add NEWS, fix all devtools::check() notes

document quiet throughout
closes #17
add ellipses (...) to almost all functions to force named argument matching
document them in one place and inherit

.github/.gitignore

@@ -0,0 +1 @@
+*.html

NEWS.md

@@ -0,0 +1,20 @@
+# clumpedr 0.3.0 (2024-05-03)
+
+* Fix package install fail: the `default(quiet)` parameter didn't work because I don't export the `default` function.
+* Document `quiet` once and inherit the docs everywhere. Explicitly list that it listens to `options(clumpedr.quiet)`.
+* Remove all the option setting functions. Users should just use e.g., `option(clumpedr.quiet = TRUE)` if they want a global setting.
+* Add `...` argument to most functions, requiring named matches (not just positions) for the more obscure function arguments.
+* Remove the `pipe_plot()` function.
+* Remove all references to `genplot` and plotting from the main function sources. Closes #17.
+* Rebuild most tests so they work and only test one function, if possible.
+* Added snapshots for tests that run the code in the vignette (ugly but it works).
+* Change `.data$COLUMN` to `"COLUMN"` in all tidyselect functions such as `tidyr::pivot_*`.
+* Add GitHub continuous integration.
+
+# clumpedr 0.2.0 (2022-05-11)
+
+* Second release to assign Zenodo DOI.
+
+# clumpedr 0.1.0 (2021-09-14)
+
+* First public release after codebase had somewhat stabilized.

R/abundance_ratios.R

@@ -15,6 +15,8 @@
 #' @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 quiet
 #' @export
 abundance_ratios <- function(.data,
                              ...,
@@ -24,6 +26,7 @@ abundance_ratios <- function(.data,
                              R45 = R45, R46 = R46, R47 = R47,
                              R48 = R48, R49 = R49,
                              quiet = NULL) {
+  # global variables and defaults
   s44 <- s45 <- s46 <- s47 <- s48 <- s49 <- NULL
 
   if (nrow(.data) == 0L) {
@@ -33,8 +36,9 @@ abundance_ratios <- function(.data,
     quiet <- default(quiet)
   }
 
-  if (!quiet)
+  if (!quiet) {
     message("Info: calculating abundance ratios R[i] = i / 44")
+  }
 
   .data %>%
     mutate({{ R45 }} := {{ i45 }} / {{ i44 }},

R/acid_fractionation.R

@@ -10,6 +10,8 @@
 #' @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 quiet
 #'
 #' @references
 #'
@@ -28,7 +30,8 @@
 #' 1057--1066.
 #'
 #' @export
-acid_fractionation <- function(.data, aff = 0.062, D47 = D47_etf,
+acid_fractionation <- function(.data, aff = 0.062, ...,
+                               D47 = D47_etf,
                                D47_out = D47_final,
                                quiet = default(quiet)) {
   # global variables and defaults

R/add_info.R

@@ -7,6 +7,8 @@
 #' @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 quiet
 #' @export
 #' @family metadata cleaning functions
 add_info <- function(.data, .info, ...,

R/append_expected_values.R

@@ -28,13 +28,15 @@
 #'
 #' @export
 #' @family empirical transfer functions
+#' @inheritParams dots
+#' @inheritParams quiet
 append_expected_values <- function(.data,
                                    ...,
                                    std_names = paste0("ETH-", 1:3),  # we don't use ETH-4!
                                    std_values = c(0.258, 0.256, 0.691) - 0.062, #, 0.507),
                                    exp = expected_D47,
                                    by = `Identifier 1`,
-                                   quiet = default(quiet)) {
+                                   quiet = NULL) {
   # global variables and defaults
   `Identifier 1` <- expected_D47 <- NULL
 

R/apply_etf.R

@@ -14,6 +14,8 @@
 #' @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 quiet
 #' @export
 apply_etf <- function(.data, ..., intercept = intercept, slope = slope, raw = D47_raw, out = D47_etf, quiet = NULL) {
   # defaults

R/bulk_and_clumping_deltas.R

@@ -16,6 +16,8 @@
 #' @param d49 Column name of d49.
 #' @inheritParams isobar_ratios
 #' @inheritParams default.params
+#' @inheritParams dots
+#' @inheritParams quiet
 #' @references Daeron, M., Blamart, D., Peral, M., & Affek, H. P., Absolute
 #'   isotopic abundance ratios and the accuracy of \eqn{\Delta_{47}}
 #'   measurements, _Chemical Geology_ **2016**, _442_, 83--96.

R/calculate_etf.R

@@ -11,7 +11,10 @@
 #' @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
-calculate_etf <- function(.data, raw = D47_raw_mean, exp = expected_D47,
+#' @inheritParams dots
+#' @inheritParams quiet
+calculate_etf <- function(.data, ...,
+                          raw = D47_raw_mean, exp = expected_D47,
                           session = Preparation, etf = etf,
                           etf_coefs = etf_coefs, slope = slope,
                           intercept = intercept, parallel = FALSE, quiet = NULL) {

R/clean_did_info.R

@@ -8,7 +8,9 @@
 #' @seealso [isoreader::iso_read_dual_inlet()]
 #' @seealso [isoreader::iso_get_file_info()]
 #' @family metadata cleaning functions
-clean_did_info  <- function(.did, masspec = NULL,
+#' @inheritParams dots
+#' @inheritParams quiet
+clean_did_info  <- function(.did, masspec = NULL, ...,
                             std_names = c(paste0("ETH-", 1:4), "IAEA-C2", "Merck"),
                             oth_name = "other",
                             quiet = NULL) {

R/collapse_cycles.R

@@ -11,6 +11,8 @@
 #' @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 quiet
 collapse_cycles <- function(.data,
                             ...,
                             cols = c(d13C_PDB, d18O_PDB, D47_raw, D47_final),
@@ -19,8 +21,11 @@ collapse_cycles <- function(.data,
                             funs = NULL,
                             alpha = 0.05,
                             na.rm = TRUE,
-                            quiet = default(quiet)) {
+                            quiet = NULL) {
   outlier_cycle <- d13C_PDB <- d18O_PDB <- D47_raw <- D47_final <- NULL
+  if (is.null(quiet)) {
+    quiet <- default(quiet)
+  }
 
   if (!quiet) {
     message("Info: collapsing cycles, calculating sample summaries.")
@@ -74,6 +79,8 @@ 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,
                             ...,
@@ -119,17 +126,25 @@ nest_cycle_data <- function(.data,
                             flags = c("R45_flag", "R46_flag"),
                             Deltas = c("D45_raw", "D46_raw", "D47_raw",
                                        "D48_raw", "D49_raw"),
-                            p49 = "param_49") {
+                            p49 = "param_49", quiet = NULL) {
 
   if (nrow(.data) == 0L) {
     return(tibble(file_id = character()))
   }
+  if (is.null(quiet)) {
+    quiet <- default(quiet)
+  }
 
   cols <- c("cycle", ratios, outlier_cycles, outliers, cycle_drop, bg_corrected, bgs,
             Rs, deltas, isotopes, params, stochastic, flags, Deltas, p49)
 
-  if (!all(cols %in% colnames(.data)))
+  if (!all(cols %in% colnames(.data))) {
     stop(glue::glue("columns {glue::glue_collapse(cols[!colnames(.data) %in% cols], sep=', ', last=' and ', width = 60)} not found in data"))
+  }
+
+  if (!quiet) {
+    message(glue::glue("Nesting by {glue::glue_collapse(cols, sep=', ', last=' and ', width = 60)}."))
+  }
 
   .data %>%
     nest(cycle_data = one_of(cols))

R/correct_backgrounds.R

@@ -7,8 +7,10 @@
 #' @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 quiet
 #' @export
-correct_backgrounds  <- function(.data, factor,
+correct_backgrounds  <- function(.data, factor, ...,
                                  i47 = v47.mV, i54 = v54.mV,
                                  quiet = default(quiet)) {
   # global variables and defaults

R/delta_values.R

@@ -4,7 +4,8 @@
 #'   [correct_backgrounds()].
 #' @details This function is a wrapper for the [abundance_ratios()],
 #'   [little_deltas()], and [bulk_and_clumping_deltas()] functions.
-#'
+#' @inheritParams dots
+#' @inheritParams quiet
 #' @export
 delta_values <- function(.data, ..., quiet = NULL) {
   R45_wg <- R46_wg <- R47_wg <- R48_wg <- R49_wg <- NULL

R/empirical_transfer_function.R

@@ -5,9 +5,13 @@
 #' then apply the ETF to all the samples and standards.
 #'
 #' @param .data A [tibble][tibble::tibble-package] resulting from [collapse_cycles()].
+#' @param id1 Column name of `Identifier 1` (default).
+#' @param outlier Column name of `outlier` (default).
 #' @inheritParams append_expected_values
 #' @inheritParams calculate_etf
-#'
+#' @inheritParams apply_etf
+#' @inheritParams dots
+#' @inheritParams quiet
 #' @details This function is a wrapper for [append_expected_values()],
 #'   [calculate_etf()], and [apply_etf()].
 #'

R/find_bad_cycles.R

@@ -19,13 +19,15 @@
 #' @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 quiet
 #' @export
 #' @family cycle functions
 find_bad_cycles <- function(.data, ...,
                             min, max, fac,
                             v44 = "v44.mV", cycle = "cycle",
                             relative_to = "init",
-                            quiet = default(quiet)) {
+                            quiet = NULL) {
   if (nrow(.data) == 0L) {
     return(tibble(file_id = character()))
   }
@@ -35,6 +37,10 @@ find_bad_cycles <- function(.data, ...,
     stop("'relative_to': ", relative_to, " should be eigher 'init' or 'prev'")
   }
 
+  if (is.null(quiet)) {
+    quiet <- default(quiet)
+  }
+
   out <- .data %>%
     mutate(outlier_cycle_low = .data[[v44]] <= .data[[min]],
            outlier_cycle_high = .data[[v44]] >= .data[[max]],
@@ -66,9 +72,10 @@ find_bad_cycles <- function(.data, ...,
            .by = "file_id") %>%
     mutate(outlier_cycle = .data$outlier_cycle_low | .data$outlier_cycle_high | .data$outlier_cycle_drop, .by = "file_id")
 
-  if (!quiet)
+  if (!quiet) {
     glue("Info: found {length(unique(pull(filter(out, .data$cycle_has_drop), file_id)))} out of {length(unique(pull(out, file_id)))} acquisitions with a drop in pressure of mass 44.") %>%
       message()
+  }
 
   out
 }