| Title: | Evaluate the Geboes Score for Histology in Ulcerative Colitis |
|---|---|
| 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. |
| Authors: | Bill Denney [aut, cre] |
| Maintainer: | Bill Denney <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 1.0.0 |
| Built: | 2024-09-05 05:38:43 UTC |
| Source: | https://github.com/billdenney/geboes.score |
Check if a value is a valid Geboes score
assert_geboes_score(x, all_categories = FALSE)assert_geboes_score(x, all_categories = FALSE)
x |
A character vector of Geboes score grades |
all_categories |
Must |
x, if the values are valid; an error otherwise
Convert a Geboes score into a factor
factor_geboes_score(x, drop_0 = FALSE) levels_geboes_score(drop_0 = FALSE)factor_geboes_score(x, drop_0 = FALSE) levels_geboes_score(drop_0 = FALSE)
x |
A character vector of Geboes score grades |
drop_0 |
Drop the ".0" levels other than "0.0" |
x as a factor, verified to be a Geboes score
levels_geboes_score(): Get all available levels of the Geboes score
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.
geboes_continuous(x)geboes_continuous(x)
x |
A character vector of Geboes score grades |
The numeric value of the continuous Geboes score (the integer value of the maximum grade)
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
# Generate all continuous scores geboes_continuous(geboes.score::geboes_grades$grade)# Generate all continuous scores geboes_continuous(geboes.score::geboes_grades$grade)
Main category
Description of the main category
Subcategory (NA if not applicable)
Description of the subcategory
Text value of the grade
Numeric value of the grade within the category/subcategory
Text description of the grade
Is the grade normal or abnormal? (see Li 2019)
geboes_gradesgeboes_grades
An object of class data.frame with 29 rows and 8 columns.
https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC1728046&blobtype=pdf
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
Values <= "3.1" or ending with ".0" are considered "normal"; values > "3.1" are considered abnormal based on Li 2019.
geboes_score_binary(x)geboes_score_binary(x)
x |
A character vector of Geboes score grades |
A character vector the same length as x with "normal" or "abnormal"
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
geboes_score_binary(c("3.1", "4.0", "3.2")) # c("Normal", "Normal", "Abnormal")geboes_score_binary(c("3.1", "4.0", "3.2")) # c("Normal", "Normal", "Abnormal")
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".
max_geboes_score(x, all_categories = TRUE, na.rm = TRUE)max_geboes_score(x, all_categories = TRUE, na.rm = TRUE)
x |
A character vector of Geboes score grades |
all_categories |
Must |
na.rm |
a logical indicating whether missing values should be removed. |
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.
The maximum value of x where values ending in ".0" are considered
as "0.0"
max_geboes_score(c("0.0", "1.2", "2A.2", "2B.1", "3.3", "4.1", "5.0")) # 4.1max_geboes_score(c("0.0", "1.2", "2A.2", "2B.1", "3.3", "4.1", "5.0")) # 4.1