added fatten

R/plot-recruitment.R

@@ -6,23 +6,22 @@
 #' @return dataframe of recruitment
 #' @author SJD Martell, DN Webber
 #'
-.get_recruitment_df <- function(M)
-{
-  #M=scset
-  #i=1
-    n <- length(M)
-    mdf <- NULL
-    for (i in 1:n)
-    {
-        A  <- M[[i]]
-        df <- data.frame(Model   = names(M)[i], rec = A$R[,2])
-        df$year <- A$R[,1]
-        df$lb <- A$R[,4]
-        df$ub <- A$R[,5]
-        df
-        mdf <- rbind(mdf, df)
-    }
-    return(mdf)
+.get_recruitment_df <- function(M) {
+  # M=scset
+  # i=1
+  n <- length(M)
+  mdf <- NULL
+  for (i in 1:n)
+  {
+    A <- M[[i]]
+    df <- data.frame(Model = names(M)[i], rec = A$R[, 2])
+    df$year <- A$R[, 1]
+    df$lb <- A$R[, 4]
+    df$ub <- A$R[, 5]
+    df
+    mdf <- rbind(mdf, df)
+  }
+  return(mdf)
 }
 
 
@@ -35,25 +34,28 @@
 #' @author SJD Martell, DN Webber
 #' @export
 #'
-plot_recruitment <- function(M, xlab = "Year", ylab = "Recruitment (millions of individuals)",xlim=c(1990.5,2019.5),fill="yellow",alpha=.9) {
-    xlab <- paste0("\n", xlab)
-    ylab <- paste0(ylab, "\n")
-    mdf <- .get_recruitment_df(M)
-    if (length(M) == 1)
-    {
-        p <- ggplot(mdf, aes(x = year, y = rec)) +
-            geom_bar(stat = "identity", alpha = 0.4, position = "dodge", col="grey60", fill=fill) +
-            scale_x_continuous(limits=xlim, breaks = seq(round(xlim[1],0),round(xlim[2],0), by = 5) ) +
-            geom_pointrange(aes(ymax = ub, ymin = lb),size=.3 ) #, position = position_dodge(width = 1.9))
-    } else {
-        p <- ggplot(mdf, aes(x = year, y = rec, col = Model, group = Model)) +
-            scale_x_continuous(limits=xlim, breaks = seq(round(xlim[1],0),round(xlim[2],0), by = 5) ) +
-#            geom_bar(stat = "identity", alpha = alpha, aes(fill = Model), limits=xlim, position = "dodge") + #Carey commented this out and added the line below
-          geom_bar(stat = "identity", alpha = alpha, aes(fill = Model), position = "dodge") +
-            geom_pointrange(aes(year, rec, ymax = ub, ymin = lb),col = "grey",  size=.6,position = position_dodge(width = 0.9))
-    }
-    p <- p + labs(x = xlab, y = ylab) + .THEME
-    if (!.OVERLAY) p <- p + facet_wrap(~Model)
-    return(p)
+plot_recruitment <- function(M, xlab = "Year",
+                             ylab = "Recruitment (millions)",
+                             xlim = c(1990.5, 2023.5),
+                             fatten = 1.5,
+                             fill = "yellow",
+                             alpha = .9) {
+  xlab <- paste0("\n", xlab)
+  ylab <- paste0(ylab, "\n")
+  mdf <- .get_recruitment_df(M)
+  if (length(M) == 1) {
+    p <- ggplot(mdf, aes(x = year, y = rec)) +
+      geom_bar(stat = "identity", alpha = 0.4, position = "dodge", col = "grey60", fill = fill) +
+      scale_x_continuous(limits = xlim, breaks = seq(round(xlim[1], 0), round(xlim[2], 0), by = 5)) +
+      geom_pointrange(aes(ymax = ub, ymin = lb), fatten = fatten, size = .3) # , position = position_dodge(width = 1.9))
+  } else {
+    p <- ggplot(mdf, aes(x = year, y = rec, col = Model, group = Model)) +
+      scale_x_continuous(limits = xlim, breaks = seq(round(xlim[1], 0), round(xlim[2], 0), by = 5)) +
+      #            geom_bar(stat = "identity", alpha = alpha, aes(fill = Model), limits=xlim, position = "dodge") + #Carey commented this out and added the line below
+      geom_bar(stat = "identity", alpha = alpha, aes(fill = Model), position = "dodge") +
+      geom_pointrange(aes(year, rec, ymax = ub, ymin = lb), col = "grey", size = .6, position = position_dodge(width = 0.9))
+  }
+  p <- p + labs(x = xlab, y = ylab) + .THEME
+  if (!.OVERLAY) p <- p + facet_wrap(~Model)
+  return(p)
 }
-