Merge Staging to Master

DESCRIPTION

@@ -35,7 +35,8 @@ Imports:
     utils,
     rlang,
     stringr,
-    ggplot2
+    ggplot2,
+    openxlsx
 Suggests:
     knitr,
     rmarkdown,

R/feed_quality.R

@@ -39,7 +39,6 @@ feed_quality <- function(para) {
 
     livestock_type_selected <- livestock_df[livestock_df$livetype_code == livestock, ]
 
-
     for (season in 1:nrow(seasons)) {
 
       feed_production <- unnest(para[["feed_items"]], cols = c(feed_type_name))
@@ -49,9 +48,7 @@ feed_quality <- function(para) {
       feed_allocation <- list()
 
       for (i in 1:length(feed_types)) {
-
-        feed_selected <- feed_production %>% dplyr::filter(feed_type_name %in%
-                                                      feed_production$feed_type_name[i])
+        feed_selected <- feed_production %>% dplyr::filter(feed_type_name %in% feed_types[i])
 
         #feed_item <- as.data.frame(feed_selected[["feed_items"]])
 
@@ -77,7 +74,7 @@ feed_quality <- function(para) {
                                                                                seasons$season_name[season])
 
         feed_item_selected <- feeding_seasons %>%
-          dplyr::filter(feed_item_code == feed_selected[["feed_item_code"]])
+          dplyr::filter(feed_item_code %in% feed_selected[["feed_item_code"]])
 
         livestock_selected <- feed_item_selected[["livestock"]] %>%
           as.data.frame() %>%
@@ -135,7 +132,7 @@ feed_quality <- function(para) {
       feed_allocation_all[is.na(feed_allocation_all)] <- 0
 
       # Bind and add into the season list
-      season_allocation[[season]] <- cbind(season_name = rep(feed_item_selected$season_name, times = nrow(feed_allocation_all)),
+      season_allocation[[season]] <- cbind(season_name = rep(feed_item_selected$season_name[1],times = nrow(feed_allocation_all)),
                                            livestock_category_code = rep(livestock_selected$livetype_code, times = nrow(feed_allocation_all)),
                                            livestock_category_name = rep(livestock_type_selected$livetype_desc, times = nrow(feed_allocation_all)),
                                            feed_allocation_all)
@@ -155,4 +152,6 @@ feed_quality <- function(para) {
   # Bind by rows
   livestock_feed_allocation <- livestock_allocation %>% bind_rows()
 
+  return(livestock_feed_allocation)
+
 }

R/ghg_emission.R

@@ -97,7 +97,7 @@ ghg_emission <- function(para, energy_required, ghg_ipcc_data, land_required, ni
   #Computing methane enteric emission factor
 
   ef <- ym1%>%
-    mutate(enteric_methane_emissions = (ge_intake*(ym/100)*no_days)/55.65) #equation 10.21
+    mutate(enteric_methane_emissions = ((ge_intake/no_days)*(ym/100)*no_days)/55.65) #equation 10.21
 
   ############################################################################################################################
   #Computing methane emission from manure management T2