in a survey |
| survey_variables_like | Get list of variable names matching the given pattern (glob... |
| symptoms | Symptoms |
| SYMPTOMS_TOPICS | Symptoms grouped by topics |
| SyndromeProvider | Syndrome provider base class |
| SyndromeProviderCountry | Syndrome Provider |
| SyndromeProviderCovid | Syndrome Provider with COVID-19 like definitions |
| SyndromeProviderIfn | Syndrome provider base class for historical Influenzanet... |
| SyndromeProviderRS2019 | Syndrome Provider with 2019 revised ILI & Ari definitions |
| syndromes_influenzanet_2011 | Compute the 2011's Influenzanet syndromes set... |
| syndromes_influenzanet_2012 | Compute syndrome classification of weekly data according to... |
| syndromes.prettify | Prettify syndrome names from InfluenzaNet DB health status... |
| syndromes_rs_2018 | Compute syndromes definitions used in Guerrisi C, Euro Surv.... |
| syndromes.set | Syndromes set definitions |
| theme_no_axis | Remove axis from plot |
| theme_with | Theme with a list of recipes |
| titlelize | Create a title from a set of character vectors |
| upset_plot | Create an upset graph, inspired from an UpsetR package, show... |
| validate_platform | Post loading function to validate platform info |
| variable_available | Define availability of variables |
| var_labels | Define a label for survey variables, labels are used to... |
| verticalize_incidence | Verticalize incidence data after computation |
| week_of_date | week_of_date(from,to) get yearweek from a date interval date... |
| week_stamp | Compute a "Week" stamp (like timestamp) : week number from... |
| with_ggplot | Init ggplot2 base theme. ggplot2 library should be loaded... |
| x_axis_vertical | Set axis to vertical |
