From 3dbe37dd72fd8881793bf3bd95ad5f5798838796 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Cl=C3=A9ment=20Turbelin?= Date: Thu, 2 Nov 2023 16:15:58 +0100 Subject: [PATCH] update docs --- man/IncidenceDailyRS2014.Rd | 30 ++++++++++---------- man/IncidenceRS2014.Rd | 30 ++++++++++---------- man/SurveyLabeller.Rd | 24 ++++++++-------- man/SyndromeProvider.Rd | 30 ++++++++++---------- man/SyndromeProviderCountry.Rd | 40 +++++++++++++-------------- man/SyndromeProviderCovid.Rd | 50 +++++++++++++++++----------------- man/SyndromeProviderIfn.Rd | 18 ++++++------ man/SyndromeProviderRS2019.Rd | 46 +++++++++++++++---------------- man/concepts.Rd | 3 +- vignettes/geography.Rmd | 2 +- 10 files changed, 137 insertions(+), 136 deletions(-) diff --git a/man/IncidenceDailyRS2014.Rd b/man/IncidenceDailyRS2014.Rd index 1c25061..d59d980 100644 --- a/man/IncidenceDailyRS2014.Rd +++ b/man/IncidenceDailyRS2014.Rd @@ -52,16 +52,16 @@ Parameters: \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{IncidenceDailyRS2014$new()}} -\item \href{#method-prepare}{\code{IncidenceDailyRS2014$prepare()}} -\item \href{#method-compute_date}{\code{IncidenceDailyRS2014$compute_date()}} -\item \href{#method-compute}{\code{IncidenceDailyRS2014$compute()}} -\item \href{#method-clone}{\code{IncidenceDailyRS2014$clone()}} +\item \href{#method-IncidenceDailyRS2014-new}{\code{IncidenceDailyRS2014$new()}} +\item \href{#method-IncidenceDailyRS2014-prepare}{\code{IncidenceDailyRS2014$prepare()}} +\item \href{#method-IncidenceDailyRS2014-compute_date}{\code{IncidenceDailyRS2014$compute_date()}} +\item \href{#method-IncidenceDailyRS2014-compute}{\code{IncidenceDailyRS2014$compute()}} +\item \href{#method-IncidenceDailyRS2014-clone}{\code{IncidenceDailyRS2014$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-IncidenceDailyRS2014-new}{}}} \subsection{Method \code{new()}}{ instanciate object \subsection{Usage}{ @@ -96,8 +96,8 @@ instanciate object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-prepare}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-IncidenceDailyRS2014-prepare}{}}} \subsection{Method \code{prepare()}}{ Prepare data before to compute Prepare participants data to be able to apply selection rules @@ -107,8 +107,8 @@ Prepare participants data to be able to apply selection rules } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-compute_date}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-IncidenceDailyRS2014-compute_date}{}}} \subsection{Method \code{compute_date()}}{ Internal function Estimate incidence with rs2014 method for a given date @@ -125,8 +125,8 @@ Estimate incidence with rs2014 method for a given date } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-compute}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-IncidenceDailyRS2014-compute}{}}} \subsection{Method \code{compute()}}{ Compute weekly incidence for all requested weeks Apply the full algorithm for rs2014 incidence computation @@ -148,8 +148,8 @@ prepare data and then compute for each week by calling estimate_incidence_rs2014 } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-IncidenceDailyRS2014-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/IncidenceRS2014.Rd b/man/IncidenceRS2014.Rd index ec6a6e7..6229e8a 100644 --- a/man/IncidenceRS2014.Rd +++ b/man/IncidenceRS2014.Rd @@ -64,16 +64,16 @@ Apply the full algorithm for rs2014 incidence computation \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{IncidenceRS2014$new()}} -\item \href{#method-prepare}{\code{IncidenceRS2014$prepare()}} -\item \href{#method-compute_week}{\code{IncidenceRS2014$compute_week()}} -\item \href{#method-compute}{\code{IncidenceRS2014$compute()}} -\item \href{#method-clone}{\code{IncidenceRS2014$clone()}} +\item \href{#method-IncidenceRS2014-new}{\code{IncidenceRS2014$new()}} +\item \href{#method-IncidenceRS2014-prepare}{\code{IncidenceRS2014$prepare()}} +\item \href{#method-IncidenceRS2014-compute_week}{\code{IncidenceRS2014$compute_week()}} +\item \href{#method-IncidenceRS2014-compute}{\code{IncidenceRS2014$compute()}} +\item \href{#method-IncidenceRS2014-clone}{\code{IncidenceRS2014$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-IncidenceRS2014-new}{}}} \subsection{Method \code{new()}}{ instanciate object \subsection{Usage}{ @@ -109,8 +109,8 @@ instanciate object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-prepare}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-IncidenceRS2014-prepare}{}}} \subsection{Method \code{prepare()}}{ Prepare data for incidence computation with RS2014 method @@ -124,8 +124,8 @@ Estimate incidence with rs2014 method for a given week } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-compute_week}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-IncidenceRS2014-compute_week}{}}} \subsection{Method \code{compute_week()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{IncidenceRS2014$compute_week(yw)}\if{html}{\out{
}} @@ -141,8 +141,8 @@ Compute incidence} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-compute}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-IncidenceRS2014-compute}{}}} \subsection{Method \code{compute()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{IncidenceRS2014$compute( @@ -168,8 +168,8 @@ Compute incidence} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-IncidenceRS2014-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/SurveyLabeller.Rd b/man/SurveyLabeller.Rd index 72cc725..aedb858 100644 --- a/man/SurveyLabeller.Rd +++ b/man/SurveyLabeller.Rd @@ -34,15 +34,15 @@ Other survey: \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{SurveyLabeller$new()}} -\item \href{#method-list}{\code{SurveyLabeller$list()}} -\item \href{#method-unprefix}{\code{SurveyLabeller$unprefix()}} -\item \href{#method-clone}{\code{SurveyLabeller$clone()}} +\item \href{#method-SurveyLabeller-new}{\code{SurveyLabeller$new()}} +\item \href{#method-SurveyLabeller-list}{\code{SurveyLabeller$list()}} +\item \href{#method-SurveyLabeller-unprefix}{\code{SurveyLabeller$unprefix()}} +\item \href{#method-SurveyLabeller-clone}{\code{SurveyLabeller$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SurveyLabeller-new}{}}} \subsection{Method \code{new()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{SurveyLabeller$new(survey, name)}\if{html}{\out{
}} @@ -60,8 +60,8 @@ Get list of labels} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-list}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SurveyLabeller-list}{}}} \subsection{Method \code{list()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{SurveyLabeller$list(.data = NULL)}\if{html}{\out{
}} @@ -77,8 +77,8 @@ Remove common prefix labels (only works with glob pattern defined labels like 'v } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-unprefix}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SurveyLabeller-unprefix}{}}} \subsection{Method \code{unprefix()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{SurveyLabeller$unprefix()}\if{html}{\out{
}} @@ -89,8 +89,8 @@ function to remove prefix, can be use as a labeller function (in ggplot2 for exa } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SurveyLabeller-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/SyndromeProvider.Rd b/man/SyndromeProvider.Rd index ea54c5f..d74c257 100644 --- a/man/SyndromeProvider.Rd +++ b/man/SyndromeProvider.Rd @@ -22,16 +22,16 @@ influenzanet base syndrome names : ili, cold, allergy, gastro ) \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-compute}{\code{SyndromeProvider$compute()}} -\item \href{#method-compute_age}{\code{SyndromeProvider$compute_age()}} -\item \href{#method-is_sudden}{\code{SyndromeProvider$is_sudden()}} -\item \href{#method-syndromes}{\code{SyndromeProvider$syndromes()}} -\item \href{#method-clone}{\code{SyndromeProvider$clone()}} +\item \href{#method-SyndromeProvider-compute}{\code{SyndromeProvider$compute()}} +\item \href{#method-SyndromeProvider-compute_age}{\code{SyndromeProvider$compute_age()}} +\item \href{#method-SyndromeProvider-is_sudden}{\code{SyndromeProvider$is_sudden()}} +\item \href{#method-SyndromeProvider-syndromes}{\code{SyndromeProvider$syndromes()}} +\item \href{#method-SyndromeProvider-clone}{\code{SyndromeProvider$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-compute}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProvider-compute}{}}} \subsection{Method \code{compute()}}{ Compute syndrome \subsection{Usage}{ @@ -52,8 +52,8 @@ data.frame() with id column from weekly and extra column for each syndrome } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-compute_age}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProvider-compute_age}{}}} \subsection{Method \code{compute_age()}}{ Compute age for each weekly using intake \subsection{Usage}{ @@ -72,8 +72,8 @@ Common function, compute sudden symptomes using both variables} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-is_sudden}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProvider-is_sudden}{}}} \subsection{Method \code{is_sudden()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{SyndromeProvider$is_sudden(r)}\if{html}{\out{
}} @@ -88,8 +88,8 @@ Common function, compute sudden symptomes using both variables} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-syndromes}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProvider-syndromes}{}}} \subsection{Method \code{syndromes()}}{ Get available syndromes names \subsection{Usage}{ @@ -101,8 +101,8 @@ character() } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProvider-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/SyndromeProviderCountry.Rd b/man/SyndromeProviderCountry.Rd index a68adc2..136bbb5 100644 --- a/man/SyndromeProviderCountry.Rd +++ b/man/SyndromeProviderCountry.Rd @@ -31,23 +31,23 @@ Syndrome Provider \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{SyndromeProviderCountry$new()}} -\item \href{#method-compute}{\code{SyndromeProviderCountry$compute()}} -\item \href{#method-clone}{\code{SyndromeProviderCountry$clone()}} -} -} -\if{html}{ -\out{
Inherited methods} -\itemize{ -\item \out{}\href{../../ifnBase/html/SyndromeProvider.html#method-compute_age}{\code{ifnBase::SyndromeProvider$compute_age()}}\out{} -\item \out{}\href{../../ifnBase/html/SyndromeProvider.html#method-is_sudden}{\code{ifnBase::SyndromeProvider$is_sudden()}}\out{} -\item \out{}\href{../../ifnBase/html/SyndromeProvider.html#method-syndromes}{\code{ifnBase::SyndromeProvider$syndromes()}}\out{} -} -\out{
} -} +\item \href{#method-SyndromeProviderCountry-new}{\code{SyndromeProviderCountry$new()}} +\item \href{#method-SyndromeProviderCountry-compute}{\code{SyndromeProviderCountry$compute()}} +\item \href{#method-SyndromeProviderCountry-clone}{\code{SyndromeProviderCountry$clone()}} +} +} +\if{html}{\out{ +
Inherited methods + +
+}} \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProviderCountry-new}{}}} \subsection{Method \code{new()}}{ Instanciate \subsection{Usage}{ @@ -80,8 +80,8 @@ Instanciate } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-compute}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProviderCountry-compute}{}}} \subsection{Method \code{compute()}}{ Compute definitions for all syndromes \subsection{Usage}{ @@ -99,8 +99,8 @@ Compute definitions for all syndromes } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProviderCountry-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/SyndromeProviderCovid.Rd b/man/SyndromeProviderCovid.Rd index 0096d51..c539943 100644 --- a/man/SyndromeProviderCovid.Rd +++ b/man/SyndromeProviderCovid.Rd @@ -40,24 +40,24 @@ To run need weekly with get_columns_for_incidence() column list \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{SyndromeProviderCovid$new()}} -\item \href{#method-syndromes}{\code{SyndromeProviderCovid$syndromes()}} -\item \href{#method-check_definitions}{\code{SyndromeProviderCovid$check_definitions()}} -\item \href{#method-compute}{\code{SyndromeProviderCovid$compute()}} -\item \href{#method-clone}{\code{SyndromeProviderCovid$clone()}} -} -} -\if{html}{ -\out{
Inherited methods} -\itemize{ -\item \out{}\href{../../ifnBase/html/SyndromeProvider.html#method-compute_age}{\code{ifnBase::SyndromeProvider$compute_age()}}\out{} -\item \out{}\href{../../ifnBase/html/SyndromeProvider.html#method-is_sudden}{\code{ifnBase::SyndromeProvider$is_sudden()}}\out{} -} -\out{
} -} +\item \href{#method-SyndromeProviderCovid-new}{\code{SyndromeProviderCovid$new()}} +\item \href{#method-SyndromeProviderCovid-syndromes}{\code{SyndromeProviderCovid$syndromes()}} +\item \href{#method-SyndromeProviderCovid-check_definitions}{\code{SyndromeProviderCovid$check_definitions()}} +\item \href{#method-SyndromeProviderCovid-compute}{\code{SyndromeProviderCovid$compute()}} +\item \href{#method-SyndromeProviderCovid-clone}{\code{SyndromeProviderCovid$clone()}} +} +} +\if{html}{\out{ +
Inherited methods + +
+}} \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProviderCovid-new}{}}} \subsection{Method \code{new()}}{ instanciate object \subsection{Usage}{ @@ -75,8 +75,8 @@ instanciate object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-syndromes}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProviderCovid-syndromes}{}}} \subsection{Method \code{syndromes()}}{ Get available syndromes names \subsection{Usage}{ @@ -88,8 +88,8 @@ character() } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-check_definitions}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProviderCovid-check_definitions}{}}} \subsection{Method \code{check_definitions()}}{ Update definitions list to compute \subsection{Usage}{ @@ -105,8 +105,8 @@ Update definitions list to compute } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-compute}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProviderCovid-compute}{}}} \subsection{Method \code{compute()}}{ Compute definitions for all syndromes \subsection{Usage}{ @@ -131,8 +131,8 @@ data.frame with each computed syndrome in column, and "id" column from weekly } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProviderCovid-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/SyndromeProviderIfn.Rd b/man/SyndromeProviderIfn.Rd index f3a9c13..5912ea4 100644 --- a/man/SyndromeProviderIfn.Rd +++ b/man/SyndromeProviderIfn.Rd @@ -20,14 +20,14 @@ Syndrome provider base class for historical Influenzanet syndromic classifier \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{SyndromeProviderIfn$new()}} -\item \href{#method-compute}{\code{SyndromeProviderIfn$compute()}} -\item \href{#method-clone}{\code{SyndromeProviderIfn$clone()}} +\item \href{#method-SyndromeProvider-new}{\code{SyndromeProviderIfn$new()}} +\item \href{#method-SyndromeProvider-compute}{\code{SyndromeProviderIfn$compute()}} +\item \href{#method-SyndromeProvider-clone}{\code{SyndromeProviderIfn$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProvider-new}{}}} \subsection{Method \code{new()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{SyndromeProviderIfn$new(version = 2012, regroup = TRUE)}\if{html}{\out{
}} @@ -44,8 +44,8 @@ Syndrome provider base class for historical Influenzanet syndromic classifier } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-compute}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProvider-compute}{}}} \subsection{Method \code{compute()}}{ Compute syndrome \subsection{Usage}{ @@ -66,8 +66,8 @@ data.frame() with id column from weekly and extra column for each syndrome } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProvider-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/SyndromeProviderRS2019.Rd b/man/SyndromeProviderRS2019.Rd index fde33c2..0b42cc2 100644 --- a/man/SyndromeProviderRS2019.Rd +++ b/man/SyndromeProviderRS2019.Rd @@ -40,24 +40,24 @@ To run need weekly with get_columns_for_incidence() column list \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-new}{\code{SyndromeProviderRS2019$new()}} -\item \href{#method-update_definitions}{\code{SyndromeProviderRS2019$update_definitions()}} -\item \href{#method-compute}{\code{SyndromeProviderRS2019$compute()}} -\item \href{#method-clone}{\code{SyndromeProviderRS2019$clone()}} -} -} -\if{html}{ -\out{
Inherited methods} -\itemize{ -\item \out{}\href{../../ifnBase/html/SyndromeProvider.html#method-compute_age}{\code{ifnBase::SyndromeProvider$compute_age()}}\out{} -\item \out{}\href{../../ifnBase/html/SyndromeProvider.html#method-is_sudden}{\code{ifnBase::SyndromeProvider$is_sudden()}}\out{} -\item \out{}\href{../../ifnBase/html/SyndromeProvider.html#method-syndromes}{\code{ifnBase::SyndromeProvider$syndromes()}}\out{} -} -\out{
} -} +\item \href{#method-SyndromeProviderRS2019-new}{\code{SyndromeProviderRS2019$new()}} +\item \href{#method-SyndromeProviderRS2019-update_definitions}{\code{SyndromeProviderRS2019$update_definitions()}} +\item \href{#method-SyndromeProviderRS2019-compute}{\code{SyndromeProviderRS2019$compute()}} +\item \href{#method-SyndromeProviderRS2019-clone}{\code{SyndromeProviderRS2019$clone()}} +} +} +\if{html}{\out{ +
Inherited methods + +
+}} \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProviderRS2019-new}{}}} \subsection{Method \code{new()}}{ instanciate object \subsection{Usage}{ @@ -81,8 +81,8 @@ instanciate object } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-update_definitions}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProviderRS2019-update_definitions}{}}} \subsection{Method \code{update_definitions()}}{ Update definitions list to compute \subsection{Usage}{ @@ -98,8 +98,8 @@ Update definitions list to compute } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-compute}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProviderRS2019-compute}{}}} \subsection{Method \code{compute()}}{ Compute definitions for all syndromes \subsection{Usage}{ @@ -129,8 +129,8 @@ data.frame with each computed syndrome in column, and "id" column from weekly } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-SyndromeProviderRS2019-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/concepts.Rd b/man/concepts.Rd index 6c76ca2..1a22f4c 100644 --- a/man/concepts.Rd +++ b/man/concepts.Rd @@ -33,7 +33,8 @@ In this package perspective, a survey is a name associated with a set of paramet A survey has a unique name, known by the package, you use to request and manipulate the data. A survey can be associated with a table name in the database (for the package to know fromwhere to fetch the data), and variable mapping (to recode database column name to -more meaningful names), and a value to label mapping ('recodes' entry recoding a value in the database to a label). It can also have a set of 'labels' (see below). +more meaningful names), and a recoding mapping ('recodes' entry, recoding a value in the database to an explicit label). It can also have a set of 'labels' (see below) +to handle variable user defined variables lists. The package also provide two survey templates for weekly, intake, and vaccination survey (see \code{\link{survey_template}()}) respectively named 'eu:weekly' and 'eu:intake', 'eu:vaccination'. diff --git a/vignettes/geography.Rmd b/vignettes/geography.Rmd index 74a36ee..464fef9 100644 --- a/vignettes/geography.Rmd +++ b/vignettes/geography.Rmd @@ -115,7 +115,7 @@ Get the structure describing the organization of geographic levels (created by * Get the areas in the given level (from the database) ```{r eval=FALSE} load_geo_zone("nuts2") # Load all areas known in nuts2 level -```` +``` *load_population(level, year)* Get the population at the given geographic level and the year