| Title: | Evaluate the Geboes Score for Histology in Ulcerative Colitis |
| Version: | 1.0.0 |
| Description: | Evaluate and validate the Geboes score for histological assessment of inflammation in ulcerative colitis. The original Geboes score from Geboes, et al. (2000) <doi:10.1136/gut.47.3.404>, binary version from Li, et al. (2019) <doi:10.1093/ecco-jcc/jjz022>, and continuous version from Magro, et al. (2020) <doi:10.1093/ecco-jcc/jjz123> are all described and implemented. |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| Depends: | R (≥ 2.10) |
| LazyData: | true |
| Imports: | checkmate |
| Suggests: | spelling, testthat (≥ 3.0.0) |
| Config/testthat/edition: | 3 |
| Language: | en-US |
| URL: | https://billdenney.github.io/geboes.score/ |
| NeedsCompilation: | no |
| Packaged: | 2024-02-01 11:11:45 UTC; wdenn |
| Author: | Bill Denney  [aut,
cre] |
| Maintainer: | Bill Denney <wdenney@humanpredictions.com> |
| Repository: | CRAN |
| Date/Publication: | 2024-02-02 19:40:13 UTC |
Check if a value is a valid Geboes score
Description
Check if a value is a valid Geboes score
Usage
assert_geboes_score(x, all_categories = FALSE)
Arguments
x |
A character vector of Geboes score grades |
all_categories |
Must |
Value
x, if the values are valid; an error otherwise
Convert a Geboes score into a factor
Description
Convert a Geboes score into a factor
Usage
factor_geboes_score(x, drop_0 = FALSE)
levels_geboes_score(drop_0 = FALSE)
Arguments
x |
A character vector of Geboes score grades |
drop_0 |
Drop the ".0" levels other than "0.0" |
Value
x as a factor, verified to be a Geboes score
Functions
-
levels_geboes_score(): Get all available levels of the Geboes score
Convert maximum Geboes scores to a continuous measurement
Description
This function returns 0 for any grade ending in ".0" fitting with the intent of the score as anything other than "0.0" cannot be a maximum.
Usage
geboes_continuous(x)
Arguments
x |
A character vector of Geboes score grades |
Value
The numeric value of the continuous Geboes score (the integer value of the maximum grade)
References
See Supplementary Table 1 in the reference below
Magro F, Lopes J, Borralho P, et al. Comparing the Continuous Geboes Score With the Robarts Histopathology Index: Definitions of Histological Remission and Response and their Relation to Faecal Calprotectin Levels. Journal of Crohn’s and Colitis. 2020;14(2):169-175. doi:10.1093/ecco-jcc/jjz123
Examples
# Generate all continuous scores
geboes_continuous(geboes.score::geboes_grades$grade)
Geboes grading source data and descriptions for assessing inflammation in ulcerative colitis
Description
- grade_category_num
Main category
- grade_category_desc
Description of the main category
- grade_subcategory_num
Subcategory (
NAif not applicable)- grade_subcategory_desc
Description of the subcategory
- grade
Text value of the grade
- grade_num
Numeric value of the grade within the category/subcategory
- description
Text description of the grade
- normal
Is the grade normal or abnormal? (see Li 2019)
Usage
geboes_grades
Format
An object of class data.frame with 29 rows and 8 columns.
Source
https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC1728046&blobtype=pdf
References
Geboes K, Riddell R, Öst A, Jensfelt B, Persson T, Löfberg R. A reproducible grading scale for histological assessment of inflammation in ulcerative colitis. Gut. 2000;47(3):404-409. doi:10.1136/gut.47.3.404
Li K, Strauss R, Marano C, et al. A Simplified Definition of Histologic Improvement in Ulcerative Colitis and its Association With Disease Outcomes up to 30 Weeks from Initiation of Therapy: Post Hoc Analysis of Three Clinical Trials. Journal of Crohn’s and Colitis. 2019;13(8):1025-1035. doi:10.1093/ecco-jcc/jjz022
Convert a Geboes score from the original value to a normal/abnormal value
Description
Values <= "3.1" or ending with ".0" are considered "normal"; values > "3.1" are considered abnormal based on Li 2019.
Usage
geboes_score_binary(x)
Arguments
x |
A character vector of Geboes score grades |
Value
A character vector the same length as x with "normal" or "abnormal"
References
Li K, Strauss R, Marano C, et al. A Simplified Definition of Histologic Improvement in Ulcerative Colitis and its Association With Disease Outcomes up to 30 Weeks from Initiation of Therapy: Post Hoc Analysis of Three Clinical Trials. Journal of Crohn’s and Colitis. 2019;13(8):1025-1035. doi:10.1093/ecco-jcc/jjz022
Examples
geboes_score_binary(c("3.1", "4.0", "3.2")) # c("Normal", "Normal", "Abnormal")
Determine the maximum value of the Geboes score
Description
Since the values ending in ".0" indicate no effect, they are not considered in which values is the maximum. In other words, "2.0" < "1.1".
Usage
max_geboes_score(x, all_categories = TRUE, na.rm = TRUE)
Arguments
x |
A character vector of Geboes score grades |
all_categories |
Must |
na.rm |
a logical indicating whether missing values should be removed. |
Details
Typical use of max_geboes_score() is to find the maximum for a single
person at a single time. For that, the all_categories argument ensures
that each category is present exactly once.
Value
The maximum value of x where values ending in ".0" are considered
as "0.0"
Examples
max_geboes_score(c("0.0", "1.2", "2A.2", "2B.1", "3.3", "4.1", "5.0")) # 4.1