Merge pull request #176 from chitrams/update-prem-174

Update Prem's Germany contact matrices 174
idem-lab · Dec 2, 2024 · 1c90a1c · 1c90a1c
2 parents 86a8702 + a3c311b
commit 1c90a1c
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diff --git a/R/data_prem_contact_matrices.R b/R/data_prem_contact_matrices.R
@@ -1,7 +1,7 @@
 #' Contact matrices as calculated by Prem. et al.
 #'
-#' Contact matrices as calculated by Prem. et al. PLoS Computational Biology.
-#' DOI: 10.1371/journal.pcbi.1005697
+#' Contact matrices as calculated by Prem. et al. (2021) PLoS Computational Biology. Updated to use the latest corrected matrices from their 2021 publication.
+#' DOI: 10.1371/journal.pcbi.1009098
 #'
 #' @format A list with 5 elements:
 #' \describe{
@@ -13,8 +13,11 @@
 #'   year age group}
 #'   \item{other}{A 16x16 matrix containing the number of other contacts, by 5
 #'   year age group}
+#'   \item{all}{A 16x16 matrix containing the number of all contacts, by 5
+#'   year age group}
 #' }
 #' All age groups are 5 year age bands, from 0 to 80.
 #'
-#' @source \url{https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005697}
+#' @source \url{https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009098}
+#' @source \url{https://github.com/kieshaprem/synthetic-contact-matrices}
 "prem_germany_contact_matrices"
diff --git a/data-raw/prem/MUestimates_home_1.xlsx b/data-raw/prem/MUestimates_home_1.xlsx
diff --git a/data-raw/prem/MUestimates_other_locations_1.xlsx b/data-raw/prem/MUestimates_other_locations_1.xlsx
diff --git a/data-raw/prem/MUestimates_school_1.xlsx b/data-raw/prem/MUestimates_school_1.xlsx
diff --git a/data-raw/prem/MUestimates_work_1.xlsx b/data-raw/prem/MUestimates_work_1.xlsx
diff --git a/data-raw/prem/contact_all.rdata b/data-raw/prem/contact_all.rdata
diff --git a/data-raw/prem/contact_home.rdata b/data-raw/prem/contact_home.rdata
diff --git a/data-raw/prem/contact_others.rdata b/data-raw/prem/contact_others.rdata
diff --git a/data-raw/prem/contact_school.rdata b/data-raw/prem/contact_school.rdata
diff --git a/data-raw/prem/contact_work.rdata b/data-raw/prem/contact_work.rdata
diff --git a/data-raw/prem/rural/contact_all_rural.rdata b/data-raw/prem/rural/contact_all_rural.rdata
diff --git a/data-raw/prem/rural/contact_home_rural.rdata b/data-raw/prem/rural/contact_home_rural.rdata
diff --git a/data-raw/prem/rural/contact_others_rural.rdata b/data-raw/prem/rural/contact_others_rural.rdata
diff --git a/data-raw/prem/rural/contact_school_rural.rdata b/data-raw/prem/rural/contact_school_rural.rdata
diff --git a/data-raw/prem/rural/contact_work_rural.rdata b/data-raw/prem/rural/contact_work_rural.rdata
diff --git a/data-raw/prem/urban/contact_all_urban.rdata b/data-raw/prem/urban/contact_all_urban.rdata
diff --git a/data-raw/prem/urban/contact_home_urban.rdata b/data-raw/prem/urban/contact_home_urban.rdata
diff --git a/data-raw/prem/urban/contact_others_urban.rdata b/data-raw/prem/urban/contact_others_urban.rdata
diff --git a/data-raw/prem/urban/contact_school_urban.rdata b/data-raw/prem/urban/contact_school_urban.rdata
diff --git a/data-raw/prem/urban/contact_work_urban.rdata b/data-raw/prem/urban/contact_work_urban.rdata
diff --git a/data-raw/prem_germany_contact_matrices.R b/data-raw/prem_germany_contact_matrices.R
@@ -1,27 +1,34 @@
-# Loads in the Prem matrices for Germany, taken from the 2015 paper.
+# Loads in the Prem matrices for Germany, taken from the 2021 paper.
 
-prem_home <- readxl::read_xlsx("data-raw/prem/MUestimates_home_1.xlsx", sheet = "Germany") %>%
-  as.matrix() %>%
+load("data-raw/prem/contact_home.rdata")
+load("data-raw/prem/contact_work.rdata")
+load("data-raw/prem/contact_school.rdata")
+load("data-raw/prem/contact_others.rdata")
+load("data-raw/prem/contact_all.rdata")
+
+# ISO3 code for Germany is DEU
+
+prem_home <- contact_home[["DEU"]] %>% 
+  t()
+
+prem_work <- contact_work[["DEU"]] %>% 
   t()
 
-prem_school <- readxl::read_xlsx("data-raw/prem/MUestimates_school_1.xlsx", sheet = "Germany") %>%
-  as.matrix() %>%
+prem_school <- contact_school[["DEU"]] %>% 
   t()
 
-prem_work <- readxl::read_xlsx("data-raw/prem/MUestimates_work_1.xlsx", sheet = "Germany") %>%
-  as.matrix() %>%
+prem_other <- contact_others[["DEU"]] %>% 
   t()
 
-prem_other <- readxl::read_xlsx("data-raw/prem/MUestimates_other_locations_1.xlsx", sheet = "Germany") %>%
-  as.matrix() %>%
+prem_all <- contact_all[["DEU"]] %>% 
   t()
 
 prem_germany_contact_matrices <- list(
   "home" = prem_home,
   "work" = prem_work,
   "school" = prem_school,
   "other" = prem_other,
-  "all" = prem_home + prem_work + prem_school + prem_other
+  "all" = prem_all
 )
 
 usethis::use_data(prem_germany_contact_matrices, overwrite = TRUE)