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Add targets branching #15

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Add targets branching #15

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4ec104d
testing new branch strategy
matthew-phelps Feb 29, 2024
22e3bd3
Branching working
matthew-phelps Mar 1, 2024
2e691a0
Update branch from dev
matthew-phelps Mar 1, 2024
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3 changes: 2 additions & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,8 @@ Suggests:
testr,
testthat (>= 3.0.0),
tidyr,
withr
withr,
whisker
VignetteBuilder:
knitr
Remotes:
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4 changes: 3 additions & 1 deletion R/apply_stats.R
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Expand Up @@ -19,10 +19,12 @@ apply_stats <-
type = c("stat_by_strata_by_trt",
"stat_by_strata_across_trt",
"stat_across_strata_across_trt")) {

checkmate::assert_data_table(ep)
# If no functions are given by the user, no results table needs to be
# produced
nm <- names(ep)
if (length(nm) <= 2 &&
if (length(nm) <= 3 &&
nm[1] == "SKIP_") {
return(data.table(NULL))
}
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2 changes: 1 addition & 1 deletion R/prepare_for_stats.R
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Expand Up @@ -49,7 +49,7 @@ prepare_for_stats <- function(

# If no functions of the type are supplied, return early
if(nrow(ep_fn)==0){
return(data.table::data.table(SKIP_=TRUE))
return(data.table::data.table(SKIP_=TRUE, endpoint_spec_id="DUMMY_"))
}


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158 changes: 116 additions & 42 deletions inst/templates/template-pipeline.R
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Expand Up @@ -6,95 +6,169 @@ chef::check_duplicate_functions(fun_dir)
## Load your R files
lapply(list.files(normalizePath(fun_dir), full.names = TRUE), source)

tar_option_set(packages = c("chef", "data.table"), format = "qs")
targets::tar_option_set(packages = c("chef", "data.table"), format = "qs")
list(
targets::tar_target(ep,
mk_endpoint_def(),
),
targets::tar_target(ep_id, add_id(ep)),
targets::tar_target(ep_fn_map,
unnest_endpoint_functions(ep_id),
cue = targets::tar_cue(mode = "always")),
mk_endpoint_def()),
tarchetypes::tar_group_by(ep_id, add_id(ep), endpoint_spec_id),
targets::tar_target(
ep_fn_map,
unnest_endpoint_functions(data.table::as.data.table(ep_id)),
cue = targets::tar_cue(mode = "always"),
pattern = map(ep_id)
),

targets::tar_target(user_def_fn,
mk_userdef_fn_dt(ep_fn_map, env = environment())),

targets::tar_target(fn_map,
merge(ep_fn_map[, .(endpoint_spec_id, fn_hash)], user_def_fn, by = c("fn_hash"))),
tarchetypes::tar_group_by(
fn_map_tibble,
merge(ep_fn_map[, .(endpoint_spec_id, fn_hash)],
user_def_fn,
by = c("fn_hash")),
endpoint_spec_id
),

targets::tar_target(
fn_map,
data.table::as.data.table(fn_map_tibble),
pattern = map(fn_map_tibble)
),

# targets::tar_target(fn_map, as.data.table(fn_map_), pattern = map(fn_map_)),
targets::tar_target(
study_data,
fetch_db_data(study_metadata = ep_id$study_metadata[[1]], fn_dt = user_def_fn),
cue = targets::tar_cue(mode = "always")
),

targets::tar_target(ep_and_data,
filter_db_data(ep_id, ep_fn_map, study_data)),
targets::tar_target(
ep_and_data,
filter_db_data(data.table::as.data.table(ep_id), ep_fn_map, study_data),
pattern = map(ep_id)
),

targets::tar_target(ep_with_data_key, ep_and_data$ep, pattern = map(ep_and_data)),
targets::tar_target(
analysis_data_container,
ep_and_data$analysis_data_container,
pattern = map(ep_and_data)
),

targets::tar_target(ep_with_data_key, ep_and_data$ep),
targets::tar_target(analysis_data_container, ep_and_data$analysis_data_container),
targets::tar_target(
ep_expanded,
expand_over_endpoints(ep_with_data_key, analysis_data_container),
pattern = map(ep_with_data_key, analysis_data_container)
),

targets::tar_target(ep_expanded, expand_over_endpoints(ep_with_data_key, analysis_data_container)),
targets::tar_target(
ep_event_index,
add_event_index(ep_expanded, analysis_data_container),
pattern = map(ep_expanded, analysis_data_container)
),

targets::tar_target(ep_event_index, add_event_index(ep_expanded, analysis_data_container)),

# `fn_map` has to be supplied to the command function of tar_targets without the
# `tar_group` variable. This is because this variable exists in the ep data
# model, and fn_map is merged onto ep. However, since the data.tables are not
# keyed by `tar_group`, this cause naming problems. It's easier to just pass
# the fn_map without this variable since no derivation of fn_map is passed to
# downstream targets.
targets::tar_target(
ep_crit_endpoint,
apply_criterion_endpoint(ep_event_index, analysis_data_container, fn_map)
apply_criterion_endpoint(ep_event_index, analysis_data_container, fn_map[,!"tar_group"]),
pattern = map(ep_event_index, analysis_data_container, fn_map)
),
targets::tar_target(
ep_crit_by_strata_by_trt,
apply_criterion_by_strata(ep_crit_endpoint, analysis_data_container, fn_map)
apply_criterion_by_strata(ep_crit_endpoint, analysis_data_container, fn_map[,!"tar_group"]),
pattern = map(ep_crit_endpoint, analysis_data_container, fn_map)
),

targets::tar_target(
ep_crit_by_strata_across_trt,
apply_criterion_by_strata(ep_crit_by_strata_by_trt, analysis_data_container, fn_map, type = "by_strata_across_trt")
apply_criterion_by_strata(
ep_crit_by_strata_by_trt,
analysis_data_container,
fn_map[,!"tar_group"],
type = "by_strata_across_trt"
),
pattern = map(ep_crit_by_strata_by_trt, analysis_data_container, fn_map)
),

tarchetypes::tar_group_size(
targets::tar_target(
ep_prep_by_strata_by_trt,
prepare_for_stats(ep_crit_by_strata_across_trt,
analysis_data_container,
fn_map,
type = "stat_by_strata_by_trt"),
size = {{branch_group_size}}
prepare_for_stats(
ep_crit_by_strata_across_trt,
analysis_data_container,
fn_map[,!"tar_group"],
type = "stat_by_strata_by_trt"
),
pattern = map(
ep_crit_by_strata_across_trt,
analysis_data_container,
fn_map
)
),

tarchetypes::tar_group_size(
targets::tar_target(
ep_prep_by_strata_across_trt,
prepare_for_stats(ep_crit_by_strata_across_trt,
analysis_data_container,
fn_map,
type = "stat_by_strata_across_trt"),
size = {{branch_group_size}}
prepare_for_stats(
ep_crit_by_strata_across_trt,
analysis_data_container,
fn_map[,!"tar_group"],
type = "stat_by_strata_across_trt"
),
pattern = map(
ep_crit_by_strata_across_trt,
analysis_data_container,
fn_map
)
),

tarchetypes::tar_group_size(
targets::tar_target(
ep_prep_across_strata_across_trt,
prepare_for_stats(ep_crit_by_strata_across_trt,
analysis_data_container,
fn_map,
type = "stat_across_strata_across_trt"),
size = {{branch_group_size}}
prepare_for_stats(
ep_crit_by_strata_across_trt,
analysis_data_container,
fn_map[,!"tar_group"],
type = "stat_across_strata_across_trt"
),
pattern = map(
ep_crit_by_strata_across_trt,
analysis_data_container,
fn_map
)
),


targets::tar_target(
ep_stat_by_strata_by_trt,
apply_stats(ep_prep_by_strata_by_trt, analysis_data_container, type = "stat_by_strata_by_trt"),
pattern = map(ep_prep_by_strata_by_trt)
apply_stats(ep_prep_by_strata_by_trt,
analysis_data_container,
type = "stat_by_strata_by_trt"),
pattern = map(ep_prep_by_strata_by_trt,
analysis_data_container)
),

targets::tar_target(
ep_stat_by_strata_across_trt,
apply_stats(ep_prep_by_strata_across_trt, analysis_data_container, type = "stat_by_strata_across_trt"),
pattern = map(ep_prep_by_strata_across_trt)
apply_stats(ep_prep_by_strata_across_trt,
analysis_data_container,
type = "stat_by_strata_across_trt"),
pattern = map(ep_prep_by_strata_across_trt,
analysis_data_container)
),

targets::tar_target(
ep_stat_across_strata_across_trt,
apply_stats(ep_prep_across_strata_across_trt, analysis_data_container, type = "stat_across_strata_across_trt"),
pattern = map(ep_prep_across_strata_across_trt)
apply_stats(
ep_prep_across_strata_across_trt,
analysis_data_container,
type = "stat_across_strata_across_trt"
),
pattern = map(ep_prep_across_strata_across_trt,
analysis_data_container)
),

targets::tar_target(
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