M_index_stan: M index of reproductive skew using Stan to conduct Bayesian...

In ctross/SkewCalc: Estimation Of Reproductive Skew

M index of reproductive skew using Stan to conduct Bayesian bootstrapping

Description

M index of reproductive skew using Stan to conduct Bayesian bootstrapping

Usage

M_index_stan(
  r,
  t,
  t0 = FALSE,
  samples = 2000,
  warmup = 1000,
  chains = 2,
  adapt_delta = 0.9,
  max_treedepth = 12,
  refresh = 100,
  agemode = "elasticity",
  priors = NULL
)

Arguments

r	A vector of RS values over time period of observation (i.e., between times t0 and t).
t	A vector of ages at death or last census.
t0	A vector of ages at first census. Defaults to zero.
samples	Number of MCMC samples per chain.
warmup	Number of warmup iterations per chain.
chains	Number of chains.
adapt_delta	A tuning parameter in Stan. See "rstan" package for more details.
max_treedepth	A tuning parameter in Stan. See "rstan" package for more details.
refresh	How often to print updates on MCMC progress.
agemode	Age control based on "elasticity" or "gaussianprocess". If Gaussian process is used, t and t0 must be integers, and max(t) not too big (e.g., < 90 or so).
priors	A 2 x 2 matrix. The first row gives the mean and sd of a normal distribution for the elasticity parameter, with default of mu=1.0, sd=0.1. The second row give the prior for the log concentration parameter, with a default of mu=0.0, sd=2.5.

Value

A Stan object "StanResults" and a data object "model_dat" are saved to the workspace. These can be used for plots and calculations. Results are also printed:

1) M. The posterior distribution of M, not accounting for diminishing RS returns to age.

2) M_age. The posterior distribution of M, accounting for diminishing RS returns to age.

3) M_raw. The posterior distribution of M_raw, not accounting for diminishing RS returns to age.

4) M_raw_age. The posterior distribution of M_raw, accounting for diminishing RS returns to age.

5) gamma The estimated elasticity of RS on exposure time.

Examples

set.seed(1)
RS = rpois(100, 5) 
Age = rpois(100, 45)
M_index_stan(RS, Age)

ctross/SkewCalc documentation built on June 11, 2025, 1:31 a.m.