From e678d230ef98a3d57500b8da42f073e41abec540 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Mon, 8 Jan 2024 22:16:02 +0000 Subject: [PATCH] Document --- man/create_clean_reported_cases.Rd | 8 +++++--- man/epinow.Rd | 2 +- man/estimate_infections.Rd | 2 +- 3 files changed, 7 insertions(+), 5 deletions(-) diff --git a/man/create_clean_reported_cases.Rd b/man/create_clean_reported_cases.Rd index 6ab35a4dc..c53830c0c 100644 --- a/man/create_clean_reported_cases.Rd +++ b/man/create_clean_reported_cases.Rd @@ -24,12 +24,14 @@ start of the time series be filtered out.} \item{zero_threshold}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} Numeric defaults to Inf. Indicates if detected zero cases are meaningful by using a threshold -number of cases based on the 7 day average. If the average is above this +number of cases based on the 7-day average. If the average is above this threshold then the zero is replaced using \code{fill}.} \item{fill}{Numeric, defaults to NA. Value to use to replace NA values or -zeros that are flagged by \code{zero_threshold}. If the default NA is used then -dates with NA values will be skipped in model fitting.} +zeroes that are flagged because the 7-day average is above the +\code{zero_threshold}. If the default NA is used then dates with NA values or with +7-day averages above the \code{zero_threshold} will be skipped in model fitting. +If this is set to 0 then the only effect is to replace NA values with 0.} } \value{ A cleaned data frame of reported cases diff --git a/man/epinow.Rd b/man/epinow.Rd index 42c42296e..a4a302f8a 100644 --- a/man/epinow.Rd +++ b/man/epinow.Rd @@ -72,7 +72,7 @@ start of the time series be filtered out.} \item{zero_threshold}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} Numeric defaults to Inf. Indicates if detected zero cases are meaningful by using a threshold -number of cases based on the 7 day average. If the average is above this +number of cases based on the 7-day average. If the average is above this threshold then the zero is replaced using \code{fill}.} \item{return_output}{Logical, defaults to FALSE. Should output be returned, diff --git a/man/estimate_infections.Rd b/man/estimate_infections.Rd index 1d7586ed2..851e3a295 100644 --- a/man/estimate_infections.Rd +++ b/man/estimate_infections.Rd @@ -68,7 +68,7 @@ start of the time series be filtered out.} \item{zero_threshold}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} Numeric defaults to Inf. Indicates if detected zero cases are meaningful by using a threshold -number of cases based on the 7 day average. If the average is above this +number of cases based on the 7-day average. If the average is above this threshold then the zero is replaced using \code{fill}.} \item{weigh_delay_priors}{Logical. If TRUE (default), all delay distribution