inst/doc/a03_LifeHistoryTraits.R

In Rage: Life History Metrics from Matrix Population Models

## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## -----------------------------------------------------------------------------
library(Rage) # load Rage
data(mpm1) # load data object 'mpm1'
mpm1 # display the contents

## -----------------------------------------------------------------------------
# mean life expectancy from "seed" stage
life_expect_mean(matU = mpm1$matU, start = 1)

# variance in life expectancy from "seed" stage
life_expect_var(matU = mpm1$matU, start = 1)

## -----------------------------------------------------------------------------
# mean life expectancy from "small" stage
life_expect_mean(matU = mpm1$matU, start = 2)

## -----------------------------------------------------------------------------
life_expect_mean(matU = mpm1$matU, start = NULL, mixdist = c(0, 0.4, 0.6, 0, 0))

## -----------------------------------------------------------------------------
longevity(matU = mpm1$matU, start = 2, lx_crit = 0.05)

## -----------------------------------------------------------------------------
longval <- NULL
startvec <- seq_len(nrow(mpm1$matU)) # vector of starting stages

for (i in startvec) {
  longval[i] <- longevity(matU = mpm1$matU, start = startvec[i], lx_crit = 0.05)
}

plot(longval,
  type = "l", xlab = "Starting stage",
  ylab = "Longevity to 5% survivorship"
)
longval

## -----------------------------------------------------------------------------
net_repro_rate(matU = mpm1$matU, matR = mpm1$matF)

## -----------------------------------------------------------------------------
gen_time(matU = mpm1$matU, matR = mpm1$matF)

## -----------------------------------------------------------------------------
mature_age(matU = mpm1$matU, matR = mpm1$matF, start = 2)

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mature_prob(matU = mpm1$matU, matR = mpm1$matF, start = 2)

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mpm1$matF # We see that the "medium" and "large" stages are reproductive

maturedist <- mature_distrib(
  matU = mpm1$matU, start = 1L,
  repro_stages = c(FALSE, FALSE, TRUE, TRUE, FALSE)
)
maturedist

## -----------------------------------------------------------------------------
# mean life expectancy from maturity
life_expect_mean(matU = mpm1$matU, start = NULL, mixdist = c(maturedist))

# mean life expectancy from "small" stage
life_expect_mean(matU = mpm1$matU, start = 2)

## -----------------------------------------------------------------------------
lx <- mpm_to_lx(matU = mpm1$matU, start = "small")
px <- mpm_to_px(matU = mpm1$matU, start = "small")
hx <- mpm_to_hx(matU = mpm1$matU, start = "small")
mx <- mpm_to_mx(matU = mpm1$matU, matR = mpm1$matF, start = "small")

## -----------------------------------------------------------------------------
lx_seed <- mpm_to_lx(matU = mpm1$matU, start = "seed")

plot(lx,
  xlab = "Survival time (years)", ylab = "Survivorship",
  type = "s", col = "black"
)
lines(lx_seed, type = "s", col = "orange")
legend("topright",
  inset = c(0.05, 0.05), c("From seed stage", "From small stage"),
  lty = c(1, 1), col = c("orange", "black")
)

## -----------------------------------------------------------------------------
entropy_d(lx, mx) # Demetrius' entropy
entropy_d(lx = mpm1$matU, mx = mpm1$matF, start = "small") # Demetrius' entropy

life_elas(lx) # Keyfitz' entropy
life_elas(lx = mpm1$matU, start = "small") # Keyfitz' entropy

entropy_k_stage(mpm1$matU)

data(leslie_mpm1) # load leslie matrix
entropy_k_age(leslie_mpm1$matU)

## -----------------------------------------------------------------------------
# shape of survival/mortality trajectory
shape_surv(lx)

# shape of fecundity trajectory
shape_rep(mx)