From 40dbea35ac7fbe4963ceb5e72a3ef9a75f35f80c Mon Sep 17 00:00:00 2001 From: Ewan Donnachie Date: Tue, 14 Apr 2020 15:06:02 +0200 Subject: [PATCH] pkgdown v1.1 --- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/LICENSE.html | 2 +- docs/articles/icd10gm_intro.html | 146 +++++++++++------------ docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 6 +- docs/news/index.html | 24 ++-- docs/pkgdown.yml | 2 +- docs/reference/get_icd_history.html | 2 +- docs/reference/get_icd_labels.html | 2 +- docs/reference/icd_expand.html | 2 +- docs/reference/icd_history.html | 2 +- docs/reference/icd_meta_blocks.html | 2 +- docs/reference/icd_meta_chapters.html | 2 +- docs/reference/icd_meta_codes.html | 11 +- docs/reference/icd_meta_transition.html | 2 +- docs/reference/icd_parse.html | 2 +- docs/reference/icd_showchanges.html | 2 +- docs/reference/icd_showchanges_icd3.html | 2 +- docs/reference/index.html | 2 +- docs/reference/is_icd_code.html | 2 +- 22 files changed, 117 insertions(+), 106 deletions(-) diff --git a/docs/404.html b/docs/404.html index d84fe63..31e81dc 100644 --- a/docs/404.html +++ b/docs/404.html @@ -76,7 +76,7 @@ ICD10gm - 1.0.5 + 1.1 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 94db7e6..031f5fa 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -76,7 +76,7 @@ ICD10gm - 1.0.5 + 1.1 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index e73415b..34f2595 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -76,7 +76,7 @@ ICD10gm - 1.0.5 + 1.1 diff --git a/docs/articles/icd10gm_intro.html b/docs/articles/icd10gm_intro.html index 4c842f3..670e43f 100644 --- a/docs/articles/icd10gm_intro.html +++ b/docs/articles/icd10gm_intro.html @@ -38,7 +38,7 @@ ICD10gm - 1.0.5 + 1.1 @@ -86,7 +86,7 @@

Introduction to the ICD10gm Package

Motivation, Basic Usage and Examples

Ewan Donnachie

-

2019-12-16

+

2020-04-14

@@ -112,7 +112,7 @@

ICD10gm is designed for use in the context of medical and health services research using routinely collected claims data. It is not suitable for use in operative coding as it does not include all relevant metadata (e.g. inclusion and exclusion notes and the detailed definitions of psychiatric diagnoses). The metadata provided in the ICD10gm package is not intended to replace the official DIMDI documentation, which should always be consulted when specifying ICD codes for analysis.

The following presents an overview of the basic functionality provided by the ICD10gm package, illustrated by means of simple examples. To access this vignette in R, type:

-
vignette("icd10gm_intro", package = "ICD10gm")
+
vignette("icd10gm_intro", package = "ICD10gm")
@@ -147,13 +147,13 @@

Example

First, we load the ICD10gm package alongside some tidyverse packages:

-
library(dplyr)
-library(purrr)
-library(tidyr)
-library(ICD10gm)
+
library(dplyr)
+library(purrr)
+library(tidyr)
+library(ICD10gm)

By way of example, we examine the coding of unspecific gastroenteritis (i.e. without identification of a specific cause), a very common diagnosis in primary care. This is currently classified under the ICD-10 code “A09”, which we can lookup for the year 2018 as follows:

-
get_icd_labels("A09", year = 2018) %>%
-  knitr::kable(row.names = FALSE)
+
get_icd_labels("A09", year = 2018) %>%
+  knitr::kable(row.names = FALSE)
@@ -191,8 +191,8 @@

year

Now, we check whether whether this code has been affected by code transitions in any revision since 2003:

-
icd_showchanges_icd3("A09") %>%
-  knitr::kable(row.names = FALSE)
+
icd_showchanges_icd3("A09") %>%
+  knitr::kable(row.names = FALSE)
@@ -254,11 +254,11 @@

year_from

Diagnoses that, prior to 2009, were coded as K52.9 are now coded as A09.9. We can investigate exactly what changed by looking the relevant codes for the years 2009 and 2010:

-
get_icd_labels(icd3 = c("A09", "K52"), year = 2009:2010) %>%
-  arrange(year, icd_sub) %>% 
-  filter(icd_sub %in% c("K529") | icd3 == "A09") %>% 
-  select(year, icd_normcode, label) %>% 
-  knitr::kable(row.names = FALSE)
+
get_icd_labels(icd3 = c("A09", "K52"), year = 2009:2010) %>%
+  arrange(year, icd_sub) %>% 
+  filter(icd_sub %in% c("K529") | icd3 == "A09") %>% 
+  select(year, icd_normcode, label) %>% 
+  knitr::kable(row.names = FALSE)
@@ -309,8 +309,8 @@

Examples

The function is_icd_code recognises ICD codes regardless of their formatting, returning TRUE if the string is recognised as an ICD code and FALSE otherwise:

-
is_icd_code(c("E10.1", "E101", "E10.1-", "J44", "This is not an ICD code"))
-#> [1]  TRUE  TRUE  TRUE  TRUE FALSE
+
is_icd_code(c("E10.1", "E101", "E10.1-", "J44", "This is not an ICD code"))
+#> [1]  TRUE  TRUE  TRUE  TRUE FALSE
@@ -321,22 +321,22 @@

Example: Scraping codes from a website

As an example of how ICD10gm can be used to extract ICD codes from arbitrary text, the following code uses the rvest package to scrape the code block “A00-A09” from the online version of the DIMDI ICD-10-GM reference. We apply the filter to exclude codes below A10, thus revealing which other ICD-10 codes are reference from this block. To simply the package building process, the code has not been evaluated. This is left as an exercise to the reader.

- +
library(dplyr)
+library(rvest)
+
+read_html("https://www.dimdi.de/static/de/klassifikationen/icd/icd-10-gm/kode-suche/htmlgm2018/block-a00-a09.htm") %>% 
+  html_text() %>%
+  icd_parse(type = "bounded") %>%
+  select(-icd_spec) %>% 
+  unique() %>% 
+  filter(icd_sub >= "A10") %>% 
+  arrange(icd_sub) %>% 
+  left_join(
+    get_icd_labels(year = 2018)[, c("icd_sub", "icd_normcode", "label")],
+    by = "icd_sub") %>% 
+  select(icd_normcode, label) %>% 
+  knitr::kable(row.names = FALSE,
+               caption = "Additional ICD-10 codes referred to in block A00-A09 (Intestional infectious diseases) of the ICD-10-GM (2018).")
@@ -347,10 +347,10 @@

Example

Irritable bowel syndrome is coded using either the three-digit code K58 (conceiving IBS as the somatic condition) or the code F45.32 (focussing on IBS as a psychosomatic condition). We can retrieve all subcodes in the year 2019 as follows:

-
icd_k58 <- data.frame(DIAG_GROUP = c("IBS", "IBS"), ICD_SPEC = c("K58", "F45.32")) %>% 
-  icd_expand(col_icd = "ICD_SPEC", year = 2019, col_meta = "DIAG_GROUP")
-  
-knitr::kable(icd_k58)
+
icd_k58 <- data.frame(DIAG_GROUP = c("IBS", "IBS"), ICD_SPEC = c("K58", "F45.32")) %>% 
+  icd_expand(col_icd = "ICD_SPEC", year = 2019, col_meta = "DIAG_GROUP")
+  
+knitr::kable(icd_k58)
year
@@ -437,24 +437,24 @@

Example

We historise the code K58, specified for the year 2019, backwards to obtain the corresponding codes for the years 2017 to 2019:

- +
icd_history(icd_k58, years = 2017:2019) %>% 
+  select(icd_spec, DIAG_GROUP, year, icd_code) %>% 
+  arrange(year, icd_code)
+#> # A tibble: 12 x 4
+#>    icd_spec DIAG_GROUP  year icd_code
+#>    <chr>    <fct>      <int> <chr>   
+#>  1 F4532    IBS         2017 F45.32  
+#>  2 K58      IBS         2017 K58.0   
+#>  3 K58      IBS         2017 K58.9   
+#>  4 F4532    IBS         2018 F45.32  
+#>  5 K58      IBS         2018 K58.0   
+#>  6 K58      IBS         2018 K58.9   
+#>  7 F4532    IBS         2019 F45.32  
+#>  8 K58      IBS         2019 K58.-   
+#>  9 K58      IBS         2019 K58.1   
+#> 10 K58      IBS         2019 K58.2   
+#> 11 K58      IBS         2019 K58.3   
+#> 12 K58      IBS         2019 K58.8
diff --git a/docs/articles/index.html b/docs/articles/index.html index 464a54a..03e9bbb 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -76,7 +76,7 @@ ICD10gm - 1.0.5 + 1.1 diff --git a/docs/authors.html b/docs/authors.html index b570e5c..8892721 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -76,7 +76,7 @@ ICD10gm - 1.0.5 + 1.1 diff --git a/docs/index.html b/docs/index.html index 3c1faeb..eb78d94 100644 --- a/docs/index.html +++ b/docs/index.html @@ -38,7 +38,7 @@ ICD10gm - 1.0.5 + 1.1 @@ -81,9 +81,9 @@
-
+

-ICD10gm +ICD10gm

An R Package for Working with the German Modification of the International Statistical Classification of Diseases and Related Health Problems

diff --git a/docs/news/index.html b/docs/news/index.html index e421d86..8fca2c2 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -76,7 +76,7 @@ ICD10gm - 1.0.5 + 1.1
@@ -126,25 +126,27 @@

Changelog

-
+

-ICD10gm 1.0.5 Unreleased +ICD10gm 1.1 Unreleased

This is a minor update:

  • Added new ICD-10-GM data for the year 2020
    • -
  • Minor improvements to documentation and cross-referencing of functions
    • +
  • Add reserved codes that are defined as needed after release of download files (e.g. COVID-19)
    • +
  • Improvements to documentation and cross-referencing of functions
    • +
  • New hex logo
-
+

-ICD10gm 1.0.4 2019-08-21 +ICD10gm 1.0.4 2019-08-21

Minor updates in preparation for tidyr 1.0, primarily ensuring consistency of type.

-
+

-ICD10gm 1.0.3 2019-02-12 +ICD10gm 1.0.3 2019-02-12

CRAN resubmission:

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 1e3b116..1296449 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.3.1 +pandoc: 2.7.3 pkgdown: 1.4.1 pkgdown_sha: ~ articles: diff --git a/docs/reference/get_icd_history.html b/docs/reference/get_icd_history.html index bd9260f..3659ead 100644 --- a/docs/reference/get_icd_history.html +++ b/docs/reference/get_icd_history.html @@ -77,7 +77,7 @@ ICD10gm - 1.0.5 + 1.1
diff --git a/docs/reference/get_icd_labels.html b/docs/reference/get_icd_labels.html index 5a32875..f003f79 100644 --- a/docs/reference/get_icd_labels.html +++ b/docs/reference/get_icd_labels.html @@ -78,7 +78,7 @@ ICD10gm - 1.0.5 + 1.1
diff --git a/docs/reference/icd_expand.html b/docs/reference/icd_expand.html index 5877226..bab1ec4 100644 --- a/docs/reference/icd_expand.html +++ b/docs/reference/icd_expand.html @@ -81,7 +81,7 @@ ICD10gm - 1.0.5 + 1.1
diff --git a/docs/reference/icd_history.html b/docs/reference/icd_history.html index 13a7d93..9c0a1f0 100644 --- a/docs/reference/icd_history.html +++ b/docs/reference/icd_history.html @@ -82,7 +82,7 @@ ICD10gm - 1.0.5 + 1.1
diff --git a/docs/reference/icd_meta_blocks.html b/docs/reference/icd_meta_blocks.html index 12429d1..d254c05 100644 --- a/docs/reference/icd_meta_blocks.html +++ b/docs/reference/icd_meta_blocks.html @@ -83,7 +83,7 @@ ICD10gm - 1.0.5 + 1.1
diff --git a/docs/reference/icd_meta_chapters.html b/docs/reference/icd_meta_chapters.html index 1ebdc5d..c08ab39 100644 --- a/docs/reference/icd_meta_chapters.html +++ b/docs/reference/icd_meta_chapters.html @@ -77,7 +77,7 @@ ICD10gm - 1.0.5 + 1.1 diff --git a/docs/reference/icd_meta_codes.html b/docs/reference/icd_meta_codes.html index c698a88..1c0b01f 100644 --- a/docs/reference/icd_meta_codes.html +++ b/docs/reference/icd_meta_codes.html @@ -78,7 +78,7 @@ ICD10gm - 1.0.5 + 1.1 @@ -183,6 +183,15 @@

Details neither the inclusion and exclusion notes nor the detailed definitions (where present, mainly in Chapter V). DIMDI provide additional reference material for operative coding and detailed research.

+

The block U00-U49 contains reserved codes that can be allocated quickly for +the documentation of new diseases or epidemiological phenomena. Such usage +is allowed only when mandated by DIMDI. In particular, the codes may not be +utilised on the initiative of other parties, for example, for clinical trials +or contractual purposes. Notable uses of the reserved codes are for the Zika +and COVID-19 viruses. These are included in the DIMDI online documentation, +but not in the download files. They are therefore added manually to this +data set as documented in the package source.

+

Die Schlüsselnummern U05.0-U05.9 dieser Kategorie sollen ein schnelles Reagieren auf aktuelle epidemiologische Phänomene ermöglichen. Sie dürfen nur zusätzlich benutzt werden, um einen anderenorts klassifizierten Zustand besonders zu kennzeichnen. Die Schlüsselnummern dieser Kategorie dürfen nur über das Deutsche Institut für Medizinische Dokumentation und Information (DIMDI) mit Inhalten belegt werden; eine Anwendung für andere Zwecke ist nicht erlaubt. DIMDI wird den Anwendungszeitraum solcher Schlüsselnummern bei Bedarf bekannt geben.

See also

Other ICD-10-GM metadata: diff --git a/docs/reference/icd_meta_transition.html b/docs/reference/icd_meta_transition.html index 319a454..7862b41 100644 --- a/docs/reference/icd_meta_transition.html +++ b/docs/reference/icd_meta_transition.html @@ -80,7 +80,7 @@ ICD10gm - 1.0.5 + 1.1

diff --git a/docs/reference/icd_parse.html b/docs/reference/icd_parse.html index bbf822d..cffadb5 100644 --- a/docs/reference/icd_parse.html +++ b/docs/reference/icd_parse.html @@ -88,7 +88,7 @@ ICD10gm - 1.0.5 + 1.1 diff --git a/docs/reference/icd_showchanges.html b/docs/reference/icd_showchanges.html index 0e6749e..256e7c3 100644 --- a/docs/reference/icd_showchanges.html +++ b/docs/reference/icd_showchanges.html @@ -80,7 +80,7 @@ ICD10gm - 1.0.5 + 1.1 diff --git a/docs/reference/icd_showchanges_icd3.html b/docs/reference/icd_showchanges_icd3.html index d7e52bc..fc887e8 100644 --- a/docs/reference/icd_showchanges_icd3.html +++ b/docs/reference/icd_showchanges_icd3.html @@ -78,7 +78,7 @@ ICD10gm - 1.0.5 + 1.1 diff --git a/docs/reference/index.html b/docs/reference/index.html index a490155..1f1c04a 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -76,7 +76,7 @@ ICD10gm - 1.0.5 + 1.1 diff --git a/docs/reference/is_icd_code.html b/docs/reference/is_icd_code.html index 6130cfc..593ca8e 100644 --- a/docs/reference/is_icd_code.html +++ b/docs/reference/is_icd_code.html @@ -88,7 +88,7 @@ ICD10gm - 1.0.5 + 1.1
icd_spec