## ---- echo = FALSE, message=FALSE---------------------------------------------
library(beset)
suppressPackageStartupMessages(library(tidyverse))
## -----------------------------------------------------------------------------
set.seed(42)
train_data <- cbind(swiss,
matrix(replicate(5, rnorm(nrow(swiss))), ncol = 5))
names(train_data)[7:11] <- paste0("noise", names(train_data)[7:11])
## -----------------------------------------------------------------------------
mod <- beset_lm(Fertility ~ ., train_data)
## ---- fig.height=4, fig.width=5-----------------------------------------------
plot(mod)
## ---- fig.height=4, fig.width=5-----------------------------------------------
plot(mod, "rsq")
## -----------------------------------------------------------------------------
summary(mod)
## ---- eval = FALSE------------------------------------------------------------
# summary(mod, n_pred = NULL, metric = "mse", oneSE = TRUE)
## -----------------------------------------------------------------------------
summary(mod, oneSE = FALSE)
## -----------------------------------------------------------------------------
summary(mod, metric = "aic")
## -----------------------------------------------------------------------------
summary(mod, metric = "mae")
## ---- fig.height=4, fig.width=5-----------------------------------------------
plot(mod)
## -----------------------------------------------------------------------------
summary(mod, n_pred = 4)
## -----------------------------------------------------------------------------
data <- partition(train_data, y = "Fertility", seed = 42, frac = .75)
## ---- fig.height=4, fig.width=5-----------------------------------------------
mod <- beset_lm(Fertility ~ ., data = data)
plot(mod)
## ---- fig.height=4, fig.width=5-----------------------------------------------
mod <- beset_lm(Fertility ~ ., data = train_data, nest_cv = TRUE, p_max = 5)
plot(mod)
## ---- fig.height=4, fig.width=5-----------------------------------------------
plot(mod, se = FALSE)
## -----------------------------------------------------------------------------
summary(mod)
## -----------------------------------------------------------------------------
summary(mod) %>% print(standardize = FALSE)
## -----------------------------------------------------------------------------
summary(mod, oneSE = FALSE)
## -----------------------------------------------------------------------------
summary(mod) %>% print(metric = "mse")
## -----------------------------------------------------------------------------
validate(mod, metric = "mse", oneSE = TRUE)
## -----------------------------------------------------------------------------
mod <- beset_lm(Fertility ~ Agriculture + Examination + Education +
Catholic + Infant.Mortality, train_data)
summary(mod)
## ---- eval = FALSE------------------------------------------------------------
# ### DO NOT RUN!
# mod <- beset_lm(Fertility ~ Agriculture * Examination * Education *
# Catholic * Infant.Mortality, train_data)
## -----------------------------------------------------------------------------
mod <- beset_lm(Fertility ~ Education * Catholic * Infant.Mortality,
train_data)
## -----------------------------------------------------------------------------
summary(mod)
## -----------------------------------------------------------------------------
mod <- beset_lm(Fertility ~ Education + Catholic + Infant.Mortality +
Education:Catholic + Education:Infant.Mortality +
Catholic:Infant.Mortality, train_data, nest_cv = TRUE,
force_in = c("Education", "Catholic", "Infant.Mortality"))
summary(mod)
## -----------------------------------------------------------------------------
mod <- beset_lm(Fertility ~ ., train_data, n_folds = 5, n_reps = 5)
summary(mod)
## ---- fig.height=4, fig.width=5-----------------------------------------------
plot(mod)
## -----------------------------------------------------------------------------
data("prostate")
summary(prostate)
## -----------------------------------------------------------------------------
mod <- beset_glm(tumor ~ ., data = prostate, family = "binomial")
## -----------------------------------------------------------------------------
summary(mod)
## ---- eval = FALSE------------------------------------------------------------
# # Incorrect syntax
# beset_glm(tumor ~ ., data = prostate, family = binomial("probit"))
## ---- eval = FALSE------------------------------------------------------------
# # Correct syntax
# beset_glm(tumor ~ ., data = prostate, family = "binomial",
# link = "probit") %>% summary()
## ---- fig.height=4, fig.width=5-----------------------------------------------
plot(mod)
## ---- fig.height=4, fig.width=5-----------------------------------------------
plot(mod) + ylab("Log-loss")
## ---- fig.height=4, fig.width=5-----------------------------------------------
plot(mod, metric = "auc")
## -----------------------------------------------------------------------------
summary(mod, metric = "auc")
## -----------------------------------------------------------------------------
data("adolescents")
qplot(x = dep, bins = 10, data = na.omit(adolescents)) + theme_classic()
## -----------------------------------------------------------------------------
mod_poisson <- beset_glm(dep ~ ., data = adolescents, family = "poisson")
## ---- fig.height=4, fig.width=5-----------------------------------------------
plot(mod_poisson)
## -----------------------------------------------------------------------------
poisson_summary <- summary(mod_poisson, n_pred = 4)
poisson_summary
## -----------------------------------------------------------------------------
mod_negbin <- beset_glm(dep ~ ., data = adolescents, family = "negbin")
## ---- fig.height=4, fig.width=5-----------------------------------------------
plot(mod_negbin)
## -----------------------------------------------------------------------------
negbin_summary <- summary(mod_negbin, oneSE = FALSE)
negbin_summary
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