Functino to run retrospective analyses
do_retrospective.Rd
Functino to run retrospective analyses
Usage
do_retrospective(
n_retro,
data,
parameters,
mapping,
random = NULL,
do_par,
n_cores,
do_francis,
n_francis_iter = NULL
)
Arguments
- n_retro
Number of retrospective peels to do
- data
Data list for RTMB model
- parameters
Parameter list for RTMB model
- mapping
Mapping list for RTMB model
- random
Random effects as a character vector - default is NULL
- do_par
Whether to do parrallelization, boolean
- n_cores
Number of cores to use for parrallelization
- do_francis
Whether to do francis reweighitng within a given retrospective peel, boolean
- n_francis_iter
Number of francis iterations to do
Examples
if (FALSE) { # \dontrun{
# Do retrospective here
ret <- do_retrospective(n_retro = 7, data, parameters, mapping, random = NULL, do_par = TRUE, n_cores = 7, do_francis = TRUE, n_francis_iter = 5)
ggplot(ret, aes(x = Year + 1959, y = value, group = peel, color = 2024 - peel)) +
geom_line(lwd = 1.3) +
facet_wrap(~Type) +
guides (color = guide_colourbar(barwidth = 10, barheight = 1.3)) +
labs(x = 'Year', y = 'Value', color = 'Retrospective Year') +
scale_color_viridis_c() +
theme_bw(base_size = 15) +
theme(legend.position = 'top')
ret %>%
dplyr::mutate(Year = Year + 1959, terminal = 2024 - peel, cohort = Year - 2, years_est = terminal-Year) %>%
filter(Type == 'Recruitment', cohort %in% c(2014:2022), terminal != Year) %>%
ggplot(aes(x = years_est - 1, y = value, group = Year, color = factor(cohort))) +
geom_line(lwd = 1.3) +
geom_point(size = 4) +
theme_bw(base_size = 15) +
labs(x = 'Years since cohort was last estimated', y = 'Recruitment (millions)', color = 'Cohort')
} # }