style closes #32

poissonconsulting · Jan 23, 2025 · 22c1e4b · 22c1e4b
1 parent 6d225d3
commit 22c1e4b
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Showing 13 changed files with 1,103 additions and 1,097 deletions.
diff --git a/R/classify-time-series-data.R b/R/classify-time-series-data.R
@@ -15,20 +15,20 @@
 #'   The data is processed by:
 #'
 #'   1. Classifying the temperature values based on their values
-#'   (questionable_min, questionable_max, erroneous_min, erroneous_max). 
-#'   
+#'   (questionable_min, questionable_max, erroneous_min, erroneous_max).
+#'
 #'   2. The
 #'   rate of change between adjacent values is calculate and values are
 #'   classified based on the rate parameters (questionable_rate,
-#'   erroneous_rate). 
-#'   
+#'   erroneous_rate).
+#'
 #'   3. Adjacent values to questionable/erroneous are coded as
-#'   questionable/erroneous. 
-#'   
+#'   questionable/erroneous.
+#'
 #'   4. A buffer is applied that any value within the
 #'   buffer is classified as questionable/erroneous based on the buffer
-#'   parameters (questionable_buffer, erroneous_buffer). 
-#'   
+#'   parameters (questionable_buffer, erroneous_buffer).
+#'
 #'   5. Reasonable values
 #'   identified between two questionable/erroneous values are coded as
 #'   questionable/erroneous based on the gap hour difference allowed
@@ -72,28 +72,29 @@ classify_time_series_data <- function(data,
     erroneous_rate = erroneous_rate,
     questionable_buffer = questionable_buffer,
     erroneous_buffer = erroneous_buffer,
-    gap_range = gap_range)
-
+    gap_range = gap_range
+  )
+
   data <- data |>
     duckplyr::rename(.date_time = date_time, .value = value) |>
     duckplyr::arrange(.data$.date_time) |>
     duckplyr::mutate(status_id = rep(NA_integer_, nrow(data))) |>
     set_status_id()
-  
+
   missing_rows <- data |>
     duckplyr::filter(is.na(.data$.value))
-  
+
   lookup <- c(".date_time", ".value") |>
     rlang::set_names(c(date_time, value))
-  
-  if(identical(nrow(missing_rows), nrow(data))) {
+
+  if (identical(nrow(missing_rows), nrow(data))) {
     data <- data |>
       duckplyr::rename(duckplyr::all_of(lookup))
-    return(data)    
+    return(data)
   }
-  
+
   tz <- attr(data$.date_time, "tzone")
-  
+
   data <- data |>
     duckplyr::filter(!is.na(.data$.value)) |>
     duckplyr::mutate(
@@ -110,37 +111,43 @@ classify_time_series_data <- function(data,
         TRUE ~ 1L
       ),
       status_id = pmax(
-        .data$status_id, 
-        duckplyr::lag(.data$status_id), 
+        .data$status_id,
+        duckplyr::lag(.data$status_id),
         duckplyr::lead(.data$status_id),
         na.rm = TRUE
-      )    
+      )
     ) |>
     duckplyr::select(
       !".rate"
     )
-  
+
   questionable_range <- data |>
     duckplyr::filter(.data$status_id == 2L) |>
-    duckplyr::mutate(.start_date_time = .data$.date_time - questionable_buffer * 3600,
-                     .end_date_time = .data$.date_time + questionable_buffer * 3600,
-                     .keep = "none")
-
+    duckplyr::mutate(
+      .start_date_time = .data$.date_time - questionable_buffer * 3600,
+      .end_date_time = .data$.date_time + questionable_buffer * 3600,
+      .keep = "none"
+    )
+
   erroneous_range <- data |>
     duckplyr::filter(.data$status_id == 3L) |>
-    duckplyr::mutate(.start_date_time = .data$.date_time - erroneous_buffer * 3600,
-                     .end_date_time = .data$.date_time + erroneous_buffer * 3600,
-                     .keep = "none")
-
+    duckplyr::mutate(
+      .start_date_time = .data$.date_time - erroneous_buffer * 3600,
+      .end_date_time = .data$.date_time + erroneous_buffer * 3600,
+      .keep = "none"
+    )
+
   gap <- data |>
     duckplyr::filter(.data$status_id != 1L) |>
-    duckplyr::mutate(.status_id = pmax(.data$status_id, duckplyr::lead(.data$status_id), na.rm = TRUE),
-                     .status_id = 2L, # TODO 2L, pmin or pmax?? - pmax
-                     .start_date_time = .data$.date_time,
-                     .end_date_time = duckplyr::lead(.data$.date_time),
-                     .keep = "none") |>
+    duckplyr::mutate(
+      .status_id = pmax(.data$status_id, duckplyr::lead(.data$status_id), na.rm = TRUE),
+      .status_id = 2L, # TODO 2L, pmin or pmax?? - pmax
+      .start_date_time = .data$.date_time,
+      .end_date_time = duckplyr::lead(.data$.date_time),
+      .keep = "none"
+    ) |>
     duckplyr::filter(.data$.end_date_time - .data$.start_date_time <= gap_range * 3600)
-  
+
   data <- data |>
     dplyr::left_join(questionable_range, by = dplyr::join_by(closest(x$.date_time >= y$.start_date_time))) |>
     duckplyr::mutate(status_id = duckplyr::if_else(.data$status_id == 1L & .data$.date_time <= .data$.end_date_time, 2L, .data$status_id, .data$status_id)) |>
@@ -172,47 +179,47 @@ check_time_series_args <- function(data,
                                    questionable_buffer = 1,
                                    erroneous_buffer = 1,
                                    gap_range = 5) {
-
   chk::chk_data(data)
   chk::chk_unused(...)
   chk::chk_string(date_time)
   chk::chk_string(value)
-  
+
   values <- list(
-    as.POSIXct("2021-05-07 08:00:00"), 
-    c(1, NA_real_)) |>
+    as.POSIXct("2021-05-07 08:00:00"),
+    c(1, NA_real_)
+  ) |>
     rlang::set_names(c(date_time, value))
-  
+
   chk::check_data(data, values = values)
   chk::chk_unique(data[[date_time]], x_name = paste0("`data$", date_time, "`"))
-  
+
   chk::chk_not_subset(colnames(data), reserved_colnames())
-  
+
   chk::chk_number(questionable_min)
   chk::chk_number(questionable_max)
   chk::chk_gt(questionable_max, questionable_min)
-  
+
   chk::chk_number(erroneous_min)
   chk::chk_number(erroneous_max)
   chk::chk_gt(erroneous_max, erroneous_min)
-  
+
   chk::chk_gte(erroneous_max, questionable_max)
   chk::chk_lte(erroneous_min, questionable_min)
-  
+
   chk::chk_number(questionable_rate)
   chk::chk_gt(questionable_rate)
-  
+
   chk::chk_number(erroneous_rate)
   chk::chk_gt(erroneous_rate)
-  
+
   chk::chk_gte(erroneous_rate, questionable_rate)
-  
+
   chk::chk_number(questionable_buffer)
   chk::chk_gte(questionable_buffer)
-  
+
   chk::chk_number(erroneous_buffer)
   chk::chk_gte(erroneous_buffer)
-  
+
   chk::chk_number(gap_range)
   chk::chk_gte(gap_range)
 }
@@ -224,7 +231,8 @@ set_status_id <- function(data) {
         .data$status_id == 3L ~ "erroneous",
         .data$status_id == 2L ~ "questionable",
         .data$status_id == 1L ~ "reasonable",
-        TRUE ~ NA_character_),
+        TRUE ~ NA_character_
+      ),
       status_id = ordered(
         .data$status_id,
         levels = c("reasonable", "questionable", "erroneous"),

diff --git a/R/date-atus.R b/R/date-atus.R
@@ -1,6 +1,6 @@
 #' Calculate Date of Accumulated Thermal Units (ATUs)
-#' 
-#' A wrapper on [gsdd::date_atus()] to calculats the date on which a 
+#'
+#' A wrapper on [gsdd::date_atus()] to calculats the date on which a
 #' specified number of Accumulated Thermal Units (ATUs) are exceeded.
 #'
 #' @inheritParams gsdd::date_atus
@@ -12,11 +12,10 @@
 date_atus <- function(
     x,
     atus = 600,
-    start_date = as.Date("1972-03-01")
-) {
-
+    start_date = as.Date("1972-03-01")) {
   gsdd::date_atus(
-    x, 
+    x,
     atus = atus,
-    start_date = start_date)
+    start_date = start_date
+  )
 }
diff --git a/R/gdd.R b/R/gdd.R
@@ -1,5 +1,5 @@
 #' Calculate Growing Degree Days (GDD)
-#' 
+#'
 #' A wrapper on [gsdd::gdd()] to get the Growing Degree Days up to a date for
 #' the longest growing season.
 #'
@@ -13,15 +13,15 @@ gdd <- function(
     x,
     end_date = as.Date("1972-09-30"),
     min_length = 60,
-    msgs = TRUE
-) {
+    msgs = TRUE) {
   chk_whole_number(min_length)
   chk_range(min_length, c(14, 213))
-  
+
   gsdd::gdd(
-    x, 
+    x,
     end_date = end_date,
-    min_length = min_length, 
+    min_length = min_length,
     pick = "longest",
-    msgs = msgs)
+    msgs = msgs
+  )
 }
diff --git a/R/gsdd-cf.R b/R/gsdd-cf.R
@@ -1,5 +1,5 @@
 #' Calculate Growing Season Degree Days (GSDD)
-#' 
+#'
 #' Soft-deprecated for [gsdd::gsdd_vctr()].
 #'
 #' @inheritParams gsdd::gsdd_vctr
@@ -14,15 +14,15 @@ gsdd_cf <- function(
     x,
     ignore_truncation = FALSE,
     min_length = 120,
-    msgs = TRUE
-) {
+    msgs = TRUE) {
   lifecycle::deprecate_soft("0.1.2", "gsdd_cf()", with = "gsdd::gsdd_vctr()")
   chk_whole_number(min_length)
   chk_range(min_length, c(14, 274))
-  
+
   gsdd::gsdd_vctr(
-    x, 
+    x,
     ignore_truncation = ignore_truncation,
-    min_length = min_length, 
-    msgs = msgs)
+    min_length = min_length,
+    msgs = msgs
+  )
 }
diff --git a/R/gsdd.R b/R/gsdd.R
@@ -2,7 +2,7 @@
 #'
 #' A wrapper on [gsdd::gsdd()] to get the Growing Season Degree Days for
 #' the longest growing season.
-#' 
+#'
 #' @inheritParams gsdd::gsdd
 #' @seealso [gsdd::gsdd()], [gsdd()] and [gss()].
 #' @export
@@ -12,14 +12,14 @@
 gsdd <- function(
     x,
     min_length = 120,
-    msgs = TRUE
-) {
+    msgs = TRUE) {
   chk_whole_number(min_length)
   chk_range(min_length, c(14, 274))
-  
+
   gsdd::gsdd(
-    x, 
-    min_length = min_length, 
+    x,
+    min_length = min_length,
     pick = "longest",
-    msgs = msgs)
+    msgs = msgs
+  )
 }
diff --git a/R/gss-plot.R b/R/gss-plot.R
@@ -1,6 +1,6 @@
 #' Plot Growing Seasons (GSS)
-#' 
-#' A wrapper on [gsdd::gss_plot()] to by default 
+#'
+#' A wrapper on [gsdd::gss_plot()] to by default
 #' plot all Growing Seasons ignoring truncation.
 #' For more information see [gsdd::gss_plot()].
 #'
@@ -18,18 +18,18 @@ gss_plot <- function(
     latex = FALSE,
     nrow = NULL,
     ncol = NULL,
-    msgs = TRUE
-) {
+    msgs = TRUE) {
   chk_whole_number(min_length)
   chk_range(min_length, c(14, 274))
-  
+
   gsdd::gss_plot(
-    x, 
-    min_length = min_length, 
+    x,
+    min_length = min_length,
     ignore_truncation = ignore_truncation,
     pick = pick,
     latex = latex,
     nrow = nrow,
     ncol = ncol,
-    msgs = msgs)
+    msgs = msgs
+  )
 }
diff --git a/R/gss.R b/R/gss.R
@@ -1,6 +1,6 @@
 #' Calculate Growing Seasons (GSS)
-#' 
-#' A wrapper on [gsdd::gss()] to by default 
+#'
+#' A wrapper on [gsdd::gss()] to by default
 #' get all Growing Seasons ignoring truncation.
 #' For more information see [gsdd::gss()].
 #'
@@ -15,15 +15,15 @@ gss <- function(
     min_length = 120,
     ignore_truncation = TRUE,
     pick = "all",
-    msgs = TRUE
-) {
+    msgs = TRUE) {
   chk_whole_number(min_length)
   chk_range(min_length, c(14, 274))
-  
+
   gsdd::gss(
-    x, 
-    min_length = min_length, 
+    x,
+    min_length = min_length,
     ignore_truncation = ignore_truncation,
     pick = pick,
-    msgs = msgs)
+    msgs = msgs
+  )
 }