Rekyt

library(ggmap)
sites = unique(df.table[, list(LON, LAT, interpreted.location, site.number)])
france = get_map("France", zoom = 6)
franceMap = ggmap(france)
franceMap + 
  geom_point(data = sites, aes(x = LON, y = LAT, color = as.factor(site.number)), size = 4) +
  labs(x = "Longitude", y = "Latitude")

Rekyt

# Fast plot for gaussian function
#
library(ggplot2)
library(grid)
library(dplyr)
# Choose a window
seq = seq(-5, 5, 0.01)

# Compute density for Gaussian function
# Mean = 0, sd = 1

Rekyt

# Multipage pdf plots with ggplot2

library(ggplot2)  # Load ggplot2 obviously
library(gridExtra)  # Load some extensions to have multiplot pdf

# Simulate data
df = data.frame(x = seq(1:30), y = rnorm(30), z = runif(30, 1, 10))

# Example plots
p.1 = ggplot(df, aes(x = x, y = y)) +

Rekyt

# Gist to simulate Growth Rate and Trait distribution
# Effects of varying coefficients
# Author: Matthias Grenié

# Packages ####

library(dplyr)  # Manipulate data
library(gtools)  # Combinations
library(ggplot2)  # Plots

Rekyt

# Example of automatic formula
# How to generate and test automatically different formulas
set.seed(1)  # Makes it reproducible

library(dplyr)
library(lmerTest)

# Test data
df = data.frame(a = runif(30, 1, 10), b_sp = rnorm(30, 5, 20), 
                b_abs = runif(30, 0, 1), c_sp = rnorm(30, -3, 10),

Rekyt

# For the moment, ggplot2 stable version cannot support the option 'geom_point(stroke = 2)' to change border size of points
# To use it we need to install ggplot2 development version
# To do that we first want to install 'devtools' package which makes packages installation from GitHub easier
install.packages("devtools")

# 'ggplot2' last version is at 'http://github.com/hadley/ggplot2/'
# thus using devtools' function 'install_github()' (install from GitHub) the syntax is simple:
devtools::install_github("hadley/ggplot2")  # Note the use of '::' not to load the entire package

# Plots

Rekyt

# Script to plot convex hull over points in ggplot2

# Packages
library(dplyr)  # To make code easier to read
library(ggplot2)

# Data Generation
set.seed(1)  # For reproducibility of example

df = data.frame(x = rnorm(100, 10, 5), y = rnorm(100, 10, 5), z = sample(letters[1:5], size =  100, replace = T))

Rekyt

# Script from a density to color quantiles area

# Packages ---------------------------------------------------------------------
library(ggplot2)
library(dplyr)

# Data -------------------------------------------------------------------------
r_data = rnorm(100)  # Computes 100 values

r_quant = quantile(r_data, probs = seq(0, 1, 0.1))  # Computes quantiles

Rekyt

# Script to plot an alpha shape on ggplot2 from a given sets of points
# Inspired by: https://rpubs.com/geospacedman/alphasimple

# Packages --------------------------------------------------------------------
library(ggplot2)
library(dplyr)
library(alphahull)
library(igraph)

Rekyt

365 Papers

Using the #365papers hashtag on Twitter to show the list of papers read in 2016

List

1. James H. Brown, "Macroecology", The University of Chicago Press, 1995;
2. Mislan et al., "Elevating The Status of Code in Ecology", TREE, Jan 2016 https://doi.org/10.1016/j.tree.2015.11.006;
3. Morueta-Holme, Blonder et al., "A network approach for inferring species associations from co-occurrence data", Ecography 22 January 2016, https://doi.org/10.1111/ecog.01892;
4. Schuldt et al., "Multitrophic diversity in a biodiverse forest is highly nonlinear across spatial scales", Nature Communications, 10 Dec 2015, https://doi.org/10.1038/ncomms10169;