Default "ML" type in plot.MLZ_data

quang-huynh · Sep 20, 2019 · b23460b · b23460b
1 parent 94e2ba4
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,6 +3,7 @@ Title: Mean Length-Based Estimators of Mortality using TMB
 Version: 0.1.3
 Authors@R: c(person("Quang", "Huynh", email = "q.huynh@oceans.ubc.ca", role = c("aut", "cre")),
   person("Todd", "Gedamke", rol = "ctb"), person("Amy", "Then", rol = "ctb"))
+Date: 2019-09-20
 Maintainer: Quang Huynh <q.huynh@oceans.ubc.ca>
 Description: Estimation functions and diagnostic tools for mean length-based total mortality estimators based on Gedamke and Hoenig (2006) <doi:10.1577/T05-153.1>.
 Depends:
@@ -28,7 +29,6 @@ Suggests:
 VignetteBuilder: knitr
 LinkingTo: TMB, RcppEigen
 NeedsCompilation: yes
-Packaged: 2017-03-01 18:29:13 UTC; qhuynh
 Author: Quang Huynh [aut, cre],
     Todd Gedamke [ctb],
     Amy Then [ctb]
diff --git a/R/methods.R b/R/methods.R
@@ -144,7 +144,7 @@ setMethod("summary", signature(object = "MLZ_model"), function(object)
 #' }
 #' @aliases plot.MLZ_data
 #' @export
-setMethod("plot", signature(x = "MLZ_data"), function(x, type = c("comp", "ML"), ggplot_layer = NULL) {
+setMethod("plot", signature(x = "MLZ_data"), function(x, type = c("ML", "comp"), ggplot_layer = NULL) {
   type <- match.arg(type)
   MLZ_data <- x
 
@@ -222,7 +222,7 @@ setMethod("plot", signature(x = "MLZ_data"), function(x, type = c("comp", "ML"),
                                               xlab = "Year", ylab = "CPUE")
       if("Effort" %in% names(summary.MLZ)) plot(Effort ~ Year, data = summary.MLZ, pch = 16, typ = "o",
                                                 xlab = "Year", ylab = "Effort")
-    } else stop("No mean lengths available.")
+    } else stop("No mean lengths available. Try plot(", substitute(x), ", type = \"comp\")")
   }
 
   return(invisible())

diff --git a/man/plot-MLZ_data-method.Rd b/man/plot-MLZ_data-method.Rd
diff --git a/vignettes/MLZ.Rmd b/vignettes/MLZ.Rmd
@@ -51,7 +51,7 @@ bin_length(SilkSnapper)
 
 The `plot` function can be used to visualize the data to aid in the selection of $L_c$.
 ```{r, fig.height = 5, fig.width = 6, message = FALSE}
-plot(new.dataset)
+plot(new.dataset, type = "comp")
 ```
 
 Once Lc is identified, `calc_ML()` can be used to mean lengths from records larger than Lc.