In atredennick/patches: Calculates metrics for analysis of alpha, beta, and gamma variability

This is a quick example for using the individual functions in the patches package.

All metrics are based on Wang and Loreau (2014, Ecology Letters). Below is a schematic for how they are all related, and the equations used in the functions.

Install and load package

Load a bunch of packages, then install patches. Also read in a test data set.

# Load relevant packages
# install.packages(c("dplyr", "plyr", "reshape2", "synchrony", "devtools"))
require(plyr)
require(dplyr)
require(reshape2)
require(synchrony)
require(devtools)

# Install package from GitHub
devtools::install_github("atredennick/patches")
require(patches)


# Read in data
setwd("/Users/atredenn/Dropbox/Patches/")
species_data_kbs <- read.csv("./Data sets/AllSpData_02282015.csv")%>%
              filter(site_code=="KBS") %>%
              filter(treatment=="T0F0")

Get all the different metrics

Species synchrony

# Start with species synchrony in each patch
phi <- species_synchrony(D = species_data_kbs)
print(phi)

First column is the plot id, second is species synchrony in that plot.

Variability of j-th species in i-th plot

CVji <- ind_spp_var(D=species_data_kbs)
# look at just the head...there are num_spp*num_plots lines
head(CVji)

Note that species that only show up once in the time series have the same CV. Here's an example of why that happens...

obs_anpp <- c(1:10)
num_years <- 10
for(i in 1:length(obs_anpp)){
  ts <- numeric(num_years)
  ts[1] <- obs_anpp[i]
  cv <- sd(ts)/mean(ts)
  print(cv)
}

So, regardless of the actual value, if there is only one observation, then the CVs are always equal.

Averaged species variability in each plot

CVspp_i <- avg_spp_var(D = species_data_kbs)
# Returns one value per plot
print(CVspp_i)

Variability of community i (CV_i^2)

CVi_sq <- community_var(D = species_data_kbs)
# Returns one value per plot
print(CVi_sq)

Alpha variability (CV_L^2)

CV_L <- alpha_var(D = species_data_kbs)
# Returns one value
print(CV_L)

Beta variability (B_1)

B_1 <- beta_var(D = species_data_kbs)
# Returns one value
print(B_1)

Gamma variability (CV_M^2)

CV_M <- gamma_var(D = species_data_kbs)
# Returns one value
print(CV_M)

atredennick/patches documentation built on May 10, 2019, 2:11 p.m.