B - Dev - Fit Model

library(FishMap)

fm_build_data_params_map

An example of the function. Only use to remove source inside the function fm_fit_model

## Settings all params

SE <- 1
data_source <- 1
data_obs <- 2
samp_process <- 0
b_constraint <- 2
const_spphab <- 1
cov_samp_process <- 0
biomass_temporal <- 1
sampling_temporal <- 0
anisotropy <- 0
lf_link <- 0
ref_data <- "com"
EM <- "est_b"
month_ref <- 1
compute_sd <- FALSE

fm_data_inputs <- readr::read_rds(system.file("examples", "part1_output_small.rds", package = "FishMap"))

species <- fm_data_inputs[["species"]]
b_com_i <- fm_data_inputs[["b_com_i"]]
mesh <- fm_data_inputs[["mesh"]]
time.step_df <- fm_data_inputs[["time.step_df"]]
loc_x <- fm_data_inputs[["loc_x"]]
y_com_i <- fm_data_inputs[["y_com_i"]]
y_sci_i <- fm_data_inputs[["y_sci_i"]]
cov_x_com <- fm_data_inputs[["cov_x_com"]]
cov_x_sci <- fm_data_inputs[["cov_x_sci"]]
c_com_x <- fm_data_inputs[["c_com_x"]]
t_com_i <- fm_data_inputs[["t_com_i"]]
t_sci_i <- fm_data_inputs[["t_sci_i"]]
spde <- fm_data_inputs[["spde"]]
Aix_ij_com <- fm_data_inputs[["Aix_ij_com"]]
Aix_w_com <- fm_data_inputs[["Aix_w_com"]]
Aix_ij_sci <- fm_data_inputs[["Aix_ij_sci"]]
Aix_w_sci <- fm_data_inputs[["Aix_w_sci"]]
cov_x_pred <- fm_data_inputs[["cov_x_pred"]]
Aix_ij_pred <- fm_data_inputs[["Aix_ij_pred"]]
Aix_w_pred <- fm_data_inputs[["Aix_w_pred"]]
W <- fm_data_inputs[["W"]]
n_survey <- fm_data_inputs[["n_survey"]]
MeshList_aniso <- fm_data_inputs[["MeshList_aniso"]]

xfb_x <- NULL # TO DELETE
weights_com <- 1 # TO DELETE

result <- fm_build_data_params_map(
  SE = SE,
  data_source = data_source,
  data_obs = data_obs,
  samp_process = samp_process,
  b_constraint = b_constraint,
  cov_samp_process = cov_samp_process,
  const_spphab = const_spphab,
  biomass_temporal = biomass_temporal,
  sampling_temporal = sampling_temporal,
  anisotropy = anisotropy,
  lf_link = lf_link,
  b_com_i = b_com_i,
  mesh = mesh,
  time.step_df = time.step_df,
  loc_x = loc_x,
  y_com_i = y_com_i,
  y_sci_i = y_sci_i,
  cov_x_com = cov_x_com,
  cov_x_sci = cov_x_sci,
  xfb_x = xfb_x,
  c_com_x = c_com_x,
  t_com_i = t_com_i,
  weights_com = weights_com,
  t_sci_i = t_sci_i,
  spde = spde,
  Aix_ij_com = Aix_ij_com,
  Aix_w_com = Aix_w_com,
  Aix_ij_sci = Aix_ij_sci,
  Aix_w_sci = Aix_w_sci,
  cov_x_pred = cov_x_pred,
  Aix_ij_pred = Aix_ij_pred,
  Aix_w_pred = Aix_w_pred,
  W = W,
  n_survey = n_survey,
  MeshList_aniso = MeshList_aniso,
  EM = EM,
  ref_data = ref_data,
  month_ref = month_ref,
  Version = Version
)

fm_fit_model(): compile model and fit to data

This function will fit the model to the observation data. It will compile the model cpp file. It will fit the model to the input data generated from fm_load_data() and provide the results as a named list.

# run part 2
fm_data_inputs <- readr::read_rds(
  system.file("examples", "part1_output_small.rds",
              package = "FishMap")
  )

fm_model_results <- fm_fit_model(fm_data_inputs = fm_data_inputs,
                                 SE = 1,
                                 data_source = 1,
                                 data_obs = 2,
                                 samp_process = 0,
                                 b_constraint = 2,
                                 cov_samp_process = 0,
                                 biomass_temporal = 1,
                                 sampling_temporal = 0,
                                 lf_link = 0,
                                 ref_data = "com",
                                 EM = "est_b",
                                 month_ref = 1)