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| 1 | +#' Create a leading outcome |
| 2 | +#' |
| 3 | +#' `step_epi_ahead` creates a *specification* of a recipe step that |
| 4 | +#' will add new columns of leading data. Leading data will |
| 5 | +#' by default include NA values where the lag was induced. |
| 6 | +#' These can be removed with [step_naomit()], or you may |
| 7 | +#' specify an alternative filler value with the `default` |
| 8 | +#' argument. |
| 9 | +#' |
| 10 | +#' @param recipe A recipe object. The step will be added to the |
| 11 | +#' sequence of operations for this recipe. |
| 12 | +#' @param ... One or more selector functions to choose variables |
| 13 | +#' for this step. See [selections()] for more details. |
| 14 | +#' @param role For model terms created by this step, what analysis role should |
| 15 | +#' they be assigned? |
| 16 | +#' @param trained A logical to indicate if the quantities for |
| 17 | +#' preprocessing have been estimated. |
| 18 | +#' @param ahead A vector of positive integers. Each specified column will be |
| 19 | +#' lead for each value in the vector. |
| 20 | +#' @param prefix A prefix for generated column names, default to "ahead_". |
| 21 | +#' @param default Determines what fills empty rows |
| 22 | +#' left by leading/lagging (defaults to NA). |
| 23 | +#' @param keys A character vector of the keys in an epi_df |
| 24 | +#' @param columns A character string of variable names that will |
| 25 | +#' be populated (eventually) by the `terms` argument. |
| 26 | +#' @param skip A logical. Should the step be skipped when the |
| 27 | +#' recipe is baked by [bake()]? While all operations are baked |
| 28 | +#' when [prep()] is run, some operations may not be able to be |
| 29 | +#' conducted on new data (e.g. processing the outcome variable(s)). |
| 30 | +#' Care should be taken when using `skip = TRUE` as it may affect |
| 31 | +#' the computations for subsequent operations. |
| 32 | +#' @param id A character string that is unique to this step to identify it. |
| 33 | +#' @template step-return |
| 34 | +#' |
| 35 | +#' @details The step assumes that the data are already _in the proper sequential |
| 36 | +#' order_ for leading. |
| 37 | +#' |
| 38 | +#' @family row operation steps |
| 39 | +#' @export |
| 40 | +#' |
| 41 | +#' @examples |
| 42 | +#' tib <- tibble( |
| 43 | +#' x = 1:5, y = 1:5, |
| 44 | +#' time_value = seq(as.Date("2020-01-01"), by = 1, length.out = 5), |
| 45 | +#' geo_value = "ca" |
| 46 | +#' ) %>% epiprocess::as_epi_df() |
| 47 | +#' |
| 48 | +#' library(recipes) |
| 49 | +#' recipe(y ~ x., data = tib) %>% |
| 50 | +#' step_epi_lag(x, lag = 2:3) %>% |
| 51 | +#' step_epi_ahead(y, ahead = 1) %>% |
| 52 | +#' prep(df) %>% |
| 53 | +#' bake(df) |
| 54 | +step_epi_ahead <- |
| 55 | + function(recipe, |
| 56 | + ..., |
| 57 | + role = "outcome", |
| 58 | + trained = FALSE, |
| 59 | + ahead = 1, |
| 60 | + prefix = "ahead_", |
| 61 | + default = NA, |
| 62 | + keys = epi_keys(recipe), |
| 63 | + columns = NULL, |
| 64 | + skip = FALSE, |
| 65 | + id = rand_id("epi_ahead")) { |
| 66 | + add_step( |
| 67 | + recipe, |
| 68 | + step_epi_ahead_new( |
| 69 | + terms = dplyr::enquos(...), |
| 70 | + role = role, |
| 71 | + trained = trained, |
| 72 | + ahead = ahead, |
| 73 | + prefix = prefix, |
| 74 | + default = default, |
| 75 | + keys = keys, |
| 76 | + columns = columns, |
| 77 | + skip = skip, |
| 78 | + id = id |
| 79 | + ) |
| 80 | + ) |
| 81 | + } |
| 82 | + |
| 83 | +step_epi_ahead_new <- |
| 84 | + function(terms, role, trained, ahead, prefix, default, keys, |
| 85 | + columns, skip, id) { |
| 86 | + step( |
| 87 | + subclass = "epi_ahead", |
| 88 | + terms = terms, |
| 89 | + role = role, |
| 90 | + trained = trained, |
| 91 | + ahead = ahead, |
| 92 | + prefix = prefix, |
| 93 | + default = default, |
| 94 | + keys = keys, |
| 95 | + columns = columns, |
| 96 | + skip = skip, |
| 97 | + id = id |
| 98 | + ) |
| 99 | + } |
| 100 | + |
| 101 | +#' @export |
| 102 | +prep.step_epi_ahead <- function(x, training, info = NULL, ...) { |
| 103 | + step_epi_ahead_new( |
| 104 | + terms = x$terms, |
| 105 | + role = x$role, |
| 106 | + trained = TRUE, |
| 107 | + ahead = x$ahead, |
| 108 | + prefix = x$prefix, |
| 109 | + default = x$default, |
| 110 | + keys = x$keys, |
| 111 | + columns = recipes_eval_select(x$terms, training, info), |
| 112 | + skip = x$skip, |
| 113 | + id = x$id |
| 114 | + ) |
| 115 | +} |
| 116 | + |
| 117 | +#' @export |
| 118 | +bake.step_epi_ahead <- function(object, new_data, ...) { |
| 119 | + if (!all(object$ahead == as.integer(object$ahead))) { |
| 120 | + rlang::abort("step_epi_ahead requires 'lag' argument to be integer valued.") |
| 121 | + } |
| 122 | + |
| 123 | + grid <- tidyr::expand_grid( |
| 124 | + col = object$columns, lag_val = -object$ahead, ahead_val = object$ahead) %>% |
| 125 | + dplyr::mutate(newname = glue::glue("{object$prefix}{ahead_val}_{col}")) %>% |
| 126 | + dplyr::select(-ahead_val) |
| 127 | + |
| 128 | + ## ensure no name clashes |
| 129 | + new_data_names <- colnames(new_data) |
| 130 | + intersection <- new_data_names %in% grid$newname |
| 131 | + if (any(intersection)) { |
| 132 | + rlang::abort( |
| 133 | + paste0("Name collision occured in `", class(object)[1], |
| 134 | + "`. The following variable names already exists: ", |
| 135 | + paste0(new_data_names[intersection], collapse = ", "), |
| 136 | + ".")) |
| 137 | + } |
| 138 | + |
| 139 | + ok <- object$keys |
| 140 | + lagged <- purrr::reduce( |
| 141 | + purrr::pmap(grid, epi_shift_single, x = new_data, key_cols = ok), |
| 142 | + dplyr::full_join, |
| 143 | + by = ok |
| 144 | + ) |
| 145 | + |
| 146 | + dplyr::full_join(new_data, lagged, by = object$keys) %>% |
| 147 | + dplyr::group_by(dplyr::across(dplyr::all_of(ok[-1]))) %>% |
| 148 | + dplyr::arrange(time_value) %>% |
| 149 | + dplyr::ungroup() |
| 150 | + |
| 151 | +} |
| 152 | + |
| 153 | +#' @export |
| 154 | +print.step_epi_ahead <- |
| 155 | + function(x, width = max(20, options()$width - 30), ...) { |
| 156 | + ## TODO add printing of the lags |
| 157 | + title <- "Leading " |
| 158 | + recipes::print_step(x$columns, x$terms, x$trained, title, width) |
| 159 | + invisible(x) |
| 160 | + } |
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