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dajmcdondajmcdon
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Rewrite main history to earlier
1 parent 910dd19 commit 168e91a

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-411
lines changed

‎DESCRIPTION

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@@ -20,7 +20,6 @@ Imports:
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glue,
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hardhat (>= 1.0.0.9000),
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magrittr,
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parsnip,
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purrr,
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recipes (>= 0.2.0.9001),
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rlang,
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tibble,
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tidyr,
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tidyselect,
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tensr,
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workflows
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Suggests:
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covidcast,

‎NAMESPACE

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@@ -1,6 +1,7 @@
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# Generated by roxygen2: do not edit by hand
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3-
S3method(bake,step_epi_shift)
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S3method(bake,step_epi_ahead)
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S3method(bake,step_epi_lag)
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S3method(epi_keys,default)
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S3method(epi_keys,epi_df)
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S3method(epi_keys,recipe)
@@ -35,7 +36,6 @@ export(smooth_arx_args_list)
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export(smooth_arx_forecaster)
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export(step_epi_ahead)
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export(step_epi_lag)
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export(step_epi_naomit)
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import(recipes)
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importFrom(magrittr,"%>%")
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importFrom(rlang,"!!")

‎R/epi_ahead.R

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@@ -63,16 +63,101 @@ step_epi_ahead <-
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columns = NULL,
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skip = FALSE,
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id = rand_id("epi_ahead")) {
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step_epi_shift(recipe,
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...,
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role = role,
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trained = trained,
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shift = ahead,
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prefix = prefix,
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default = default,
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keys = keys,
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columns = columns,
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skip = skip,
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id = id
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add_step(
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recipe,
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step_epi_ahead_new(
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terms = dplyr::enquos(...),
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role = role,
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trained = trained,
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ahead = ahead,
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prefix = prefix,
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default = default,
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keys = keys,
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columns = columns,
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skip = skip,
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id = id
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)
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)
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}
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step_epi_ahead_new <-
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function(terms, role, trained, ahead, prefix, default, keys,
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columns, skip, id) {
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step(
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subclass = "epi_ahead",
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terms = terms,
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role = role,
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trained = trained,
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ahead = ahead,
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prefix = prefix,
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default = default,
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keys = keys,
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columns = columns,
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skip = skip,
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id = id
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)
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}
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#' @export
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prep.step_epi_ahead <- function(x, training, info = NULL, ...) {
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step_epi_ahead_new(
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terms = x$terms,
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role = x$role,
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trained = TRUE,
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ahead = x$ahead,
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prefix = x$prefix,
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default = x$default,
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keys = x$keys,
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columns = recipes_eval_select(x$terms, training, info),
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skip = x$skip,
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id = x$id
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)
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}
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#' @export
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bake.step_epi_ahead <- function(object, new_data, ...) {
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if (!all(object$ahead == as.integer(object$ahead))) {
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rlang::abort("step_epi_ahead requires 'ahead' argument to be integer valued.")
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}
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grid <- tidyr::expand_grid(
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col = object$columns, lag_val = -object$ahead) %>%
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dplyr::mutate(
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ahead_val = -lag_val,
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newname = glue::glue("{object$prefix}{ahead_val}_{col}")
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) %>%
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dplyr::select(-ahead_val)
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## ensure no name clashes
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new_data_names <- colnames(new_data)
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intersection <- new_data_names %in% grid$newname
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if (any(intersection)) {
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rlang::abort(
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paste0("Name collision occured in `", class(object)[1],
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"`. The following variable names already exists: ",
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paste0(new_data_names[intersection], collapse = ", "),
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"."))
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}
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ok <- object$keys
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lagged <- purrr::reduce(
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purrr::pmap(grid, epi_shift_single, x = new_data, key_cols = ok),
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dplyr::full_join,
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by = ok
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)
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dplyr::full_join(new_data, lagged, by = ok) %>%
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dplyr::group_by(dplyr::across(dplyr::all_of(ok[-1]))) %>%
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dplyr::arrange(time_value) %>%
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dplyr::ungroup()
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}
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#' @export
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print.step_epi_ahead <-
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function(x, width = max(20, options()$width - 30), ...) {
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## TODO add printing of the lags
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title <- "Leading "
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recipes::print_step(x$columns, x$terms, x$trained, title, width)
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invisible(x)
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}

‎R/epi_lag.R

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@@ -29,17 +29,95 @@ step_epi_lag <-
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columns = NULL,
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skip = FALSE,
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id = rand_id("epi_lag")) {
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step_epi_shift(recipe,
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...,
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role = role,
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trained = trained,
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shift = -lag,
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prefix = prefix,
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default = default,
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keys = keys,
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columns = columns,
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skip = skip,
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id = id
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add_step(
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recipe,
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step_epi_lag_new(
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terms = dplyr::enquos(...),
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role = role,
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trained = trained,
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lag = lag,
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prefix = prefix,
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default = default,
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keys = keys,
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columns = columns,
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skip = skip,
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id = id
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)
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)
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}
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step_epi_lag_new <-
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function(terms, role, trained, lag, prefix, default, keys,
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columns, skip, id) {
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step(
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subclass = "epi_lag",
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terms = terms,
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role = role,
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trained = trained,
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lag = lag,
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prefix = prefix,
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default = default,
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keys = keys,
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columns = columns,
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skip = skip,
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id = id
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)
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}
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#' @export
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prep.step_epi_lag <- function(x, training, info = NULL, ...) {
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step_epi_lag_new(
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terms = x$terms,
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role = x$role,
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trained = TRUE,
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lag = x$lag,
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prefix = x$prefix,
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default = x$default,
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keys = x$keys,
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columns = recipes_eval_select(x$terms, training, info),
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skip = x$skip,
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id = x$id
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)
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}
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#' @export
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bake.step_epi_lag <- function(object, new_data, ...) {
85+
if (!all(object$lag == as.integer(object$lag))) {
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rlang::abort("step_epi_lag requires 'lag' argument to be integer valued.")
87+
}
88+
89+
grid <- tidyr::expand_grid(col = object$columns, lag_val = object$lag) %>%
90+
dplyr::mutate(newname = glue::glue("{object$prefix}{lag_val}_{col}"))
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## ensure no name clashes
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new_data_names <- colnames(new_data)
94+
intersection <- new_data_names %in% grid$newname
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if (any(intersection)) {
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rlang::abort(
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paste0("Name collision occured in `", class(object)[1],
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"`. The following variable names already exists: ",
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paste0(new_data_names[intersection], collapse = ", "),
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"."))
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}
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ok <- object$keys
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lagged <- purrr::reduce(
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purrr::pmap(grid, epi_shift_single, x = new_data, key_cols = ok),
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dplyr::full_join,
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by = ok
107+
)
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109+
dplyr::full_join(new_data, lagged, by = ok) %>%
110+
dplyr::group_by(dplyr::across(dplyr::all_of(ok[-1]))) %>%
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dplyr::arrange(time_value) %>%
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dplyr::ungroup()
113+
114+
}
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116+
#' @export
117+
print.step_epi_lag <-
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function(x, width = max(20, options()$width - 30), ...) {
119+
## TODO add printing of the lags
120+
title <- "Lagging "
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recipes::print_step(x$columns, x$terms, x$trained, title, width)
122+
invisible(x)
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}

‎R/epi_shift_internal.R

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This file was deleted.

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