Create quality indicators — create

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.

Usage

create_quality(x, ..., decimal = 2)

# S3 method for class 'canreg'
create_quality(x, ..., cancer_type = "big")

# S3 method for class 'canregs'
create_quality(x, ..., cancer_type = "big")

# S3 method for class 'fbswicds'
create_quality(x, ..., decimal = 2)

# S3 method for class 'fbswicd'
create_quality(x, ..., decimal = 2)

Arguments

x: 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.
decimal: The number of decimal places to include in the resulting quality indicator values. Defaults to 2.
cancer_type: 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'.

Value

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.

Examples

data <- load_canreg()
qua <- create_quality(data, year, sex, cancer, cancer_type = "big")
head(qua)
#> # A tibble: 6 × 14
#>    year   sex cancer    rks   fbs    fbl   sws    swl    mi    mv   dco    ub
#>   <int> <int>  <int>  <int> <int>  <dbl> <int>  <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1  2016     1     60 455653  1183 260.     920 202.    0.78  65.8  2.62  0.68
#> 2  2016     1     61 455653  1175 258.     917 201.    0.78  65.5  2.64  0.68
#> 3  2016     1    101 455653    13   2.85    10   2.19  0.77 100    0     0   
#> 4  2016     1    102 455653     7   1.54     7   1.54  1    100    0     0   
#> 5  2016     1    103 455653   157  34.5    127  27.9   0.81  86.0  2.55  0   
#> 6  2016     1    104 455653   135  29.6    107  23.5   0.79  91.1  2.22  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    fbl   sws    swl    mi    mv   dco    ub
#>   <int> <int>  <int>  <int> <int>  <dbl> <int>  <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1  2016     1     60 455653  1155 253.     897 197.    0.78  66.4  2.68  0.69
#> 2  2016     1     61 455653  1147 252.     894 196.    0.78  66.2  2.7   0.7 
#> 3  2016     1    201 455653    20   4.39    17   3.73  0.85 100    0     0   
#> 4  2016     1    202 455653   591 130.     475 104.    0.8   67.7  2.88  0.17
#> 5  2016     1    203 455653   336  73.7    284  62.3   0.85  54.8  2.38  0   
#> 6  2016     1    204 455653    21   4.61    12   2.63  0.57  81.0  4.76  0   
#> # ℹ 2 more variables: sub <dbl>, m8000 <dbl>