ensure ellipses (...) are empty using rlang::check_dots_empty()

R/abundance_ratios.R

@@ -15,7 +15,7 @@
 #' @param R47 Desired new name of the calculated ratio for mass 47.
 #' @param R48 Desired new name of the calculated ratio for mass 48.
 #' @param R49 Desired new name of the calculated ratio for mass 49.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @export
 abundance_ratios <- function(.data,
@@ -26,6 +26,7 @@ abundance_ratios <- function(.data,
                              R45 = R45, R46 = R46, R47 = R47,
                              R48 = R48, R49 = R49,
                              quiet = NULL) {
+  rlang::check_dots_empty0(...)
   # global variables and defaults
   s44 <- s45 <- s46 <- s47 <- s48 <- s49 <- NULL
 

R/acid_fractionation.R

@@ -10,7 +10,7 @@
 #' @param D47 The column name of the \eqn{\Delta_47} values to use for the acid
 #'   fractionation calculation.
 #' @param D47_out The desired new column name.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #'
 #' @references
@@ -34,6 +34,7 @@ acid_fractionation <- function(.data, aff = 0.062, ...,
                                D47 = D47_etf,
                                D47_out = D47_final,
                                quiet = default(quiet)) {
+  rlang::check_dots_empty0(...)
   # global variables and defaults
   D47_etf <- D47_final <- NULL
 

R/add_info.R

@@ -7,12 +7,13 @@
 #' @param .info A [tibble][tibble::tibble-package], resulting from
 #'   [clean_did_info()].
 #' @param cols  A character vector with column names in info to add to the data.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @export
 #' @family metadata cleaning functions
 add_info <- function(.data, .info, ...,
                      cols = NULL, quiet = NULL) {
+  rlang::check_dots_empty0(...)
   if (nrow(.data) == 0) {
     return(tibble(file_id = character()))
   }

R/append_expected_values.R

@@ -28,7 +28,7 @@
 #'
 #' @export
 #' @family empirical transfer functions
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 append_expected_values <- function(.data,
                                    ...,
@@ -39,6 +39,7 @@ append_expected_values <- function(.data,
                                    quiet = NULL) {
   # global variables and defaults
   `Identifier 1` <- expected_D47 <- NULL
+  rlang::check_dots_empty0(...)
 
   if (length(std_names) != length(std_values))
     stop("std_names should be of equal length to std_values.")

R/apply_etf.R

@@ -14,12 +14,13 @@
 #' @param raw The column with raw values to apply the ETF to.
 #' @param out The new column name.
 #' @family empirical transfer functions
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @export
 apply_etf <- function(.data, ..., intercept = intercept, slope = slope, raw = D47_raw, out = D47_etf, quiet = NULL) {
   # defaults
   D47_raw <- D47_etf <- NULL
+  rlang::check_dots_empty0(...)
   if (is.null(quiet)) {
     quiet <- default(quiet)
   }

R/bulk_and_clumping_deltas.R

@@ -16,7 +16,7 @@
 #' @param d49 Column name of d49.
 #' @inheritParams isobar_ratios
 #' @inheritParams default.params
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @references Daeron, M., Blamart, D., Peral, M., & Affek, H. P., Absolute
 #'   isotopic abundance ratios and the accuracy of \eqn{\Delta_{47}}
@@ -36,6 +36,7 @@ bulk_and_clumping_deltas  <- function(.data, ...,
                                       R18_PDBCO2 = default(R18_PDBCO2),
                                       lambda = default(lambda),
                                       D17O = default(D17O), quiet = NULL) {
+  rlang::check_dots_empty0(...)
   if (nrow(.data) == 0L) {
     return(tibble(file_id = character()))
   }

R/calculate_etf.R

@@ -11,7 +11,7 @@
 #' @param intercept The column name of the new intercept.
 #' @param parallel Whether or not (default) to process this in parallel, using package `furrr`.
 #' @importFrom stats na.exclude
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @family empirical transfer functions
 #' @export
@@ -20,6 +20,7 @@ calculate_etf <- function(.data, ...,
                           session = Preparation, etf = etf,
                           etf_coefs = etf_coefs, slope = slope,
                           intercept = intercept, parallel = FALSE, quiet = NULL) {
+  rlang::check_dots_empty(...)
   # global variables and defaults
   if (parallel & !requireNamespace("furrr", quietly = TRUE)) {
     stop("Package \"furrr\" is needed for this function to work.\n Please install it or run this with `parallel = FALSE`",

R/clean_did_info.R

@@ -8,12 +8,13 @@
 #' @seealso [isoreader::iso_read_dual_inlet()]
 #' @seealso [isoreader::iso_get_file_info()]
 #' @family metadata cleaning functions
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 clean_did_info  <- function(.did, masspec = NULL, ...,
                             std_names = c(paste0("ETH-", 1:4), "IAEA-C2", "Merck"),
                             oth_name = "other",
                             quiet = NULL) {
+  rlang::check_dots_empty(...)
   if (is.null(quiet)) {
     quiet <- default(quiet)
   }

R/collapse_cycles.R

@@ -11,7 +11,7 @@
 #' @param alpha The confidence level for the summary functions.
 #' @param na.rm a logical value indicating wheter NA values should be stripped
 #'   before the computation proceeds.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @export
 collapse_cycles <- function(.data,
@@ -24,6 +24,7 @@ collapse_cycles <- function(.data,
                             na.rm = TRUE,
                             quiet = NULL) {
   outlier_cycle <- d13C_PDB <- d18O_PDB <- D47_raw <- D47_final <- NULL
+  rlang::check_dots_empty0(...)
   if (is.null(quiet)) {
     quiet <- default(quiet)
   }
@@ -65,6 +66,7 @@ collapse_cycles <- function(.data,
 #' columns that have cycle information based on previous computation steps.
 #'
 #' @param .data A [tibble][tibble::tibble-package] resulting from [bulk_and_clumping_deltas()].
+#' @param ... Additional chacter vectors to nest by.
 #' @param masses The masses that are present in the mass spectrometer. Defaults to 44:49 and 54.
 #' @param ratios Ratio columns, based on masses.
 #' @param outlier_cycles Columns with outlier_cycle information.
@@ -80,7 +82,6 @@ collapse_cycles <- function(.data,
 #' @param flags Flag columns.
 #' @param Deltas Big delta values.
 #' @param p49 Param 49.
-#' @inheritParams dots
 #' @inheritParams quiet
 #' @export
 nest_cycle_data <- function(.data,

R/correct_backgrounds.R

@@ -7,14 +7,15 @@
 #' @param factor Factor by which to multiply the half-cup before subtraction.
 #' @param i47 Column with mass 47 intensities to correct.
 #' @param i54 Column with mass 47.5 intensities to use for correction.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @export
 correct_backgrounds  <- function(.data, factor, ...,
                                  i47 = v47.mV, i54 = v54.mV,
                                  quiet = default(quiet)) {
   # global variables and defaults
   v47.mV <- v54.mV <- NULL
+  rlang::check_dots_empty0(...)
 
   if (!quiet)
     glue("Info: adding background based on half-mass with factor {factor}") %>%

R/delta_values.R

@@ -4,11 +4,12 @@
 #'   [correct_backgrounds()].
 #' @details This function is a wrapper for the [abundance_ratios()],
 #'   [little_deltas()], and [bulk_and_clumping_deltas()] functions.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @export
 delta_values <- function(.data, ..., quiet = NULL) {
   R45_wg <- R46_wg <- R47_wg <- R48_wg <- R49_wg <- NULL
+  rlang::check_dots_empty0(...)
   if (nrow(.data) == 0L) {
     return(tibble(file_id = character()))
   }

R/empirical_transfer_function.R

@@ -10,7 +10,7 @@
 #' @inheritParams append_expected_values
 #' @inheritParams calculate_etf
 #' @inheritParams apply_etf
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @details This function is a wrapper for [append_expected_values()],
 #'   [calculate_etf()], and [apply_etf()].
@@ -41,6 +41,7 @@ empirical_transfer_function <- function(.data,
                                         parallel = FALSE) {
   # defaults from above
   D47_raw <- expected_D47 <- D47_etf <- `Identifier 1` <- Preparation <- NULL
+  rlang::check_dots_empty0(...)
   if (is.null(quiet)) {
     quiet <- default(quiet)
   }

R/find_bad_cycles.R

@@ -19,7 +19,7 @@
 #' @param cycle Column name of the column with the measurement cycle number.
 #' @param relative_to cycle Drop detection occurs relative to either the first
 #'   cycle ("init", default) or to the previous cycle ("prev").
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @export
 #' @family cycle functions
@@ -28,6 +28,7 @@ find_bad_cycles <- function(.data, ...,
                             v44 = "v44.mV", cycle = "cycle",
                             relative_to = "init",
                             quiet = NULL) {
+  rlang::check_dots_empty0(...)
   if (nrow(.data) == 0L) {
     return(tibble(file_id = character()))
   }

R/find_outliers.R

@@ -19,7 +19,7 @@
 #' @param D47 The column with \eqn{\Delta_{47}} values.
 #' @param session Column name that defines correction session.
 #' @param id1 Column name of the sample/standard identifier.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @export
 find_outliers <- function(.data,
@@ -36,6 +36,7 @@ find_outliers <- function(.data,
                           quiet = NULL) {
   # default quoted arguments are bad, hmkay
   D47_raw <- Preparation <- `Identifier 1` <- NULL
+  rlang::check_dots_empty0(...)
 
   if (is.null(quiet)) {
     quiet <- default(quiet)
@@ -72,13 +73,14 @@ find_outliers <- function(.data,
 ##' @param init_low Column in .data with minimum initial intensity threshold for mass 44.
 ##' @param init_high Column in .data with maximum initial intensity threshold for mass 44.
 ##' @param init_diff Column in .data with maximum initial difference in mass 44 threshold between standard and sample gas.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 ##' @export
 find_init_outliers <- function(.data,
                                init_low, init_high, init_diff,
                                ...,
                                quiet = NULL) {
+  rlang::check_dots_empty0(...)
   if (nrow(.data) == 0L) {
     return(tibble(file_id = character()))
   }
@@ -107,9 +109,10 @@ find_init_outliers <- function(.data,
 ##' Find measurements with a param49 value that is greater than \code{param49_off}.
 ##' @param .data A [tibble][tibble::tibble-package] with raw Delta values and file information.
 ##' @param param49_off The absolute cutoff value for the parameter 49 value.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 find_param49_outliers <- function(.data, param49_off, ..., quiet = NULL) {
+  rlang::check_dots_empty0(...)
   if (nrow(.data) == 0L) {
     return(tibble(file_id = character()))
   }
@@ -134,12 +137,13 @@ find_param49_outliers <- function(.data, param49_off, ..., quiet = NULL) {
 ##' @param .data A [tibble][tibble::tibble-package] with raw Delta values and file information.
 ##' @param internal_sd The internal standard deviation cutoff value.
 ##' @param D47 The column to calculate the internal sd value for.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 ##' @export
 find_internal_sd_outlier <- function(.data, internal_sd = .15, ...,
                                      D47 = D47_raw,
                                      quiet = NULL) {
+  rlang::check_dots_empty0(...)
   `Identifier 1` <- D47_raw <- NULL
   if (is.null(quiet)) {
     quiet <- default(quiet)
@@ -166,12 +170,13 @@ find_internal_sd_outlier <- function(.data, internal_sd = .15, ...,
 #' @param session The session for which to calculate the standard deviation and median values.
 #' @param outlier_session Column name of new output column.
 #' @export
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 find_session_outlier <- function(.data, ...,
                                  n = 5, nsd_off = 4, D47 = D47_raw, outlier_session = outlier_session_D47,
                                  session = Preparation, quiet = NULL) {
   D47_raw <- Preparation <- outlier_session_D47 <- NULL
+  rlang::check_dots_empty0(...)
   if (is.null(quiet)) {
     quiet <- default(quiet)
   }
@@ -200,13 +205,14 @@ find_session_outlier <- function(.data, ...,
 #' @param D47 The column to calculate the internal sd value for.
 #' @param session The session for which to calculate the standard deviation and median values.
 #' @param id1 The column that defines the sample/standard name.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 ##' @export
 find_session_id1_outlier <- function(.data, ...,
                                      n_id1 = 5, nsd_off = 4, D47 = D47_raw,
                                  session = Preparation, id1 = `Identifier 1`, quiet = NULL) {
   D47_raw <- Preparation <- `Identifier 1` <- outlier <- NULL
+  rlang::check_dots_empty0(...)
 
   if (is.null(quiet)) {
     quiet <- default(quiet)
@@ -235,10 +241,11 @@ find_session_id1_outlier <- function(.data, ...,
 #'
 #' @param .data A [tibble][tibble::tibble-package] with raw Delta values and file information.
 #' @param out_column The name of the outlier column.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @export
 summarise_outlier <- function(.data, out_column = outlier, ..., quiet = NULL) {
+  rlang::check_dots_empty0(...)
   if (nrow(.data) == 0L) {
     return(tibble(file_id = character()))
   }

R/isobar_ratios.R

@@ -15,7 +15,7 @@
 #' @param R48 The output column name for R48.
 #' @param R49 The output column name for R49.
 #' @inheritParams default.params
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #'
 #' @references Daeron, M., Blamart, D., Peral, M., & Affek, H. P., Absolute
@@ -38,6 +38,7 @@ isobar_ratios <- function(.data,
                           D47 = default(D47),
                           D48 = default(D48),
                           D49 = default(D49)) {
+  rlang::check_dots_empty0(...)
   .data %>%
     mutate(
       # Compute R17

R/little_deltas.R

@@ -4,10 +4,11 @@
 #' \deqn{\delta_i = (R_i / R_iwg - 1) \times 1000}
 #'
 #' @param .data A [tibble][tibble::tibble-package] with abundance ratios.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @export
 little_deltas <- function(.data, ..., quiet = NULL) {
+  rlang::check_dots_empty0(...)
   if (nrow(.data) == 0L) {
     return(tibble(file_id = character()))
   }

R/reference_gas_delta.R

@@ -4,14 +4,15 @@
 #' @param .did An iso file, resulting from [isoreader::iso_read_dual_inlet()].
 #' @param d13C_PDB_wg \eqn{\delta^{13}C} reference gas value to overwrite.
 #' @param d18O_PDBCO2_wg \eqn{\delta^{18}O} reference gas value to overwrite.
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @export
 append_ref_deltas <- function(.data, .did = NULL,
                               ...,
                               d13C_PDB_wg = NULL,
                               d18O_PDBCO2_wg = NULL,
                               quiet = NULL) {
+  rlang::check_dots_empty0(...)
   if (!any(class(.data) %in% c("data.frame", "tbl_df", "tbl"))) {
     stop("`.data` must be a data.frame or tibble", call. = FALSE)
   }

R/remove_outliers.R

@@ -12,7 +12,7 @@
 #'   Preparation of the standards.
 #' @param D47 The column with \eqn{\Delta_47} values. Defaults to `D47_raw_mean`.
 #' @inheritParams find_outliers
-#' @inheritParams dots
+#' @inheritParams rlang::args_dots_empty
 #' @inheritParams quiet
 #' @export
 remove_outliers <- function(.data,
@@ -30,6 +30,7 @@ remove_outliers <- function(.data,
                             quiet = NULL) {
   # global variables and defaults
   D47_raw <- file_datetime <- Preparation <- `Identifier 1` <- NULL
+  rlang::check_dots_empty0(...)
   if (is.null(quiet)) {
     quiet <- default(quiet)
   }