create_quality()calculate quality indicators from object with class
of canreg, canregs, fbswicd, or fbswicds. The quality indicators for
population-based cancer registries (PBCRs) including:
fbs: Number of incident cases.
inci: Cancer incidence rate.
sws: Number of death cases.
mort: 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'.
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'.
data("canregs")
fbsws <- count_canreg(canregs, cancer_type = "system")
qua2 <- create_quality(fbsws, year, sex, cancer)
head(qua2)
#> # A tibble: 6 × 15
#> areacode year sex cancer rks fbs inci sws mort mi mv dco
#> <int> <int> <dbl> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 410103 2021 0 201 687356 43 6.26 14 2.04 0.33 69.8 2.33
#> 2 410103 2021 0 202 687356 665 96.8 433 63 0.65 69.8 1.35
#> 3 410103 2021 0 203 687356 534 77.7 288 41.9 0.54 69.7 0.75
#> 4 410103 2021 0 204 687356 41 5.96 7 1.02 0.17 75.6 0
#> 5 410103 2021 0 205 687356 244 35.5 53 7.71 0.22 83.2 1.64
#> 6 410103 2021 0 206 358941 142 39.6 38 10.6 0.27 86.6 0
#> # ℹ 3 more variables: ub <dbl>, sub <dbl>, m8000 <dbl>
# Calculate the quality indicators based on object with class of `canreg`
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 687356 38 5.53 13 1.89 0.34 73.7 2.63 0
#> 2 2021 0 102 687356 5 0.73 0 0 0 40 0 0
#> 3 2021 0 103 687356 59 8.58 50 7.27 0.85 74.6 0 0
#> 4 2021 0 104 687356 123 17.9 82 11.9 0.67 71.5 1.63 0
#> 5 2021 0 105 687356 236 34.3 103 15.0 0.44 77.5 0.85 0
#> 6 2021 0 106 687356 128 18.6 101 14.7 0.79 54.7 1.56 0
#> # ℹ 2 more variables: sub <dbl>, m8000 <dbl>
# Calculate the quality indicators based on object with class of `canregs`
qua <- create_quality(canregs, year, sex, cancer, cancer_type = "big")
head(qua)
#> # A tibble: 6 × 15
#> areacode year sex cancer rks fbs inci sws mort mi mv dco
#> <int> <int> <dbl> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 410103 2021 0 101 687356 38 5.53 13 1.89 0.34 73.7 2.63
#> 2 410103 2021 0 102 687356 5 0.73 0 0 0 40 0
#> 3 410103 2021 0 103 687356 59 8.58 50 7.27 0.85 74.6 0
#> 4 410103 2021 0 104 687356 123 17.9 82 11.9 0.67 71.5 1.63
#> 5 410103 2021 0 105 687356 236 34.3 103 15.0 0.44 77.5 0.85
#> 6 410103 2021 0 106 687356 128 18.6 101 14.7 0.79 54.7 1.56
#> # ℹ 3 more variables: ub <dbl>, sub <dbl>, m8000 <dbl>
# Calculate the quality indicators based on object with class of `fbswicds`
fbsws <- count_canreg(canregs, cancer_type = "small")
qua <- create_quality(fbsws, year, sex, cancer)
head(qua)
#> # A tibble: 6 × 15
#> areacode year sex cancer rks fbs inci sws mort mi mv dco
#> <int> <int> <dbl> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 410103 2021 0 10 687356 59 8.58 50 7.27 0.85 74.6 0
#> 2 410103 2021 0 11 687356 123 17.9 82 11.9 0.67 71.5 1.63
#> 3 410103 2021 0 12 687356 13 1.89 4 0.58 0.31 84.6 0
#> 4 410103 2021 0 13 687356 129 18.8 63 9.17 0.49 77.5 0.78
#> 5 410103 2021 0 14 687356 104 15.1 39 5.67 0.38 76.9 0.96
#> 6 410103 2021 0 15 687356 3 0.44 0 0 0 100 0
#> # ℹ 3 more variables: ub <dbl>, sub <dbl>, m8000 <dbl>
# Calculate the quality indicators based on object with class of `fbswicd`
fbsw <- count_canreg(canregs[[1]], cancer_type = "big")
qua <- create_quality(fbsw, year, sex, cancer)
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 687356 38 5.53 13 1.89 0.34 73.7 2.63 0
#> 2 2021 0 102 687356 5 0.73 0 0 0 40 0 0
#> 3 2021 0 103 687356 59 8.58 50 7.27 0.85 74.6 0 0
#> 4 2021 0 104 687356 123 17.9 82 11.9 0.67 71.5 1.63 0
#> 5 2021 0 105 687356 236 34.3 103 15.0 0.44 77.5 0.85 0
#> 6 2021 0 106 687356 128 18.6 101 14.7 0.79 54.7 1.56 0
#> # ℹ 2 more variables: sub <dbl>, m8000 <dbl>