## generate some data
set.seed(111)
n <- 200
## regressor
dat <- data.frame(x = runif(n, -3, 3))
## response
dat$y <- with(dat, 1.5 + sin(x) + rnorm(n, sd = 0.6))
## estimate models with
## bayesx REML and MCMC
b1 <- bayesx(y ~ sx(x), method = "REML", data = dat)
## same using mgcv syntax
b1 <- bayesx(y ~ s(x, bs = "ps", k = 20), method = "REML", data = dat)
## now with MCMC
b2 <- bayesx(y ~ sx(x), method = "MCMC",
iter = 1200, burnin = 200, data = dat)
## compare reported output
summary(c(b1, b2))
## plot the effect for both models
plot(c(b1, b2), residuals = TRUE)
## use confint
confint(b1, level = 0.99)
confint(b2, level = 0.99)
## more examples
set.seed(111)
n <- 500
## regressors
dat <- data.frame(x = runif(n, -3, 3), z = runif(n, -3, 3),
w = runif(n, 0, 6), fac = factor(rep(1:10, n/10)))
## response
dat$y <- with(dat, 1.5 + sin(x) + cos(z) * sin(w) +
c(2.67, 5, 6, 3, 4, 2, 6, 7, 9, 7.5)[fac] + rnorm(n, sd = 0.6))
## estimate models with
## bayesx MCMC and REML
## and compare with
## mgcv gam()
b1 <- bayesx(y ~ sx(x) + sx(z, w, bs = "te") + fac,
data = dat, method = "MCMC")
b2 <- bayesx(y ~ sx(x) + sx(z, w, bs = "te") + fac,
data = dat, method = "REML")
b3 <- gam(y ~ s(x, bs = "ps") + te(z, w, bs = "ps") + fac,
data = dat)
## summary statistics
summary(b1)
summary(b2)
summary(b3)
## plot the effects
op <- par(no.readonly = TRUE)
par(mfrow = c(3, 2))
plot(b1, term = "sx(x)")
plot(b1, term = "sx(z,w)")
plot(b2, term = "sx(x)")
plot(b2, term = "sx(z,w)")
plot(b3, select = 1)
vis.gam(b3, c("z","w"), theta = 40, phi = 40)
par(op)
## combine models b1 and b2
b <- c(b1, b2)
## summary
summary(b)
## only plot effect 2 of both models
plot(b, term = "sx(z,w)")
## with residuals
plot(b, term = "sx(z,w)", residuals = TRUE)
## same model with kriging
b <- bayesx(y ~ sx(x) + sx(z, w, bs = "kr") + fac,
method = "REML", data = dat)
plot(b)
## now a mrf example
## note: the regional identification
## covariate and the map regionnames
## should be coded as integer
set.seed(333)
## simulate some geographical data
data("MunichBnd")
N <- length(MunichBnd); n <- N*5
names(MunichBnd) <- 1:N
## regressors
dat <- data.frame(x1 = runif(n, -3, 3),
id = as.factor(rep(names(MunichBnd), length.out = n)))
dat$sp <- with(dat, sort(runif(N, -2, 2), decreasing = TRUE)[id])
## response
dat$y <- with(dat, 1.5 + sin(x1) + sp + rnorm(n, sd = 1.2))
## estimate models with
## bayesx MCMC and REML
b1 <- bayesx(y ~ sx(x1) + sx(id, bs = "mrf", map = MunichBnd),
method = "MCMC", data = dat)
b2 <- bayesx(y ~ sx(x1) + sx(id, bs = "mrf", map = MunichBnd),
method = "REML", data = dat)
## summary statistics
summary(b1)
summary(b2)
## plot the effects
op <- par(no.readonly = TRUE)
par(mfrow = c(1,3))
plot(b1, term = "sx(id)", map = MunichBnd,
main = "bayesx() MCMC estimate")
plot(b2, term = "sx(id)", map = MunichBnd,
main = "bayesx() REML estimate")
plotmap(MunichBnd, x = dat$sp, id = dat$id,
main = "Truth")
par(op)
## try geosplines instead
b <- bayesx(y ~ sx(id, bs = "gs", map = MunichBnd) + sx(x1), data = dat)
summary(b)
plot(b, term = "sx(id)", map = MunichBnd)
plot(b, term = "sx(id)", map = MunichBnd, pos = "right")
## geokriging
b <- bayesx(y ~ sx(id, bs = "gk", map = MunichBnd) + sx(x1),
method = "REML", data = dat)
summary(b)
plot(b, term = "sx(id)", map = MunichBnd)
## perspective plot of the effect
plot(b, term = "sx(id)")
## image and contour plot
plot(b, term = "sx(id)", image = TRUE,
contour = TRUE, grid = 200)
## model with random effects
set.seed(333)
N <- 30
n <- N*10
## regressors
dat <- data.frame(id = sort(rep(1:N, n/N)), x1 = runif(n, -3, 3))
dat$re <- with(dat, rnorm(N, sd = 0.6)[id])
## response
dat$y <- with(dat, 1.5 + sin(x1) + re + rnorm(n, sd = 0.6))
## estimate model
b <- bayesx(y ~ sx(x1) + sx(id, bs = "re"), data = dat)
summary(b)
plot(b)
## extract estimated random effects
## and compare with true effects
plot(fitted(b, term = "sx(id)")$Mean ~ unique(dat$re))
## now a spatial example
## with structured and
## unstructered spatial
## effect
set.seed(333)
## simulate some geographical data
data("MunichBnd")
N <- length(MunichBnd); names(MunichBnd) <- 1:N
n <- N*5
## regressors
dat <- data.frame(id = rep(1:N, n/N), x1 = runif(n, -3, 3))
dat$sp <- with(dat, sort(runif(N, -2, 2), decreasing = TRUE)[id])
dat$re <- with(dat, rnorm(N, sd = 0.6)[id])
## response
dat$y <- with(dat, 1.5 + sin(x1) + sp + re + rnorm(n, sd = 0.6))
## estimate model
b <- bayesx(y ~ sx(x1) +
sx(id, bs = "mrf", map = MunichBnd) +
sx(id, bs = "re"), method = "MCMC", data = dat)
summary(b)
## plot all spatial effects
op <- par(no.readonly = TRUE)
par(mfrow = c(1, 3))
plot(b, term = "sx(id):mrf", map = MunichBnd,
main = "Structured spatial effect")
plot(b, term = "sx(id):re", map = MunichBnd,
main = "Unstructured spatial effect")
plot(b, term = "sx(id):total", map = MunichBnd,
main = "Total spatial effect", digits = 4)
par(mfrow = op)
## some experiments with the
## stepwise algorithm
## generate some data
set.seed(321)
n <- 1000
## regressors
dat <- data.frame(x1 = runif(n, -3, 3), x2 = runif(n),
x3 = runif(n, 3, 6), x4 = runif(n, 0, 1))
## response
dat$y <- with(dat, 1.5 + sin(x1) + 0.6 * x2 + rnorm(n, sd = 0.6))
## estimate model with STEP
b <- bayesx(y ~ sx(x1) + sx(x2) + sx(x3) + sx(x4),
method = "STEP", algorithm = "cdescent1", CI = "MCMCselect",
iter = 10000, step = 10, data = dat)
summary(b)
plot(b)
## a probit example
set.seed(111)
n <- 1000
dat <- data.frame(x <- runif(n, -3, 3))
dat$z <- with(dat, sin(x) + rnorm(n))
dat$y <- rep(0, n)
dat$y[dat$z > 0] <- 1
b <- bayesx(y ~ sx(x), family = "binomialprobit", data = dat)
summary(b)
plot(b)
## estimate varying coefficient models
set.seed(333)
n <- 1000
dat <- data.frame(x = runif(n, -3, 3), id = factor(rep(1:4, n/4)))
## response
dat$y <- with(dat, 1.5 + sin(x) * c(-1, 0.2, 1, 5)[id] + rnorm(n, sd = 0.6))
## estimate model
b <- bayesx(y ~ sx(x, by = id, center = TRUE),
method = "REML", data = dat)
summary(b)
plot(b, resid = TRUE, cex.resid = 0.1)Run the code above in your browser using DataLab