Description Usage Arguments Examples
Define arguments for hook and line simulations Used in initialize_population
1 2 3 4 5 6 7 8 9 10 11 | make_ctl(numrow = 10, numcol = 10, nfish1 = 10000, nfish2 = 0,
prob1 = 0.1, prob2 = 0, distribute = "uniform", maxfish = 10,
percent = 0.3, area = NULL, seed = 300, move_out_prob = 0.4,
location = data.frame(vessel = c(1, 1, 2), x = c(3, 3, 8), y = c(3, 5, 8)),
scope = 1, nhooks = 5, ndrops = 5, nangs = 3,
process = "equal_prob", p0 = 0.4, nyear = 10, browser = FALSE,
cpue_method = "average", mortality, movement_function = move_fish_none,
max_prob = 0.1, min_prob = 0.1, comp_coeff = NA, rec_rate = NA,
rec_years = NA, hs_loc = NA, hs_scope = NA, delta = NA, shapes = NA,
niters = 1, par_func = "change_two", depletion_type = "none",
prop_moving = 0)
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numrow |
Number of rows in matrix |
numcol |
Number of columns in matrix |
nfish1 |
Number of fish1 to allocate among matrix |
nfish2 |
Number of fish2 to allocate among matrix |
prob1 |
Probability of catching species 1 |
prob2 |
Probability of catching species 2 |
distribute |
Specify fish distribution to be 'uniform', 'patchy', or 'area' specific |
maxfish |
Maximum number of fish that can be sampled at a time; default is 10 |
percent |
percentage of area to sample. Only necessary if distribute == 'patchy'; default is 0.3 |
area |
Specify area to distribute fish, options are 'upperleft', 'upperright', 'lowerleft', 'lowerright', 'upperhalf', 'lowerhalf', 'righthalf', 'lefthalf' Only necessary if distribute == 'area' |
seed |
Set seed if distribute == random, defaults to 300 |
move_out_prob |
Probability of moving out of fishing area |
location |
Data frame of locations with column for vessel, rows, and columns of fish are to fish in. |
scope |
the scope of fishing movement, default to 1 so fish in surrounding 1 cells can move in; default is 1 |
nhooks |
number of hooks at the smallest sampling size; default is 5 |
ndrops |
number of drops, default is 5 following hook and line protocol; default is 5 |
nangs |
number of anglers, Default is 3 |
process |
specify process by which fish are sampled, options are 'multinomial', 'hypergeometric', and 'equal_prob'. 'equal_prob' is based on CIE comments from 2012. |
p0 |
Probability that fish detects gear, used in the hook_prob function; default is 0.4 |
nyear |
Number of years in survey; default is 10 |
browser |
Switch to turn on browser for debugging |
cpue_method |
Method of aggregating cpue. For use in calc_cpue function. Currently |
mortality |
Natural mortality values, can be input as single value or matrix. Percentage mortality each year if single value options are 'average', '75hooks' to aggregate by hooks, and 'weighted_average' is in development. |
movement_function |
Specify the movement function, this occurs in year 2 of the survey, defaults to no movement |
max_prob |
Maximum movement probability for movement functions; defaults to 0.1 |
min_prob |
Minimum movement probability for movement functions; defaults to 0.1 |
comp_coeff |
Competition coefficient, how likely to catch species 1? Defaults to NA |
rec_rate |
Recruitment rate |
rec_years |
Years of recruitment |
hs_loc |
Locations of hotspots |
hs_scope |
Scope of hotspot range. Amount of diffusion of fish |
delta |
Difference between center of hotspot and surrounding cells |
shapes |
Shape Parameters for beta distribution in initialize_population |
niters |
Number of iterations to run for each scenario |
par_func |
parameter function to parallelize |
depletion_type |
Specify the type of depletion, increasing, decreasing or the default none |
prop_moving |
Specify proportion of fish moving in or out of fishing locations |
1 | make_ctl(p0 = .2)
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