Merge pull request #865 from mmitsuyo/0719

fix xlim in plot_residual_vpa
ichimomo · Jul 19, 2024 · 97106f8 · 97106f8
2 parents cc2ca10 + a178791
commit 97106f8
Showing 1 changed file with 11 additions and 10 deletions.
diff --git a/R/diagnostics_vpa.R b/R/diagnostics_vpa.R
@@ -746,7 +746,7 @@ plot_residual_vpa2 <- function(res, index_name = NULL, plot_smooth = FALSE, plot
       facet_wrap(~Index_Label, scale = if(plot_scale) "free" else "fixed",axes="all_x")+
       geom_hline(yintercept = 0, linewidth = 1)+
       xlab("Year") +
-      xlim(xlim_year) +
+      #xlim(xlim_year) +
       ylab("log(Residual)") +
       theme_SH(base_size = 14)+
       geom_label(data = rho_data,
@@ -755,15 +755,15 @@ plot_residual_vpa2 <- function(res, index_name = NULL, plot_smooth = FALSE, plot
                                              ", rho=", round(ar1,2), signif)),
                  vjust="inward", hjust="inward")+
 	  guides(x=guide_axis(minor.ticks = TRUE))+
-	  scale_x_continuous(breaks=scales::breaks_pretty(),minor_breaks=scales::breaks_width(1))
+	  scale_x_continuous(limits=xlim_year,breaks=scales::breaks_pretty(),minor_breaks=scales::breaks_width(1))
     g1_sd <- ggplot(d_tidy) +
       geom_ribbon(aes(x = year, ymin = -qnorm(0.025), ymax = qnorm(0.025)), alpha=0.05)+
       geom_ribbon(aes(x = year, ymin = -qnorm(0.1), ymax = qnorm(0.1)), alpha=0.1)+
       geom_point(aes(x=year, y=sd.resid, colour = Index_Label), size = 2) +
       facet_wrap(~Index_Label, scale = if(plot_scale) "fixed" else "free",axes="all_x")+
       geom_hline(yintercept = 0, linewidth = 1)+
       xlab("Year") +
-      xlim(xlim_year) +
+      #xlim(xlim_year) +
       ylab("log(Residual)") +
       theme_SH(base_size = 14)+
       geom_label(data = rho_data,
@@ -772,14 +772,14 @@ plot_residual_vpa2 <- function(res, index_name = NULL, plot_smooth = FALSE, plot
                                              ", rho=", round(ar1,2), signif)),
                  vjust="inward", hjust="inward")+
 	  guides(x=guide_axis(minor.ticks = TRUE))+
-	  scale_x_continuous(breaks=scales::breaks_pretty(),minor_breaks=scales::breaks_width(1))
+	  scale_x_continuous(limits=xlim_year, breaks=scales::breaks_pretty(),minor_breaks=scales::breaks_width(1))
   } else {
     g1 <- ggplot(d_tidy) +
       geom_point(aes(x=year, y=resid, colour = Index_Label), size = 2) +
       facet_wrap(~Index_Label, scale = if(plot_scale) "free" else "fixed",axes="all_x")+
       geom_hline(yintercept = 0, linewidth = 1)+
       xlab("Year") +
-      xlim(xlim_year) +
+      #xlim(xlim_year) +
       ylab("log(Residual)") +
       theme_SH(base_size = 14)+
       geom_label(data = rho_data,
@@ -788,13 +788,13 @@ plot_residual_vpa2 <- function(res, index_name = NULL, plot_smooth = FALSE, plot
                                              ", rho=", round(ar1,2), signif)),
                  vjust="inward", hjust="inward")+
 	  guides(x=guide_axis(minor.ticks = TRUE))+
-	  scale_x_continuous(breaks=scales::breaks_pretty(),minor_breaks=scales::breaks_width(1))
+	  scale_x_continuous(limits=xlim_year, breaks=scales::breaks_pretty(),minor_breaks=scales::breaks_width(1))
     g1_sd <- ggplot(d_tidy) +
       geom_point(aes(x=year, y=sd.resid, colour = Index_Label), size = 2) +
       facet_wrap(~Index_Label, scale = if(plot_scale) "fixed" else "free",axes="all_x")+
       geom_hline(yintercept = 0, linewidth = 1)+
       xlab("Year") +
-      xlim(xlim_year) +
+      #xlim(xlim_year) +
       ylab("log(Residual)") +
       theme_SH(base_size = 14)+
       geom_label(data = rho_data,
@@ -803,7 +803,7 @@ plot_residual_vpa2 <- function(res, index_name = NULL, plot_smooth = FALSE, plot
                                              ", rho=", round(ar1,2), signif)),
                  vjust="inward", hjust="inward")+
 	  guides(x=guide_axis(minor.ticks = TRUE))+
-	  scale_x_continuous(breaks=scales::breaks_pretty(),minor_breaks=scales::breaks_width(1))
+	  scale_x_continuous(limits=xlim_year, breaks=scales::breaks_pretty(),minor_breaks=scales::breaks_width(1))
   }
   if(plot_smooth) g1 <- g1 + geom_smooth(aes(x=year, y=resid, colour = Index_Label), lwd = 0.5, se=FALSE, lty=2)
   if(plot_smooth) g1_sd <- g1_sd + geom_smooth(aes(x=year, y=sd.resid, colour = Index_Label), lwd = 0.5, se=FALSE, lty=2)
@@ -812,12 +812,13 @@ plot_residual_vpa2 <- function(res, index_name = NULL, plot_smooth = FALSE, plot
     geom_point(aes(x=year, y=obs, colour = Index_Label), size = 2) +
     geom_line(aes(x=year, y=pred, colour = Index_Label), linewidth = 1) +
     facet_wrap(~Index_Label, scale="free") +
-    xlim(xlim_year) + ylim(0, NA) +
+    #xlim(xlim_year) + 
+	ylim(0, NA) +
     ylab("Abundance index") +
     xlab("Year") +
     theme_SH(base_size = 14)+
 	guides(x=guide_axis(minor.ticks = TRUE))+
-	scale_x_continuous(breaks=scales::breaks_pretty(),minor_breaks=scales::breaks_width(1))
+	scale_x_continuous(limits=xlim_year, breaks=scales::breaks_pretty(),minor_breaks=scales::breaks_width(1))
 
   # 資源量と指数の（非）線形性のプロット
   Lab_tmp <- unique(d_tidy$Index_Label)