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_targets.R
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_targets.R
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# === Targets: socprod model ----------------------------------------------
# Alec Robitaille
# Source ------------------------------------------------------------------
lapply(dir('R', '*.R', full.names = TRUE), source)
# Options -----------------------------------------------------------------
# Targets
tar_option_set(format = 'qs',
workspace_on_error = TRUE)
# Stan
options(mc.cores = 2,
scipen = 999,
digits = 2,
cmdstanr_draws_format = "draws_df")
compiled_dir <- file.path('stan', 'compiled')
output_stan_dir <- file.path('output', 'stan')
# Data --------------------------------------------------------------------
# w05 wines
# w06 grants
# w07 trolley
# w08 frogs (1), bangladesh (2), trolley (3)
# w09 bangladesh
# Targets: data -----------------------------------------------------------
targets_data <- c(
# data.tables
tar_target(
DT_wines,
data_wines()
),
tar_target(
DT_grants,
data_grants()
),
tar_target(
DT_trolley,
data_trolley()
),
tar_target(
DT_reedfrogs,
data_reedfrogs()
),
tar_target(
DT_bangladesh,
data_bangladesh()
),
# model data as lists
tar_target(
model_data_wines,
data_wines_list()
),
tar_target(
model_data_grants,
data_grants_list()
),
tar_target(
model_data_trolley,
data_trolley_list()
),
tar_target(
model_data_reedfrogs,
data_reedfrogs_list()
),
tar_target(
model_data_bangladesh,
data_bangladesh_list()
)
)
targets_stan <- c(
tar_stan_mcmc(
stan,
dir('stan', 'w05', full.names = TRUE),
data = model_data_wines,
cpp_options = list(stan_threads = TRUE),
chains = 4,
quiet = FALSE,
parallel_chains = 4,
threads_per_chain = 4,
dir = compiled_dir,
output_dir = output_stan_dir
),
tar_stan_mcmc(
stan_b,
dir('stan', 'w06', full.names = TRUE),
data = model_data_grants,
cpp_options = list(stan_threads = TRUE),
chains = 4,
quiet = FALSE,
parallel_chains = 4,
threads_per_chain = 4,
dir = compiled_dir,
output_dir = output_stan_dir
),
tar_stan_mcmc(
stan_c,
dir('stan', 'w07|w08_model_trolley', full.names = TRUE),
data = model_data_trolley,
cpp_options = list(stan_threads = TRUE),
chains = 4,
quiet = FALSE,
parallel_chains = 4,
threads_per_chain = 4,
dir = compiled_dir,
output_dir = output_stan_dir
),
tar_stan_mcmc(
stan_d,
dir('stan', 'w08_model_frogs', full.names = TRUE),
data = model_data_reedfrogs,
cpp_options = list(stan_threads = TRUE),
chains = 4,
quiet = FALSE,
parallel_chains = 4,
threads_per_chain = 4,
dir = compiled_dir,
output_dir = output_stan_dir
),
tar_stan_mcmc(
stan_e,
dir('stan', 'w09|w08_model_bang', full.names = TRUE),
data = model_data_bangladesh,
cpp_options = list(stan_threads = TRUE),
chains = 4,
quiet = FALSE,
parallel_chains = 4,
threads_per_chain = 4,
dir = compiled_dir,
output_dir = output_stan_dir
)
)
# Targets: render ---------------------------------------------------------
targets_render <- c(
tar_files(
rmd_files,
c(dir('notes', '.Rmd', full.names = TRUE),
dir('homework', '.Rmd', recursive = TRUE, full.names = TRUE))
),
tar_file(
index,
'index.Rmd'
),
tar_file(
book_yml,
'_bookdown.yml'
),
tar_file(
out_yml,
'_output.yml'
),
tar_file(
readme,
'README.md'
),
tar_target(
book,
render_with_deps(index, c(rmd_files, book_yml, out_yml, readme))
)
)
# Targets: all ------------------------------------------------------------
# Automatically grab all the "targets_*" lists above
lapply(grep('targets', ls(), value = TRUE), get)