Takes list output from tidy_rema and returns the same list with
enhanced versions of the biomass_by_strata and cpue_by_strata
when appropriate. These enhanced dataframes include three new columns,
tot_log_obs_cv, tot_obs_lci, and tot_obs_uci, which
represent combined log-space standard error and associated confidence
intervals that include both assumed and estimated additional observation
error.
Arguments
- tidy_rema
list out output from
tidy_rema, which includes model results but also inputs- save
(optional) logical (T/F) save figures as
filetypeinpath. Default = FALSE. NOT YET IMPLEMENTED.- path
(optional) directory path to location where figure files are to be saved if
save = TRUE. NOT YET IMPLEMENTED.- alpha_ci
(optional) the significance level for generating confidence intervals. Default = 0.05
Value
a list with the following items:
$parameter_estimatesA data.frame of fixed effects parameters in REMA (e.g. log_PE and log_q) with standard errors and confidence intervals that have been transformed from log space to natural space for ease of interpretation.
$biomass_by_strataA tidy, long format data.frame of model predicted and observed biomass by biomass survey strata. This data.frame is now enhanced with new columns that include log-space standard error and associated confidence intervals that account for additional estimated observation error.
$cpue_by_strataA tidy, long format data.frame of model predicted and observed CPUE by CPUE survey strata. This data.frame is now enhanced with new columns that include log-space standard error and associated confidence intervals that account for additional estimated observation error. If REMA is not run in multi-survey mode, or if CPUE data are not provided, an explanatory character string with instructions for fitting to CPUE data is returned.
$biomass_by_cpue_strataA tidy, long format data.frame of model predicted biomass by CPUE survey strata. Note that observed/summed biomass observations are not returned in case there are missing values in one stratum but not another within a given year. This output is reserved for instances when the number of biomass strata exceeds that of CPUE survey strata, but the user wants to visualize predicted biomass at the same resolution as the CPUE predictions. In other scenarios, a character string is returned explaining the special use case for this object.
$total_predicted_biomassA tidy, long format data.frame of total model predicted biomass summed across all biomass survey strata. If only one stratum is used (i.e. the univariate RE), the predicted values will be the same as
output$biomass_by_strata.$total_predicted_cpueA tidy, long format data.frame of total model predicted CPUE summed across all CPUE survey strata. If only one stratum is used (i.e. the univariate RE), the predicted values will be the same as
output$cpue_by_strata. If The CPUE survey index provided was defined as not summable in prepare_rema_input(), an character string will be returned explaining how to change this using the 'sum_cpue_index' in?prepare_rema_inputif appropriate.