dsjohnson

library(glmmTMB)
library(mgcv)

#########################################################################
## Function to create prediction matrices from mgcv for glmmTMB
##   from ?mgcv::smooth2random
########################################################################
s2rPred <- function(sm,re,data) {
## Function to aid prediction from smooths represented as type==2
## random effects. re must be the result of smooth2random(sm,...,type=2).

dsjohnson

#' @title Find the sections of a path that pass thorugh a restricted area
#' @description This function is used to identify sections of a path that pass through 
#' restricted areas. the CTCRW model in crawl cannot actively steer paths away 
#' from restricted areas as it knows nothing of spatial information. So, this function
#' will identify areas that for which the unrestrained path passes through these areas.
#' If the path/points end within the restricted area, those records will be removed.
#' The user can then use this information to adjust the path as desired. 
#' @param xy A \code{SpatialPoints} object from the \code{sp} package or a 
#' 2-column matrix of x and y locations
#' @param res_raster A \code{raster} object from the raster package that indicates 

dsjohnson

### Load packages ###
# Must have 'marked' v >= 1.1.8
library(marked)
# The splines package is only necessary for fitting b-spline curves used in the paper
# It is not required for the multivate models in the marked package
library(splines)


### Import and process data ###

dsjohnson

library(cowplot)
library(coda)
load("Sig_test_DJ.RData")
data = all_model
data$Year = factor(data$Year)
data = droplevels(data)

### Add beach variables
data$Beach4 = ifelse(data$Beach=="4", 1, 0)
data$Beach7 = ifelse(data$Beach=="7", 1, 0)

dsjohnson

library(rstan)
devtools::source_gist("8f675b9aa74ab9900fb4")
load("Sig_test_DJ.RData")
data = all_model
data$Year = factor(data$Year)
data = droplevels(data)

### Add beach variables
data$Beach4 = ifelse(data$Beach=="4", 1, 0)
data$Beach7 = ifelse(data$Beach=="7", 1, 0)

dsjohnson

### New growth function
logistic_growth = function(x, phi1, phi2, phi3){
  phi1/(1 + exp(-(x-phi2)/phi3))
} 

ll_logistic = function(par, y, xvar, phi1_dm, phi2_dm, phi3_dm, sigma_dm, sigma=1, predict=FALSE, scale=-2){
  n1 = ncol(phi1_dm)
  n2 = ncol(phi2_dm)
  n3 = ncol(phi3_dm)
  if(!missing(sigma_dm)) n4 = ncol(sigma_dm)

dsjohnson

After you have installed gfortran from homebrew using 
$ brew install gfortran

After installing R... add the following lines to ~/.R/Makevars
FC = /usr/local/bin/gfortran
F77 = /usr/local/bin/gfortran
FLIBS = -L/usr/local/Cellar/gcc/4.9.2_1/lib/gcc/4.9 -lgfortran -lquadmath -lm

and openblas using
$ brew install openblas

dsjohnson

library("marked")

#### Some preliminaries ###
ilogit = function(x){log(x/(1-x))}
min.adult.age=5
additional.resight=3
adult.age="stable"

set.seed(111)
n.rel.pup=c(138,57,38,250,rep(100,4))

dsjohnson

library(sp)
library(rgdal)
library(raster)
library(gstat)
library(rgeos)
library(automap)
library(adehabitatHR)
source("stpp_rsf_helper.R")

# Read in telemtry

dsjohnson

library(sp)
library(rgdal)
library(raster)
library(gstat)
library(rgeos)
library(automap)
library(mgcv)
source("stpp_rsf_helper.R")
load("nfs_analysis/JAE_analysis_data_st.RData")
# load("stQuadList_countVersion.RData")