Updates to DemoKin up to uploading to CRAN #1

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alburezg wants to merge 104 commits into MPIDR:main from IvanWilli:main

.Rbuildignore

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     ^\.Rproj\.user$
     ^README\.Rmd$
     ^LICENSE\.md$
+    ^cran-comments\.md$
+    ^CRAN-SUBMISSION$
+    ^_pkgdown\.yml$
+    ^docs$
+    ^pkgdown$
+    ^\.github$

.github/.gitignore

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		*.html

.github/workflows/pkgdown.yaml

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+    # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+    # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+    on:
+      push:
+        branches: [main, master]
+      pull_request:
+      release:
+        types: [published]
+      workflow_dispatch:
+    name: pkgdown.yaml
+    permissions: read-all
+    jobs:
+      pkgdown:
+        runs-on: ubuntu-latest
+        # Only restrict concurrency for non-PR jobs
+        concurrency:
+          group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+        permissions:
+          contents: write
+        steps:
+          - uses: actions/checkout@v4
+          - uses: r-lib/actions/setup-pandoc@v2
+          - uses: r-lib/actions/setup-r@v2
+            with:
+              use-public-rspm: true
+          - uses: r-lib/actions/setup-r-dependencies@v2
+            with:
+              extra-packages: any::pkgdown, local::.
+              needs: website
+          - name: Build site
+            run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+            shell: Rscript {0}
+          - name: Deploy to GitHub pages 🚀
+            if: github.event_name != 'pull_request'
+            uses: JamesIves/github-pages-deploy-action@v4.5.0
+            with:
+              clean: false
+              branch: gh-pages
+              folder: docs

.gitignore

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     .m
     .mat
     .csv
+    docs

CRAN-SUBMISSION

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+    Version: 1.0.3
+    Date: 2023-06-04 13:27:38 UTC
+    SHA: f54cd023b2e6bb2de1e74d1d0c89c13828149c44

DESCRIPTION

            
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    Package: DemoKin

    Title: Demokin

    Description: Estimate population kin counts and its distribution by type and age

    Version: 1.0.0

    Title: Estimate Population Kin Distribution  

    Description: Estimate population kin counts and its distribution by type, age and sex.

        The package implements one-sex and two-sex framework for studying living-death availability,

        with time varying rates or not, and multi-stage model.

    Version: 1.0.3

    Authors@R: c(

        person("Iván", "Williams", email = "act.ivanwilliams@gmail.com", role = "cre"),

        person("Iván", "Williams", email = "act.ivanwilliams@gmail.com", role = c("aut", "cre")),

        person("Diego", "Alburez-Gutierrez", email = "alburezgutierrez@demogr.mpg.de", role = "aut"),

        person("Xi", "Song", email = "xisong@sas.upenn.edu", role = "ctb"))

        person("Xi", "Song", email = "xisong@sas.upenn.edu", role = "ctb"),

        person("Hal", "Caswell", email = "caswell@demogr.mpg.de", role = "ctb"),

        person("Benjamin", "Schlüter", email = "benjamin.schluter@utoronto.ca", role = "ctb"),

        person("Joe", "Butterick", email = "J.Butterick@soton.ac.uk", role = "ctb"),

        person("Sha", "Jiang", email = "jiang@demogr.mpg.de", role = "ctb"))

    License: MIT + file LICENSE

    Encoding: UTF-8

    LazyData: true

    Roxygen: list(markdown = TRUE)

    RoxygenNote: 7.2.1

    RoxygenNote: 7.2.3

    Suggests: 

        knitr,

        rmarkdown,

        testthat (>= 3.0.0)

        testthat (>= 3.0.0),

        ggplot2,

        pkgdown

    VignetteBuilder: knitr

    Imports: 

        dplyr,

        tidyr,

        purrr,

        HMDHFDplus,

        progress,

        matrixcalc,

        Matrix,

        MASS,

        stats,

        igraph,

        magrittr,

        lifecycle

        data.table,

        lifecycle,

        tictoc,

        reshape2

    URL: https://github.com/IvanWilli/DemoKin,

        https://ivanwilli.github.io/DemoKin/

    BugReports: https://github.com/IvanWilli/DemoKin/issues

    Depends: 

        R (>= 2.10)

NAMESPACE

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     # Generated by roxygen2: do not edit by hand
     export("%>%")
-    export(demokin_codes)
-    export(get_HMDHFD)
     export(kin)
+    export(kin2sex)
     export(kin_multi_stage)
+    export(kin_multi_stage_time_variant_2sex)
     export(kin_time_invariant)
+    export(kin_time_invariant_2sex)
+    export(kin_time_invariant_2sex_cod)
     export(kin_time_variant)
+    export(kin_time_variant_2sex)
+    export(kin_time_variant_2sex_cod)
+    export(output_period_cohort_combination)
     export(plot_diagram)
     export(rename_kin)
+    export(timevarying_kin)
+    export(timevarying_kin_2sex)
+    export(timevarying_kin_2sex_cod)
     importFrom(magrittr,"%>%")

NEWS.md

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+    # DemoKin 1.0.3
+    # DemoKin 1.0.2
+    # DemoKin 1.0.1
     # DemoKin 1.0.0
     * Added a `NEWS.md` file to track changes to the package.
     * Change stable/non-stable references to time varying/non-varying rates.
     * Add multi-state process.
+    # DemoKin 1.0.1
+    * Submitted to CRAN
+    * Death counts are placed in the age where Focal experience the death.
+    * Aggregated kin types are allowed (`s` for older and younger sisters, for example).

R/aux_funs.R

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-    #' print kin codes
-    #' @description Print kin codes and labels
-    #' @export
-    demokin_codes <- function(){
-      codes <- c("coa", "cya", "d", "gd", "ggd", "ggm", "gm", "m", "nos", "nys", "oa", "ya", "os", "ys")
-      caswell_codes <- c("t", "v", "a", "b", "c", "h", "g", "d", "p", "q", "r", "s", "m", "n")
-      labels <- c("Cousins from older aunt", "Cousins from younger aunt", "Daughter", "Grand-daughter", "Great-grand-daughter", "Great-grandmother", "Grandmother", "Mother", "Nieces from older sister", "Nieces from younger sister", "Aunt older than mother", "Aunt younger than mother", "Older sister", "Younger sister")
-      data.frame(DemoKin = codes, Caswell = caswell_codes, Label = labels, row.names = NULL)
-    }
     #' rename kin
-    #' @description Rename kin labels depending consolidate some types
-    #' @export
-    rename_kin <- function(df, consolidate_column = "no"){
-      stopifnot("Argument 'consolidate_column' should be 'no' or a valid column name" = consolidate_column %in% c("no", colnames(df)))
-      if(consolidate_column == "no"){
-        relatives <- c("Cousins from older aunt", "Cousins from younger aunt", "Daughter", "Grand-daughter", "Great-grand-daughter", "Great-grandmother", "Grandmother", "Mother", "Nieces from older sister", "Nieces from younger sister", "Aunt older than mother", "Aunt younger than mother", "Older sister", "Younger sister")
-        names(relatives) <- c("coa", "cya", "d", "gd", "ggd", "ggm", "gm", "m", "nos", "nys", "oa", "ya", "os", "ys")
-      } else {
-        # Combine kin types irrespective of whether they come from older
-        # or younger sibling lines
-        consolidate_vec <- c("c", "c", "d", "gd", "ggd", "ggm", "gm", "m", "n", "n", "a", "a", "s", "s")
-        names(consolidate_vec) <- c("coa", "cya", "d", "gd", "ggd", "ggm", "gm", "m", "nos", "nys", "oa", "ya", "os", "ys")
-        # Rename kin types from codes to actual words
-        relatives <- c("Cousins", "Daughter", "Grand-daughter", "Great-grand-daughter", "Great-grandmother", "Grandmother", "Mother", "Nieces", "Aunt", "Sister")
-        names(relatives) <-  unique(consolidate_vec)
-        df <- as.data.frame(df)
-        df$count <- df[ , consolidate_column]
-        df <-
-          df %>%
-          dplyr::mutate(kin = consolidate_vec[kin]) %>%
-          dplyr::group_by(age_focal, kin) %>%
-          dplyr::summarise(count = sum(count)) %>%
-          dplyr::ungroup()
-      }
-      df$kin <- relatives[df$kin]
-      df
+    #' @description Add kin labels depending the sex
+    #' @details See table `demokin_codes` to know label options.
+    #' @param df data.frame. A data frame with variable `kin` with `DemoKin` codes to be labelled.
+    #' @param sex character. "f" for female, "m" for male or "2sex" for both sex naming.
+    #' @return Add a column with kin labels in the input data frame.
+    #' @export
+    rename_kin <- function(df, sex = "f"){
+      if(!"kin" %in% names(df)) stop("Input df needs a column named kin.")
+      if(sex == "f") demokin_codes_sex <- DemoKin::demokin_codes[,c("DemoKin", "Labels_female")]
+      if(sex == "m") demokin_codes_sex <- DemoKin::demokin_codes[,c("DemoKin", "Labels_male")]
+      if(sex == "2sex") demokin_codes_sex <- DemoKin::demokin_codes[,c("DemoKin", "Labels_2sex")]
+      colnames(demokin_codes_sex) <- c("kin", "kin_label")
+      df %>%
+        dplyr::left_join(demokin_codes_sex)
     }

R/data.R

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-    #' Female swedish survival ratios from 1900 to 2015
-    #'
+    #' Singapore: List of matrices that redistribute newborns to age-class 1 and "no education" category
+    #' @docType data
+    #' @format
+    #'   The data is aggregated into 5-year age groups and 5-year time intervals
+    #' @source
+    #'   Wittgenstein Center
+    "H_mat_edu"
+    #' Singapore: Lists of transition matrices showing probabilities of moving between education states. Females
+    #' @docType data
+    #' @format
+    #'   The data is aggregated into 5-year age groups and 5-year time intervals
+    #' @source
+    #'   Wittgenstein Center
+    "T_mat_fem_edu"
+    #' Singapore: Lists of transition matrices showing probabilities of moving between education states. Males
+    #' @docType data
+    #' @format
+    #'   The data is aggregated into 5-year age groups and 5-year time intervals
+    #' @source
+    #'   Wittgenstein Center
+    "T_mat_male_edu"
+    #' Singapore: Lists of matrices containing fertility rates by age and education. Females
+    #' @docType data
+    #' @format
+    #'   The data is aggregated into 5-year age groups and 5-year time intervals
+    #' @source
+    #'   Wittgenstein Center
+    "F_mat_fem_edu"
+    #' Singapore: Lists of matrices containing fertility rates by age and education. Males
+    #' @docType data
+    #' @format
+    #'   The data is aggregated into 5-year age groups and 5-year time intervals
+    #' @source
+    #'   Wittgenstein Center
+    "F_mat_male_edu"
+    #' Singapore: Lists of matrices containing survival probabilities by age (rows) and education (columns) from 2020-2090. Females
+    #' @docType data
+    #' @format
+    #'   The data is aggregated into 5-year age groups and 5-year time intervals
+    #' @source
+    #'   Wittgenstein Center
+    "U_mat_fem_edu"
+    #' Singapore: Lists of matrices containing survival probabilities by age (rows) and education (columns) from 2020-2090. Males
+    #' @docType data
+    #' @format
+    #'   The data is aggregated into 5-year age groups and 5-year time intervals
+    #' @source
+    #'   Wittgenstein Center
+    "U_mat_male_edu"
+    #' UK female fertility from 1965 to 2022
+    #' @docType data
+    #' @format
+    #'   list of age by stage matrices, entries give female fert. List starting 1965 ending 2022.
+    #' @source
+    #'   HFD and ONS
+    "Female_parity_fert_list_UK"
+    #' UK female parity transitions from 1965 to 2022
+    #' @docType data
+    #' @format
+    #'   list of age by stage matrices, entries give female parity transitions. List starting 1965 ending 2022.
+    #' @source
+    #'   HFD and ONS
+    "Parity_transfers_by_age_list_UK"
+    #' UK female parity mortality from 1965 to 2022
+    #' @docType data
+    #' @format
+    #'   list of age by stage matrices, entries give female parity mortality List starting 1965 ending 2022.
+    #' @source
+    #'   HFD and ONS
+    "Female_parity_mortality_list_UK"
+    #' UK male parity mortality from 1965 to 2022
+    #' @docType data
+    #' @format
+    #'   list of age by stage matrices, entries give male parity mortality List starting 1965 ending 2022.
+    #' @source
+    #'   HFD and ONS
+    "Male_parity_mortality_list_UK"
+    #' UK parity assign parity at birth
+    #' @docType data
+    #' @format
+    #'   list of matrices which redistributes newborns to age-class 1 and parity 0. No time-variation.
+    #' @source
+    #'   None
+    "Redistribution_by_parity_list_UK"
     #' Female swedish survival ratios from 1900 to 2015
     #' @docType data
     #' @format
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     #' @source
     #'   Caswell (2021)
     "kin_svk1990_caswell2020"
+    #' Fertility for France (2012) by sex in Caswell (2022).
+    #'
+    #' Fertility for France (2012) by sex in Caswell (2022).
+    #' @docType data
+    #' @format
+    #' A data.frame with age specific fertility rates by age and sex.
+    #'
+    #' @source
+    #'   Caswell (2022)
+    "fra_asfr_sex"
+    #' Survival probability for France (2012) by sex in Caswell (2022).
+    #'
+    #' Survival probability for France (2012) by sex in Caswell (2022).
+    #' @docType data
+    #' @format
+    #' A data.frame with survival probabilities by age and sex.
+    #'
+    #' @source
+    #'   Caswell (2022)
+    "fra_surv_sex"
+    #' DemoKin codes, Caswell (2020) codes, and useful labels.
+    #'
+    #' DemoKin codes, Caswell (2020) codes, and useful labels.
+    #' @docType data
+    #' @format
+    #' A data.frame with codes and labels for distinction between kin types.
+    "demokin_codes"

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