Fix feeding.mat()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ReactiveAtlantis
 Title: Multiple Reactive HTML tools to help in the calibration of the Atlantis ecosystem model (AEM)
-Version: 0.0.2.1
+Version: 0.0.2.2
 Authors@R: person("Javier", "Porobic", email = "jporobicg@gmail.com", role = c("aut", "cre"))
 Description: This package has tools that help in the calibration of an AEM. These tools are reactive HTML pages that help you analyze AEM data outputs and inputs during the calibration process.
 Depends:
@@ -9,5 +9,5 @@ License: GPL-3
 Imports: shiny, ncdf4, tidyverse, stringr, data.table, RColorBrewer, Rdpack, reshape2, plotrix, DT, dplyr, ggplot2,  plotly, scales, proj4, tidyr, stats, rlang
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.3
 RdMacros: Rdpack

R/catch.R

@@ -635,9 +635,9 @@ theme_atlantis <- function(){
                  ## color background 2)
                  panel.background = ggplot2::element_rect(fill = scales::alpha('#fcda96', 0.1)),
                  ## modify grid 3)
-                 panel.grid.major.x = ggplot2::element_line(colour = "#844D14", linetype = 3, size = 0.5),
+                 panel.grid.major.x = ggplot2::element_line(colour = "#844D14", linetype = 3, linewidth = 0.5),
                  panel.grid.minor.x = ggplot2::element_blank(),
-                 panel.grid.major.y =  ggplot2::element_line(colour = "#844D14", linetype = 3, size = 0.5),
+                 panel.grid.major.y =  ggplot2::element_line(colour = "#844D14", linetype = 3, linewidth = 0.5),
                  panel.grid.minor.y = ggplot2::element_blank(),
                  ## modify text, axis and colour 4) and 5)
                  axis.text = ggplot2::element_text(colour = "#292B15", face = "italic", family = "Times New Roman", size = ggplot2::rel(1.2)),

R/pprey.mat.R

@@ -142,7 +142,7 @@ feeding.mat <- function(prm.file, grp.file, nc.file, bgm.file, cum.depths, quiet
         predator    <- gsub(pattern = "[[:digit:]]+", '\\1', c.pred)
         a.pred.prey <- as.numeric(unlist(strsplit(c.pred, predator)))
         pry.loc     <- which(bio.adl[, 1] %in% predator)
-        if(length(a.pred.prey) == 0 || is.na(a.pred.prey)) a.pred.prey[2] <- 2
+        if(length(a.pred.prey) == 0 || any(is.na(a.pred.prey))) a.pred.prey[2] <- 2
         ## Young Predator
         if(a.pred.prey[2] == 1){
             ## Young Prey
@@ -442,7 +442,7 @@ feeding.mat <- function(prm.file, grp.file, nc.file, bgm.file, cum.depths, quiet
             Press_out <- shiny::reactive({
                 dat.P <- reshape2::melt(rff2(), value.name = 'value')
                 dat.P[which(dat.P == 0,  arr.ind = TRUE)] <- NA
-                p <- ggplot2::ggplot(data = dat.P, ggplot2::aes(x = .data$Var1, y = .data$Var2, fill = .data$value)) + geom_tile(colour="grey45", size = 0.2)
+                p <- ggplot2::ggplot(data = dat.P, ggplot2::aes(x = .data$Var1, y = .data$Var2, fill = .data$value)) + geom_tile(colour="grey45", linewidth = 0.2)
                 p <- p + scale_fill_distiller(palette = "RdPu",, limits=c(0, 100), name = 'Precentage of pressure', na.value = 'white', direction = 1)
                 p <- p + theme(panel.background = element_blank(), axis.text.x = element_text(angle = 90, hjust = 1)) + labs(x = 'Prey', y = 'Predator') + scale_x_discrete(position = "top")
                 p <- p + annotate("rect", xmin = linex() -.5, xmax = linex() +.5, ymin = 0, ymax = ncol(rff2()) + 1, alpha = .1, colour = 'goldenrod')
@@ -467,14 +467,14 @@ feeding.mat <- function(prm.file, grp.file, nc.file, bgm.file, cum.depths, quiet
             })
             output$plot5 <- shiny::renderPlot({
                 ggplot2::ggplot(data = b.juv, ggplot2::aes(x = .data$FG, y = log(.data$Biomass), fill=.data$FG)) +
-                    geom_bar(colour="black", stat="identity") +
-                    guides(fill = FALSE)+
+                    geom_bar(colour="#ad2c2c", stat="identity") +
+                    guides(colour = "black")+
                     xlab("Functional Groups") + ylab("Biomass [MgN] or Density [MgNm-3]")
             })
             output$plot6 <- shiny::renderPlot({
                 ggplot2::ggplot(data = b.adl, ggplot2::aes(x = .data$FG, y = log(.data$Biomass), fill=.data$FG)) +
                     geom_bar(colour="black", stat="identity") +
-                    guides(fill = FALSE)+
+                    guides(colour = "black")+
                     xlab("Functional Groups") + ylab("Biomass [MgN] or Density [MgNm-3]")
             })
             output$plot10 <- shiny::renderPlot({
@@ -550,7 +550,6 @@ Bio.func <- function(nc.file, groups.csv, numlayers){
         ## ~                       Age structured biomass pools and biomass pool                    ~ ##
         ## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ##
         if(groups.csv$numcohorts[code] == 1 || TY[code] %in% special){
-            browser()
             for(coh in 1 : groups.csv$numcohorts[code]){
                 if(grepl("ice", FG[code])) {
                     # If group name contains "Ice", the nc file will only contain one value per polygon, instead of values for all depths in the water column.
@@ -831,7 +830,7 @@ Over.mat.func <- function(Ava.mat, Gape){
             a.pred.prey <- as.numeric(unlist(strsplit(c.pred, predator)))
             pry.loc     <- which(Gape$FG %in% Prey[py])
             prd.loc     <- which(Gape$FG %in% predator)
-            if(length(pry.loc) == 0 || is.na(a.pred.prey)){
+            if (length(pry.loc) == 0 || any(is.na(a.pred.prey))){
                 Over.mat [pd, py] <- 1
             } else {
                 if(a.pred.prey[1] == 1){