Overview
Canregtools is an R package designed to streamline the analysis workflow for Population-Based Cancer Registry (PBCR) data. It aims to improve the efficiency, accuracy, and reproducibility of cancer registry data processing, thereby supporting standardized, and routine PBCR analytical workflows.
Install
Currently, the package is not available on CRAN, but you can install the development version of canregtools from https://gigu003.r-universe.dev/.
install.packages('canregtools', repos = c('https://gigu003.r-universe.dev', 'https://cloud.r-project.org'))Usage
# Load sample data
library(canregtools)
data("canregs")
data <- canregs[[1]]
# Convert `canreg` to `fbswicd`
fbsw <- count_canreg(data, cancer_type = "big")
# 1. Age-standardized rate (ASR)
create_asr(fbsw, year, sex, cancer) |>
add_labels(lang = "en")
#> # A tibble: 84 × 14
#> year sex sex_en cancer cancer_en no_cases cr asr_cn2000 asr_wld85
#> <int> <dbl> <fct> <chr> <fct> <dbl> <dbl> <dbl> <dbl>
#> 1 2021 0 Total 101 Oral Cavity & P… 38 5.53 3.74 3.79
#> 2 2021 0 Total 102 Nasopharynx 5 0.73 0.71 0.71
#> 3 2021 0 Total 103 Esophagus 59 8.58 4.53 4.85
#> 4 2021 0 Total 104 Stomach 123 17.9 11.1 11.2
#> 5 2021 0 Total 105 Conlon, Rectum … 236 34.3 20.6 20.2
#> # ℹ 79 more rows
#> # ℹ 5 more variables: truncr_cn2000 <dbl>, truncr_wld85 <dbl>, cumur <dbl>,
#> # prop <dbl>, rank <int>
# 2. Quality indicators
create_quality(fbsw, cancer) |>
add_labels(label_type = "abbr", lang = "en")
#> # A tibble: 28 × 16
#> year sex sex_en cancer cancer_en rks fbs inci sws mort mi mv
#> <int> <dbl> <fct> <chr> <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 9000 0 T 101 Oral Cav… 687356 38 5.53 20 2.91 0.53 73.7
#> 2 9000 0 T 102 Nasophar… 687356 5 0.73 2 0.29 0.4 40
#> 3 9000 0 T 103 Esophagus 687356 59 8.58 58 8.44 0.98 74.6
#> 4 9000 0 T 104 Stomach 687356 123 17.9 82 11.9 0.67 71.5
#> 5 9000 0 T 105 Colorect… 687356 236 34.3 103 15.0 0.44 77.5
#> # ℹ 23 more rows
#> # ℹ 4 more variables: dco <dbl>, ub <dbl>, sub <dbl>, mvs <dbl>
# 3. Age-specific rates
create_age_rate(fbsw) |>
add_labels(lang = "en")
#> # A tibble: 19 × 8
#> year sex sex_en cancer cancer_en agegrp cases rate
#> <int> <dbl> <fct> <chr> <fct> <fct> <dbl> <dbl>
#> 1 9000 0 Total 60 All Cancers 0 岁 3 44.3
#> 2 9000 0 Total 60 All Cancers 1-4 岁 12 31.4
#> 3 9000 0 Total 60 All Cancers 5-9 岁 9 16.4
#> 4 9000 0 Total 60 All Cancers 10-14 岁 13 32.5
#> 5 9000 0 Total 60 All Cancers 15-19 岁 8 26.2
#> # ℹ 14 more rows
