Man pages for cturbelin/ifnBase
InfluenzaNet Data Analysis Base

add_path_prefixRegister a path prefix
as_mappingCreate a mapping to recode variable value to labels
axis_weekAxis for yearweek data
base_onset_designBase onset design, used for incidence computation
calc_adjusted_incidenceCompute crude & adjusted incidence from a count data
calc_ageAge of participants from a Year-month birth date
calc.conf.intCompute confidence interval for rate using poisson...
calc_seasonReturn the season number of a yearweek or a Date
calc_season_fixedCompute a season index of each year week
calc_weekly_delayCompute delay between 2 surveys for each participant
calc_weekly_orderCompute order of weekly response
can_use_countryCheck if the platform is allowed to use "country" value
check_list_mappingCheck if two named list are compatible to merge
check_survey_templateCheck if a survey definition is compatible with a survey...
check_uniqueCheck if list values are unique
complete_intakeComplete intake for a survey using intake from the past...
complete_intake_strategyComplete intake according to platform's strategy
compute_onsetCompute the onset date from a design object
compute_weekly_syndromesCreate syndrome columns in the weekly data
conceptsPackage concepts
constantsConstants values
create_pathInternal function create the path from the current paths...
create_step_trackerCreate a step counter
create_survey_definitionCreate a survey definition
create_syndrome_columnsCreate syndrom columns from factor encoded column
cut_ageCut age values into categories using breaks and defining...
dbConnectConnect or Reconnect to DB
db_equalCreate an equal criteria
dbQueryRun a query
design_incidenceDescribe the stratification to use for incidence computation...
episode_buildBuild Episodes data from survey data
episode_computeCompute episodes in weekly data
episode_compute_arizaCompute episodes using M Ariza's algorithm The onset date is...
episode_compute_ecollanCompute Episodes using Marie Ecollan's strategy
episode_compute_soutyCompute Episodes using Cecile Souty's strategy
episode_designCreate a design definition for episodes computation
episode_fusionApply function strategy
episode_fusion.simple_strategyMerge episodes using a simple function as merge strategy
episode_fusion_strategyCompute episode dataset
episode_fusion.worst_strategyApply 'worst' fusion strategy
episode_onset_designOnset definition used for episodes
episode_prepare_dataPrepare data and select participants using given rules
episode_select_participantsSelect participants based on a list of rules
episode_strategyDefine a strategy to merge data of the same episode of a...
FEVER.CODESList of coded values for fever names are pretty labels,...
format_weekFormat a yearweek value to a human readable format
geo_base_levelGet base level of geographic tables (lowest level)
geo_base_tableGet Base geographic tables It should contains all levels,...
geo_columnGet geographic column name for a given level
geo_definitionGet geographic structure description
geo_hierarchyGet a hierarchy path of geographic levels
geo_is_typeAllow to define "type" of geographic levels & area
geo_levelCreate a geographic level object
geo_level_navNavigate through geographic levels (get the upper level, the...
geo_level_tableGet geographic table definition for a given geographic level
get_columns_for_incidenceReturns list of columns needed of weekly survey to compute...
get_current_pathsGet the current paths defined by 'init.path()' or...
get_db_handleget database connexion handle
get_default_colorGet default color
get_geo_joinGet information needed to make a join with geo tables from...
get_historical_seasonsGet list of available season names
get_historical_tablesGet Historical tables
get_optionGet package option from name From 'ifn' options() entry
get_season_datesGet dates of the season
get_symptoms_aliasesAliases for symptom columns
gg_barplot_percentPercentage barplot
graph.closeEnd a graphic export to a file. Use it instead of
graph_colorsReturn a list of n colors by the "best" color generator...
graph_get_lastget last output graph
graph.hookDeclare a hook function called when graph.close() is called
graph.openOpen a graph using standard library
graph.saveExport a ggplot2 and run graph hooks. To be used with ggplot2...
i18nTranslate a string
i18n_inflectInflexion for a count
i18n_loadLoad i18n translations from a list of files
i18n_namestranslate names attribute
ifnBase-packageInfluenzaNet Data Analysis Base Package
IncidenceDailyRS2014Incidence estimator using rs2014 method implemented using...
IncidenceRS2014Compute Incidence using rs2014 method Active participants are...
init.pathDefine an path for files, usable by my.path()
is_syndrome_providerTest if object is a syndrome provider object
join_surveyuserCreate join clause to survey_surveyuser table for a survey
keep_last_surveyKeep the last survey for each participant
load_geo_zoneLoad areas defined at a given geographic level
load_platformLoad platform file containing definitions and specific...
load_populationLoad global population for a geographic level and a census...
load_population_ageLoad popuplation by age-group & sex
load_population_age.implLoad Population by age
load_results_for_incidenceLoad data for incidence computation
make_week_indexMake an index data.frame associating week index (wid) to a...
merge_by_valueMerge two named lists by their values (survey recoding)
monday_of_dateMonday of the week of the date
monday_of_weekDate of the monday of a yearweek
monday_of_yearDate of the first monday of the year
multiple_freqCompute frequency table for multiple options matrix
multiple_xfreqFrequency for multiple options by group
my.pathReturn the path of a file in the current ouput path
output_incidenceDefine structure containing incidence results output and some...
overrideAllow override of mapping or recoding from template
parse_seasonCheck if input is a season number
platform_define_surveyDescribe a survey of a platform and register it
platform_envGet the platform env
platform_geographic_levelsCreate structure defining an geographic table system
platform_geographic_tablesCreate geographic tables description
platform_importImport a file in the platform enviroment
platform_optionsDefine platform options
platform_pathPath to platform definition files
platform_season_historyDefine historical data
plot_age_pyramidPlot Age Pyramid
polygon_icDraw confidence interval with polygon
print.fusion_strategyPrint fusion strategy
print.fusion_strategy_dictPrint fusion strategy
print.paths_definitionPrint path definition
print.survey_definitionprint survey definition
print.survey_errorPrint checks results
print.survey_labelsprint survey labels mapping
print.survey_mappingprint survey variable mapping
print.survey_recodeprint survey recoding
PROTECTED_QUESTIONSList of not usable for data variable names in survey mapping
raw_valueCreate a list of values marked as "raw"
recode_aliascreate a recoding alias
recode_intakeRecode Intake variables to more error-proof labels Value to...
recode_varRecode values with a given mapping
recode_weeklyApply common recoding for weekly data
recode_weekly_dateRecode weekly dates Recode weekly dates
recode_ynprecode Y/N/DNK where Y=0 to boolean (wow!) Used to recode...
regroup.syndromeRegroup mixed syndromes to non-specific for the 2012's...
relative_seasonsGet relative season numbers to a reference season number
scale_x_widScale from wid to Yearweek values
season_definitionGet historical season definition
share.cache.pathreturn the path of a file in cache files of a file in data
share.libLoad a share library
share.lib.pathGet file in lib path
share.optionget options for the ifn environment
share_pathpath of a file in share/ directory
strategy_create_codingCreate a encoding dictionnary for each variable used in a...
survey_aliasesConvert DB column name from and to question variable name...
survey_default_languageGet the default language used for survey Uses...
survey_definitionGet survey definition
survey_labelsReturn the "labels" for a given question variable name
survey_load_allLoad all definition data about a survey
survey_load_health_statusLoad health status for each weekly responses
survey_load_optionsload options of a question from the database, identified by...
survey_load_participantsLoad participants data
survey_load_participationsLoad last participation date for intake & weekly survey for...
survey_load_questionsload questions of a survey from the database
survey_load_resultsload a survey results set
survey_load_results_historicLoad historical data for a set of users
survey_load_translationload a translation for a survey for a given language
survey_options_forGet the options for a survey's varname This is not the...
survey_participant_previous_seasonList of participants registred in weekly at least once in...
survey_participant_seasonGet list of participant id (person_id = survey_user_id) List...
survey_question_idget the question_id (id in the question table in the...
survey_recodeRecode data from the DB storage code to the R labels (or to...
survey_recodingsGet all the recodings defined in a survey
survey_single_tableReturns TRUE if the survey's data are store using a single...
survey_templateSurvey Template definitions
survey_variable_availableCheck if variables are available for a given season
survey_variable_recodingGet the recoding mapping of a variable in a survey
survey_variables_likeGet list of variable names matching the given pattern (glob...
SyndromeProviderSyndrome provider base class
SyndromeProviderCountrySyndrome Provider
SyndromeProviderRS2019Syndrome Provider with 2019 revised ILI & Ari definitions
syndromes_influenzanet_2011Compute the 2011's Influenzanet syndromes set...
syndromes_influenzanet_2012Compute syndrome classification of weekly data according to...
syndromes.prettifyPrettify syndrome names from InfluenzaNet DB health status...
syndromes_rs_2018Compute syndromes definitions used in Guerrisi C, Euro Surv....
syndromes.setSyndromes set definitions
theme_no_axisRemove axis from plot
theme_withTheme with a list of recipes
titlelizeCreate a title from a set of character vectors
validate_platformPost loading function to validate platform info
variable_availableDefine availability of variables
verticalize_incidenceVerticalize incidence data after computation
week_of_dateweek_of_date(from,to) get yearweek from a date interval date...
week_stampCompute a "Week" stamp (like timestamp) : week number from...
with_ggplotInit ggplot2 base theme. ggplot2 library should be loaded...
x_axis_verticalSet axis to vertical
cturbelin/ifnBase documentation built on Dec. 11, 2019, 9:52 a.m.