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  "Package": "msSPChelpR",
  "Title": "Helper Functions for Second Primary Cancer Analyses",
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  "Description": "A collection of helper functions for analyzing Second\nPrimary Cancer data, including functions to reshape data, to\ncalculate patient states and analyze cancer incidence.",
  "License": "GPL-3",
  "URL": "https://marianschmidt.github.io/msSPChelpR/",
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  "Date/Publication": "2024-01-24 21:36:00 UTC",
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    "pat_status_tt",
    "renumber_time_id",
    "renumber_time_id_tt",
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    "reshape_long_tidyr",
    "reshape_long_tt",
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    "reshape_wide_tidyr",
    "reshape_wide_tt",
    "sir_byfutime",
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    "sir_ratio_lci",
    "sir_ratio_uci",
    "summarize_sir_results",
    "vital_status",
    "vital_status_tt"
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        "year",
        "sex",
        "age",
        "race",
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        "population_n_per_year"
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      "object": "standard_population",
      "class": [
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      ],
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        "sex",
        "age",
        "population_n",
        "group_proportion"
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    },
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      "title": "US Reference Rates for Cancer Data (ICD-O 2digit code)",
      "object": "us_refrates_icd2",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
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        "region",
        "year",
        "sex",
        "age",
        "race",
        "comment",
        "incidence_cases",
        "population_pyar",
        "population_n_per_year",
        "incidence_crude_rate"
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      "table": true,
      "tojson": true
    },
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      "name": "us_second_cancer",
      "title": "US Second Cancer Data",
      "object": "us_second_cancer",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "fake_id",
        "SEQ_NUM",
        "registry",
        "sex",
        "race",
        "datebirth",
        "t_datediag",
        "t_site_icd",
        "t_dco",
        "t_hist",
        "fc_age",
        "datedeath",
        "p_alive",
        "p_dodmin",
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        "t_yeardiag"
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      "table": true,
      "tojson": true
    }
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      "title": "Calculate age-standardized incidence rates",
      "topics": [
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      ]
    },
    {
      "page": "calc_futime",
      "title": "Calculate follow-up time per case until end of follow-up depending on pat_status - tidyverse version",
      "topics": [
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    },
    {
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      "title": "Calculate follow-up time per case until end of follow-up depending on pat_status - tidytable version",
      "topics": [
        "calc_futime_tt"
      ]
    },
    {
      "page": "calc_refrates",
      "title": "Calculate age-, sex-, cohort-, region-specific incidence rates from a cohort",
      "topics": [
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      ]
    },
    {
      "page": "histgroup_iarc",
      "title": "Create variable for groups of malignant neoplasms considered to be histologically 'different' for the purpose of defining multiple tumors, ICD-O-3",
      "topics": [
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      ]
    },
    {
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      "topics": [
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    },
    {
      "page": "ir_crosstab_byfutime",
      "title": "Calculate crude incidence rates and cross-tabulate results by break variables; cumulative FU-times as are used as xbreak_var",
      "topics": [
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      ]
    },
    {
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      "title": "Determine patient status at specific end of follow-up - tidyverse version",
      "topics": [
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      ]
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      "title": "Determine patient status at specific end of follow-up - tidytable version",
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    },
    {
      "page": "population_us",
      "title": "US Populations Data",
      "topics": [
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    },
    {
      "page": "renumber_time_id",
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      "topics": [
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      ]
    },
    {
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      "topics": [
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      ]
    },
    {
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      "topics": [
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    },
    {
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    {
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      "title": "Reshape dataset to wide format",
      "topics": [
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      "topics": [
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      "topics": [
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      "title": "Calculate standardized incidence ratios with custom grouping variables stratified by follow-up time",
      "topics": [
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    },
    {
      "page": "sir_ratio",
      "title": "Calculate Ratio of two SIRs or SMRs",
      "topics": [
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      "source": "introduction.Rmd",
      "filename": "introduction.html",
      "title": "Introduction to the msSPChelpR package - from long dataset to SIR analyses",
      "author": "Marian Eberl",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Recommended Workflows",
        "Calculate follow-up times",
        "Calculate Standardized Incidence Ratios (SIR)",
        "Theory behind SIRs",
        "Examples",
        "SEER lung cancer",
        "Step 1 - Long dataset",
        "Step 2 - Filter long dataset",
        "Step 3 - Renumber time_id",
        "Step 4 - Reshape to wide dataset",
        "Step 5 - Recalculate p_spc",
        "Step 6 - Determine patient status at end of FU",
        "Step 6b - Remove patients irrelevant to analysis depending on status",
        "Step 7 - Calculate FU time",
        "Step 8 - Calculate SIR",
        "Step 9 - Summarize SIR results",
        "Built with"
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      "created": "2020-03-11 08:31:00",
      "modified": "2023-06-14 15:27:02",
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