THREE BIG THINGS THIS WEEK
All of the case studies have been worked on but the advanced one is still having some trouble. We will be working on both the advanced and Pacific Hake case studies this week.
Google Summer of Code ideas need to be submitted today! We have two submitted so far, one related to turning on and off uncertainty for derived quantities and one related to adding Empirical Dynamic Modeling (EDM) to FIMS. EDM models were presented last week for brown shrimp at NSAW.
We have an Implementation Team Meeting and a tutorial on FIMSdiags this week. Please attend both and spread the news about the tutorial.
FIMS ANNOUNCEMENTS
- If you attended the FIMS Training on Monday, please fill out the survey on Google Cloud Workstations.
UPCOMING EVENTS
Wednesday, February 04
FIMS Implementation Team Meeting (Priorities)
Time: 15:30–16:30 E; 12:30–13:30 P; 11:30–12:30 AK; 9:30–10:30 H Location: Virtual Online: Google meet
Thursday, February 05
FIMSdiags Tutorial
Time: 14:00–15:00 E; 11:00–12:00 P; 10:00–11:00 AK; 8:00–9:00 H Location: Virtual Online: Google meet
PHOTO OF THE WEEK
We have diagnostics thanks to Meg and Ian. Below is some sample code for running a likelihood profile over R_zero. Attend the tutorial on Thursday to learn more about {FIMSdiags}.
# data
data("data1", package = "FIMS")
data_4_model <- FIMS::FIMSFrame(data1)
# Create parameters
parameters <- data_4_model |>
FIMS::create_default_configurations() |>
FIMS::create_default_parameters(data = data_4_model)
# Run the model with optimization
base_model <- parameters |>
FIMS::initialize_fims(data = data_4_model) |>
FIMS::fit_fims(optimize = TRUE)
FIMS::clear()
# Run a likelihood profile on R_zero
like_fit <- FIMSdiags::run_fims_likelihood(
model = base_model,
parameters = parameters,
parameter_name = "log_rzero",
data = data1,
n_cores = 1,
min = -1,
max = 1,
length = 5
)