In pbs-assess/gfsynopsis: Data Synopsis Reports for PBS Groundfish

library(gfplot)

# On PBS network:
# d <- gfdata::get_survey_samples("lingcod")
# Or load cached data:
d <- readRDS(here::here("report/data-cache/lingcod.rds"))$survey_samples
survs <- c(
  # "4B: STRAIT OF GEORGIA",
  "5C: SOUTHERN HECATE STRAIT",
  "5E: WEST COAST Q.C. ISLANDS",
  "5D: NORTHERN HECATE STRAIT",
  "5B: NORTHERN Q.C. SOUND",
  "3D: N.W. VANCOUVER ISLAND",
  "3C: S.W. VANCOUVER ISLAND",
  "5A: SOUTHERN Q.C. SOUND"
  # "2B:CAPE BLANCO TO CAPE PERPETUA (42 50' TO 44 18')"
)
surv_samp <- dplyr::filter(d, major_stat_area_name %in% survs)

Available samples:

tidy_sample_avail(surv_samp) %>% plot_sample_avail() +
  ggplot2::scale_fill_viridis_c()

Length-age fits (using a Stan Bayesian model):

# mf <- fit_vb(surv_samp, sex = "female")
# mm <- fit_vb(surv_samp, sex = "male")
# plot_vb(object_female = mf, object_male = mm)
# 
# TMB::sdreport(mf$model)
# TMB::sdreport(mm$model)

mf_stan <- fit_vb(surv_samp, sex = "female", method = "mcmc", iter = 2000L)
mm_stan <- fit_vb(surv_samp, sex = "male", method = "mcmc", iter = 2000L)
plot_vb(object_female = mf_stan, object_male = mm_stan)

mf_stan$model
mm_stan$model

You can see the model and priors here: https://github.com/pbs-assess/gfplot/blob/master/inst/stan/vb.stan

linf_upper_sd gets set to the 99% quantile of the sampled fish lengths.

mf <- fit_length_weight(surv_samp, sex = "female")
mm <- fit_length_weight(surv_samp, sex = "male")
plot_length_weight(object_female = mf, object_male = mm)

TMB::sdreport(mf$model)
TMB::sdreport(mm$model)

Maturity ogives. F50 and M50 give you the age (or length) at 50% maturity. 05 and 95 give you the 90% confidence interval.

m_age <- fit_mat_ogive(surv_samp, type = "age")
plot_mat_ogive(m_age)

m_length <- fit_mat_ogive(surv_samp, type = "length")
plot_mat_ogive(m_length)

See detailed figure captions in the initial pages of https://www.dfo-mpo.gc.ca/csas-sccs/Publications/ResDocs-DocRech/2019/2019_041-eng.html

pbs-assess/gfsynopsis documentation built on March 26, 2024, 7:30 p.m.