## ----eval=FALSE---------------------------------------------------------------
#  install.packages('coffee')

## -----------------------------------------------------------------------------
library(coffee)

## ----fig.width=4, fig.asp=1.3-------------------------------------------------
sim.rings(age.start=1000, length=400, gaps=20)
mytree <- rings()

## ----eval=FALSE---------------------------------------------------------------
#  ?rings

## ----eval=FALSE---------------------------------------------------------------
#  set.seed(123)
#  sim.strat()
#  strat(its=2e5) # note that this run will take a few minutes

## -----------------------------------------------------------------------------
# The run's files will be put in this folder: strats/mystrat
#   |>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>| 100%
# Done running...
# Removed a burn-in of 100
# Thinning the MCMC by storing every 8 iterations
# 79.71% of the model's ages fit within the 95% hpd ranges of the dates,
# with worst-fitting date 2 (51.38%) and best-fitting date 4 (93.89%)
# Run took 3.17 minutes

## ----eval=FALSE, fig.width=4, fig.asp=1.3-------------------------------------
#  set.seed(234)
#  sim.strat()
#  strat(burnin=0, thinning=1, internal.thinning=1, its=2000,
#    init.ages=rbind(seq(3000, 4000, length=5), rbind(seq(3010, 4010, length=5))))

## ----eval=FALSE, fig.width=4, fig.asp=1.3-------------------------------------
#  strat("block_example", its=2e6, thinning=20, internal.thinning=20) # takes long to run

## ----eval=FALSE---------------------------------------------------------------
#  strat("undated_example") # will need a longer run for reliable results (the example below used 600,000 iterations)

## ----fig.width=4, fig.asp=1.3-------------------------------------------------
sim.strat(n=5)
strat(its=100, burnin=0, thinning=1, internal.thinning=1, show.progress=FALSE) # much too short
layout(1) # new plot
undated_1.5 <- ages.undated(1.5) # ages between positions 1 and 2
summary(undated_1.5)

## ----eval=FALSE---------------------------------------------------------------
#  strat("gaps_example") # will need a longer run for reliable results (the example below used 1 million iterations, followed by thinning using the thinner() function)