Package: msSPChelpR 0.9.1.9000

msSPChelpR: Helper Functions for Second Primary Cancer Analyses

A collection of helper functions for analyzing Second Primary Cancer data, including functions to reshape data, to calculate patient states and analyze cancer incidence.

Authors:Marian Eberl [aut, cre]

msSPChelpR_0.9.1.9000.tar.gz
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msSPChelpR_0.9.1.9000.tgz(r-4.6-any)msSPChelpR_0.9.1.9000.tgz(r-4.5-any)
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msSPChelpR_0.9.1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
msSPChelpR/json (API)

# Install 'msSPChelpR' in R:

install.packages('msSPChelpR', repos = c('https://marianschmidt.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/marianschmidt/msspchelpr/issues

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

Datasets:

population_us - US Populations Data
standard_population - Standard Populations Data
us_refrates_icd2 - US Reference Rates for Cancer Data
us_second_cancer - US Second Cancer Data

On CRAN:

4.30 score 2 stars 20 scripts 286 downloads 25 exports 27 dependencies

Last updated from:7a074d3c63. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	155
source / vignettes	OK	194
linux-release-x86_64	OK	152
macos-release-arm64	OK	219
macos-oldrel-arm64	OK	172
windows-devel	OK	107
windows-release	OK	103
windows-oldrel	OK	106
wasm-release	OK	113

Exports:%>%asir calc_futime calc_futime_tt calc_refrates histgroup_iarc ir_crosstab ir_crosstab_byfutime pat_status pat_status_tt renumber_time_id renumber_time_id_tt reshape_long reshape_long_tidyr reshape_long_tt reshape_wide reshape_wide_tidyr reshape_wide_tt sir_byfutime sir_ratio sir_ratio_lci sir_ratio_uci summarize_sir_results vital_status vital_status_tt

Dependencies:cli cpp11 data.table datawizard dplyr generics glue insight lifecycle lubridate magrittr pillar pkgconfig purrr R6 rlang sjlabelled stringi stringr tibble tidyr tidyselect tidytable timechange utf8 vctrs withr

Introduction to the msSPChelpR package - from long dataset to SIR analyses

Rendered fromintroduction.Rmdusingknitr::rmarkdown

Last update: 2023-06-14
Started: 2020-03-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate age-standardized incidence rates	asir
Calculate follow-up time per case until end of follow-up depending on pat_status - tidyverse version	calc_futime
Calculate follow-up time per case until end of follow-up depending on pat_status - tidytable version	calc_futime_tt
Calculate age-, sex-, cohort-, region-specific incidence rates from a cohort	calc_refrates
Create variable for groups of malignant neoplasms considered to be histologically 'different' for the purpose of defining multiple tumors, ICD-O-3	histgroup_iarc
Calculate crude incidence rates and crosstabulate results by break variables	ir_crosstab
Calculate crude incidence rates and cross-tabulate results by break variables; cumulative FU-times as are used as xbreak_var	ir_crosstab_byfutime
Determine patient status at specific end of follow-up - tidyverse version	pat_status
Determine patient status at specific end of follow-up - tidytable version	pat_status_tt
US Populations Data	population_us
Renumber the time ID per case (i.e. Tumor sequence)	renumber_time_id
Renumber the time ID per case (i.e. Tumor sequence) - tidytable version	renumber_time_id_tt
Reshape dataset to long format - stats::reshape version	reshape_long
Reshape dataset to wide format - tidyr version	reshape_long_tidyr
Reshape dataset to wide format - tidytable version	reshape_long_tt
Reshape dataset to wide format	reshape_wide
Reshape dataset to wide format - tidyr version	reshape_wide_tidyr
Reshape dataset to wide format - tidytable version	reshape_wide_tt
Calculate standardized incidence ratios with custom grouping variables stratified by follow-up time	sir_byfutime
Calculate Ratio of two SIRs or SMRs	sir_ratio sir_ratio_lci sir_ratio_uci
Standard Populations Data	standard_population
Summarize detailed SIR results	summarize_sir_results
US Reference Rates for Cancer Data (ICD-O 2digit code)	us_refrates_icd2
US Second Cancer Data	us_second_cancer
Determine vital status at end of follow-up depending on pat_status - tidyverse version	vital_status
Determine vital status at end of follow-up depending on pat_status - tidytable version	vital_status_tt