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.pdf |msSPChelpR.html✨
msSPChelpR/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

4.48 score 2 stars 15 scripts 235 downloads 25 exports 28 dependencies

Last updated 10 months agofrom:7a074d3c63. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-winOKOct 27 2024
R-4.5-linuxOKOct 27 2024
R-4.4-winOKOct 27 2024
R-4.4-macOKOct 27 2024
R-4.3-winOKOct 27 2024
R-4.3-macOKOct 27 2024

Exports:%>%asircalc_futimecalc_futime_ttcalc_refrateshistgroup_iarcir_crosstabir_crosstab_byfutimepat_statuspat_status_ttrenumber_time_idrenumber_time_id_ttreshape_longreshape_long_tidyrreshape_long_ttreshape_widereshape_wide_tidyrreshape_wide_ttsir_byfutimesir_ratiosir_ratio_lcisir_ratio_ucisummarize_sir_resultsvital_statusvital_status_tt

Dependencies:clicpp11data.tabledatawizarddplyrfansigenericsglueinsightlifecyclelubridatemagrittrpillarpkgconfigpurrrR6rlangsjlabelledstringistringrtibbletidyrtidyselecttidytabletimechangeutf8vctrswithr

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

Marian Eberl

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Oct 27 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Calculate age-standardized incidence ratesasir
Calculate follow-up time per case until end of follow-up depending on pat_status - tidyverse versioncalc_futime
Calculate follow-up time per case until end of follow-up depending on pat_status - tidytable versioncalc_futime_tt
Calculate age-, sex-, cohort-, region-specific incidence rates from a cohortcalc_refrates
Create variable for groups of malignant neoplasms considered to be histologically 'different' for the purpose of defining multiple tumors, ICD-O-3histgroup_iarc
Calculate crude incidence rates and crosstabulate results by break variablesir_crosstab
Calculate crude incidence rates and cross-tabulate results by break variables; cumulative FU-times as are used as xbreak_varir_crosstab_byfutime
Determine patient status at specific end of follow-up - tidyverse versionpat_status
Determine patient status at specific end of follow-up - tidytable versionpat_status_tt
US Populations Datapopulation_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 versionrenumber_time_id_tt
Reshape dataset to long format - stats::reshape versionreshape_long
Reshape dataset to wide format - tidyr versionreshape_long_tidyr
Reshape dataset to wide format - tidytable versionreshape_long_tt
Reshape dataset to wide formatreshape_wide
Reshape dataset to wide format - tidyr versionreshape_wide_tidyr
Reshape dataset to wide format - tidytable versionreshape_wide_tt
Calculate standardized incidence ratios with custom grouping variables stratified by follow-up timesir_byfutime
Calculate Ratio of two SIRs or SMRssir_ratio sir_ratio_lci sir_ratio_uci
Standard Populations Datastandard_population
Summarize detailed SIR resultssummarize_sir_results
US Reference Rates for Cancer Data (ICD-O 2digit code)us_refrates_icd2
US Second Cancer Dataus_second_cancer
Determine vital status at end of follow-up depending on pat_status - tidyverse versionvital_status
Determine vital status at end of follow-up depending on pat_status - tidytable versionvital_status_tt