From bab45ae287ece19eadb2f67da243a2705f1a70cd Mon Sep 17 00:00:00 2001
From: Maria Voigt <maria.voigt@idiv.de>
Date: Wed, 8 Feb 2017 13:37:43 +0100
Subject: [PATCH] adding option to vary ESW
---
src/model_fitting/abundance_model.R | 12 +++++++++++-
1 file changed, 11 insertions(+), 1 deletion(-)
diff --git a/src/model_fitting/abundance_model.R b/src/model_fitting/abundance_model.R
index 2a5ec31..fbb54a1 100644
--- a/src/model_fitting/abundance_model.R
+++ b/src/model_fitting/abundance_model.R
@@ -30,6 +30,10 @@ option_list <- list (
make_option(c("-o", "--output-directory"), dest = "output_directory",
type = "character", help = "directory with output files",
metavar = "/path/to/output-dir"),
+ make_option("--ESW-aerial-index",
+ dest = "ESW_aerial_index",
+ type = "double",
+ help = "index aerial effective strip width"),
make_option("--exclude-year", dest = "exclude_year", type = "integer",
default = NA, help = "year to exclude", metavar = "2015"),
make_option("--include-aerial",
@@ -74,6 +78,9 @@ if(is_verbose){print(paste("indir", indir))}
outdir <- options$output_directory
if(is_verbose){print(paste("outdir", outdir))}
+ESW_aerial_index <- options$ESW_aerial_index
+if(is_verbose){print(paste("Aerial ESW index", ESW_aerial_index))}
+
do_stability <- options$stability
if(is_verbose){print(paste("stability", do_stability))}
@@ -102,7 +109,10 @@ source(file.path(indir_fun, "roger_functions/get_conf_set.r"))
#define offset ground
ESW <- 0.01595 #effective strip width in km
-ESW_aerial <- 0.075 # effective strip width for aerial transects
+
+ESW_aerial_options <- seq(from = 0.01, to = 0.15, by = 0.01)
+ESW_aerial <- ESW_aerial_options[ESW_aerial_index]
+print(paste("this is ESW aerial:", ESW_aerial))
NCS <- 1.12 #nest construction rate from Spehar et al. 2010
PNB <- 0.88 # proportion of nest builders from Spehar et al. 2010
--
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