| Title: | Classification of Cancer Using Administrative Data |
|---|---|
| Description: | Classifies the type of cancer using routinely collected data commonly found in cancer registries from pathology reports. The package implements the International Classification of Diseases for Oncology, 3rd Edition site (topography), histology (morphology), and behaviour codes of neoplasms to classify cancer type <https://www.who.int/standards/classifications/other-classifications/international-classification-of-diseases-for-oncology>. Classification in children utilize the International Classification of Childhood Cancer by Steliarova-Foucher et al. (2005) <doi:10.1002/cncr.20910>. Adolescent and young adult cancer classification is based on Barr et al. (2020) <doi:10.1002/cncr.33041>. |
| Authors: | Giancarlo Di Giuseppe [aut, cre, cph]
|
| Maintainer: | Giancarlo Di Giuseppe <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 0.1.0 |
| Built: | 2025-02-16 06:31:54 UTC |
| Source: | https://github.com/giancarlodigi/cancerr |
This function classifies the type of adolescent and young adult cancer cases based on the histology, site, and behaviour codes of the cancer. It uses the International Classification of Diseases for Oncology (ICD-O), 3rd edition codes to determine the classification. The function returns a value is based on the method specified and the depth level of the classification hierarchy to be determined.
aya_class( histology, site, behaviour, method = "Barr 2020", depth = 1, verbose = FALSE )aya_class( histology, site, behaviour, method = "Barr 2020", depth = 1, verbose = FALSE )
histology |
Histology code of the cancer. |
site |
Site (aka topography) code of the cancer. |
behaviour |
Behaviour code of the cancer. |
method |
Method used for the diagnosis classification of the cancer.
Default is |
depth |
Depth level of the classification hierarchy to be determined.
If set to |
verbose |
Logical value to print messages to the console if unable to
classify or duplicates found. Default is |
Returns the diagnostic classification of the cancer based on the specified method and depth level.
# First position in the classification hierarchy aya_class("9020", "C50.1", "3", method = "Barr 2020", depth = 1) # Second position in the classification hierarchy aya_class("9020", "C50.1", "3", method = "Barr 2020", depth = 2) # Third position in the classification hierarchy aya_class(9020, "C50.1", "3", method = "Barr 2020", depth = 3)# First position in the classification hierarchy aya_class("9020", "C50.1", "3", method = "Barr 2020", depth = 1) # Second position in the classification hierarchy aya_class("9020", "C50.1", "3", method = "Barr 2020", depth = 2) # Third position in the classification hierarchy aya_class(9020, "C50.1", "3", method = "Barr 2020", depth = 3)
Determines the type of childhood cancer cases based on the histology and site codes of the cancer. It uses the International Classification of Childhood Cancer (ICCC) codes to determine the classification. The function returns a value based on the method specified and the depth level of the classification hierarchy to be determined.
kid_class(histology, site, method = "iccc3", depth = 1, verbose = FALSE)kid_class(histology, site, method = "iccc3", depth = 1, verbose = FALSE)
histology |
Histology code of the cancer. |
site |
Site (aka topography) code of the cancer. |
method |
Method to use for diagnosis classification.
Default is |
depth |
Depth level of the classification hierarchy to be determined.
If set to |
verbose |
Logical value to print messages to the console if unable to
classify or duplicates found. Default is |
Returns the diagnostic classification of the childhood cancer based on the specified method and depth level.
kid_class("8522", "C50.1", method = "iccc3", depth = 1) kid_class("8970", "C22.0", method = "iccc3", depth = 2)kid_class("8522", "C50.1", method = "iccc3", depth = 1) kid_class("8970", "C22.0", method = "iccc3", depth = 2)
Converts ICD-O-3 topography codes in to a numeric format. It removes the "C" from the beginning of the string if present, and ensures that the codes are valid ICD-O-3 site codes.
site_convert(x, validate = TRUE)site_convert(x, validate = TRUE)
x |
The ICD-O-3 site codes to be converted. |
validate |
Logical indicating whether to make the converted values
have valid ICD-O-3 sites codes between C00.0 and C97.0, setting any invalid
codes to |
Takes in a character or numeric vector of ICD-O-3 site codes and converts them to a standardized numeric format. The function will remove the "C" from the beginning of the string if present. It will also automatically detect if the codes have are in decimal ("C34.1") or integer ("C341") format and convert them.
If validate is set to TRUE, the function checks if the topography
codes are valid ICD-O-3 site codes for neoplasms which range from
C00.0 to C97.0. Any invalid codes will be set to NA and a warning will be
issued indicating the number of invalid codes found.
Returns a converted ICD-O-3 topography code in a numeric format.
# Character input with and without "C" at the beginning site_convert(c("C80.1", "C34.1", "C50.3", "C424", "80.9")) # Numeric input site_convert(c(80.1, 8.1, 81, 708)) # Numeric input# Character input with and without "C" at the beginning site_convert(c("C80.1", "C34.1", "C50.3", "C424", "80.9")) # Numeric input site_convert(c(80.1, 8.1, 81, 708)) # Numeric input