Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----message = FALSE----------------------------------------------------------
# install.packages(c("semEff", "ggplot2"))
library(semEff)
library(ggplot2)
## -----------------------------------------------------------------------------
knitr::kable(head(shipley))
## ----eval = FALSE-------------------------------------------------------------
# shipley.sem <- list(
# DD = lme4::lmer(DD ~ lat + (1 | site) + (1 | tree), data = shipley),
# Date = lme4::lmer(Date ~ DD + (1 | site) + (1 | tree), data = shipley),
# Growth = lme4::lmer(Growth ~ Date + (1 | site) + (1 | tree), data = shipley),
# Live = lme4::glmer(Live ~ Growth + (1 | site) + (1 | tree), data = shipley,
# family = binomial)
# )
## ----eval = FALSE-------------------------------------------------------------
# shipley.sem.boot <- bootEff(shipley.sem, R = 1000, seed = 13, ran.eff = "site")
## -----------------------------------------------------------------------------
(shipley.sem.eff <- semEff(shipley.sem.boot))
## -----------------------------------------------------------------------------
summary(shipley.sem.eff, "Growth")
## -----------------------------------------------------------------------------
tot <- getTotEff(shipley.sem.eff, "Growth")
tot.b <- getTotEff(shipley.sem.eff, "Growth", type = "boot")
## -----------------------------------------------------------------------------
dat <- na.omit(shipley)
mod <- shipley.sem$Growth
fit <- sapply(c("Date", "DD"), function(i) {
x <- data.frame(seq(min(dat[i]), max(dat[i]), length = 100)); names(x) <- i
f <- predEff(mod, newdata = x, effects = tot[i], eff.boot = tot.b)
c(x, f)
}, simplify = FALSE)
## -----------------------------------------------------------------------------
plotFit <- function(x, y, fit, x.lab = NULL, y.lab = NULL) {
d <- fit[[1]]
f <- fit$fit
ci.l <- fit$ci.lower
ci.u <- fit$ci.upper
ggplot () +
geom_point(aes(x, y)) +
geom_ribbon(aes(d, ymin = ci.l, ymax = ci.u, alpha = "0.15"), fill = "blue") +
geom_line(aes(d, f), color = "blue", size = 1) +
xlab(x.lab) +
ylab(y.lab) +
theme_bw() +
theme(legend.position = "none")
}
## ----warning = FALSE----------------------------------------------------------
plotFit(x = dat$Date, y = dat$Growth, fit = fit$Date,
x.lab = "Julian Date of Bud Burst (direct effect)", y.lab = "Stem Growth (mm)")
## ----warning = FALSE----------------------------------------------------------
plotFit(x = dat$DD, y = dat$Growth, fit = fit$DD,
x.lab = "Degree Days to Bud Burst (indirect effect)", y.lab = "Stem Growth (mm)")
## -----------------------------------------------------------------------------
c(r2_marg = R2(mod, re.form = NA)[[1]],
r2_cond = R2(mod)[[1]])
## -----------------------------------------------------------------------------
c(r2_site = R2(mod, re.form = ~ 1 | site)[[1]],
r2_tree = R2(mod, re.form = ~ 1 | tree)[[1]])
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