Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup--------------------------------------------------------------------
library(HTLR)
library(bayesplot)
## -----------------------------------------------------------------------------
SEED <- 1234
n <- 510
p <- 2000
means <- rbind(
c(0, 1, 0),
c(0, 0, 0),
c(0, 0, 1),
c(0, 0, 1),
c(0, 0, 1),
c(0, 0, 1),
c(0, 0, 1),
c(0, 0, 1),
c(0, 0, 1),
c(0, 0, 1)
) * 2
means <- rbind(means, matrix(0, p - 10, 3))
A <- diag(1, p)
A[1:10, 1:3] <-
rbind(
c(1, 0, 0),
c(2, 1, 0),
c(0, 0, 1),
c(0, 0, 1),
c(0, 0, 1),
c(0, 0, 1),
c(0, 0, 1),
c(0, 0, 1),
c(0, 0, 1),
c(0, 0, 1)
)
set.seed(SEED)
dat <- gendata_FAM(n, means, A, sd_g = 0.5, stdx = TRUE)
str(dat)
## -----------------------------------------------------------------------------
# require(corrplot)
cor(dat$X[ , 1:11]) %>% corrplot::corrplot(tl.pos = "n")
## -----------------------------------------------------------------------------
set.seed(SEED)
dat <- split_data(dat$X, dat$y, n.train = 500)
str(dat)
## -----------------------------------------------------------------------------
set.seed(SEED)
system.time(
fit.t <- htlr(dat$x.tr, dat$y.tr)
)
print(fit.t)
## -----------------------------------------------------------------------------
set.seed(SEED)
system.time(
fit.t2 <- htlr(X = dat$x.tr, y = dat$y.tr,
prior = htlr_prior("t", df = 1, logw = -20, sigmab0 = 1500),
iter = 4000, init = "bcbc", keep.warmup.hist = T)
)
print(fit.t2)
## -----------------------------------------------------------------------------
summary(fit.t2, features = c(1:10, 100, 200, 1000, 2000), method = median)
## -----------------------------------------------------------------------------
post.t <- as.matrix(fit.t2, k = 2)
## signal parameters
mcmc_intervals(post.t, pars = c("Intercept", "V1", "V2", "V3", "V1000"))
## -----------------------------------------------------------------------------
as.matrix(fit.t2, k = 2, include.warmup = T) %>%
mcmc_trace(c("V1", "V1000"), facet_args = list("nrow" = 2), n_warmup = 2000)
## -----------------------------------------------------------------------------
y.class <- predict(fit.t, dat$x.te, type = "class")
y.class
print(paste0("prediction accuracy of model 1 = ",
sum(y.class == dat$y.te) / length(y.class)))
y.class2 <- predict(fit.t2, dat$x.te, type = "class")
print(paste0("prediction accuracy of model 2 = ",
sum(y.class2 == dat$y.te) / length(y.class)))
## -----------------------------------------------------------------------------
predict(fit.t, dat$x.te, type = "response") %>%
evaluate_pred(y.true = dat$y.te)
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