diff --git a/DESCRIPTION b/DESCRIPTION index df2e6c1a..908ea3be 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -53,7 +53,8 @@ VignetteBuilder: knitr Remotes: cmu-delphi/epidatr, - reconverse/outbreaks + reconverse/outbreaks, + glmgen/genlasso Config/testthat/edition: 3 Encoding: UTF-8 LazyData: true diff --git a/man/as_epi_archive.Rd b/man/as_epi_archive.Rd index a98798cc..d13ba4d6 100644 --- a/man/as_epi_archive.Rd +++ b/man/as_epi_archive.Rd @@ -91,15 +91,11 @@ examples. } \details{ This simply a wrapper around the \code{new()} method of the \code{epi_archive} -class, so for example: - -\if{html}{\out{
}}\preformatted{x <- as_epi_archive(df, geo_type = "state", time_type = "day") -}\if{html}{\out{
}} - -would be equivalent to: +class, so for example:\preformatted{x <- as_epi_archive(df, geo_type = "state", time_type = "day") +} -\if{html}{\out{
}}\preformatted{x <- epi_archive$new(df, geo_type = "state", time_type = "day") -}\if{html}{\out{
}} +would be equivalent to:\preformatted{x <- epi_archive$new(df, geo_type = "state", time_type = "day") +} } \examples{ # Simple ex. with necessary keys diff --git a/man/as_epi_df.Rd b/man/as_epi_df.Rd index 851aed7e..6d7592e4 100644 --- a/man/as_epi_df.Rd +++ b/man/as_epi_df.Rd @@ -52,9 +52,9 @@ examples. } \section{Methods (by class)}{ \itemize{ -\item \code{as_epi_df(epi_df)}: Simply returns the \code{epi_df} object unchanged. +\item \code{epi_df}: Simply returns the \code{epi_df} object unchanged. -\item \code{as_epi_df(tbl_df)}: The input tibble \code{x} must contain the columns +\item \code{tbl_df}: The input tibble \code{x} must contain the columns \code{geo_value} and \code{time_value}. All other columns will be preserved as is, and treated as measured variables. If \code{as_of} is missing, then the function will try to guess it from an \code{as_of}, \code{issue}, or \code{version} column of \code{x} @@ -62,14 +62,14 @@ will try to guess it from an \code{as_of}, \code{issue}, or \code{version} colum (stored in its attributes); if this fails, then the current day-time will be used. -\item \code{as_epi_df(data.frame)}: Works analogously to \code{as_epi_df.tbl_df()}. +\item \code{data.frame}: Works analogously to \code{as_epi_df.tbl_df()}. -\item \code{as_epi_df(tbl_ts)}: Works analogously to \code{as_epi_df.tbl_df()}, except that +\item \code{tbl_ts}: Works analogously to \code{as_epi_df.tbl_df()}, except that the \code{tbl_ts} class is dropped, and any key variables (other than "geo_value") are added to the metadata of the returned object, under the \code{other_keys} field. - }} + \examples{ # Convert a `tsibble` that has county code as an extra key # Notice that county code should be a character string to preserve any leading zeroes diff --git a/man/epi_archive.Rd b/man/epi_archive.Rd index 026f27e1..0b198eab 100644 --- a/man/epi_archive.Rd +++ b/man/epi_archive.Rd @@ -114,18 +114,18 @@ toy_epi_archive \section{Methods}{ \subsection{Public methods}{ \itemize{ -\item \href{#method-epi_archive-new}{\code{epi_archive$new()}} -\item \href{#method-epi_archive-print}{\code{epi_archive$print()}} -\item \href{#method-epi_archive-as_of}{\code{epi_archive$as_of()}} -\item \href{#method-epi_archive-fill_through_version}{\code{epi_archive$fill_through_version()}} -\item \href{#method-epi_archive-merge}{\code{epi_archive$merge()}} -\item \href{#method-epi_archive-slide}{\code{epi_archive$slide()}} -\item \href{#method-epi_archive-clone}{\code{epi_archive$clone()}} +\item \href{#method-new}{\code{epi_archive$new()}} +\item \href{#method-print}{\code{epi_archive$print()}} +\item \href{#method-as_of}{\code{epi_archive$as_of()}} +\item \href{#method-fill_through_version}{\code{epi_archive$fill_through_version()}} +\item \href{#method-merge}{\code{epi_archive$merge()}} +\item \href{#method-slide}{\code{epi_archive$slide()}} +\item \href{#method-clone}{\code{epi_archive$clone()}} } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-epi_archive-new}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-new}{}}} \subsection{Method \code{new()}}{ Creates a new \code{epi_archive} object. \subsection{Usage}{ @@ -195,8 +195,8 @@ An \code{epi_archive} object. } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-epi_archive-print}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-print}{}}} \subsection{Method \code{print()}}{ \subsection{Usage}{ \if{html}{\out{
}}\preformatted{epi_archive$print()}\if{html}{\out{
}} @@ -204,8 +204,8 @@ An \code{epi_archive} object. } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-epi_archive-as_of}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-as_of}{}}} \subsection{Method \code{as_of()}}{ Generates a snapshot in \code{epi_df} format as of a given version. See the documentation for the wrapper function \code{\link[=epix_as_of]{epix_as_of()}} for details. @@ -215,8 +215,8 @@ See the documentation for the wrapper function \code{\link[=epix_as_of]{epix_as_ } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-epi_archive-fill_through_version}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-fill_through_version}{}}} \subsection{Method \code{fill_through_version()}}{ Fill in unobserved history using requested scheme by mutating \code{self} and potentially reseating its fields. See @@ -237,8 +237,8 @@ version, which doesn't mutate the input archive but might alias its fields. } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-epi_archive-merge}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-merge}{}}} \subsection{Method \code{merge()}}{ Merges another \code{epi_archive} with the current one, mutating the current one by reseating its \code{DT} and several other fields, but avoiding @@ -267,8 +267,8 @@ does not alias either archive's \code{DT}. } } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-epi_archive-slide}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-slide}{}}} \subsection{Method \code{slide()}}{ Slides a given function over variables in an \code{epi_archive} object. See the documentation for the wrapper function \code{\link[=epix_slide]{epix_slide()}} for @@ -290,8 +290,8 @@ details. } \if{html}{\out{
}} -\if{html}{\out{}} -\if{latex}{\out{\hypertarget{method-epi_archive-clone}{}}} +\if{html}{\out{}} +\if{latex}{\out{\hypertarget{method-clone}{}}} \subsection{Method \code{clone()}}{ The objects of this class are cloneable with this method. \subsection{Usage}{ diff --git a/man/epi_slide.Rd b/man/epi_slide.Rd index 1b620b69..c64bbce1 100644 --- a/man/epi_slide.Rd +++ b/man/epi_slide.Rd @@ -107,16 +107,12 @@ incomplete windows) is therefore left up to the user, either through the specified function or formula \code{f}, or through post-processing. If \code{f} is missing, then an expression for tidy evaluation can be specified, -for example, as in: - -\if{html}{\out{
}}\preformatted{epi_slide(x, cases_7dav = mean(cases), n = 7) -}\if{html}{\out{
}} - -which would be equivalent to: +for example, as in:\preformatted{epi_slide(x, cases_7dav = mean(cases), n = 7) +} -\if{html}{\out{
}}\preformatted{epi_slide(x, function(x, ...) mean(x$cases), n = 7, +which would be equivalent to:\preformatted{epi_slide(x, function(x, ...) mean(x$cases), n = 7, new_col_name = "cases_7dav") -}\if{html}{\out{
}} +} Thus, to be clear, when the computation is specified via an expression for tidy evaluation (first example, above), then the name for the new column is diff --git a/man/epix_as_of.Rd b/man/epix_as_of.Rd index 4053cd28..6dc72a44 100644 --- a/man/epix_as_of.Rd +++ b/man/epix_as_of.Rd @@ -29,15 +29,11 @@ examples. } \details{ This is simply a wrapper around the \code{as_of()} method of the -\code{epi_archive} class, so if \code{x} is an \code{epi_archive} object, then: - -\if{html}{\out{
}}\preformatted{epix_as_of(x, max_version = v) -}\if{html}{\out{
}} - -is equivalent to: +\code{epi_archive} class, so if \code{x} is an \code{epi_archive} object, then:\preformatted{epix_as_of(x, max_version = v) +} -\if{html}{\out{
}}\preformatted{x$as_of(max_version = v) -}\if{html}{\out{
}} +is equivalent to:\preformatted{x$as_of(max_version = v) +} } \examples{ # warning message of data latency shown diff --git a/man/epix_slide.Rd b/man/epix_slide.Rd index 79e9c1c3..2acae1a1 100644 --- a/man/epix_slide.Rd +++ b/man/epix_slide.Rd @@ -115,15 +115,11 @@ should never be used in place of \code{epi_slide()}, and only used when version-aware sliding is necessary (as it its purpose). Finally, this is simply a wrapper around the \code{slide()} method of the -\code{epi_archive} class, so if \code{x} is an \code{epi_archive} object, then: - -\if{html}{\out{
}}\preformatted{epix_slide(x, new_var = comp(old_var), n = 120) -}\if{html}{\out{
}} - -is equivalent to: +\code{epi_archive} class, so if \code{x} is an \code{epi_archive} object, then:\preformatted{epix_slide(x, new_var = comp(old_var), n = 120) +} -\if{html}{\out{
}}\preformatted{x$slide(x, new_var = comp(old_var), n = 120) -}\if{html}{\out{
}} +is equivalent to:\preformatted{x$slide(x, new_var = comp(old_var), n = 120) +} } \examples{ # these dates are reference time points for the 3 day average sliding window