added fuimus namespace calls, updated pkgdown site, removed utility f…

…unctions

DESCRIPTION

@@ -25,6 +25,7 @@ Imports:
     vctrs (>= 0.6.5)
 Suggests: 
     qs,
+    fuimus,
     gt,
     knitr,
     rmarkdown,
@@ -33,6 +34,8 @@ Suggests:
     testthat (>= 3.0.0)
 VignetteBuilder: 
     knitr
+Remotes: 
+    github::andrewallenbruce/fuimus
 Config/roxyglobals/filename: roxyglobals-generated.R
 Config/roxyglobals/unique: TRUE
 Encoding: UTF-8

NAMESPACE

@@ -6,16 +6,13 @@ export(appendix_B)
 export(appendix_C)
 export(apply_age_edits)
 export(case_chapter_icd10)
-export(display_long)
 export(ex_data)
-export(gt_marks)
 export(gt_style)
 export(icd10api)
 export(icd10cm)
 export(is_valid_icd)
 export(mount_board)
 export(remove_dot)
 export(search_edits)
-export(search_in)
 export(search_msdrg)
 export(years_floor)

R/appendices.R

@@ -31,11 +31,12 @@ appendix_A <- function(drg  = NULL,
 
   msd <- pins::pin_read(mount_board(), "msdrg_41.1")
 
-  if (!is.null(type)) {msd <- vctrs::vec_slice(msd, msd$drg_type == type)}
+  if (!is.null(type)) {
+    msd <- vctrs::vec_slice(msd, msd$drg_type == type)
+  }
 
-  if (!is.null(drg)) {msd <- search_in(msd, msd$drg, drg)}
-
-  if (!is.null(mdc)) {msd <- search_in(msd, msd$mdc, mdc)}
+  msd <- fuimus::search_in_if(msd, msd$drg, drg)
+  msd <- fuimus::search_in_if(msd, msd$mdc, mdc)
 
   return(msd)
 }

R/icd_10_cm.R

@@ -30,7 +30,7 @@ icd10cm <- function(icd = NULL,
       ) |>
       tidyr::unnest(icd_sec_code)
 
-    icd10 <- search_in(icd10, icd10$icd_code, icd)
+    icd10 <- fuimus::search_in(icd10, icd10$icd_code, icd)
 
     edit <- search_edits(icd = icd)
 

R/icd_edits.R

@@ -25,7 +25,7 @@ search_edits <- function(icd = NULL,
 
   edt <- pins::pin_read(mount_board(), "code_edits")
 
-  if (!is.null(icd)) {edt <- search_in(edt, edt$icd_code, icd)}
+  edt <- fuimus::search_in_if(edt, edt$icd_code, icd)
 
   return(edt)
 }
@@ -48,10 +48,17 @@ search_edits <- function(icd = NULL,
 #'
 #' @export
 years_floor <- function(from, to) {
-  floor(as.integer(difftime(to, from, units = "weeks", tz = "UTC")) / 52.17857)
+  floor(
+    as.integer(
+      difftime(
+        to,
+        from,
+        units = "weeks",
+        tz = "UTC"
+        )
+      ) / 52.17857)
 }
 
-
 #' Apply Age Conflict Edits
 #'
 #' @param rule `<chr>` ICD-10-CM Conflict Rule

R/msdrg.R

@@ -38,12 +38,11 @@ search_msdrg <- function(drg  = NULL,
                          ...) {
 
   ms <- pins::pin_read(mount_board(), "msdrg")
+  ms <- fuimus::search_in_if(ms, ms$drg, drg)
+  ms <- fuimus::search_in_if(ms, ms$mdc, mdc)
 
-  if (!is.null(type)) {ms <- vctrs::vec_slice(ms, ms$drg_type == type)}
-
-  if (!is.null(drg)) {ms <- search_in(ms, ms$drg, drg)}
-
-  if (!is.null(mdc)) {ms <- search_in(ms, ms$mdc, mdc)}
-
+  if (!is.null(type)) {
+    ms <- vctrs::vec_slice(ms, ms$drg_type == type)
+  }
   return(ms)
 }

R/utils.R

@@ -1,37 +1,3 @@
-#' Search in data frame
-#'
-#' @template args-df
-#'
-#' @param dfcol `<sym>` unquoted column to search, in the form of `df$col`
-#'
-#' @param search `<chr>` vector of strings to search for in `df$col`
-#'
-#' @template returns
-#'
-#' @keywords internal
-#'
-#' @autoglobal
-#'
-#' @export
-search_in <- function(df, dfcol, search) {
-  vctrs::vec_slice(
-    df,
-    vctrs::vec_in(
-      dfcol,
-      collapse::funique(
-        search
-      )
-    )
-  )
-}
-
-#' Return GitHub raw url
-#'
-#' @noRd
-gh_raw <- function(x) {
-  paste0("https://raw.githubusercontent.com/", x)
-}
-
 #' Mount [pins][pins::pins-package] board
 #'
 #' @param `<chr>` string; whether source is `"local"` or `"remote"`
@@ -51,34 +17,12 @@ mount_board <- function(source = c("local", "remote")) {
   switch(
     source,
     local  = pins::board_folder(fs::path_package("extdata/pins", package = "pathologie")),
-    remote = pins::board_url(gh_raw(
+    remote = pins::board_url(fuimus::gh_raw(
       "andrewallenbruce/pathologie/master/inst/extdata/pins/"
     ))
   )
 }
 
-#' Pivot data frame to long format for easy printing
-#'
-#' @template args-df
-#'
-#' @param cols `<syms>` vector of bare column name to pivot, default is [dplyr::everything()]
-#'
-#' @template returns
-#'
-#' @keywords internal
-#'
-#' @autoglobal
-#'
-#' @export
-display_long <- function(df,
-                         cols = dplyr::everything()) {
-
-  df |> dplyr::mutate(
-    dplyr::across(
-      dplyr::everything(), as.character)) |>
-    tidyr::pivot_longer({{ cols }})
-}
-
 #' gt Theme
 #'
 #' @param tbl `<gt_tbl>` object
@@ -128,36 +72,6 @@ gt_style <- function(tbl,
     )
 }
 
-#' gt Marks
-#'
-#' @param tbl `<gt_tbl>` object
-#'
-#' @param cols `<syms>` vector of bare column names, e.g. `c(mdc, drg)`
-#'
-#' @template returns
-#'
-#' @keywords internal
-#'
-#' @autoglobal
-#'
-#' @export
-gt_marks <- function(tbl, cols) {
-
-  tbl |>
-    gt::text_case_when(
-      x == TRUE ~ gt::html(
-        fontawesome::fa("check",
-                        prefer_type = "solid",
-                        fill = "red")),
-      x == FALSE ~ gt::html(
-        fontawesome::fa("xmark",
-                        prefer_type = "solid",
-                        fill = "white")),
-      .default = NA,
-      .locations = gt::cells_body(
-        columns = {{ cols }}))
-}
-
 #' Example data set
 #'
 #' @template returns

_pkgdown.yml

@@ -1,4 +1,12 @@
 url: https://andrewallenbruce.github.io/pathologie/
 template:
   bootstrap: 5
+  theme: tango
+  bslib:
+    font_scale: 1.1
+    base_font: {google: "Atkinson Hyperlegible"}
+    heading_font: {google: "Atkinson Hyperlegible"}
+    code_font: "Hack, mono"
+  includes:
+    in_header: <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/hack-font@3/build/web/hack-subset.css">
 

vignettes/pathologie.Rmd

@@ -22,6 +22,7 @@ knitr::opts_chunk$set(
 library(dplyr)
 library(gt)
 library(pathologie)
+library(fuimus)
 ```
 
 ```{r}