This function generates a data frame or a list of data frames containing the quality indicators for population-based cancer registries (PBCRs). These indicators include various metrics such as:
fbs: Number of incident cases.
fbl: Incidence rate.
sws: Number of death cases.
swl: Mortality rate.
mv: Percentage of cases with microscopic verification.
mi: Mortality-to-incidence ratio.
And other relevant quality metrics for cancer data evaluation.
create_quality(x, ..., decimal = 2, collapse = TRUE)
# S3 method for class 'canreg'
create_quality(x, ..., cancer_type = "big")
# S3 method for class 'canregs'
create_quality(x, ..., cancer_type = "big", collapse = TRUE)
# S3 method for class 'fbswicds'
create_quality(x, ..., decimal = 2, collapse = TRUE)
# S3 method for class 'fbswicd'
create_quality(x, ..., decimal = 2)The input data, object with class of 'fbswicd', 'fbswicds',
'canreg', or 'canregs'.
One or more variables used for stratification. For example, you
can stratify by sex, year, cancer, or just by year. If sex
is not passed as a parameter, the output will be the result for the
combined gender.
The number of decimal places to include in the resulting quality indicator values. Defaults to 2.
Logical value whether output result as quality or qualites.
A character string specifying the classification method
used to categorize ICD-10 codes. This determines how ICD-10 codes are
classified. Options include "big" (classify ICD-10 codes into 26
cancer categories), "small" (classify ICD-10 codes into 59 cancer
categories, more specific categories), "system" (classify ICD-10
codes into organ system), and "gco" (classify ICD-10 code into
cancer categories same as classification published by the Global
Cancer Observatory). This parameter is only available when the
input data is a vector of ICD-10 codes, or object with class of
'canreg' or 'canregs'.
The function returns a data frame (if applied to a single registry
object, 'canreg' or 'fbswicd') or a list of data frames (if applied to a
grouped registry object, 'canregs' or 'fbswicds') with a class of either
'quality' or 'qualities'. Each output data frame contains the computed
quality indicators for the registry or subgroup.
data("canregs")
data <- canregs[[1]]
qua <- create_quality(data, year, sex, cancer, cancer_type = "big")
head(qua)
#> # A tibble: 6 × 14
#> year sex cancer rks fbs inci sws mort mi mv dco ub
#> <int> <dbl> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 2021 0 101 683110 27 3.95 10 1.46 0.37 55.6 3.7 0
#> 2 2021 0 102 683110 7 1.02 2 0.29 0.29 57.1 0 0
#> 3 2021 0 103 683110 65 9.52 43 6.29 0.66 86.2 1.54 0
#> 4 2021 0 104 683110 101 14.8 78 11.4 0.77 71.3 2.97 0
#> 5 2021 0 105 683110 180 26.4 102 14.9 0.57 81.7 2.78 0
#> 6 2021 0 106 683110 127 18.6 99 14.5 0.78 67.7 3.15 0
#> # ℹ 2 more variables: sub <dbl>, m8000 <dbl>
fbsw <- count_canreg(data, cancer_type = "system")
qua2 <- create_quality(fbsw, year, sex, cancer)
head(qua2)
#> # A tibble: 6 × 14
#> year sex cancer rks fbs inci sws mort mi mv dco ub
#> <int> <dbl> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 2021 0 201 683110 34 4.98 14 2.05 0.41 55.9 2.94 0
#> 2 2021 0 202 683110 574 84.0 422 61.8 0.74 74.6 2.61 0.35
#> 3 2021 0 203 683110 466 68.2 228 33.4 0.49 76.6 1.29 0
#> 4 2021 0 204 683110 44 6.44 15 2.2 0.34 79.6 0 0
#> 5 2021 0 205 683110 245 35.9 41 6 0.17 90.6 0 0
#> 6 2021 0 208 683110 115 16.8 45 6.59 0.39 76.5 1.74 0
#> # ℹ 2 more variables: sub <dbl>, m8000 <dbl>