Package: canregtools 0.2.11

canregtools: Analyzing Population-Based Cancer Registry Data

Provides tools for working with Population-Based Cancer Registry (PBCR) data, including cleaning, restructuring, classification, summary tabulation, rate estimation, age-standardization, quality assessment, visualization, and report preparation. It supports routine cancer registry workflows based on standardized CanReg-style data structures and helps make registry analyses more reproducible and consistent.

Authors:Qiong Chen [aut, cre, cph]

canregtools_0.2.11.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
canregtools/json (API)

# Install 'canregtools' in R:
install.packages('canregtools', repos = c('https://gigu003.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gigu003/canregtools/issues

Pkgdown/docs site:https://gigu003.github.io

Datasets:
  • canregs - Example Population-Based Cancer Registry Data
  • quality - Quality Indicators from the China Cancer Registry Annual Report

On CRAN:

Conda:

cancer-epidemiologycancer-registrationstatistical-analysisvisualization

2.48 score 4 scripts 55 exports 27 dependencies

Last updated from:758c9cd413. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK204
source / vignettesOK175
linux-release-x86_64OK200
macos-release-arm64OK129
macos-oldrel-arm64OK117
windows-develOK161
windows-releaseOK152
windows-oldrelOK156
wasm-releaseOK123

Exports:add_labelsadd_var_labelsageadjustas_canregcalc_agecalc_axclassify_areacodeclassify_areacode2classify_childhoodclassify_icd10classify_morpclassify_topocombine_tpcount_canregcr_cleancr_filtercr_mergecr_reframecr_selectcreate_age_ratecreate_asrcreate_canreg_report_datacreate_qualitycreate_reportcreate_site_morpcumratecumriskcutagedel_dict_filesdraw_barchartdraw_dumbbelldraw_linechartdraw_pyramiddrop_othersdrop_totalesti_fbswicdesti_popexpand_age_popexpand_lxget_popget_stdpopls_attrsls_dictls_dict_filesls_varsltnew_canreg_reportread_canregtidy_agetidy_sextidy_vartruncratevalidate_canreg_reportwrite_areacodewrite_registry

Dependencies:cellrangerclicpp11crayondplyrgenericsgluehmslifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6readxlrematchrlangstringistringrtibbletidyrtidyselectutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Add variable labels for data set.add_labels
Add Variable Labels with Unitsadd_var_labels
Calculate the age standardized rate using the direct methodageadjust
Construct a canreg objectas_canreg
Calculate the actual age in completed years between two datescalc_age
Calculate ax for life tablecalc_ax
Example Population-Based Cancer Registry Data ('canregs')canregs
Classify codes for the administrative divisions of Chinaclassify_areacode
Classify codes for the administrative divisions of Chinaclassify_areacode2
Classify childhood cancer according to the ICCC3 standardsclassify_childhood
Classify ICD10 codes to cancer categoriesclassify_icd10
Classify ICD-O-3 morphology codes into categoriesclassify_morp
Classify ICD-O-3 topography codes into categoriesclassify_topo
Sum named numeric vectorscombine_tp
Count and classify 'canreg' datacount_canreg count_canreg.canreg count_canreg.canregs
Clean canreg data.cr_clean cr_clean.canreg cr_clean.canregs cr_clean.FBcases cr_clean.POP cr_clean.SWcases
Filter rows from canregtools objectscr_filter cr_filter.age_rates cr_filter.asrs cr_filter.canreg cr_filter.canregs cr_filter.default cr_filter.fbswicd cr_filter.fbswicds cr_filter.qualities
Merge elements from objects of class 'canregs', 'fbswicds', or 'asrs'cr_merge cr_merge.age_rates cr_merge.asrs cr_merge.canregs cr_merge.checks cr_merge.fbswicds cr_merge.qualities cr_merge.site_morps cr_merge.summaries
Reframe data of class canregs or fbswicdscr_reframe cr_reframe.canregs cr_reframe.fbswicds
Select elements from objects with class '"canregs"', or '"fbswicds"'cr_select cr_select.age_rates cr_select.asrs cr_select.canregs cr_select.fbswicds cr_select.summaries
Calculate age specific ratecreate_age_rate create_age_rate.canreg create_age_rate.canregs create_age_rate.fbswicd create_age_rate.fbswicds
Calculate age-standardized rate (ASR)create_asr create_asr.canreg create_asr.canregs create_asr.fbswicd create_asr.fbswicds
Create a standardized cancer registry report data objectcreate_canreg_report_data
Calculate quality indicatorscreate_quality create_quality.canreg create_quality.canregs create_quality.fbswicd create_quality.fbswicds
Render standardized cancer registry reports from built-in templatescreate_report create_report.canreg create_report.canregs
Count ICD-10 site and morphology groups by stratacreate_site_morp create_site_morp.canreg create_site_morp.canregs create_site_morp.fbswicd create_site_morp.fbswicds
Calculate the cumulative incidence or mortality ratecumrate
Calculate the cumulative riskcumrisk
Group ages into categoriescutage
Delete a dictionary file from canregtools configdel_dict_files
Draw Grouped Bar Charts with Facetsdraw_barchart
Plot dumbbell chartdraw_dumbbell
Draw a Custom Line Chart Using Base Rdraw_linechart
Plot a population pyramiddraw_pyramid
Drop “other” cancer codesdrop_others
Drop the total cancerdrop_total
Estimate object of fbswicdesti_fbswicd
Estimating population structure using interpolation method.esti_pop
Expand population data from 5-year age groups to single-year agesexpand_age_pop
Expand a five-year abridged life table to a complete life tableexpand_lx
Subset or summarize population dataget_pop get_pop.canreg get_pop.canregs get_pop.fbswicd get_pop.fbswicds
Get standardized population dataget_stdpop
list built-in attributes name used in 'cr_reframe()'ls_attrs
list dictionary used in packagels_dict
List dictionary files used by canregtoolsls_dict_files
List variable names and their descriptions by categoryls_vars
Construct a life table from age-specific mortality rateslt
Construct a 'canreg_report' objectnew_canreg_report
Quality Indicators from the China Cancer Registry Annual Reportquality
Read cancer registration dataread_canreg
Summary object of class 'canreg'summary.canreg summary.canregs
Tidy age descriptiontidy_age
Tidy gender variabletidy_sex
Reformat variable values for Cancer Registration in Chinatidy_var
Calculate truncated age standardized ratetruncrate
Validate a 'canreg_report' objectvalidate_canreg_report
Write custom six-digit administrative division codes to dictionarywrite_areacode
Write registry attributes to a user-defined dictionarywrite_registry write_registry.character write_registry.data.frame write_registry.list write_registry.NULL