Merge pull request #625 from cmu-delphi/lcb/doc-fixups

Doc cleanup

Author: brookslogan

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: epiprocess
 Title: Tools for basic signal processing in epidemiology
-Version: 0.11.6
+Version: 0.11.7
 Authors@R: c(
     person("Jacob", "Bien", role = "ctb"),
     person("Logan", "Brooks", , "[email protected]", role = c("aut", "cre")),

NEWS.md

@@ -10,8 +10,20 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.x.y will indicat
 - `epix_as_of_current()` introduced as an alias for `epix_as_of(.$versions_end)`.
 - Added `dplyr::filter` implementation for `epi_archive`s.
 
+## Improvements
+
+- Various documentation has been updated, simplified, and improved with better
+  examples.
+
 # epiprocess 0.11
 
+## Highlights
+
+`{epiprocess}` should once again not require Rtools or a compiler to be able to
+install! We've also updated some function interfaces to be more consistent
+throughout the package & with tidyverse, and improved the generality of and
+fixed bugs in various functions and documentation.
+
 ## Breaking changes
 
 - `growth_rate()` argument order and names have changed. You will need to

R/archive.R

@@ -322,6 +322,9 @@ new_epi_archive <- function(
 
 #' Perform second (costly) round of validation that `x` is a proper `epi_archive`
 #'
+#' Does not validate `geo_type` or `time_type` against `geo_value` and
+#' `time_value` columns. These are assumed to have been set to compatibly.
+#'
 #' @return * Of `validate_epi_archive`: an `epi_archive`,
 #'   [invisibly][base::invisible] (or raises an error if `x` was invalid)
 #'

R/autoplot.R

@@ -1,7 +1,7 @@
 #' Automatically plot an epi_df or epi_archive
 #'
 #' @param object,x An `epi_df` or `epi_archive`
-#' @param ... <[`tidy-select`][dplyr_tidy_select]> One or more unquoted
+#' @param ... <[`tidy-select`][dplyr::dplyr_tidy_select]> One or more unquoted
 #'   expressions separated by commas. Variable names can be used as if they
 #'   were positions in the data frame, so expressions like `x:y` can
 #'   be used to select a range of variables.
@@ -22,7 +22,7 @@
 #' @param .max_facets `r lifecycle::badge("deprecated")`
 #' @param .facet_filter Select which facets will be displayed. Especially
 #'   useful for when there are many `geo_value`'s or keys. This is a
-#'   <[`rlang`][args_data_masking]> expression along the lines of [dplyr::filter()].
+#'   <[`rlang`][rlang::args_data_masking]> expression along the lines of [dplyr::filter()].
 #'   However, it must be a single expression combined with the `&` operator. This
 #'   contrasts to the typical use case which allows multiple comma-separated expressions
 #'   which are implicitly combined with `&`. When multiple variables are selected

R/epi_df.R

@@ -6,18 +6,20 @@
 #' which can be seen as measured variables at each key. In brief, an `epi_df`
 #' represents a snapshot of an epidemiological data set at a point in time.
 #'
-#' @details An `epi_df` is a tibble with (at least) the following columns:
+#' @details An `epi_df` is a kind of tibble with (at least) the following
+#'   columns:
 #'
 #' - `geo_value`: A character vector representing the geographical unit of
 #'    observation. This could be a country code, a state name, a county code,
 #'    etc.
 #' - `time_value`: A date or integer vector representing the time of observation.
 #'
 #' Other columns can be considered as measured variables, which we also refer to
-#'   as signal variables. An `epi_df` object also has metadata with (at least)
-#'   the following fields:
+#'   as indicators or signals. An `epi_df` object also has metadata with (at
+#'   least) the following fields:
 #'
 #' * `geo_type`: the type for the geo values.
+#' * `time_type`: the type for the time values.
 #' * `as_of`: the time value at which the given data were available.
 #'
 #' Most users should use `as_epi_df`. The input tibble `x` to the constructor

R/grouped_epi_archive.R

@@ -203,13 +203,12 @@ ungroup.grouped_epi_archive <- function(x, ...) {
 }
 
 
-#' @rdname epix_slide
-#'
 #' @importFrom data.table key address rbindlist setDF copy
 #' @importFrom tibble as_tibble new_tibble validate_tibble
 #' @importFrom dplyr group_by groups
 #' @importFrom rlang !! !!! enquo quo_is_missing enquos is_quosure sym syms
 #'  env missing_arg
+#'
 #' @export
 epix_slide.grouped_epi_archive <- function(
     .x,

R/inline-roxygen.R

@@ -7,7 +7,7 @@
 #'
 #' @keywords internal
 tidyselect_arg_roxygen <- '
-  <[`tidy-select`][dplyr_tidy_select]> An unquoted column
+  <[`tidy-select`][dplyr::dplyr_tidy_select]> An unquoted column
   name (e.g., `cases`), multiple column names (e.g., `c(cases, deaths)`),
   [other tidy-select expression][tidyselect::language], or a vector of
   characters (e.g. `c("cases", "deaths")`). Variable names can be used as if