From e7ccaa39620134773a06c0a1f698bf905b279a42 Mon Sep 17 00:00:00 2001
From: Rose McKeon <rose@rosemckeon.co.uk>
Date: Wed, 31 Jul 2019 00:24:40 +0000
Subject: [PATCH] for #89 @bradduthie does this make sense to do?

---
 R/disturploidy.R | 16 ++++++++++++----
 R/functions.R    | 11 ++++++++++-
 2 files changed, 22 insertions(+), 5 deletions(-)

diff --git a/R/disturploidy.R b/R/disturploidy.R
index 30f2430..87e0738 100644
--- a/R/disturploidy.R
+++ b/R/disturploidy.R
@@ -318,9 +318,15 @@ disturploidy <- function(
       if(nrow(seeds) > 0){
         tic("Germination")
         # decide which seeds germimate
-        seeds <- seeds %>% germinate(
-          germination_prob
-        )
+        if(seed_survival_prob == 0){
+          # we decided the germination fate already to reduce computation
+          # so germinate all seeds
+          seeds <- seeds %>% germinate(1)
+          message("  Germinating all seeds (germination fate already decided).")
+        } else {
+          # germination needs to happen as usual
+          seeds <- seeds %>% germinate(germination_prob)
+        }
         new_juveniles <- seeds %>% filter(
           life_stage == 1
         )
@@ -461,7 +467,9 @@ disturploidy <- function(
           genome_size,
           ploidy_prob,
           mutation_rate,
-          grid_size
+          grid_size,
+          germination_prob,
+          seed_survival_prob
         )
         # make sure we have some new seeds
         # (stop any mutate errors)
diff --git a/R/functions.R b/R/functions.R
index c0aecfc..7c3fc77 100644
--- a/R/functions.R
+++ b/R/functions.R
@@ -83,7 +83,9 @@ reproduce <- function(
   genome_size = 10,
   ploidy_prob = .01,
   mutation_rate = .001,
-  grid_size
+  grid_size = 100,
+  germination_prob = .5,
+  seed_survival_prob = 0
 ){
   # make sure we have the right kind of parameters
   stopifnot(
@@ -190,6 +192,13 @@ reproduce <- function(
   }
   message("  ", nrow(zygotes), " zygotes created in TOTAL.")
   if(nrow(zygotes) > 0){
+    # see if we can reduce computation and decide the germination fate now
+    if(seed_survival_prob == 0){
+      # seeds with genomes will not persist so we don't need to fill them
+      # we'll check for this at the germination stage too
+      zygotes <- zygotes %>% survive(germination_prob)
+      message("  ", nrow(zygotes), " zygotes destined to become seeds that will germinate.")
+    }
     # make sure all the new zygotes become seeds with genetic info
     seeds <- create_seeds(
       zygotes, adults, generation, genome_size, mutation_rate