arcaravaggi

# A wrapper for download and cleaning of IOC bird lists
# This function downloads a given list, defined by the URL,
# completes rows with relevant information, and outputs a data frame.
# Further functions may be added and a small package developed, in time.
# 
# There's almost certainly a more elegant way of doing this.
#
# earl = URL of IOC master List (see https://www.worldbirdnames.org/new/ioc-lists/master-list-2); currently defaults to v13.1
#
# E.g. 

arcaravaggi

##Generates a set of autocorrelated random normal variates
#
#INPUT
# n: number of variates to generate
# mean, sd: mean and standard deviation of the normal distribution
# r: the autocorrelation coefficient (between 0 and 1)
rautonorm <- function(n,mean=0,sd=1,r){
  ranfunc <- function(i,z,r) sqrt(1-r^2) * sum(z[2:(i+1)]*r^(i-(1:i))) + z[1]*r^i
  z <- rnorm(n)
  mean + sd*c(z[1], sapply(1:(n-1), ranfunc, z, r))

arcaravaggi

# Plot histogram with density curve, and measures of dispersion from the mean
#
# dispersion x axis:
# V = Sample variance
# IQR = inter-quartile range (balanced)
# SD = standard deviation
# SE = Standard error
# CI = Confidence interval (see inputs)
#
# CV = coefficent of variation

arcaravaggi

# Function to reduce multiple columns to single binary vector
# c = data frame or columns of interest
binRC <- function(c){
 d <- as.integer(rowSums(c)>0)
 return(d)
}                 

# Here's an example, using a randomly generated data frame
set.seed(42)
df <- data.frame(col1 = rbinom(n=100, size=1, prob=0.05), 

arcaravaggi

# Function to load a list of packages
# Installs if package is absent
#
# Pass character vector
# E.g. ipak(c("beepr", "dplyr", "adehabitat"))
#
ipak <- function(pkg){
  new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
  if (length(new.pkg)) 
    install.packages(new.pkg, dependencies = TRUE)

arcaravaggi

# There's probably a much neater way to do this but if it works, it works. And this? It works. 

set.seed(24)
df <- data.frame(col1 = rep(LETTERS[1:4], 10),
                col2 = rep(1:10, 4))

# Function to create network data objects ####
# - a data frame of usernames that interact with >1 hashtag ('dataframe')
# - edges and nodes used in creating networks ('edges', 'nodes')
# - the network object ('routes')

arcaravaggi

# From https://stackoverflow.com/questions/17022553/adding-r2-on-graph-with-facets
# Function for calculating R^2
# Adjust the lm call as required
lm_eqn = function(df){
  m = lm(min_t ~ max_t, df);
  eq <- substitute(r2, 
             list(r2 = format(summary(m)$r.squared, digits = 3)))
  as.character(as.expression(eq));                 
}

arcaravaggi

# Copy all rows in a dataframe according to their maximum value. 
# Copy all other integers an appropriate number of times, filling the last cell with 0.
#
# By StackOverflow user, CPak: https://stackoverflow.com/a/50930471/9962100
# 
# Example
# df <- data.frame(A1 = c(0,2,0,3), A2 = c(1,0,2,0), A3 = c(0,1,3,2))
# ans <- data.frame(A1 = c(0,2,2,0,0,0,3,3,3), A2 = c(1,0,0,2,2,0,0,0,0), A3 = c(0,1,0,3,3,3,2,2,0))
# library(magrittr)
# test <- do.call(rbind, lapply(seq_len(nrow(df)), function(x) explodeR(df[x, ]))) %>% as.data.frame

arcaravaggi

# By Stack user forlooper 
# https://stackoverflow.com/a/37332382
#
# e.g.
# p <- extractCoords(SST_start)
extractCoords <- function(sp.df)
{
  results <- list()
  for(i in 1:length(sp.df@polygons[[1]]@Polygons))
  {

arcaravaggi

# Function for truncation of normal distribution
# n = number of iterations (default = 1000)
# m = mean
# s = SD/SE/CI
# l = lower bounds (default = -100)
# u = upper bounds (default = 100)
# r = round to x integers (default = 5)
tnorm <- function(n = 1000, m, s, l = -100, u = 100, r = 5) {   
  tdist <- round(rnorm(n, m, s), r)
  tdist[tdist < l] <- l