v0.15.0 - experiment with a second SDG mode that allows changes in in…

…dividual causes of

death;

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: lemur
 Title: Life expectancy monitor upscaled in R
-Version: 0.14.4
+Version: 0.15.0
 Authors@R: c(
   person("Marius D.", "Pascariu", role = c("aut", "cre", "cph"), email = "rpascariu@outlook.com", comment = c(ORCID = "0000-0002-2568-6489")),
   person("Jose Manuel", "Aburto", role = "aut", comment = c(ORCID = "0000-0002-2926-6879")),
@@ -42,7 +42,7 @@ Imports:
   RPostgres (>= 1.4.5)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Suggests: 
   testthat (>= 3.0.0)
 Depends: 

NEWS

@@ -1,3 +1,7 @@
+version 0.15.0
+- experiment with a second SDG mode that allows changes in individual causes of
+death;
+
 version 0.14.2
 - Update docker container;
 

R/app_captions.R

@@ -1,6 +1,6 @@
 # -------------------------------------------------------------- #
 # Author: Marius D. PASCARIU
-# Last Update: Wed Nov  8 13:50:34 2023
+# Last Update: Tue Jan 16 18:21:29 2024
 # -------------------------------------------------------------- #
 
 # ALL THE INFORMATIVE CAPTIONS FOR FIGURES AND TABLES ARE CODED HERE
@@ -56,7 +56,7 @@ generate_table_captions <- function(mode,
     "SDG accomplishment levels applied to one or more risks factors ",
     "as specified in the dashboard.") 
 
-  if (mode %in% c("mode_cod", "mode_sdg")) {
+  if (mode %in% c("mode_cod", "mode_sdg", "mode_sdg2")) {
     lt_initial <- paste0(
       "TABLE 1 -- Life table for ", part1, ". ", part2,
       " TABLE 2 below includes such alterations."
@@ -79,7 +79,7 @@ generate_table_captions <- function(mode,
     )
   }
 
-  if (mode == "mode_sdg") {
+  if (mode %in% c("mode_sdg", "mode_sdg2")) {
 
     lt_final <- paste0(
       "TABLE 2 -- Hypothetical life table for ", part1, ". ", part4
@@ -194,7 +194,7 @@ generate_fig2_captions <- function(mode,
   }
 
   # Part 3 - Life expectancy before and after
-  if (mode %in% c("mode_cod", "mode_sdg")) {
+  if (mode %in% c("mode_cod", "mode_sdg", "mode_sdg2")) {
     prefix1 <- "Before: "
     prefix2 <- "After the changes: "
   }

R/app_process_data.R

@@ -3,7 +3,7 @@
 # Last Update: Tue Dec 19 22:08:15 2023
 # -------------------------------------------------------------- #
 
-# somebody should merge these functions in 1?
+# somebody should merge these functions into 1 function?
 
 # ----------------------------------------------------------------------------
 # PROCESS DATA

R/app_server.R

@@ -1,6 +1,6 @@
 # -------------------------------------------------------------- #
 # Author: Marius D. PASCARIU
-# Last Update: Tue Dec  5 22:23:04 2023
+# Last Update: Tue Jan 16 18:31:54 2024
 # -------------------------------------------------------------- #
 
 #' The application server-side
@@ -22,7 +22,7 @@ app_server <- function(input, output, session) {
 
   # 1) cod data ---
   data_cod <- reactive({
-    if (input$mode != "mode_sdg") {
+    if (input$mode %in% c("mode_cod", "mode_sex", "mode_cntr") ) {
 
       dataSource <- if (serverMode()) "cod" else lemur::data_gbd2019_cod
 
@@ -44,7 +44,7 @@ app_server <- function(input, output, session) {
 
   # 2) sdg data ---
   data_sdg <- reactive({
-    if (input$mode == "mode_sdg") {
+    if (input$mode %in% c("mode_sdg", "mode_sdg2")) {
 
       dataSource <- if (serverMode()) "sdg" else lemur::data_gbd2019_sdg
 
@@ -146,7 +146,39 @@ app_server <- function(input, output, session) {
         }
       }
 
+    } else if (input$mode == 'mode_sdg2') {
+
+      M <- build_reduction_matrix(
+        data       = data_sdg(),
+        select_cod = as.character(unique(data_sdg()$cause_name)),
+        select_x   = 0:110,
+        cod_change = 0
+      )
+
+      M[  , "Cardiovascular Diseases"] <- input$sdg2_1  
+      M[  , "Chronic Respiratory Diseases"] <- input$sdg2_2  
+      M[  , "Diabetes"] <- input$sdg2_3  
+      M[  , "Enteric Infections"] <- input$sdg2_4  
+      M[  , "Exposure to Forces of Nature"] <- input$sdg2_5  
+      M[  , "HIV/ AIDS / STD"] <- input$sdg2_6  
+      M[  , "Injuries (excl. Poisonings)"] <- input$sdg2_7  
+      M[  , "Interpersonal Violence"] <- input$sdg2_8  
+      M[  , "Kidney Disease"] <- input$sdg2_9  
+      M[  , "Malaria"] <- input$sdg2_10  
+      if (input$sex != 'male') M[  , "Maternal disorders"] <- input$sdg2_11
+      M[  , "Neglected Tropical Diseases (excl. Malaria)"] <- input$sdg2_12  
+      M[  , "Neonatal disorders"] <- input$sdg2_13  
+      M[  , "Neoplasms"] <- input$sdg2_14  
+      M[  , "Other Communicable"] <- input$sdg2_15  
+      M[  , "Other Non-Communicable"] <- input$sdg2_16  
+      M[  , "Poisonings"] <- input$sdg2_17  
+      M[  , "Respiratory Infections (excl. Tuberculosis)"] <- input$sdg2_18  
+      M[  , "Self-Harm"] <- input$sdg2_19  
+      M[  , "Transport Injuries"] <- input$sdg2_20  
+      M[  , "Tuberculosis"] <- input$sdg2_21  
+
     } else {
+
       M <- build_reduction_matrix(
         data = data_cod(),
         select_cod = input$cod_target,
@@ -199,7 +231,16 @@ app_server <- function(input, output, session) {
         region2    = input$region2,
         sex        = input$sex,
         cod_change = data_cod_change()
-        )
+        ),
+
+      mode_sdg2 = prepare_data_mode_cod(
+        cod        = data_sdg(),
+        lt         = data_lt(),
+        region1    = input$region1,
+        region2    = input$region2,
+        sex        = input$sex,
+        cod_change = data_cod_change()
+        ) 
     )
   })
 
@@ -419,7 +460,7 @@ app_server <- function(input, output, session) {
         type = "barplot") +
         facet_wrap("sex")
 
-    } else if (input$mode == "mode_sdg") {
+    } else if (input$mode %in% c("mode_sdg", "mode_sdg2")) {
       p <- plot_cod(
         cod  = data_fig()$cod_final,
         perc = input$perc,
@@ -531,6 +572,28 @@ app_server <- function(input, output, session) {
     updateSliderInput(session, 'sdg_5', value = 0)
     updateSliderInput(session, 'sdg_6', value = 0)
     updateSliderInput(session, 'sdg_7', value = 0)
+
+    updateSliderInput(session, 'sdg2_1', value = 0)
+    updateSliderInput(session, 'sdg2_2', value = 0)
+    updateSliderInput(session, 'sdg2_3', value = 0)
+    updateSliderInput(session, 'sdg2_4', value = 0)
+    updateSliderInput(session, 'sdg2_5', value = 0)
+    updateSliderInput(session, 'sdg2_6', value = 0)
+    updateSliderInput(session, 'sdg2_7', value = 0)
+    updateSliderInput(session, 'sdg2_8', value = 0)
+    updateSliderInput(session, 'sdg2_9', value = 0)
+    updateSliderInput(session, 'sdg2_10', value = 0)
+    updateSliderInput(session, 'sdg2_11', value = 0)
+    updateSliderInput(session, 'sdg2_12', value = 0)
+    updateSliderInput(session, 'sdg2_13', value = 0)
+    updateSliderInput(session, 'sdg2_14', value = 0)
+    updateSliderInput(session, 'sdg2_15', value = 0)
+    updateSliderInput(session, 'sdg2_16', value = 0)
+    updateSliderInput(session, 'sdg2_17', value = 0)
+    updateSliderInput(session, 'sdg2_18', value = 0)
+    updateSliderInput(session, 'sdg2_19', value = 0)
+    updateSliderInput(session, 'sdg2_20', value = 0)
+    updateSliderInput(session, 'sdg2_21', value = 0)
     updatePrettyCheckboxGroup(session, 'cod_target', selected = lemur::data_app_input$cause_name)
   })