creat pkgdown website for the package

.github/.gitignore

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

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -1,2 +1,3 @@
 /.Rhistory
 /.Rbuildignore
+docs

DESCRIPTION

@@ -30,3 +30,4 @@ Imports:
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
+URL: https://japhir.github.io/clumpedcalib/

NAMESPACE

@@ -7,3 +7,4 @@ export(d18Osw_calc)
 export(filter_outliers)
 export(temp_calc)
 export(temp_d18Osw_calc)
+importFrom(stats,coef)

R/apply_calib_and_d18O_boot.R

@@ -1,9 +1,13 @@
-#' Calculate bootstrapped mean values for age, d18O, d13C, and D47 and calculate temperature and d18Osw
+#' Calculate bootstrapped means with temperature and d18Osw
+#'
+#' For age, d18O, d13C, and D47, from which we calculate temperature and d18Osw.
 #'
 #' @inheritParams filter_outliers
 #' @inheritParams bootstrap_means
 #' @inheritParams temp_d18Osw_calc
 #' @inheritParams our_summary
+#' @param output Character vector specifying whether to return a `"summary"` or
+#'   the `"raw"` bootstrapped samples.
 #' @export
 apply_calib_and_d18O_boot <- function(data,
                                       calib,

R/clumped_calib_boot.R

@@ -3,6 +3,7 @@
 #' @param data A data.frame with columns D47, X, sd_X, and sd_D47. X stands for
 #'   the commonly-used temperature scale, 10^6 / T^2 with T in K.
 #' @param Nsim Number of simulations to do for bootstrapping.
+#' @returns A [tibble][tibble::tibble-package] with bootstrapped slope--intercept pairs.
 #' @export
 clumped_calib_boot <- function(data, Nsim = 1e5) {
   bs <- function(data, indices) {

R/clumpedcalib-package.R

@@ -0,0 +1,7 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @importFrom stats coef
+## usethis namespace: end
+NULL

R/equation_supported.R

@@ -1,6 +1,19 @@
 #' Parse equation name into our internal simplified code.
 #'
-#' Throws an error if not supported.
+#' See details for which equations are currently supported.
+#'
+#' - 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.
+#' @returns Character vector of cleaned up equation reference. Gives an error if it's currently not supported.
 equation_supported <- function(equation) {
   supported_equations <- c(
     "KimONeil1997", # NOTE: as recalculated in Bemis 1998!

R/temp_calc.R

@@ -11,12 +11,9 @@
 #' @export
 temp_calc <- function(d18Occ, d18Osw, equation = NULL) {
   equation <- equation_supported(equation)
-  if (!equation %in% supported_equations()) {
-    cli::cli_abort(c("Equation {equation} is not implemented",
-                     "i" = "Feel free to submit a pull request!"))
-  }
-
   if (equation == "KimONeil1997") {
+    # T (°C) = a + b(δc - δw) + c(δc - δw)^2
+    # with a = 16.1, b = -4.64, and c = 0.09
     d18Osw <- d18Osw - 0.27 # convert from VSMOW to VPDB
     temp <- 16.1 - 4.64 * (d18Occ - d18Osw) + 0.09 * (d18Occ - d18Osw)^2
   } else if (equation == "Marchitto2014") {

README.md

@@ -0,0 +1,53 @@
+# `clumpedcalib`: Calculate and Apply Clumped Isotope Calibrations Using Bootstrapping
+
+[![](https://zenodo.org/badge/657580630.svg)](https://zenodo.org/badge/latestdoi/657580630)
+
+Written by [Ilja J. Kocken](https://orcid.org/0000-0003-2196-8718) Feel
+free to use this stuff, as long as you adhere to the
+[file:LICENSE.md](LICENSE.md)
+
+-   Calculate bootstrapped York regression from clumped isotope
+    calibration data.
+-   Calculate bootstrapped sample means for the age, d13C, d18O, and
+    D47.
+-   Apply the bootstrapped calibration to calculate temperature and
+    d18Osw.
+-   Also comes with the classic d18Occ calibrations. See
+    [temp_calc()](R/temp_calc.R).
+-   As well as the inverses, for when you have constraints on
+    temperature and wish to calculate d18Osw. See
+    [d18Osw_calc()](R/d18Osw_calc.R) .
+
+## How to calculate bootstrapped averages and apply a clumped-isotope specific temperature calibration.
+
+To use this:
+
+1.  Install this package `clumpedcalib`, see
+    [#installation](#installation).
+2.  Update the input calibration data
+    [file:dat/example_calib.csv](dat/example_calib.csv). Make sure the
+    column names include `X`, `D47`, `sd_X`, `sd_D47`.
+3.  Add your sample data at the replicate level.
+4.  Check to see if you like [the function that calculates
+    d18Osw](R/d18Osw_calc.R). Currently, you can choose from the Kim &
+    O\'Neil 1997 calibration, as adjusted by Bemis et al., 1998, or the
+    Marchitto et al., 2014 calibration.
+5.  Create your own definition of [filter outliers](R/filter_outliers.R)
+    so that it filters out bad measurements and NA\'s for your data.
+6.  Walk through [the example workflow](clumped-bootstrap-calibration.org)
+    step-by-step.
+7.  Have a look at [the functions](R) to better understand what's
+    happening.
+
+The bootstrapped calibration idea is based on a Matlab script written by
+Alvaro Fernandez.
+
+# installation
+
+To install this development package:
+
+```{R}
+remotes::install_github("japhir/clumpedcalib")
+```
+
+Or you can look at all the [functions](R) and only copy what you like.

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: https://japhir.github.io/clumpedcalib/
+template:
+  bootstrap: 5
+

tests/testthat/test-d18Osw_temp_calculations.R

@@ -3,13 +3,13 @@ test_that("They're reversible", {
   temp_calc(d18Occ = 2, d18Osw = 0)
   d18Osw_calc(d18Occ = 2, temperature = 5)
   # is it reversible?
-  expect_equal(d18Osw = d18Osw_calc(d18Occ = 3,
-                                    temp = temp_calc(d18Occ = 3,
-                                                     d18Osw = 0)),
-               0)
+  expect_equal(d18Osw_calc(d18Occ = 3,
+                           temp = temp_calc(d18Occ = 3,
+                                            d18Osw = 0)),
+               expected = 0)
   expect_equal(temp_calc(d18Occ = 3,
                          d18Osw = d18Osw_calc(d18Occ = 3, temp = 5)),
-               5)
+               expected = 5)
   expect_error(d18Osw_calc(5, 3, equation = "hoi"))
   expect_error(temp_calc(5, 3, equation = "hoi"))
 
@@ -21,12 +21,12 @@ test_that("They're reversible", {
                                             d18Osw = 0,
                                             equation = "Marchitto2014"),
                            equation = "Marchitto2014"),
-               0)
+               expected = 0)
   expect_equal(temp_calc(d18Occ = 3,
                          d18Osw = d18Osw_calc(d18Occ = 3, temp = 5,
                                               equation = "Marchitto2014"),
                          equation = "Marchitto2014"),
-               5)
+               expected = 5)
 
   ## # set up a plot for comparison between equations
   ## comparison <- expand.grid(d18Occ = seq(-10, 10),