change AUDPC and add AUDPC_rel

R/Methods-LandsepiParams.R

@@ -2068,7 +2068,7 @@ loadOutputs <- function(epid_outputs = "all", evol_outputs = "all"){
                      , evol_outputs = evol_outputs
                      , thres_breakdown = 50000
                      , GLAnoDis = 1.48315
-                     , audpc100S = 0.38)
+                     , audpc100S = 0.76)
   return(outputList)
 }
 

R/RcppExports.R

@@ -118,7 +118,7 @@
 #'              L = as.numeric(cultivars$yield_L),
 #'              I = as.numeric(cultivars$yield_I),
 #'              R = as.numeric(cultivars$yield_R)),
-#'              production_cost_perHa = as.numeric(cultivars$production_cost),
+#'              planting_cost_perHa = as.numeric(cultivars$planting_cost),
 #'              market_value = as.numeric(cultivars$market_value))
 #'             
 #' evol_res <- evol_output(, time_param, Npoly, cultivars, genes)

R/output.R

@@ -110,7 +110,7 @@
 epid_output <- function(types = "all", time_param, Npatho, area, rotation, croptypes, cultivars_param, eco_param,
                         GLAnoDis = cultivars_param$max_density[1] ## true for non-growing host
                         , ylim_param = list(
-                          audpc = c(0, 0.38),
+                          audpc = c(0, 0.76), #0.38),
                           audpc_rel = c(0, 1),
                           gla = c(0, 1.48),
                           gla_rel = c(0, 1),
@@ -356,7 +356,11 @@ epid_output <- function(types = "all", time_param, Npatho, area, rotation, cropt
           switch(type,
             "audpc" = {
               numerator <- sum(as.numeric(I_host[host, ts_year]), as.numeric(R_host[host, ts_year]))
-              denominator <- sum(as.numeric(K_host[host, y] * length(ts_year)))
+              denominator <- nTSpY * areaTot   ## sum(as.numeric(K_host[host, y] * length(ts_year)))
+            },
+            "audpc_rel" = {
+              numerator <- sum(as.numeric(I_host[host, ts_year]), as.numeric(R_host[host, ts_year]))
+              denominator <- sum(as.numeric(N_host[host, ts_year]))
             },
             "gla" = {
               numerator <- sum(as.numeric(H_host[host, ts_year]))
@@ -384,9 +388,16 @@ epid_output <- function(types = "all", time_param, Npatho, area, rotation, cropt
 
         ## metrics for all landscape
         switch(type,
-          "audpc" = {
+          # "audpc" = {
+          #   numerator_tot <- sum(as.numeric(I_host[, ts_year]), as.numeric(R_host[, ts_year]))
+          #   denominator_tot <- sum(as.numeric(K_host[, y] * length(ts_year)))
+          #   if (denominator_tot > 0) {
+          #     output_matrix[y, "total"] <- numerator_tot / denominator_tot
+          #   }
+          # },
+          "audpc_rel" = {
             numerator_tot <- sum(as.numeric(I_host[, ts_year]), as.numeric(R_host[, ts_year]))
-            denominator_tot <- sum(as.numeric(K_host[, y] * length(ts_year)))
+            denominator_tot <- sum(as.numeric(N_host[, ts_year]))
             if (denominator_tot > 0) {
               output_matrix[y, "total"] <- numerator_tot / denominator_tot
             }
@@ -398,7 +409,7 @@ epid_output <- function(types = "all", time_param, Npatho, area, rotation, cropt
               output_matrix[y, "total"] <- numerator_tot / denominator_tot
             }
           },
-          { ## i.e. if gla | substr(type,1,3)=="eco"
+          { ## i.e. if audpc | gla | substr(type,1,3)=="eco"
             output_matrix[y, "total"] <- sum(output_matrix[y, 1:Nhost], na.rm = TRUE)
           }
         )
@@ -436,7 +447,11 @@ epid_output <- function(types = "all", time_param, Npatho, area, rotation, cropt
 
         switch(type, "audpc" = {
           main_output <- "AUDPC"
-          ylab_output <- "Proportion of diseased hosts: (I+R)/K"
+          ylab_output <- expression("Equivalent nb of diseased hosts / time step / m"^2) ## expression('title'^2)
+          round_ylab_output <- 2
+        }, "audpc_rel" = {
+          main_output <- expression("Relative AUDPC")
+          ylab_output <- "Proportion of diseased hosts: (I+R)/N"
           round_ylab_output <- 2
         }, "gla" = {
           main_output <- expression("Green leaf area (GLA)") ## expression('title'[2])

R/simul_landsepi.R

@@ -241,7 +241,7 @@ simul_landsepi <- function(seed = 12345, time_param = list(Nyears = 20, nTSpY =
                            genes, landscape = NULL, area,
                            rotation, basic_patho_param, disp_patho, disp_host, pI0 = 5e-4,
                            epid_outputs = "all", evol_outputs = "all", thres_breakdown = 50000,
-                           GLAnoDis = 1.48315, audpc100S = 0.38,
+                           GLAnoDis = 1.48315, audpc100S = 0.76, #0.38,
                            writeTXT = TRUE, graphic = TRUE, videoMP4 = FALSE, keepRawResults = FALSE) {
 
   # Host parameters