#test
#Descriptions of new scripts
run_sim has been edited to work for our purposes. This includes eliminating fishing and allowing for a sequence of move_cov matrices to be used
init_movCov_Bens (original, 2 and 3) each create temperature covariate matrices that extend longer than 1 year
init_movCov_Bens edits init_movCov in 2 ways 1) changes trend from decreasing temperature over the course of a year to increasing temp 2) each year it extends the temp further This one is not ideal because it starts at the same temp each year and extends further
init_movCov_Bens2 edits init_movCov by starting at a higher temp point each year but following the same trend problem with this trend is that it just increases temp over the course of a year and then jumps back to a lower value
init_movCov_Bens3 is an attempt at an oscillating relationship rather than just increasing over the course of a year and then jumping back to a lower value
init_movCov_Bens4 is same as init_moveCov except only creates first matrix. Then this matrix is adjusted, sine is applied, second half stretched, and finally copied 52 times
init_pop_Bens same as init_pop except I also record the lambda parameter for use in creating movement probabilities
init_sim_Bens creates different week.breaks (called week.breaks.all) that will run from week 1 to week n where n is total week in simulation week.breaks.all will be used to call the temperature covariate matrix for each week in the simulation (rather than looping back each year)
init_sim_Bens_nofish is the same as init_sim_Bens except it also creates a day.seq and day.breaks that allows us to intialize a fleet where no fishing is taking place (ghost fleet fishes 1 day per week)
Bens_plot_spatiotemp_hab takes plot_spatiotemp_hab and allows only certain weeks to be plotted, as specified by plot_wk
Bens_plot_spatiotemp_hab_justtemp takes plot_spatiotemp_hab and plots only the temperature gradient (no habitat preferences). Also allows only certain weeks to be plotted, as specified by plot_wk
go_fish_Bens eliminates most of the script to avoid decision about where to fish and instead chooses a random location for the single vessel. At the bottom the catchability value is replaced with a 0