Added getMeanLength function. Description and tests needed.

DESCRIPTION

@@ -70,6 +70,7 @@ Collate:
     getYieldVsFcurve.R
     validSim.R
     plots.R
+    getMeanLength.R
 Encoding: UTF-8
 RoxygenNote: 7.1.2
 Roxygen: list(markdown = TRUE)

R/getMeanLength.R

@@ -0,0 +1,40 @@
+#' Calculate the mean length of the community
+#'
+#' Calculates the mean length of the community through time. This is simply the
+#' total biomass of the community divided by the abundance in numbers then converted 
+#' the weights into species specific lengths based on species params. You can
+#' specify minimum and maximum length or length range for the species. Lengths
+#' take precedence over lengths (i.e. if both min_l and min_w are supplied, only
+#' min_l will be used). You can also specify the species to be used in the
+#' calculation.
+#'
+#' @param sim A \linkS4class{MizerSim} object
+#' @inheritParams valid_species_arg
+#' @inheritDotParams get_size_range_array -params
+#'
+#' @return A vector containing the mean length of the community through time
+#' @export
+#' @family functions for calculating indicators
+#' @concept summary_function
+#' @examples
+#' mean_length <- getMeanlength(NS_sim)
+#' years <- c("1967", "2010")
+#' mean_length[years]
+#' getMeanLength(NS_sim, species = c("Herring", "Sprat", "N.pout"))[years]
+#' getMeanLength(NS_sim, min_w = 10, max_w = 5000)[years]
+
+getMeanLength <- function (sim, species = NULL, ...) 
+{
+  assert_that(is(sim, "MizerSim"))
+  species <- valid_species_arg(sim, species)
+  n_species <- getN(sim, ...)
+  biomass_species <- getBiomass(sim, ...)
+  n_total <- apply(n_species[, species, drop = FALSE], 1, sum)
+  biomass_total <- apply(biomass_species[, species, drop = FALSE], 
+                         1, sum)
+  mean_weight_species <- biomass_species/n_species
+  conversion <- function() exp(log(mean_weight_species[, species, drop = FALSE]/sim@params@species_params["a"])/sim@params@species_params["b"]) 
+  mean_length_species<- conversion()
+  mean_length <- apply(mean_weight_species[, species,drop = FALSE], 1, sum)
+  return(mean_length)
+}