update for cran check

emitanaka · Nov 12, 2023 · 3bbd04e · 3bbd04e
1 parent bdb85e8
commit 3bbd04e
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Showing 23 changed files with 362 additions and 346 deletions.
diff --git a/R/anatomy.R b/R/anatomy.R
@@ -9,7 +9,7 @@
 #' @param ... Any other arguments parsed to `dae::designAnatomy`.
 #' @examples
 #' split <- takeout(menu_split(t1 = 3, t2 = 2, r = 2))
-#' anatomy(split)
+#' design_anatomy(split)
 #' @return An object of class "des_anatomy".
 #' @export
 design_anatomy <- function(.edibble, ...) {

diff --git a/R/assign.R b/R/assign.R
@@ -67,7 +67,7 @@ assign_trts <- function(.edibble, order = "random", seed = NULL, constrain = nes
       vanc <- prov$fct_id_ancestor(id = unit_id, role = "edbl_unit")
       units_df_with_id <- units_df <- tibble::as_tibble(prov$serve_units(id = vanc))
       units_df_with_id$..id.. <- 1:nrow(units_df_with_id)
-      ptrts_df <- na.omit(tibble::as_tibble(prov$serve_trts(id = parent_trts)))
+      ptrts_df <- stats::na.omit(tibble::as_tibble(prov$serve_trts(id = parent_trts)))
 
       if(nrow(ptrts_df) == 0L) abort(paste0("The treatment factor, ",
                                             .combine_words(prov$fct_names(id = trts_id), fun = cli::col_blue),
@@ -104,7 +104,7 @@ assign_trts <- function(.edibble, order = "random", seed = NULL, constrain = nes
                                    {
                                      vparents <- prov$fct_id(name = constrain[[unit_nm]])
                                      order_name <- structure(order[igroup], class = order[igroup])
-                                     order_trts(order_name, trts_table = sub_trts_df, units_table = sub_units_df, unit = setNames(unit_id, unit_nm), constrain = vparents, Provenance = prov, ...)
+                                     order_trts(order_name, trts_table = sub_trts_df, units_table = sub_units_df, unit = stats::setNames(unit_id, unit_nm), constrain = vparents, Provenance = prov, ...)
                                    })
         permutation[units_df_with_id$..id..[locs]] <- sub_trts_df_with_id[permute, "..id..", drop = TRUE]
       }
@@ -144,7 +144,7 @@ assign_trts <- function(.edibble, order = "random", seed = NULL, constrain = nes
                               units_df <- tibble::as_tibble(prov$serve_units(id = vanc))
                               vparents <- prov$fct_id(name = constrain[[unit_nm]])
                               order_name <- structure(order[igroup], class = order[igroup])
-                              order_trts(order_name, trts_table = trts_df, units_table = units_df, unit = setNames(unit_id, unit_nm), constrain = vparents, Provenance = prov, ...)
+                              order_trts(order_name, trts_table = trts_df, units_table = units_df, unit = stats::setNames(unit_id, unit_nm), constrain = vparents, Provenance = prov, ...)
                             })
 
     }

diff --git a/R/attrs.R b/R/attrs.R
@@ -39,6 +39,7 @@ fct_attrs <- fct
 #'
 #'
 #' @param value A vector of the level values.
+#' @param n The number of replicate (if applicable).
 #' @param data A list or data frame of the same size as the `levels`.
 #' @param ... Name-value pair denoting other level attributes. The value should be the same
 #'  length as `levels` or a single value.

diff --git a/R/design.R b/R/design.R
@@ -85,7 +85,7 @@ design_model <- function(data, type = c("anova", "lmer")) {
   des <- edbl_design(data)
   type <- match.arg(type)
   unit_str <- des$anatomy
-  units <- attr(terms(unit_str), "term.labels")
+  units <- attr(stats::terms(unit_str), "term.labels")
   trts <- map_lgl(prov$fct_levels(name = prov$trt_names(), return = "value"),
                   function(x) inherits(x, "numeric") |  inherits(x, "integer"))
   tnames <- names(trts)

diff --git a/R/edibble.R b/R/edibble.R
@@ -127,8 +127,6 @@ not_edibble <- function(x) {
 #' @param ... Passed to `new_tibble`.
 #' @param .design An edibble graph object.
 #' @param .class Subclasses for edibble table. The default is NULL.
-#' @param units The data columns that are units.
-#' @param trts The data columns that are treatments.
 #' @importFrom tibble new_tibble
 #' @importFrom vctrs vec_size_common
 #' @return An edibble table.

diff --git a/R/latin.R b/R/latin.R
@@ -8,7 +8,7 @@
 #' @examples
 #' latin_square(n = 3)
 #' latin_rectangle(3, 3, 3)
-#' latin_array(3, c(3, 3, 3))
+#' latin_array(c(3, 3, 3), 3)
 NULL
 
 #' @describeIn latin Latin square design

diff --git a/R/pivot.R b/R/pivot.R
@@ -21,7 +21,7 @@
 #' @param .remove_empty Remove empty combinations. Default is TRUE.
 #' @examples
 #' spd <- takeout(menu_split())
-#' spd %>% split(trt1)
+#' split(spd, spd$trt1)
 #' spd %>% split_by(trt1)
 #' spd %>% split_by(trt2)
 #' spd %>% split_by(mainplot)

diff --git a/R/simulate.R b/R/simulate.R
@@ -204,7 +204,7 @@ get_censored_value <- function(y, valid, censor) {
     switch(valid$operator,
            "greaterThan" = return_censor_value(y, y > value, censor, valid_env = valid_env),
            "greaterThanOrEqual" = return_censor_value(y, y >= value, censor, valid_env = valid_env),
-           "equal" = return_censor_value(y, y == value, .censor, valid_env = valid_env),
+           "equal" = return_censor_value(y, y == value, censor, valid_env = valid_env),
            "between" = return_censor_value(y, y > value[1] & y < value[2], censor, value, valid_env = valid_env),
            "lessThanOrEqual" = return_censor_value(y, y <= value, censor, valid_env = valid_env),
            "lessThan" = return_censor_value(y, y < value, censor, valid_env = valid_env))
@@ -291,7 +291,7 @@ aggregate_values <- function(y, group, fn) {
 #' @param .interaction Whether there should be treatment interaction effects.
 #' @param .discrete Whether to make the response value discrete or not.
 #' @param .linear Whether to include non-linear term or not. The value is always additive.
-#' @param .dist The random distribution to use for numerical values
+#' @param .error_dist The random distribution to use for numerical values
 #'  (either "normal", "uniform", "exponential", "gamma", "beta", "cauchy", "chisq", "f", "t", "poisson", "weibull").
 #'  The default choice is random out of these with higher chances of "normal".
 #' @seealso [autofill_rcrds()]
@@ -506,7 +506,7 @@ examine_process <- function(data, process = NULL) {
     NULL
   } else {
     if(!is_null(process)) {
-      res <- setNames(list(res), process)
+      res <- stats::setNames(list(res), process)
     }
     structure(res, class = c("sim_process", class(res)))
   }

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,8 +1,29 @@
 ## Release summary
 
-This is a major internal change that the R6 class is completely changed to a Provenance class object that ensures a more consistent and cognitive access to internal structure. 
+This update makes a number of bug fixes, addition of new features and 
+quality of life improvements as shown below.
 
-Other changes include the change of dependency to use `openxlsx2` instead of `openxlsx` and the change in print for the object with class `ebdl_table`.
+Bug fixes
+
+* Bug fix for export_design when no record factor exists
+* Bug fix for order assignment
+
+Quality of life improvements
+
+* Format change for the title page in the export
+* Change behaviour of `fct_attrs()` when levels supplied as numeric or vector 
+  instead of `lvls()`. 
+* Change the print out of edibble table.
+* Improve the assignment algorithm.
+
+New features 
+
+* Added new functions `count_by()` and `split_by()`.
+* Added ability to specify conditional treatment.
+* The `simuluate_rcrds()` has now a facelift with delineation of the process specification to `simulate_process()`. 
+* `autofill_rcrds()` implemented.
+* Added ability to add two designs by `+`.
+* Ability to add metadata through design().
 
 ## R CMD check results
 

diff --git a/man/design_anatomy.Rd b/man/design_anatomy.Rd
diff --git a/man/latin.Rd b/man/latin.Rd
diff --git a/man/lvls.Rd b/man/lvls.Rd
diff --git a/man/new_edibble.Rd b/man/new_edibble.Rd
diff --git a/man/split_by.Rd b/man/split_by.Rd
diff --git a/man/with_variables.Rd b/man/with_variables.Rd