hello.Rd
Testing sampling designs for selecting samples for age and growth of fishes. This is a IBM to generate a population and catch from the population to test sampling approaches of POS or FOS, sample size, supplemental sampling, and constraining or not constraining t0. It uses a von Bertalanffy growth function.
S1_Auric_lowF <- simulate_population_harvest(Linf = 32.5, Linf_sd = 2.5,
M = 0.18, F = 0.09, Lorenzen = TRUE,
mincat = 10, catsd = 2.5, maxcat = 200, maxcatsd = 0,
L0 = 10, L0_sd = 2.5, k = 0.6, k_sd = 0,
Amax = 32, age_max = 15, N = 100000)
summary(S1_Auric_lowF$harvest$length)
#> Min. 1st Qu. Median Mean 3rd Qu. Max.
#> 15.59 26.18 29.67 29.04 32.37 41.92
str(S1_Auric_lowF$harvest$length)
#> num [1:14701] 19.5 19.7 20.1 20.7 20.6 ...
S1_hist_length_harv <- hist(S1_Auric_lowF$harvest$length, breaks = seq(0,50,2),include.lowest=TRUE, right=FALSE,plot=FALSE)
##### A. S1_Auric_lowF#######
#FOS examples with differing sample size, constained vs unconstrained, supplemental samples added
S1_A1 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 300,
sample_type = 'FOS', supp_large = FALSE, supp_small = FALSE, constrained = FALSE,
save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A2 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 75,
sample_type = 'FOS', supp_large = FALSE, supp_small = FALSE, constrained = FALSE,
save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A3 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 300,
sample_type = 'FOS', supp_large = FALSE, supp_small = FALSE, constrained = TRUE,
save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A4 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 75,
sample_type = 'FOS', supp_large = FALSE, supp_small = FALSE, constrained = TRUE,
save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A5 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 300,
sample_type = 'FOS', supp_large = FALSE, supp_large_n_per_bin = 3,
supp_small = TRUE, constrained = FALSE, supp_small_n_per_bin = 3,
supp_min_length = 10, save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A6 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 75,
sample_type = 'FOS', supp_large = FALSE, supp_large_n_per_bin = 3,
supp_small = TRUE, constrained = FALSE, supp_small_n_per_bin = 3,
supp_min_length = 10, save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A7 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 300,
sample_type = 'FOS', supp_large = FALSE, supp_large_n_per_bin = 3,
supp_small = TRUE, constrained = TRUE, supp_small_n_per_bin = 3,
supp_min_length = 10, save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A8 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 75,
sample_type = 'FOS', supp_large = FALSE, supp_large_n_per_bin = 3,
supp_small = TRUE, constrained = TRUE, supp_small_n_per_bin = 3,
supp_min_length = 10, save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
#POS examples with differing sample size, constained vs unconstrained, supplemental samples added
S1_A9 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 300,
sample_type = 'POS', supp_large = FALSE, supp_small = FALSE, constrained = FALSE,
save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A10 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 75,
sample_type = 'POS', supp_large = FALSE, supp_small = FALSE, constrained = FALSE,
save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A11 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 300,
sample_type = 'POS', supp_large = FALSE, supp_small = FALSE, constrained = TRUE,
save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A12 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 75,
sample_type = 'POS', supp_large = FALSE, supp_small = FALSE, constrained = TRUE,
save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A13 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 300,
sample_type = 'POS', supp_large = TRUE, supp_large_n_per_bin = 3,
supp_small = FALSE, constrained = FALSE,
save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A14 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 75,
sample_type = 'POS', supp_large = TRUE, supp_large_n_per_bin = 3,
supp_small = FALSE, constrained = FALSE,
save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A15 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 300,
sample_type = 'POS', supp_large = TRUE, supp_large_n_per_bin = 3,
supp_small = FALSE, constrained = TRUE,
save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A16 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 75,
sample_type = 'POS', supp_large = TRUE, supp_large_n_per_bin = 3,
supp_small = FALSE, constrained = TRUE,
save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A17 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 300,
sample_type = 'POS', supp_large = FALSE, supp_large_n_per_bin = 3,
supp_small = TRUE, constrained = FALSE, supp_small_n_per_bin = 3,
supp_min_length = 10, save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A18 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 75,
sample_type = 'POS', supp_large = FALSE, supp_large_n_per_bin = 3,
supp_small = TRUE, constrained = FALSE, supp_small_n_per_bin = 3,
supp_min_length = 10, save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A19 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 300,
sample_type = 'POS', supp_large = FALSE, supp_large_n_per_bin = 3,
supp_small = TRUE, constrained = TRUE, supp_small_n_per_bin = 3,
supp_min_length = 10, save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A20 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 75,
sample_type = 'POS', supp_large = FALSE, supp_large_n_per_bin = 3,
supp_small = TRUE, constrained = TRUE, supp_small_n_per_bin = 3,
supp_min_length = 10, save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A21 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 300,
sample_type = 'POS', supp_large = TRUE, supp_large_n_per_bin = 3,
supp_small = TRUE, constrained = FALSE, supp_small_n_per_bin = 3,
supp_min_length = 10, save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A22 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 75,
sample_type = 'POS', supp_large = TRUE, supp_large_n_per_bin = 3,
supp_small = TRUE, constrained = FALSE, supp_small_n_per_bin = 3,
supp_min_length = 10, save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A23 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 300,
sample_type = 'POS', supp_large = TRUE, supp_large_n_per_bin = 3,
supp_small = TRUE, constrained = TRUE, supp_small_n_per_bin = 3,
supp_min_length = 10, save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"
S1_A24 <- LH_sample(sim_output = S1_Auric_lowF, n_boots = 1000, samp_size = 75,
sample_type = 'POS', supp_large = TRUE, supp_large_n_per_bin = 3,
supp_small = TRUE, constrained = TRUE, supp_small_n_per_bin = 3,
supp_min_length = 10, save_bootstraps = TRUE, Lbin_width = 2)
#> [1] "2022-09-29 12:27:14 HST"
#> Error in population_harv %>% group_by(binL) %>% mutate(prop = n()) %>% group_by() %>% mutate(n = sum(n())) %>% mutate(propL = prop/n): could not find function "%>%"