wpetry

#################################################
## Illuminating the dark corners of demography
## W.K. Petry
##
## README: This code reproduces the analyses shown on the COM(P)ADRE blog. The analyses were run
## at a spatial resolution of 1/12° (>9.3 million cells to cover the Earth!), and will take several hours
## to run the necessary calculations on a standard desktop/laptop. It's recommended that the code be run
## at a coarser spatial resolution first, increasing the resolution only when accuracy is needed. See the
## 'res' parameter under the 'Preliminaries' heading.
#################################################

wpetry

# dplyr pipe ligature ideas:

## %>%	forward-pipe operator
˙>.

## %T>%	tee operator
˙T>.

## %<>%	compound assignment pipe-operator
˙◇.

wpetry

#################################################
## Format p-values for use in Rmarkdown documents
## This function modifies base::format.pval() to automate
## the inclusion of equalities and inequalities
## Author: W.K. Petry
#################################################
# Arguments:
# pv            a numeric vector
# digits        how many significant digits to use; recommended value is 3
# eps           numerical tolerance; effectively the smallest p-value to report; recommended value is 10^(-digits)

wpetry

library(ggplot2)
library(grid)
# define consistent ggplot theme to apply to all figures
theme_ms <- function(base_size=12, base_family="Helvetica") {
  library(grid)
  (theme_bw(base_size = base_size, base_family = base_family)+
      theme(text=element_text(color="black"),
            axis.title=element_text(face="bold", size = rel(1.3)),
            axis.text=element_text(size = rel(1), color = "black"),
            legend.title=element_text(face="bold"),

wpetry

library(lubridate)

wtr_yr <- function(dates, start_month = 9) {
  # Convert dates into POSIXlt
  dates.posix <- as.POSIXlt(dates)
  # Year offset
  offset <- ifelse(dates.posix$mon >= start_month - 1, 1, 0)
  # Water year
  adj.year <- dates.posix$year + 1900 + offset
  # Return the water year

wpetry

# somewhat hackish solution to:
# https://twitter.com/EamonCaddigan/status/646759751242620928
# based mostly on copy/pasting from ggplot2 geom_violin source:
# https://github.com/hadley/ggplot2/blob/master/R/geom-violin.r

library(ggplot2)
library(dplyr)


"%||%" <- function(a, b) {

wpetry

## Generate random compositions that sum to <=1

library(gtools)
library(ggtern)
library(scatterplot3d)

rCompos <- function(n, subsamples, alphas = NULL){
  if(is.null(alphas)) alphas <- rep(1, subsamples)
  sums <- matrix(runif(n), ncol = 1)
  dirichlet <- gtools::rdirichlet(n, alphas)

wpetry

#################################################-
## Evaluate color palettes for colorblindness accessibility ----
## W.K. Petry
#################################################-
## Preliminaries ----
#################################################-
library(colorspace)
library(colorscience)
library(paletteer)  # devtools::install_github("EmilHvitfeldt/paletteer")
library(tidyverse)

wpetry

#' Retrieve attached or loaded package names and their version numbers
#'
#' @param L an object of class 'sessionInfo'. Default is to retrieve the current
#'     workspace session information.
#' @param n character specifying whether to use attached packages ('otherPkgs') or
#'     packages only loaded via a namespace ('loadedOnly'). Base packages are always
#'     omitted.
#'
#' @return a data frame with two columns: the package name and the package version number.
#' @export

wpetry

# WindRose.R
# modified from https://stackoverflow.com/questions/17266780/wind-rose-with-ggplot-r
require(ggplot2)
require(RColorBrewer)
require(dplyr)
require(tidyr)

plot.windrose <- function(data,
                          spd,
                          dir,