update outputs in video

R/Methods-LandsepiParams.R

@@ -465,7 +465,7 @@ saveDeploymentStrategy <- function(params, outputGPKG = "landsepi_landscape.gpkg
 #' @param writeTXT a logical indicating if outputs must be written in text files (TRUE, default) 
 #' or not (FALSE).
 #' @param videoMP4 a logical indicating if a video must be generated (TRUE) or not (FALSE, default).
-#' Works only if graphic=TRUE and audpc is computed.
+#' Works only if graphic=TRUE and audpc_rel is computed.
 #' @param keepRawResults a logical indicating if binary files must be kept after the end of 
 #' the simulation (default=FALSE). Careful, many files may be generated if keepRawResults=TRUE.
 #' @details See ?landsepi for details on the model, assumptions and outputs, and our vignettes 
@@ -2089,7 +2089,7 @@ loadOutputs <- function(epid_outputs = "all", evol_outputs = "all"){
 #' \item GLAnoDis = the absolute Green Leaf Area in absence of disease (used to compute 
 #' economic outputs).
 #' \item audpc100S = the audpc in a fully susceptible landscape (used as reference value 
-#' for graphics and video).
+#' for graphics).
 #' }
 #' @details "epid_outputs" is a character string (or a vector of character strings if several 
 #' outputs are to be computed) specifying the type of epidemiological and economic outputs 

R/output.R

@@ -178,15 +178,15 @@ epid_output <- function(types = "all", time_param, Npatho, area, rotation, cropt
   C_host[C_host == 0] <- NA
   area_host[, Nhost + 1] <- areaTot
 
-  ## IMPORTATION OF THE SIMULATION OUTPUT (only those required depending on parameter "types")
-  requireH <- sum(is.element(substr(types, 1, 3), c("gla", "eco"))) > 0
-  requireL <- sum(is.element(types, c("audpc_rel", "gla_rel", "eco_yield", "eco_product", "eco_cost", "eco_margin"))) > 0
-  requireIR <- sum(is.element(types, c("audpc", "audpc_rel", "gla_rel", "eco_yield", "eco_product", "eco_cost", "eco_margin"))) > 0
-  if (graphic & sum(substr(types, nchar(types) - 7, nchar(types)) == "dynamics") > 0) {
-    requireH <- 1
-    requireL <- 1
-    requireIR <- 1
-  }
+  ## IMPORTATION OF THE SIMULATION OUTPUT (only those required depending on parameter "types" --> not necessary any more)
+  # requireH <- sum(is.element(substr(types, 1, 3), c("gla", "eco"))) > 0
+  # requireL <- sum(is.element(types, c("audpc_rel", "gla_rel", "eco_yield", "eco_product", "eco_cost", "eco_margin"))) > 0
+  # requireIR <- sum(is.element(types, c("audpc", "audpc_rel", "gla_rel", "eco_yield", "eco_product", "eco_cost", "eco_margin"))) > 0
+  # if (graphic & sum(substr(types, nchar(types) - 7, nchar(types)) == "dynamics") > 0) {
+  #   requireH <- 1
+  #   requireL <- 1
+  #   requireIR <- 1
+  # }
   H <- as.list(1:nTS)
   # Hjuv <- as.list(1:nTS)
   # P <- as.list(1:nTS)
@@ -198,11 +198,11 @@ epid_output <- function(types = "all", time_param, Npatho, area, rotation, cropt
   # print("Reading binary files to compute epidemiological model outputs")
   for (year in 1:Nyears) {
     # print(paste("year", year, "/", Nyears))
-    if (requireH) {
+    # if (requireH) {
       binfileH <- file(paste(path, sprintf("/H-%02d", year), ".bin", sep = ""), "rb")
       H.tmp <- readBin(con = binfileH, what = "int", n = Npoly * Nhost * nTSpY, size = 4, signed = T, endian = "little")
       close(binfileH)
-    }
+    # }
     # binfileHjuv = file(paste(path, sprintf("/Hjuv-%02d", year), ".bin",sep=""), "rb")
     #  Hjuv.tmp <- readBin(con=binfileHjuv, what="int", n=Npoly*Nhost*nTSpY, size = 4, signed=T,endian="little")
     # close(binfileHjuv)
@@ -214,12 +214,12 @@ epid_output <- function(types = "all", time_param, Npatho, area, rotation, cropt
     #                  signed = T,
     #                  endian = "little")
     # close(binfileP)
-    if (requireL) {
+    # if (requireL) {
       binfileL <- file(paste(path, sprintf("/L-%02d", year), ".bin", sep = ""), "rb")
       L.tmp <- readBin(con = binfileL, what = "int", n = Npoly * Npatho * Nhost * nTSpY, size = 4, signed = T, endian = "little")
       close(binfileL)
-    }
-    if (requireIR) {
+    # }
+    # if (requireIR) {
       binfileI <- file(paste(path, sprintf("/I-%02d", year), ".bin", sep = ""), "rb")
       I.tmp <- readBin(con = binfileI, what = "int", n = Npoly * Npatho * Nhost * nTSpY, size = 4, signed = T, endian = "little")
       close(binfileI)
@@ -227,21 +227,21 @@ epid_output <- function(types = "all", time_param, Npatho, area, rotation, cropt
       binfileR <- file(paste(path, sprintf("/R-%02d", year), ".bin", sep = ""), "rb")
       R.tmp <- readBin(con = binfileR, what = "int", n = Npoly * Npatho * Nhost * nTSpY, size = 4, signed = T, endian = "little")
       close(binfileR)
-    }
+    # }
 
     for (t in 1:nTSpY) {
-      if (requireH) {
+      # if (requireH) {
         H[[t + index]] <- matrix(H.tmp[((Nhost * Npoly) * (t - 1) + 1):(t * (Nhost * Npoly))], ncol = Nhost, byrow = T)
-      }
+      # }
       # Hjuv[[t + index]] <- matrix(Hjuv.tmp[((Nhost*Npoly)*(t-1)+1):(t*(Nhost*Npoly))],ncol=Nhost,byrow=T)
       # P[[t + index]] <- matrix(P.tmp[((Npatho * Npoly) * (t - 1) + 1):(t * (Npatho * Npoly))], ncol = Npatho, byrow = T)
-      if (requireL) {
+      # if (requireL) {
         L[[t + index]] <- array(
           data = L.tmp[((Npatho * Npoly * Nhost) * (t - 1) + 1):(t * (Npatho * Npoly * Nhost))],
           dim = c(Nhost, Npatho, Npoly)
         )
-      }
-      if (requireIR) {
+      # }
+      # if (requireIR) {
         I[[t + index]] <- array(
           data = I.tmp[((Npatho * Npoly * Nhost) * (t - 1) + 1):(t * (Npatho * Npoly * Nhost))],
           dim = c(Nhost, Npatho, Npoly)
@@ -250,7 +250,7 @@ epid_output <- function(types = "all", time_param, Npatho, area, rotation, cropt
           data = R.tmp[((Npatho * Npoly * Nhost) * (t - 1) + 1):(t * (Npatho * Npoly * Nhost))],
           dim = c(Nhost, Npatho, Npoly)
         )
-      }
+      # }
     } ## for t
 
     index <- index + nTSpY
@@ -261,22 +261,22 @@ epid_output <- function(types = "all", time_param, Npatho, area, rotation, cropt
   L_host <- NULL
   I_host <- NULL
   R_host <- NULL
-  if (requireH) {
+  # if (requireH) {
     for (t in 1:nTS) {
       H_host <- cbind(H_host, apply(H[[t]], 2, sum))
     }
-  }
-  if (requireL) {
+  # }
+  # if (requireL) {
     for (t in 1:nTS) {
       L_host <- cbind(L_host, apply(L[[t]], 1, sum))
     }
-  }
-  if (requireIR) {
+  # }
+  # if (requireIR) {
     for (t in 1:nTS) {
       I_host <- cbind(I_host, apply(I[[t]], 1, sum))
       R_host <- cbind(R_host, apply(R[[t]], 1, sum))
     }
-  }
+  # }
   N_host <- H_host + L_host + I_host + R_host
 
 
@@ -877,7 +877,7 @@ evol_output <- function(types = "all", time_param, Npoly, cultivars_param, genes
 #' used to delimit durabilities of the resistance genes. No line is drawn if keyDates=NULL (default).
 #' @param nMapPY an integer specifying the number of epidemic maps per year to generate.
 #' @param path path where binary files are located and where the video will be generated.
-#' @details The left panel shows the year-after-year dynamics of AUDPC, relative to a fully susceptible landscape,
+#' @details The left panel shows the year-after-year dynamics of AUDPC, 
 #' for each cultivar as well as the global average. The right panel illustrates the landscape,
 #' where fields are hatched depending on the cultivated croptype, and coloured depending on the prevalence of the disease.
 #' Note that up to 9 different croptypes can be represented properly in the right panel.

R/simul_landsepi.R

@@ -125,11 +125,11 @@
 #' above which a pathogen genotype is unlikely to go extinct, used to characterise the time to invasion
 #' of resistant hosts (several values are computed if several thresholds are given in a vector).
 #' @param GLAnoDis the absolute Green Leaf Area in absence of disease (used to compute economic outputs).
-#' @param audpc100S the audpc in a fully susceptible landscape (used as reference value for graphics and video).
+#' @param audpc100S the audpc in a fully susceptible landscape (used as reference value for graphics).
 #' @param writeTXT a logical indicating if outputs must be written in text files (TRUE, default) or not (FALSE).
 #' @param graphic a logical indicating if graphics must be generated (TRUE, default) or not (FALSE).
 #' @param videoMP4 a logical indicating if a video must be generated (TRUE) or not (FALSE, default).
-#' Works only if graphic=TRUE and epid_outputs="audpc" (or epid_outputs="all").
+#' Works only if graphic=TRUE and epid_outputs="audpc_rel" (or epid_outputs="all").
 #' @param keepRawResults a logical indicating if binary files must be kept after the end of the simulation (default=FALSE).
 #' Careful, many files may be generated if keepRawResults=TRUE.
 #' @details See ?landsepi for details on the model and assumptions.  
@@ -346,7 +346,7 @@ simul_landsepi <- function(seed = 12345, time_param = list(Nyears = 20, nTSpY =
   }
 
   ## Video
-  if (videoMP4 & !is.null(epid_res[["audpc"]])) {
+  if (videoMP4 & !is.null(epid_res[["audpc_rel"]])) {
     video(
       epid_res[["audpc_rel"]], time_param, Npatho, landscape, area, rotation, croptypes_cultivars_prop,
       croptype_names, cultivars_param

inst/shiny-landsepi/server.R

@@ -7,7 +7,7 @@ simul_params <- setInoculum(simul_params, 5e-4)
 
 ## Outputs
 simul_params <- setOutputs(simul_params, list(
-  epid_outputs = "audpc", evol_outputs = "",
+  epid_outputs = "audpc_rel", evol_outputs = "",
   thres_breakdown = 50000,
   GLAnoDis = 1.48315,
   audpc100S = 0.76