* getting started vignette

* added display_long helper

DESCRIPTION

@@ -24,6 +24,7 @@ Imports:
     tidyr (>= 1.3.1),
     vctrs (>= 0.6.5)
 Suggests: 
+    gt,
     knitr,
     rmarkdown,
     roxyglobals

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(case_chapter_icd10)
+export(display_long)
 export(icd10api)
 export(icd10cm)
 export(is_valid_icd)

NEWS.md

@@ -1,3 +1,3 @@
 # pathologie (development version)
 
-* Initial CRAN submission.
+* Initial commit.

R/utils.R

@@ -6,7 +6,7 @@ gh_raw <- function(x) {
 
 #' Mount [pins][pins::pins-package] board
 #' @param source `"local"` or `"remote"`
-#' @return `<pins_board_folder>` or `<pins_board_url>`
+#' @return `<pins_board_folder>` if `source = "local"` or `<pins_board_url>` if `source = "remote"`
 #' @noRd
 mount_board <- function(source = c("local", "remote")) {
 
@@ -16,7 +16,22 @@ mount_board <- function(source = c("local", "remote")) {
     source,
     local  = pins::board_folder(fs::path_package("extdata/pins", package = "pathologie")),
     remote = pins::board_url(gh_raw(
-      "andrewallenbruce/northstar/master/inst/extdata/pins/"
+      "andrewallenbruce/pathologie/master/inst/extdata/pins/"
     ))
   )
 }
+
+#' Pivot data frame to long format for easy printing
+#' @param df `<data.frame>`
+#' @param cols `<chr>` vector of columns to pivot long, default is [dplyr::everything()]
+#' @return A [tibble][tibble::tibble-package] of the pivoted data frame.
+#' @autoglobal
+#' @export
+#' @keywords internal
+display_long <- function(df, cols = dplyr::everything()) {
+
+  df |> dplyr::mutate(
+    dplyr::across(
+      dplyr::everything(), as.character)) |>
+    tidyr::pivot_longer({{ cols }})
+}

README.Rmd

@@ -22,7 +22,7 @@ The goal of pathologie is to ...
 
 ## Installation
 
-You can install the development version of **pathologie** from [GitHub](https://github.com/) with:
+You can install **pathologie** from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("pak")
@@ -33,6 +33,19 @@ pak::pak("andrewallenbruce/pathologie")
 
 This is a basic example which shows you how to solve a common problem:
 
-```{r example}
+```{r setup}
 library(pathologie)
+library(dplyr)
 ```
+
+
+```{r}
+icd10cm(code = c("I10", "I15.0")) |> 
+  glimpse()
+```
+
+
+```{r}
+icd10api(code = "I1")
+```
+

README.md

@@ -10,8 +10,7 @@ The goal of pathologie is to …
 
 ## Installation
 
-You can install the development version of **pathologie** from
-[GitHub](https://github.com/) with:
+You can install **pathologie** from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("pak")
@@ -24,4 +23,55 @@ This is a basic example which shows you how to solve a common problem:
 
 ``` r
 library(pathologie)
+library(dplyr)
+#> 
+#> Attaching package: 'dplyr'
+#> The following objects are masked from 'package:stats':
+#> 
+#>     filter, lag
+#> The following objects are masked from 'package:base':
+#> 
+#>     intersect, setdiff, setequal, union
+```
+
+``` r
+icd10cm(code = c("I10", "I15.0")) |> 
+  glimpse()
+#> Rows: 2
+#> Columns: 10
+#> $ ch            <int> 9, 9
+#> $ abb           <chr> "CARDIO", "CARDIO"
+#> $ chapter_name  <chr> "Diseases of the circulatory system", "Diseases of the c…
+#> $ chapter_range <chr> "I00 - I99", "I00 - I99"
+#> $ section_name  <chr> "Other rheumatic heart diseases", "Secondary hypertensio…
+#> $ section_range <chr> "I09 - I10", "I15 - I15.9"
+#> $ order         <int> 11397, 11411
+#> $ valid         <int> 1, 1
+#> $ code          <chr> "I10", "I15.0"
+#> $ description   <chr> "Essential (primary) hypertension", "Renovascular hypert…
+```
+
+``` r
+icd10api(code = "I1")
+#> # A tibble: 18 × 2
+#>    code   description                                                           
+#>    <chr>  <chr>                                                                 
+#>  1 I10    Essential (primary) hypertension                                      
+#>  2 I11.0  Hypertensive heart disease with heart failure                         
+#>  3 I11.9  Hypertensive heart disease without heart failure                      
+#>  4 I12.0  Hypertensive chronic kidney disease with stage 5 chronic kidney disea…
+#>  5 I12.9  Hypertensive chronic kidney disease with stage 1 through stage 4 chro…
+#>  6 I13.0  Hypertensive heart and chronic kidney disease with heart failure and …
+#>  7 I13.10 Hypertensive heart and chronic kidney disease without heart failure, …
+#>  8 I13.11 Hypertensive heart and chronic kidney disease without heart failure, …
+#>  9 I13.2  Hypertensive heart and chronic kidney disease with heart failure and …
+#> 10 I15.0  Renovascular hypertension                                             
+#> 11 I15.1  Hypertension secondary to other renal disorders                       
+#> 12 I15.2  Hypertension secondary to endocrine disorders                         
+#> 13 I15.8  Other secondary hypertension                                          
+#> 14 I15.9  Secondary hypertension, unspecified                                   
+#> 15 I16.0  Hypertensive urgency                                                  
+#> 16 I16.1  Hypertensive emergency                                                
+#> 17 I16.9  Hypertensive crisis, unspecified                                      
+#> 18 I1A.0  Resistant hypertension
 ```

vignettes/pathologie.Rmd

@@ -7,13 +7,108 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
-```{r, include = FALSE}
+```{r setup, include = FALSE}
 knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>"
-)
+  collapse  = FALSE,
+  echo      = TRUE,
+  message   = FALSE, 
+  warning   = FALSE,
+  error     = TRUE,
+  comment   = "#>",
+  dpi       = 600, 
+  out.width = "100%"
+  )
+
+library(dplyr)
+library(gt)
+library(pathologie)
 ```
 
-```{r setup}
+```{r}
 library(pathologie)
 ```
+
+
+# ICD-10-CM
+
+```{r}
+icd10cm(code = "I10") |> 
+  mutate(Chapter = paste0("* ", chapter_name, " \n ", "* Range: [", chapter_range, "]"),
+         Section = paste0("* ", section_name, " \n ", "* Range: [", section_range, "]")
+         ) |>
+  select("ICD-10-Code"   = code, 
+         Description     = description, 
+         Chapter,
+         Section,
+         Abbreviation    = abb) |> 
+  display_long() |>
+  gt(groupname_col       = "name", 
+     row_group_as_column = TRUE) |>
+  fmt_markdown() |> 
+  gt_style(tablign       = "right", 
+           tabsize       = 16, 
+           tabwt         = "bold") |> 
+  tab_style(
+      style              = cell_text(
+      font               = google_font(name = "Fira Code")),
+      locations          = cells_body(
+        columns          = contains("value"))) |>
+  tab_style(
+    style                = list(
+      cell_fill(color    = "powderblue"),
+      cell_text(weight   = "bold"),
+      cell_borders(
+      sides              = c("all"),
+      color              = "powderblue",
+      weight             = px(3))
+      ),
+    locations            = cells_row_groups())
+```
+
+
+# The NLM's ICD-10-CM API
+
+The [National Library of Medicine](https://clinicaltables.nlm.nih.gov/apidoc/icd10cm/v3/doc.html)'s ICD-10-CM API is a RESTful API that provides access to the current ICD-10-CM code set. 
+
+The API allows users to search for codes by code or keyword(term), and returns the code and its description. Searching is case insensitive and greedy The following are some examples:
+
+
+> Returns the seven ICD-10 codes beginning with `A15`:
+
+```{r}
+icd10api(code = "A15")
+```
+
+> Returns all 344 ICD-10 codes associated with tuberculosis:
+
+```{r}
+icd10api(term = "tuber")
+```
+
+> Returns the two ICD-10 codes associated with pleurisy:
+
+```{r}
+icd10api(term = "pleurisy")
+```
+
+## The `field` Parameter
+
+The `field` parameter allows users to specify whether they want to search for ICD-10-CM codes by the codes themselves or by terms associated with their description. It defaults to `"code"` and it's behavior warrants some explanation.
+
+If you're searching for codes beginning with a certain letter, you must set the `field` parameter to `"code"` or it will return both codes and terms that contain that letter. 
+
+
+For instance, the following call returns ICD-10 **codes** and **descriptions** containing the letter "Z":
+
+
+```{r}
+icd10api(code = "z", limit = 50)
+```
+
+
+While the call below returns only the ICD-10 **codes** containing "Z":
+
+
+```{r}
+icd10api(code = "z", field = "code", limit = 50)
+```