Updates to DemoKin up to uploading to CRAN

.Rbuildignore

@@ -2,3 +2,5 @@
 ^\.Rproj\.user$
 ^README\.Rmd$
 ^LICENSE\.md$
+^cran-comments\.md$
+^CRAN-SUBMISSION$

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.0.3
+Date: 2023-06-04 13:27:38 UTC
+SHA: f54cd023b2e6bb2de1e74d1d0c89c13828149c44

DESCRIPTION

@@ -1,34 +1,39 @@
 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 = "[email protected]", role = "cre"),
     person("Diego", "Alburez-Gutierrez", email = "[email protected]", role = "aut"),
-    person("Xi", "Song", email = "[email protected]", role = "ctb"))
+    person("Xi", "Song", email = "[email protected]", role = "ctb"),
+    person("Caswell", "Hal", email = "[email protected]", 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
 VignetteBuilder: knitr
 Imports: 
     dplyr,
     tidyr,
     purrr,
-    HMDHFDplus,
     progress,
     matrixcalc,
     Matrix,
     MASS,
     stats,
     igraph,
     magrittr,
+    data.table,
     lifecycle
+URL: https://github.com/IvanWilli/DemoKin
 BugReports: https://github.com/IvanWilli/DemoKin/issues
 Depends: 
     R (>= 2.10)

NAMESPACE

@@ -1,12 +1,19 @@
 # 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_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

@@ -1,6 +1,16 @@
+# 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

@@ -1,49 +1,17 @@
-
-#' 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

@@ -127,3 +127,34 @@
 #' @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"