valentinitnelav

# ======================================================================================
# Create a simple world map in Robinson projection with labeled graticules using ggplot
# ======================================================================================

# Set a working directory with setwd() or work with an RStudio project

# __________ Set libraries
library(rgdal)      # for spTransform() & project()
library(ggplot2)    # for ggplot()

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# ======================================================================================
# Pacific centered world map with ggplot
# Enhanced aspect with graticules and labels
# The central/prime meridian can be shifted with any positive value towards west
# Can use any project of known PROJ.4 string
# ======================================================================================

# ~~~~~~~~~~~ Load needed libraries ~~~~~~~~~~~ #
library(data.table)
library(ggplot2)

valentinitnelav

# Converting coordinates from DMS or DdM formats to decimal
# DMS = "degrees minutes seconds"; DdM = "degrees decimal minutes" 
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dg2dec <- function(varb, Dg=NA, Min=NA, Sec=NA, SW.Hemisphere="S|W") {
  # Dg=decimal, Min=minutes and Sec=seconds; 
  # NOTE 1 - if the format is "degrees decimal minutes - DdM" (e.g. 40° 26.767′ N) and not 
  # "degrees minutes seconds - DMS" (e.g. 40° 26′ 46″ N), then call the function only with 
  # Dg and Min arguments, like dg2dec(varb, Dg="°", Min="′N"). 
  # Same applies when there is no seconds symbol (e.g. 45°12'7.38).
  # Note that one should not use blank spaces in Dg, Min or Sec arguments (will return NA).

valentinitnelav

# ==========================================================================
# Example of plot for publication with inwards ticks in ggplot
# ==========================================================================

library(ggplot2)

# ==================================
# create some data
# ==================================
set.seed(1)

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make_GeodesicBuffer <- function(XY.dg, dg.step=5, dst.m, crs){
    #######################################################################################################
    ## Function to make a circle-buffer around given points (long-lat coordinates)
    ## Is different from rgeos::gBuffer() by the fact that it allows the user to create 
    ## a geodesic buffer with a width expressed in metric units.
    ## Otherwise the user needs to project and apply an Euclidian buffer with rgeos::gBuffer(),
    ## which will introduce distortions that vary greatly with latitude and the radius of the circle buffer. 
    ## See also my question addressed here:
    ## https://gis.stackexchange.com/questions/250389/euclidean-and-geodesic-buffering-in-r
    ##

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# extract long-lat coordinates from a bunch of kmz files
# first unzips the KMZ-s then reads coordinates from each KML with getKMLcoordinates {maptools}
# (worth checking this as well: https://gist.github.com/holstius/6631918 )

library(maptools)

# list the kmz files in a given folder path
KMZs <- list.files(path="Data/kmz-files", pattern="*.kmz", full.names=FALSE)

# unzip each KMZ file and read coordinates with getKMLcoordinates()

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# =============================================================================================================
# Scraps the TPL web page for all families of angiosperms and downloads the corresponding *csv files. 
# Then grabs the unique species names from this pile of data and builds a custom dictionary for a spell checker. 
# =============================================================================================================

# _________ Read the family names from the TPL web page (Angiosperms only) _________ #
# I adapted code from http://www.stat.berkeley.edu/~spector/s133/Readexample.html for parsing through web pages
thepage <- readLines("http://www.theplantlist.org/1.1/browse/A/")
# One can notice that family names are in rows of such patern:
# <i class=\"family\">Piperaceae</i></a>"

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# ==========================================================================
# Dotplot with CI/error bars for publication - ggplot
# see also: http://www.cookbook-r.com/Graphs/Plotting_means_and_error_bars_(ggplot2)/
# ==========================================================================

library(ggplot2)

# ==================================
# create some data
# ==================================

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# -----------------------------------------------------------------------------
# Example to check some taxa names with Taxonstand & wikitaxa
# -----------------------------------------------------------------------------
my_sp <- fread("Output/taxa_to_check_VS.csv")
my_sp
# taxa
# Thereianthus_spicatus
# Eriocnema_fulva
# Hebe_macrocarpa
# Aspalathus_cymbriformis

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library(ggplot2)
library(ggsci) # for cool palettes

# read data
my_data <- read.csv("data/chickengrowthdiet.csv")
str(my_data)
# Diet should not be numeric but factor (or categorical)
my_data$Diet <- factor(my_data$Diet)

# -------------------------------------