In brouwern/popcycles: What the Package Does (One Line, Title Case)

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

library(popcycles)

An excellent introduction to matrix population models can be found here:

Stevens, H. 2020. A primer of ecology in R Chapter 4 Density-independent Demography Sections 4.1 to 4.6 https://hankstevens.github.io/Primer-of-Ecology/DID.html

Key concepts:

• life cycle graph
• matrices and matrix math
• life stages
• matrix representation of life cycles
• population projection
• population growth rate
• population growth rate from eigenanalysis
• sensitivity and elasticity analysis
• what's missing from this model: spatial structure, density dependence

Example: Gopher Tortise

Desert tortoise "medium-high" fertility matrix from Doak et al. 1994 Used for examples in Caswell 2002 book, Wisdom et al, and elsewhere. Results reported in Table 6 of Doak et al. 1994.

Data

Data for testing / demonstrating functions. Could add this to help files for the functionss.

tortoise <- matrix(data = c(0.000,0.000,0.000,0.000,0.000,1.300,1.980,2.57,
0.716,0.567,0.000,0.000,0.000,0.000,0.000,0.00,
0.000,0.149,0.567,0.000,0.000,0.000,0.000,0.00,
0.000,0.000,0.149,0.604,0.000,0.000,0.000,0.00,
0.000,0.000,0.000,0.235,0.560,0.000,0.000,0.00,
0.000,0.000,0.000,0.000,0.225,0.678,0.000,0.00,
0.000,0.000,0.000,0.000,0.000,0.249,0.851,0.00,
0.000,0.000,0.000,0.000,0.000,0.000,0.016,0.86),
byrow = T,nrow = 8)

n <- c("yearling",  "juv1",  "juv2",  "imm1",  "imm2", "subadult", "adult1", "adult2")
rownames(tortoise) <- n
colnames(tortoise) <- n

Test calc_lam

calc_lam(tortoise) #Matches "Average" - "All" result, Table 1, Doak et al 1994.

Sensitivities

max(calc_S(tortoise)$E) # matches sensitivity reported in Caswell 2002 pg 256

Note: elasticities sum to 1.

sum(calc_S(tortoise)$E)

brouwern/popcycles documentation built on June 10, 2021, 3:23 p.m.