restoring repo contents

Author: Archaeo-Programmer

Diff for: .Rbuildignore

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+^.*\.Rproj$
+^\.Rproj\.user$

Diff for: .gitignore

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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# Mac Files
+.DS_Store
+vignettes/.DS_Store
+

Diff for: DESCRIPTION

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+Package: cropDiffusionR
+Type: Package
+Title: Exploring the Diffusion of Agricultural Crops
+Version: 1.0.0
+Date: 2022-09-23
+Authors@R: 
+    c(
+    person(given = "Andrew",
+           family = "Gillreath-Brown",
+           role = c("aut", "cre"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0002-2272-5542")),
+    person(given = "Timothy",
+           family = "Kohler",
+           role = c("aut", "ctb"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0002-3414-6660"))
+           )
+Maintainer: Andrew Gillreath-Brown <[email protected]>
+Description: This R package repository is to accompany the submission for Gillreath-Brown and Kohler 2022, which examines the effects temperature on the spread of maize agriculture to the southwestern United States.
+License: MIT + file LICENSE
+Depends: 
+    magrittr,
+    R (>= 3.5.0),
+    vegan
+Imports: 
+    rebus.numbers,
+    leaflet,
+    sp,
+    rgdal,
+    plotly,
+    RColorBrewer,
+    here,
+    lubridate,
+    units,
+    rcarbon, 
+    DescTools, 
+    sf,
+    readr,
+    purrr,
+    dplyr,
+    tibble,
+    tidyr,
+    raster,
+    reshape2, 
+    mgcv,
+    ggplot2,
+    maps,
+    ggh4x,
+    usmap,
+    shadowtext,
+    knitr,
+    data.table,
+    httr,
+    ggpubr,
+    gganimate,
+    ggsci,
+    p3k14c,
+    terra
+Remotes: 
+    zeehio/facetscales,
+    Archaeo-Programmer/paleomat
+LazyData: TRUE
+Suggests: testthat
+Encoding: UTF-8
+URL: https://github.com/Archaeo-Programmer/cropDiffusionR
+BugReports: https://github.com/Archaeo-Programmer/cropDiffusionR/issues
+RoxygenNote: 7.2.1
+Roxygen: list(markdown = TRUE)

Diff for: LICENSE

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+MIT License
+
+Copyright (c) 2022 Andrew Gillreath-Brown
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Diff for: NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(extract_GDD)
+export(extract_diffusion)
+export(extract_earliest_crop)
+importFrom(magrittr,`%<>%`)
+importFrom(magrittr,`%>%`)

Diff for: R/data.R

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+#' Annual Accumulated Growing Degree Days from SAGE.
+#'
+#' A `raster` containing annual global accumulated growing degree days for the year with a base temperature of 5°C.
+#'
+#' @format An object of class `RasterLayer`.
+#' @source \url{https://sage.nelson.wisc.edu/data-and-models/atlas-of-the-biosphere/mapping-the-biosphere/ecosystems/growing-degree-days/}
+"global_gdd"
+
+#' North American Southwest Ancient Maize Database.
+#'
+#' A `tibble` containing calibrated radiocarbon data for ancient maize macrosamples across the North American Southwest.
+#'
+#' @format An object of class `tibble`.
+#' @source \url{https://doi.org/10.1038/s41597-022-01118-7}
+#' @source \url{https://doi.org/10.48512/XCV8459173}
+#' @source \url{http://en.ancientmaize.com/}
+#' @source \url{https://www.canadianarchaeology.ca/}
+#' @references
+#' Bocinsky, R. Kyle, Darcy Bird, and Erick Robinson, (2020). Compendium of R code and data for p3k14c: A synthetic global database of archaeological radiocarbon dates. Accessed on September 12, 2022. https://github.com/people3k/p3k14c
+#'
+#' Bird, D., Miranda, L., Vander Linden, M. et al. p3k14c, a synthetic global database of archaeological radiocarbon dates. Sci Data 9, 27 (2022). https://doi.org/10.1038/s41597-022-01118-7
+#' 
+#' Blake, M., B. Benz, D. Moreiras, L. Masur, N. Jakobsen and R. Wallace. 2017. Ancient Maize Map, Version 2.1: An Online Database and Mapping Program for Studying the Archaeology of Maize in the Americas. http://en.ancientmaize.com/. Laboratory of Archaeology, University of B.C., Vancouver. Accessed on February 24, 2021.
+#' 
+#' Martindale, Andrew, Richard Morlan, Matthew Betts, Michael Blake, Konrad Gajewski, Michelle Chaput, Andrew Mason, and Pierre Vermeersch (2016) Canadian Archaeological Radiocarbon Database (CARD 2.1), accessed September 10, 2022.
+"maizeDB"
+
+#' Annual Accumulated Growing Degree Days from WorldClim.
+#'
+#' A `raster` containing annual accumulated growing degree days for the year with a base temperature of 10°C and maximum temperature of 30°C. 
+#' GDD was calculated from the tavg 30 seconds (~1 \ifelse{html}{\out{km<sup>2</sup>}}{\eqn{km^2}}).
+#'
+#' @format An object of class `RasterLayer`.
+#' @source \url{https://www.worldclim.org/data/worldclim21.html}
+"NASW_gdd"
+
+#' Southwestern United States and Mexico States Polygon.
+#'
+#' A `MULTIPOLYGON` containing the state boundaries for the southwestern United States (i.e., Arizona, Colorado, New Mexico, and Utah) and Mexico.
+#'
+#' @format An object of class `sfc_MULTIPOLYGON`.
+#' @source \url{https://www.arcgis.com/home/item.html?id=ac9041c51b5c49c683fbfec61dc03ba8}
+"usa_mexico_states"
+
+#' Digital Elevation Model for the Southwestern United States and Mexico States.
+#'
+#' A `raster` containing elevation for the southwestern United States (i.e., Arizona, Colorado, New Mexico, and Utah) and Mexico.
+#'
+#' @format An object of class `RasterLayer`.
+#' @source \url{https://github.com/jhollist/elevatr}
+"NASW_elevation"
+

Diff for: R/extract_GDD.R

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+#' @name extract_GDD
+#' @title Extract annual accumulated growing degree days
+#'
+#' @description `extract_GDD()` extracts annual accumulated growing degree days from WorldClim 2.0 for 1970 to 2000 at site locations.
+#'
+#' @param sites A data.frame with an ID and sfc_Point geometry containing site locations.
+#' @return A tibble with growing degree days for each ID.
+#' @importFrom magrittr `%<>%` `%>%`
+#' @export
+extract_GDD <-
+  function(sites) {
+
+    # Get annual accumulated growing degree days.
+    terra::extract(x = cropDiffusionR::NASW_gdd,
+                    y = sites) %>%
+      dplyr::bind_cols(LabID = sites$LabID, GDD = .)
+    
+  }

Diff for: R/extract_diffusion.R

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+#' @name extract_diffusion
+#' @title Extract latitudinal diffusion of a crop
+#'
+#' @description `extract_diffusion()` extracts the diffusion of a crop by latitude.
+#'
+#' @param database A data.frame containing a crop database.
+#' @param direction A string stating the direction of diffusion (i.e., north).
+#' @return A tibble that has the frontier of a crop through time using 100 year time bins.
+#' @importFrom magrittr `%<>%` `%>%`
+#' @export
+extract_diffusion <-
+  function(database, direction = "north") {
+    database <- database %>%
+      # Create 100 year bins.
+      dplyr::mutate(bin = cut(
+        MedianBP,
+        breaks = seq(
+          plyr::round_any(min(MedianBP), 100, f = floor),
+          plyr::round_any(max(MedianBP), 100, f = ceiling),
+          by = 100
+        ),
+        include.lowest = TRUE
+      ))
+    
+    if (direction == "north")
+      database %>%
+      dplyr::group_by(bin) %>%
+      dplyr::slice_max(Lat) %>%
+      dplyr::slice_max(MedianBP) %>%
+      dplyr::ungroup() %>%
+      dplyr::arrange(desc(MedianBP)) %>%
+      dplyr::filter(Lat == cummax(Lat)) %>%
+      dplyr::group_by(SiteName) %>%
+      dplyr::slice_min(Date, with_ties = FALSE) %>%
+      dplyr::ungroup() %>% 
+      dplyr::arrange(Date)
+    else
+      stop(
+        "The direction is not north. Please use north for direction. We will be updating this function in the fugure to do other directions."
+      )
+  }

Diff for: R/extract_earliest_crop.R

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+#' @name extract_earliest_crop
+#' @title Extract earliest date for a crop by province
+#'
+#' @description `extract_earliest_crop()` extracts the sample with the earliest date for a crop by province.
+#'
+#' @param database A data.frame containing the crop database.
+#' @return A tibble that contains the earliest date for each province.
+#' @importFrom magrittr `%<>%` `%>%`
+#' @export
+extract_earliest_crop <-
+  function(database) {
+    database %>%
+      dplyr::group_by(Province) %>%
+      dplyr::slice_max(MedianBP) %>%
+      dplyr::ungroup() %>% 
+      dplyr::arrange(Latitude)
+    
+  }

Diff for: README.md

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+# cropDiffusionR: Exploring the Diffusion of Agricultural Crops
+
+`cropDiffusionR` is an *R* package implementing functions to perform
+analysis on the relationship between maize agriculture and temperature changes in prehistory.
+
+This is the official R package for [cropDiffusionR](https://github.com/Archaeo-Programmer/cropDiffusionR), 
+which contains all code associated with the analyses described and presented, including figures and tables, in Gillreath-Brown et al. 2022 (submitted): 
+
+Gillreath-Brown, A., and T. A. Kohler (2022). Children of El Niño: How Maize Farmers in the US Southwest Grew and Prospered under El Niño but Suffered under La Niña. Submitted to *KIVA* for review.
+    
+All code for analysis, figures, and tables is in [Maize_Analysis.Rmd](vignettes/Maize_Analysis.Rmd).
+
+## Installation
+
+You can install `cropDiffusionR` from GitHub with these lines of R code (Windows users are recommended to install a separate program, Rtools, before proceeding with this step):
+
+``` r
+if (!require("devtools")) install.packages("devtools")
+devtools::install_github("Archaeo-Programmer/cropDiffusionR")
+```
+
+## Repository Contents
+
+The [:file\_folder: vignettes](vignettes) directory contains:
+
+  - [:page\_facing\_up: Maize_Analysis](vignettes/Maize_Analysis.Rmd): R
+    Markdown document with all analysis and code to reproduce the figures and tables for the submitted paper (Gillreath-Brown and Kohler 2022).
+    It also has a rendered version, [Maize_Analysis.html](vignettes/Maize_Analysis.html), which shows figure and table output.
+  - [:file\_folder: figures](vignettes/figures): Plots, figures, and illustrations in the paper, including supplementary materials.
+  - [:file\_folder: tables](vignettes/tables): Tables in the paper, including supplementary materials.
+  
+  ## How to Run the Code?
+
+To reproduce the analysis, output, figures, and tables, you will need to clone the repository. To clone the repository, you can do the following from your Terminal:
+
+```bash
+git clone https://github.com/Archaeo-Programmer/cropDiffusionR.git
+cd cropDiffusionR
+```
+
+After installing the `cropDiffusionR` package (via `install_github` as shown above or by using `devtools::install()`), then you can render the analysis, visualizations, and tables.
+You can compile the `cropDiffusionR` analysis within R by entering the following in the console:
+
+``` r
+rmarkdown::render(here::here('vignettes/Maize_Analysis.Rmd'), output_dir = here::here('vignettes'))
+```
+
+If you do not want to compile the R Markdowns, then you can retrieve a readable HTML file by navigating to [Maize_Analysis.html](vignettes/Maize_Analysis.html). Then, click "Raw" and save the file as "Maize_Analysis.html" (i.e., save file with `.html` extension or as HTML file type). Another option, after installing the `cropDiffusionR` package, is to use `rstudioapi::viewer` in the R console:
+
+``` r
+rstudioapi::viewer(here::here('vignettes/cropDiffusionR.html'))
+```
+
+Another option for reproducing the results is to use the package itself and follow along with the vignette, [ cropDiffusionR](vignettes/cropDiffusionR.Rmd). Data and functions are already loaded into the package. 
+
+## Licenses
+
+**Code:** [GNU GPLv3](LICENSE.md)
+
+**Data:** [CC-0](http://creativecommons.org/publicdomain/zero/1.0/)
+attribution requested in reuse
+
+## Acknowledgements
+
+This material is based upon work supported by the National Science Foundation under Grants [SMA-1637171](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1637171) 
+and [SMA-1620462](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1620462), and by the Office of the Chancellor, [Washington State University-Pullman](https://wsu.edu/).

Diff for: cropDiffusionR.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace,vignette