update docs somewhat

add references to (d18Osw)|(temp)_calc and inherit them in the parent function

R/bootstrap_means.R

@@ -12,7 +12,7 @@
 #' @param D47 The column name in `data` with the clumped isotope values.
 #' @param Nsim The number of bootstraps you want to run. Defaults to the
 #'   number of rows in `calib`.
-#' @return A tibble with bootstrapped slope-intercept pair.
+#' @returns A tibble with bootstrapped slope-intercept pair.
 #' @export
 bootstrap_means <- function(data,
                             group,

R/d18Osw_calc.R

@@ -4,12 +4,11 @@
 #'
 #' @param temperature  The formation temperature (in °C).
 #' @inheritParams temp_calc
-#' @return The oxygen isotope composition of the sea water in VSMOW.
+#' @returns The oxygen isotope composition of the sea water in VSMOW.
 #' @author Ilja J. Kocken
-#' @references
-#' Kim, S.-T., & O’Neil, J. R. (1997). Equilibrium and nonequilibrium oxygen isotope effects in synthetic carbonates. Geochimica et Cosmochimica Acta, 61(16), 3461–3475. https://doi.org/10.1016/S0016-7037(97)00169-5
-#'
-#' Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation of the oxygen isotopic composition of planktonic foraminifera: Experimental results and revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070
+#' @inherit supported_equations references
+#' @examples
+#' d18Osw_calc(3, 2, "KimONeil1997")
 #' @export
 d18Osw_calc <- function(d18Occ, temperature, equation = NULL) {
   equation <- equation_supported(equation)

R/equation_supported.R

@@ -3,29 +3,9 @@
 #' Also parses equation name into our internal simplified code.
 #' See details for which equations are currently supported.
 #'
-#' - TODO: add all supported equations and references somewhere.
-#'
-#' - Kim & O'Neil 1997 as recalculated by Bemis et al., 1998:
-#'
-#'   \eqn{T = a + b(\delta_{c} - \delta_{w}) + c(\delta_{c} - \delta_{w})^2}{T = a + b(delta_c - delta_w) + c(delta_c - delta_w)^2},
-#'
-#'   where T is in °C, \eqn{\delta_{c}}{delta_c} is in VPDB and \eqn{\delta_{w}}{delta_w} is in VMOW.
-#'
-#' - Marchitto et al., 2014:
-#'
-#'   \eqn{(\delta_{cp} - \delta_{ws} + 0.27) = -0.245\pm0.005t + 0.0011\pm0.0002t^{2} + 3.58±0.02}{(delta_cp - delta_ws + 0.27) = -0.245+-0.005t + 0.0011+-0.0002t^2 + 3.58+-0.02}.
-#'
-#' @param equation Character vector with equation reference.
+#' @param equation Character vector with equation reference. Must be one of [supported_equations()].
 #' @returns Character vector of cleaned up equation reference. Gives an error if it's currently not supported.
 equation_supported <- function(equation) {
-  supported_equations <- c(
-    "Shackleton1974",
-    "ErezLuz1983",
-    "KimONeil1997", # NOTE: as recalculated in Bemis 1998!
-    ## "Bemis1998",
-    "Marchitto2014"
-  )
-
   # default
   if (is.null(equation)) {
     equation <- "KimONeil1997"
@@ -65,10 +45,47 @@ equation_supported <- function(equation) {
     }
   }
 
-  if (!equation %in% supported_equations) {
-    cli::cli_abort(c("Equation {.var {equation}} is not implemented",
-                     "i" = "Supported equation{?s}: {.and {supported_equations}}",
-                     "i" = "Feel free to submit a pull request!"))
+  if (!equation %in% supported_equations()) {
+    cli::cli_abort(c("Equation {.var {equation}} is not implemented/reckognized.",
+                     "i" = "Supported equation{?s}: {.and {supported_equations()}}.",
+                     "x" = "Maybe you have misspelled it?",
+                     "i" = "Feel free to submit a pull request to add the equation!"))
   }
   return(equation)
 }
+
+#' Supported d18Osw, d18Occ, temperature relationship equations.
+#'
+#' Defaults to Kim & O'neil 1997 as modified by Bemis et al., 1998.
+# #'
+# #' - Kim & O'Neil 1997 as recalculated by Bemis et al., 1998:
+# #'
+# #'   \eqn{T = a + b(\delta_{c} - \delta_{w}) + c(\delta_{c} - \delta_{w})^2}{T = a + b(delta_c - delta_w) + c(delta_c - delta_w)^2},
+# #'
+# #'   where T is in °C, \eqn{\delta_{c}}{delta_c} is in VPDB and \eqn{\delta_{w}}{delta_w} is in VMOW.
+# #'
+# #' - Marchitto et al., 2014:
+# #'
+# #'   \eqn{(\delta_{cp} - \delta_{ws} + 0.27) = -0.245\pm0.005t + 0.0011\pm0.0002t^{2} + 3.58±0.02}{(delta_cp - delta_ws + 0.27) = -0.245+-0.005t + 0.0011+-0.0002t^2 + 3.58+-0.02}.
+# #'
+#' @examples
+#' supported_equations()
+#' @references
+#' Shackleton, N. J. (1974). Attainment of isotopic equilibrium between ocean water and the benthic foraminifera genus _Uvigerina_: Isotopic changes in the ocean during the last glacial. _Colloques Internationaux Du CNRS_, _219_, 203–209.
+#'
+#' Erez, J., & Luz, B. (1983). Experimental paleotemperature equation for planktonic foraminifera. _Geochimica et Cosmochimica Acta_, _47(6)_, 1025–1031. https://doi.org/10.1016/0016-7037(83)90232-6
+#'
+#' Kim, S.-T., & O’Neil, J. R. (1997). Equilibrium and nonequilibrium oxygen isotope effects in synthetic carbonates. _Geochimica et Cosmochimica Acta_, _61(16)_, 3461–3475. https://doi.org/10.1016/S0016-7037(97)00169-5
+#'
+#' Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation of the oxygen isotopic composition of planktonic foraminifera: Experimental results and revised paleotemperature equations. _Paleoceanography_, _13(2)_, 150–160. https://doi.org/10.1029/98PA00070
+#'
+#' Marchitto, T. M., Curry, W. B., Lynch-Stieglitz, J., Bryan, S. P., Cobb, K. M., & Lund, D. C. (2014). Improved oxygen isotope temperature calibrations for cosmopolitan benthic foraminifera. _Geochimica et Cosmochimica Acta_, _130_, 1–11. https://doi.org/10.1016/j.gca.2013.12.034
+supported_equations <- function() {
+  c(
+    "Shackleton1974",
+    "ErezLuz1983",
+    "KimONeil1997", # NOTE: as recalculated in Bemis 1998!
+    ## "Bemis1998",
+    "Marchitto2014"
+  )
+}

R/filter_outliers.R

@@ -2,7 +2,7 @@
 #'
 #' @param data A dataframe with columns `outlier`, `broadid`
 #' @param group Column name of the groups.
-#' @return A dataframe with outliers, standards, and NAs filtered out.
+#' @returns A dataframe with outliers, standards, and NAs filtered out.
 #' @export
 filter_outliers <- function(data, group) {
   data |>

R/temp_calc.R

@@ -6,13 +6,12 @@
 #' @param d18Occ The oxygen isotope composition of the carbonate in VPDB.
 #' @param d18Osw The oxygen isotope composition of the sea water in VSMOW
 #' @param equation Character vector with the equation to use. Defaults to Kim & O'Neil, 1997.
-#' @return The temperature in degrees Celsius.
+#' @returns The temperature in degrees Celsius.
 #' @author Ilja J. Kocken
+#' @inherit supported_equations references
+#' @examples
+#' temp_calc(3, 0, "KimONeil1997")
 #' @export
-#' @references
-#' Kim, S.-T., & O’Neil, J. R. (1997). Equilibrium and nonequilibrium oxygen isotope effects in synthetic carbonates. Geochimica et Cosmochimica Acta, 61(16), 3461–3475. https://doi.org/10.1016/S0016-7037(97)00169-5
-#'
-#' Bemis, B. E., Spero, H. J., Bijma, J., & Lea, D. W. (1998). Reevaluation of the oxygen isotopic composition of planktonic foraminifera: Experimental results and revised paleotemperature equations. Paleoceanography, 13(2), 150–160. https://doi.org/10.1029/98PA00070
 temp_calc <- function(d18Occ, d18Osw, equation = NULL) {
   equation <- equation_supported(equation)
   if (equation == "Shackleton1974") {

R/temp_d18Osw_calc.R

@@ -6,7 +6,7 @@
 #' @param calib A dataframe with draws from the bootstrapped (or Bayesian)
 #'   temperature regression. Should have columns `slope` and `intercept`.
 #' @inheritParams d18Osw_calc
-#' @return Same as boot but with additional columns `temp` and `d18Osw`.
+#' @returns Same as boot but with additional columns `temp` and `d18Osw`.
 #' @export
 temp_d18Osw_calc <- function(boot, calib, equation = NULL, Nsim = NULL) {
   if (is.null(Nsim)) {