In ha0ye/portalDS: Compute Dynamic Stability for Rodents at Portal

knitr::opts_chunk$set(echo = TRUE)

Introduction

This report documents applying the dynamic stability analysis to the Portal dataset.

First, some setup for the environment:

library(portalDS)
library(dplyr)
library(ggplot2)

set.seed(42)
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Workflow

Data

We use data from the 8 control plots, up to the 2015 treatment-switch. Abundances are summed, and scaled according to the number of plots sampled in each census (sometimes, incomplete sampling occurred). Only species with at least 50% non-zero abundance across the time series were kept. Missing censuses had abundances imputed using linear interpolation for each individual species.

block <- make_portal_block(filter_q = 0.5)
str(block)

Analysis

We do not go through the full analysis here. Instead, see the Maizuru Dynamic Stability vignette or (eventual methdos write-up).

We specify a results file for storing the outputs of the analysis. The compute_dynamic_stability() function will check for the presence of individual output components and will skip them if they've already been computed.

results_file <- here::here("output/portal_ds_results_50.RDS")
results <- compute_dynamic_stability(block, results_file)
str(results, max.level = 1)

Results

Abundance time series

plot_time_series(results$block)

Eigenvalues & Eigenvectors

Highlighted segments are the posterior estimates of regime shifts from Christensen et al. 2018.

plot_eigenvalues(results$eigenvalues, 
                 num_values = 3) %>% 
    add_regime_shift_highlight()

plot_eigenvectors(results$eigenvectors) %>% 
    add_regime_shift_highlight()

Singular values and SVD vectors

Again, highlighted segments are the posterior estimates of regime shifts from Christensen et al. 2018.

plot_svd_values(results$svd_decomp$d, 
                num_values = 3) %>% 
    add_regime_shift_highlight()

plot_svd_vectors(results$svd_decomp$u) %>% 
    add_regime_shift_highlight()

ha0ye/portalDS documentation built on March 28, 2020, 1:21 p.m.