Man pages for jBernardADFG/ChenaSalchaTowerSonar
Apportion and enumerate salmon on the Chena and Salcha
| allison_plot | Plot sonar + hamachan estimates for 2020 analysis |
| calculate_totals | Calculate totals, according to a user-input date range. |
| compile_estimates | Compile visual and sonar estimates into a single data.frame. |
| expand_counts | Expand visual and sonar counts. |
| extract_final_results | Extract the final results from the model. |
| extract_length_priors | Extract relavant data from posterior samples. |
| extract_runtiming_priors | Extract relavant data from posterior samples. |
| find_convergence_issues | Identify parameters with Rhat values > 1.1 |
| gather_mixture_data | Gather and format data for mixture model. |
| get_length_samples | Estimate mean, sd, and se of carcass lengths. |
| get_runtiming_samples | Estimate parameters of hierarchical logistic regression using... |
| prepare_historical_counts | Prepare the historical fish counts for Hamachan's... |
| prepare_length_data | Reads in carcass length data. |
| prepare_runtiming_data | Read in Historical Run Timing Data. |
| prepare_sonar_counts_for_expansion | Formats mixture model output and visual count data for... |
| prepare_sonar_counts_for_expansion_2 | Formats mixture model output and visual count data for... |
| prepare_visual_counts_for_expansion | Format the visual counts for expansion. |
| ProcessFiles_ARIS | Processes all ARIS files within a specified directory. |
| ProcessFiles_DIDSON | Processes all DIDSON files within a specified directory. |
| ReadFile_ARIS | Reads ARIS files. |
| ReadFile_DIDSON | Reads DIDSON files. |
| run_hamachan | Run Hamachan's hierarchical run-timing model. |
| run_mixture_model | Use sonar data to apportion and enumerate fish passage by... |
| run_mixture_model_2 | Use sonar data to apportion and enumerate fish passage by... |
| run_mixture_model_3 | Use sonar data to apportion and enumerate fish passage by... |
| runningavg_interp | Apply the running-average interpolation method where... |
| standardize_ARIS | Converts ARIS data to a standardized format. |
| standardize_DIDSON | Converts DIDSON data to a standardized format. |
| visual_sonar_plot | Plot expanded visual and sonar counts. |
