creates exploratory plots of the data.

given an ITIS/stock and a metric to be plotted. All assessments are plotted

NAMESPACE

@@ -4,5 +4,6 @@ export(get_available_ts)
 export(get_latest_full_assessment)
 export(get_latest_metrics)
 export(get_species_itis)
+export(plot_ts)
 importFrom(magrittr,"%>%")
 importFrom(rlang,.data)

R/plot_ts.R

@@ -0,0 +1,103 @@
+#' Plot time series data for a particular species
+#'
+#' Exploratory plots of Catch, Abundance, F, Recruitment for all assessments for a particular species
+#'
+#' @param itis Numeric. Species ITIS code
+#' @param stock Character. Full name of stock (only required if more than one stock exists for ITIS code)
+#' @param metric Character vector. Specifying which metric to plot (Catch, Abundance, Fmort, Recruitment)
+#' @param plotAs Character. How to plpot results. Plot all assessments on a single plot ("one") or
+#' plot each assessment in its own facet ("facet")
+#'
+#' @section Units:
+#' The units of some of the metrics change over time. For example, catch for one assessment may be presented in metric tons
+#' whereas other assessments may be in thousand metric tons. This is not resolved in the plotting. When this arises it is best
+#' to use \code{plotAs = "facet"} since each facet uses its own yaxis scale
+#'
+#' @return A ggplot object is returned. A figure is also returned
+#'
+#' @importFrom magrittr "%>%"
+#' @importFrom rlang .data
+#'
+#' @export
+
+plot_ts <- function(itis=NULL, stock=NULL, metric = "Catch", plotAs="one") {
+
+
+  #error check for metric names
+  if (is.null(itis)) {
+    stop("If you do not know the ITIS code then please use get_species_itis()")
+  }
+  if (!metric %in% c("Catch","Fmort","Recruitment","Abundance","Index")) {
+    stop("Please use of the defined metrics to plot. Catch, Fmort, Recruitment, Abundance, Index")
+  }
+
+
+  # filter by ITIS and Metric
+  dataToPlot <- stocksmart::stockAssessmentData %>%
+    dplyr::filter(.data$ITIS == itis,Metric == metric) %>%
+    dplyr::mutate(AssessmentYear = as.factor(AssessmentYear))
+
+  if(nrow(dataToPlot) ==0){
+    message("The metric you selected doesn't exist for this stock")
+    return()
+  }
+
+  # select stocks for this ITIS
+  stocks <- dataToPlot %>%
+    dplyr::distinct(StockName)
+
+  # if multiple stocks and user argument - NULL
+  if ((nrow(stocks) > 1) && (is.null(stock))){
+    message(paste0("There are multiple stocks for ITIS = ",itis,". Please specify which stock you'd like to plot"))
+    stop(stocks)
+  }
+  # if multiple stocks and user argument doesn't match
+  if ((nrow(stocks) > 1) && (!stock %in% (stocks %>% dplyr::pull()))){
+    message(paste0("Please specify a valid stock to plot "))
+    stop(stocks)
+  }
+
+  # if only a single stock and user argument doesn't match
+  if (nrow(stocks) == 1) {
+    if (is.null(stock)) { # user left blank
+      stock = stocks
+    } else { # user entereres a string
+      if (!stock %in% (stocks %>% dplyr::pull())) {
+        message(paste0("Please specify a valid stock to plot "))
+        stop(stocks)
+      }
+    }
+
+  }
+
+  # filter out stock
+  stockToPlot <- dataToPlot %>%
+    dplyr::filter(StockName == stock)
+
+  # units check and standardize
+  # eg if units change over time from say mt to thousands mt
+
+
+  # plot data
+  if (plotAs == "facet"){
+    p <- ggplot2::ggplot(stockToPlot) +
+      ggplot2::geom_line(ggplot2::aes(x=Year,y=Value)) +
+      ggplot2::facet_wrap(~AssessmentYear,scales = "free_y")
+  } else {
+    if ((stockToPlot %>% dplyr::distinct(Units) %>% nrow()) >1) {
+      message("The units change over time. Plotting as a facet plot will be better")
+    }
+    p <- ggplot2::ggplot(stockToPlot) +
+      ggplot2::geom_line(ggplot2::aes(x=Year,y=Value,color = AssessmentYear))
+  }
+
+  p <- p +
+    ggplot2::ylab(paste0(metric," (",stockToPlot %>% dplyr::distinct(Units),")")) +
+    ggplot2::ggtitle(stockToPlot %>% dplyr::distinct(StockName))
+
+  print(p)
+
+  return(p)
+
+
+}