Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.width = 5,
fig.height = 5
)
## -----------------------------------------------------------------------------
library(paleoTS)
set.seed(10) # to make example replicatable
x <- sim.GRW(ns = 20, ms = 0.5, vs = 0.1)
plot(x)
## -----------------------------------------------------------------------------
print(str(x))
## -----------------------------------------------------------------------------
x.sub <- sub.paleoTS(x, ok = 10:15) # select only populations 10 through 15
plot(x)
plot(x.sub, add = TRUE, col = "red")
## -----------------------------------------------------------------------------
library(mnormt) # should omit this later
w.grw <- fitSimple(x, model = "GRW")
print(w.grw$parameters) # look at estimated parameters
## -----------------------------------------------------------------------------
plot(x, modelFit = w.grw)
## -----------------------------------------------------------------------------
w.urw <- fitSimple(x, model = "URW")
compareModels(w.grw, w.urw) # convenient table comparing model support
## -----------------------------------------------------------------------------
w.punc <- fitGpunc(x, ng = 2) # ng is the number of segments (= number of punctuations + 1)
## -----------------------------------------------------------------------------
plot(x, modelFit = w.punc)
## -----------------------------------------------------------------------------
compareModels(w.grw, w.urw, w.punc)
## -----------------------------------------------------------------------------
fit3models(x)
## -----------------------------------------------------------------------------
data(dorsal.spines)
ok1 <- dorsal.spines$nn > 0 # levels without measured fossils
ok2 <- dorsal.spines$tt > 4.4 # levels before the new species invades
ds.sub <- sub.paleoTS(dorsal.spines, ok = ok1 & ok2, reset.time = TRUE) # subsample
ds.sub.pool <- pool.var(ds.sub, minN = 5, ret.paleoTS = TRUE) # replace some pooled variance
w.ou <- fitSimple(ds.sub.pool, pool = FALSE, model = "OU")
plot(ds.sub.pool, modelFit = w.ou)
## -----------------------------------------------------------------------------
set.seed(90)
y <- sim.GRW(ns = 40, ms = 0.2, vs = 0.1, vp = 4) # high vp gives broader error bars
plot(y)
fit3models(y, method = "Joint") # GRW clearly wins
fit3models(y, method = "AD") # GRW only barely beats URW
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