Merge branch 'master' into master

idem-lab · Aug 19, 2024 · f8cb4f5 · f8cb4f5
2 parents 29e00f8 + ecf3fe8
commit f8cb4f5
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Showing 18 changed files with 2,889 additions and 12 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -13,3 +13,4 @@
 ^pkgdown$
 ^touchstone$
 ^cran-comments\.md$
+^paper$
diff --git a/.gitignore b/.gitignore
@@ -10,3 +10,8 @@ README_cache
 .vscode/launch.json
 .pre-commit-config.yaml
 tests/README.md
+paper/*.html
+paper/*.pdf
+paper/paper_cache/
+paper/paper_files/
+chitra/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -35,14 +35,13 @@ Description: Builds contact matrices using GAMs and population data. This packag
   Electoral Commission and Australian Bureau of Statistics) 2020.
 License: MIT + file LICENSE
 Depends: 
-    R (>= 2.10)
+    R (>= 4.1.0)
 Suggests: 
     covr,
     knitr,
     vdiffr,
     testthat (>= 3.0.0),
     rmarkdown,
-    stringr,
     future,
     spelling,
     deSolve
@@ -54,7 +53,7 @@ Language: en-US
 LazyData: true
 LazyDataCompression: xz
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports: 
     mgcv,
     dplyr (>= 1.0.9),
@@ -75,6 +74,7 @@ Imports:
     vctrs,
     scales,
     english,
-    waldo
+    waldo,
+    stringr
 URL: https://github.com/idem-lab/conmat
 BugReports: https://github.com/idem-lab/conmat/issues
diff --git a/NAMESPACE b/NAMESPACE
@@ -53,6 +53,7 @@ export(abs_age_state)
 export(abs_age_work_lga)
 export(abs_age_work_state)
 export(abs_unabbreviate_states)
+export(add_age_partial_sum)
 export(add_intergenerational)
 export(add_modelling_features)
 export(add_offset)
@@ -68,8 +69,11 @@ export(apply_vaccination)
 export(as_conmat_population)
 export(as_setting_prediction_matrix)
 export(autoplot)
+export(clean_term_names)
 export(conmat_population)
+export(create_age_grid)
 export(estimate_setting_contacts)
+export(extract_term_names)
 export(extrapolate_polymod)
 export(fit_setting_contacts)
 export(fit_single_contact_model)
@@ -86,16 +90,21 @@ export(get_polymod_per_capita_household_size)
 export(get_polymod_population)
 export(get_polymod_setting_data)
 export(get_setting_transmission_matrices)
+export(gg_age_partial_pred_long)
+export(gg_age_partial_sum)
+export(gg_age_terms_settings)
 export(matrix_to_predictions)
 export(new_age_matrix)
 export(new_ngm_setting_matrix)
 export(new_setting_data)
 export(per_capita_household_size)
+export(pivot_longer_age_preds)
 export(polymod)
 export(population)
 export(population_label)
 export(predict_contacts)
 export(predict_contacts_1y)
+export(predict_individual_terms)
 export(predict_setting_contacts)
 export(predictions_to_matrix)
 export(prepare_population_for_modelling)
@@ -104,6 +113,14 @@ export(scaling)
 export(setting_prediction_matrix)
 export(transmission_probability_matrix)
 import(rlang)
+importFrom(ggplot2,aes)
 importFrom(ggplot2,autoplot)
+importFrom(ggplot2,coord_fixed)
+importFrom(ggplot2,facet_grid)
+importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_tile)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,scale_fill_viridis_c)
+importFrom(ggplot2,theme_minimal)
 importFrom(magrittr,"%>%")
 importFrom(stats,predict)
diff --git a/R/checkers.R b/R/checkers.R
@@ -142,13 +142,16 @@ check_if_var_numeric <- function(data, var, attribute) {
   }
 }
 
-check_if_data_frame <- function(x) {
+check_if_data_frame <- function(x,
+                                arg = rlang::caller_arg(x),
+                                call = rlang::caller_env()) {
   if (!is.data.frame(x)) {
     cli::cli_abort(
-      c(
-        "x must be a {.cls data.frame}",
-        "i" = "x is {.cls {class(x)}}"
-      )
+      message = c(
+        "{.arg {arg}} must be a {.cls data.frame}",
+        "i" = "{.arg {arg}} is {.cls {class(x)}}"
+      ),
+      call = call
     )
   }
 }