Merge pull request #623 from cmu-delphi/lint-for-0.11

Lint + lint config updates for 0.11

Author: brookslogan

.lintr

@@ -1,6 +1,5 @@
 linters: linters_with_defaults(
   line_length_linter(120),
-  cyclocomp_linter = NULL,
   object_length_linter(length = 40L)
   )
 exclusions: list(

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: epiprocess
 Title: Tools for basic signal processing in epidemiology
-Version: 0.10.5
+Version: 0.11.0
 Authors@R: c(
     person("Jacob", "Bien", role = "ctb"),
     person("Logan", "Brooks", , "[email protected]", role = c("aut", "cre")),

R/archive.R

@@ -497,15 +497,13 @@ is_locf <- function(vec, abs_tol, is_key) { # nolint: object_usage_linter
   if (is.vector(vec, mode = "numeric") && !is_key) {
     # (integer or double vector, no class (& no dims); maybe names, which we'll
     # ignore like `vec_equal`); not a key column
-    res <- unname(if_else(
+    unname(if_else(
       !is.na(vec) & !is.na(lag_vec),
       abs(vec - lag_vec) <= abs_tol,
       is.na(vec) & is.na(lag_vec)
     ))
-    return(res)
   } else {
-    res <- vec_equal(vec, lag_vec, na_equal = TRUE)
-    return(res)
+    vec_equal(vec, lag_vec, na_equal = TRUE)
   }
 }
 
@@ -808,5 +806,5 @@ clone <- function(x) {
 #' @export
 clone.epi_archive <- function(x) {
   x$DT <- data.table::copy(x$DT)
-  return(x)
+  x
 }

R/correlation.R

@@ -120,8 +120,8 @@ epi_cor <- function(x, var1, var2, dt1 = 0, dt2 = 0, shift_by = geo_value, # nol
 # Function to perform time shifts, lag or lead
 shift <- function(var, n) {
   if (n < 0) {
-    return(dplyr::lag(var, -n))
+    dplyr::lag(var, -n)
   } else {
-    return(dplyr::lead(var, n))
+    dplyr::lead(var, n)
   }
 }

R/epi_df.R

@@ -218,7 +218,7 @@ as_epi_df <- function(x, ...) {
 #' @export
 as_epi_df.epi_df <- function(x, ...) {
   x <- ungroup(x)
-  return(x)
+  x
 }
 
 #' @rdname epi_df

R/grouped_epi_archive.R

@@ -76,12 +76,12 @@ new_grouped_epi_archive <- function(x, vars, drop) {
   private$vars <- vars
   private$drop <- drop
 
-  return(structure(
+  structure(
     list(
       private = private
     ),
     class = "grouped_epi_archive"
-  ))
+  )
 }
 
 
@@ -431,7 +431,7 @@ epix_slide.grouped_epi_archive <- function(
     }
 
     # Fast conversion:
-    return(validate_tibble(new_tibble(res)))
+    validate_tibble(new_tibble(res))
   }
 
   out <- lapply(.versions, function(.version) {
@@ -493,16 +493,14 @@ epix_slide.grouped_epi_archive <- function(
       }
     }
 
-    return(
-      dplyr::bind_rows(dplyr::group_map( # note: output will be ungrouped
-        dplyr::group_by(as_of_df, !!!syms(.x$private$vars), .drop = .x$private$drop),
-        group_map_fn,
-        .slide_comp = .slide_comp, ...,
-        .version = .version,
-        .new_col_name = .new_col_name,
-        .keep = TRUE
-      ))
-    )
+    dplyr::bind_rows(dplyr::group_map( # note: output will be ungrouped
+      dplyr::group_by(as_of_df, !!!syms(.x$private$vars), .drop = .x$private$drop),
+      group_map_fn,
+      .slide_comp = .slide_comp, ...,
+      .version = .version,
+      .new_col_name = .new_col_name,
+      .keep = TRUE
+    ))
   })
   # Combine output into a single tibble (allowing for packed columns)
   out <- vctrs::vec_rbind(!!!out)

R/growth_rate.R

@@ -192,9 +192,9 @@ growth_rate <- function(
         a <- mean(yy[left])
         hh <- mean(xx[right]) - mean(xx[left])
         if (log_scale) {
-          return((b - a) / hh)
+          (b - a) / hh
         } else {
-          return((b / a - 1) / hh)
+          (b / a - 1) / hh
         }
       } else {
         # Linear regression
@@ -203,9 +203,9 @@ growth_rate <- function(
         b <- sum(xm * ym) / sum(xm^2)
         a <- mean(yy - b * xx)
         if (log_scale) {
-          return(b)
+          b
         } else {
-          return(b / (a + b * x_ref))
+          b / (a + b * x_ref)
         }
       }
     })
@@ -381,5 +381,5 @@ parse_trendfilter_params <- function(params) {
   # If we got here, we fit TF. There are two possibilities:
   # 1. df is NULL and lambda is a scalar
   # 2. df is numeric and lambda is either NULL or a vector (vec_lambda = TRUE)
-  return(params)
+  params
 }

R/methods-epi_archive.R

@@ -604,10 +604,10 @@ epix_detailed_restricted_mutate <- function(.data, ...) {
     out_archive <- .data
     out_archive$DT <- out_dt
     request_names <- names(col_modify_cols)
-    return(list(
+    list(
       archive = out_archive,
       request_names = request_names
-    ))
+    )
     # (We might also consider special-casing when `mutate` hands back something
     # equivalent (in some sense) to the input (probably only encountered when
     # we're dealing with `group_by`), and using just `$DT`, not a shallow copy,
@@ -879,8 +879,7 @@ epix_slide.epi_archive <- function(
 #' @noRd
 epix_slide_versions_default <- function(ea) {
   versions_with_updates <- c(ea$DT$version, ea$versions_end)
-  ref_time_values <- tidyr::full_seq(versions_with_updates, guess_period(versions_with_updates))
-  return(ref_time_values)
+  tidyr::full_seq(versions_with_updates, guess_period(versions_with_updates))
 }
 
 
@@ -920,7 +919,7 @@ epix_truncate_versions_after.epi_archive <- function(x, max_version) {
     x$clobberable_versions_start <- NA
   }
   x$versions_end <- max_version
-  return(x)
+  x
 }
 
 

R/methods-epi_df.R

@@ -17,7 +17,7 @@ as_tibble.epi_df <- function(x, ...) {
   # first instead.
   destructured <- tibble::as_tibble(vctrs::vec_data(x), ...)
   if (attr(x, "decay_to_tibble") %||% TRUE) {
-    return(destructured)
+    destructured
   } else {
     # We specially requested via attr not to decay epi_df-ness but to drop any
     # grouping.
@@ -39,12 +39,10 @@ as_tibble.epi_df <- function(x, ...) {
 #' @export
 as_tsibble.epi_df <- function(x, key, ...) {
   if (missing(key)) key <- c("geo_value", attributes(x)$metadata$other_keys)
-  return(
-    as_tsibble(
-      tibble::as_tibble(x),
-      key = tidyselect::all_of(key), index = "time_value",
-      ...
-    )
+  as_tsibble(
+    tibble::as_tibble(x),
+    key = tidyselect::all_of(key), index = "time_value",
+    ...
   )
 }
 
@@ -351,8 +349,8 @@ unnest.epi_df <- function(data, ...) {
 # Simple reclass function
 reclass <- function(x, metadata) {
   class(x) <- unique(c("epi_df", class(x)))
-  attributes(x)$metadata <- metadata
-  return(x)
+  attr(x, "metadata") <- metadata
+  x
 }
 
 #' Arrange an epi_df into a standard order
@@ -376,7 +374,7 @@ arrange_canonical.default <- function(x, ...) {
   cli::cli_abort(c(
     "`arrange_canonical()` is only meaningful for an {.cls epi_df}."
   ))
-  return(x)
+  x
 }
 
 #' @export
@@ -397,7 +395,7 @@ arrange_row_canonical.default <- function(x, ...) {
   cli::cli_abort(c(
     "`arrange_row_canonical()` is only meaningful for an {.cls epi_df}."
   ))
-  return(x)
+  x
 }
 
 #' @export
@@ -417,7 +415,7 @@ arrange_col_canonical.default <- function(x, ...) {
   cli::cli_abort(c(
     "`arrange_col_canonical()` is only meaningful for an {.cls epi_df}."
   ))
-  return(x)
+  x
 }
 
 #' @export

R/outliers.R

@@ -122,7 +122,7 @@ detect_outlr <- function(x = seq_along(y), y,
 
     # Update column names with model abbreviation
     colnames(results) <- paste(abbr, colnames(results), sep = "_")
-    return(results)
+    results
   })
 
   # Combine information about detected outliers

R/revision_analysis.R

@@ -280,9 +280,9 @@ get_last_run <- function(bool_vec, values_from) {
 f_no_na <- function(f, x) {
   x <- x[!is.na(x)]
   if (length(x) == 0) {
-    return(Inf)
+    Inf
   } else {
-    return(f(x))
+    f(x)
   }
 }
 
@@ -313,8 +313,8 @@ time_delta_summary <- function(time_delta, time_type) {
       check.names = FALSE
     ) %>%
       mutate(across(c(min, median, mean, max), ~ .x * unit_time_delta(time_type)))
-    return(res)
+    res
   } else {
-    return(data.frame())
+    data.frame()
   }
 }

R/slide.R

@@ -281,7 +281,7 @@ epi_slide <- function(
       i <<- i + 1L
       .slide_comp(.x, .group_key, .ref_time_value, ...)
     }
-    return(slide_comp_wrapper)
+    slide_comp_wrapper
   }
 
   # - If .x is not grouped, then the trivial group is applied:
@@ -398,11 +398,11 @@ epi_slide_one_group <- function(
   # back.
   return_types <- purrr::map_chr(slide_values_list, function(x) {
     if (is.data.frame(x)) {
-      return("data.frame")
+      "data.frame"
     } else if (vctrs::obj_is_vector(x) && is.null(vctrs::vec_names(x))) {
-      return("vector")
+      "vector"
     } else {
-      return("other")
+      "other"
     }
   }) %>% unique()
   # Returned values must be data.frame or vector.
@@ -512,7 +512,7 @@ epi_slide_one_group <- function(
     res[[.new_col_name]] <- slide_values
   }
 
-  return(res)
+  res
 }
 
 get_before_after_from_window <- function(window_size, align, time_type) {
@@ -544,7 +544,7 @@ get_before_after_from_window <- function(window_size, align, time_type) {
       after <- window_size - 1
     }
   }
-  return(list(before = before, after = after))
+  list(before = before, after = after)
 }
 
 #' Optimized slide functions for common cases
@@ -952,7 +952,7 @@ epi_slide_opt <- function(
       }
     }
 
-    return(.data_group)
+    .data_group
   }
 
   result <- mutate(.x, .real = TRUE) %>%
@@ -1147,9 +1147,9 @@ full_date_seq <- function(x, before, after, time_type) {
     }
   }
 
-  return(list(
+  list(
     all_dates = all_dates,
     pad_early_dates = pad_early_dates,
     pad_late_dates = pad_late_dates
-  ))
+  )
 }

R/utils.R

@@ -617,7 +617,7 @@ guess_geo_type <- function(geo_value) {
     }
   }
 
-  return("custom")
+  "custom"
 }
 
 
@@ -679,7 +679,7 @@ time_column_names <- function() {
   )
   substitutions <- upcase_snake_case(substitutions)
   names(substitutions) <- rep("time_value", length(substitutions))
-  return(substitutions)
+  substitutions
 }
 #
 #' potential geo_value columns
@@ -696,7 +696,7 @@ geo_column_names <- function() {
   )
   substitutions <- upcase_snake_case(substitutions)
   names(substitutions) <- rep("geo_value", length(substitutions))
-  return(substitutions)
+  substitutions
 }
 
 #' potential version columns
@@ -711,7 +711,7 @@ version_column_names <- function() {
   )
   substitutions <- upcase_snake_case(substitutions)
   names(substitutions) <- rep("version", length(substitutions))
-  return(substitutions)
+  substitutions
 }
 
 #' rename potential time_value columns
@@ -753,7 +753,7 @@ guess_column_name <- function(x, column_name, substitutions) {
       }
     )
   }
-  return(x)
+  x
 }
 
 ##########

README.md

@@ -120,7 +120,7 @@ edf
 #> 
 #> # A tibble: 2,808 × 4
 #>   geo_value time_value cases_cumulative cases_daily
-#> * <chr>     <date>                <dbl>       <dbl>
+#>   <chr>     <date>                <dbl>       <dbl>
 #> 1 ca        2020-03-01               19          19
 #> 2 ca        2020-03-02               23           4
 #> 3 ca        2020-03-03               29           6
@@ -144,7 +144,7 @@ edf
 #> 
 #> # A tibble: 2,808 × 5
 #>   geo_value time_value cases_cumulative cases_daily smoothed_cases_daily
-#> * <chr>     <date>                <dbl>       <dbl>                <dbl>
+#>   <chr>     <date>                <dbl>       <dbl>                <dbl>
 #> 1 ca        2020-03-01               19          19                19   
 #> 2 ca        2020-03-02               23           4                11.5 
 #> 3 ca        2020-03-03               29           6                 9.67