dfa_cv: Apply cross validation to DFA model

Description Usage Arguments Examples

View source: R/dfa_cv.R

Description

Apply cross validation to DFA model

Usage

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dfa_cv(
  stanfit,
  cv_method = c("loocv", "lfocv"),
  fold_ids = NULL,
  n_folds = 10,
  iter = 2000,
  chains = 4,
  thin = 1,
  ...
)

Arguments

stanfit

A stanfit object, to preserve the model structure from a call to fit_dfa()

cv_method

The method used for cross validation. The options are 'loocv', where time is ignored and each data point is assigned randomly to a fold. The method 'ltocv' is leave time out cross validation, and time slices are iteratively held out out. Finally the method 'lfocv' implements leave future out cross validation to do one-step ahead predictions.

fold_ids

A vector whose length is the same as the number of total data points. Elements are the fold id of each data point. If not all data points are used (e.g. the lfocv or ltocv approach might only use 10 time steps) the value can be something other than a numbber, e.g. NA

n_folds

Number of folds, defaults to 10

iter

Number of iterations in Stan sampling, defaults to 2000.

chains

Number of chains in Stan sampling, defaults to 4.

thin

Thinning rate in Stan sampling, defaults to 1.

...

Any other arguments to pass to rstan::sampling().

Examples

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## Not run: 
set.seed(42)
s <- sim_dfa(num_trends = 1, num_years = 20, num_ts = 3)
obs <- c(s$y_sim[1, ], s$y_sim[2, ], s$y_sim[3, ])
long <- data.frame("obs" = obs, "ts" = sort(rep(1:3, 20)),
"time" = rep(1:20, 3))
m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long",
sample = FALSE)
# random folds
fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1)

# folds can also be passed in
fold_ids <- sample(1:5, size = nrow(long), replace = TRUE)
m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long",
sample = FALSE)
fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1,
fold_ids = fold_ids)

# do an example of leave-time-out cross validation where years are dropped
fold_ids <- long$time
m <- fit_dfa(y = long, iter = 50, chains = 1, data_shape = "long",
sample = FALSE)
fit_cv <- dfa_cv(m, cv_method = "loocv", iter = 100, chains = 1,
fold_ids = fold_ids)

# example with covariates and long format data
obs_covar <- expand.grid("time" = 1:20, "timeseries" = 1:3,
"covariate" = 1:2)
obs_covar$value <- rnorm(nrow(obs_covar), 0, 0.1)
obs <- c(s$y_sim[1, ], s$y_sim[2, ], s$y_sim[3, ])
m <- fit_dfa(y = long, iter = 50, chains = 1, obs_covar = obs_covar,
data_shape = "long", sample = FALSE)
fit_cv <- dfa_cv(m, cv_method = "loocv", n_folds = 5, iter = 50, chains = 1)

## End(Not run)

bayesdfa documentation built on May 29, 2021, 1:06 a.m.