Man pages for pbs-assess/PACea
An R package of Pacific ecosystem information to help facilitate an ecosystem approach to fisheries management
| a | Shorthand for 'as.data.frame()' for printing all of a tibble. |
| add_tickmarks | Add tickmarks to an existing plot |
| alpi | ALPI - Aleutian Low Pressure Index |
| ao | AO - Arctic Oscillation |
| area_mean | Isobath (200m) separated summary of values across an area |
| bccm_all_variables | Download all BCCM data |
| bccm_all_variables_full | Download all 22 BCCM full model results from Zenodo to a... |
| bccm_bottom_oxygen | BCCM environmental variable data |
| bccm_bottom_oxygen_full | Use BCCM model output for the full domain of the model (not... |
| bccm_data | BCCM data layers |
| bccm_eez_poly | Polygons masking layers for BC waters |
| bc_coast | BC coastline |
| bc_eez | BC Exclusive Economic Zone (EEZ) |
| bi | BI - North Pacific Current Bifurcation Index |
| buoy_metadata | Metadata regarding buoys for sea surface temperature. |
| buoy_sst | Daily average sea surface temperatures for 19 buoys (yielding... |
| calc_anom | Calculate anomaly |
| calc_clim | Calculate climatology |
| check_index_changed | Check if a newly downloaded pacea object has changed from one... |
| create_data | Create package data with one call. Taken from hake package. |
| create_herring_object | Create herring object to then save as data (five regions so... |
| get_pacea_data | Get large pacea data from repository |
| get_zenodo_data | Get large data products from Zenodo (if the file is not... |
| grid26 | Geospatial pacea grid - BC coastline grid template |
| grid26_depth | Geospatial pacea grid - BC coastline grid template with depth... |
| hake_biomass | Pacific Hake annual spawning stock biomass (females only) as... |
| hake_recruitment | Pacific Hake annual age-0 recruitments as estimated by the... |
| hake_recruitment_deviations | Pacific Hake annual log-scale age-0 recruitment deviations... |
| hake_recruitment_over_2010 | Pacific Hake annual age-0 recruitments divided by... |
| hake_recruitment_over_R0 | Pacific Hake annual age-0 recruitments divided by unfished... |
| hake_total_biomass_age_1 | Pacific Hake annual total biomass of age-1 fish as estimated... |
| harbour_seals | Estimated abundance of Pacific Harbour Seals in each of seven... |
| harbour_seals_data_final_year | Final year of Pacific Harbour Seals survey in each of seven... |
| herring_recruitment | Pacific Herring annual age-2 recruitments as estimated by the... |
| herring_spawning_biomass | Pacific Herring annual spawning stock biomass (males and... |
| hotssea_all_variables | Download all 40 HOTSSea model results from Zenodo to a local... |
| hotssea_data | HOTSSea data layers |
| hotssea_surface_salinity_min | Load or download the HOTSSea model output |
| isobath_200m | 200m isobath for separating inshore and offshore Pacific... |
| last_npi_annual | Year-month stamp of last downloaded 'npi_annual' file; not... |
| last_npi_monthly | Year-month stamp of last downloaded 'npi_monthly' file; not... |
| lubridate_pacea_series | Convert an object that represents a time seris ('pacea_index'... |
| mei | ENSO MEI - Multivariate ENSO Index |
| npgo | NPGO - North Pacific Gyre Oscillation |
| npi_annual | NPI - North Pacific Index annual values and anomalies |
| npi_monthly | NPI - North Pacific Index monthly values |
| oisst_7day | Optimal interpolation SST |
| oni | ONI - Oceanographic Niño Index |
| overlap | Restrict two time series to only the overlapping dates (only... |
| pacea_cache | Get directory of where to cache large data sets |
| pacea_clear_cache | pacea clear cache |
| pacea_import_from | pacea package importFrom requirements |
| pacea_indices | Summary of climatic and oceanographic indices in pacea |
| pacea_installed | Check the date of the last local installation of 'pacea' |
| pacea_long | pacea spatiotemporal data convert to long/wide format |
| pdo | PDO - Pacific Decadal Oscillation |
| plot_buoy_sst_single | Plot buoy SST data for a single station; called by... |
| plot.pacea_biomass | Plot a pacea biomass time series object (currently assumes... |
| plot.pacea_biomass_herring | Plot a herring biomass time series object for one or all... |
| plot.pacea_buoy | Plot buoy SST data for one or multiple stations |
| plot.pacea_harbour_seals | Plot the Pacific Harbour Seals abundance estimates |
| plot.pacea_index | Plot a pacea climatic or oceanographic index |
| plot.pacea_oi | Plot OISST data |
| plot.pacea_oianom | Plot anomaly of OISST spatiotemporal data layer |
| plot.pacea_recruitment | Plot a pacea recruitment time series object (currently... |
| plot.pacea_recruitment_herring | Plot a herring recruitment time series object for one or all... |
| plot.pacea_st | Plot a pacea spatiotemporal data layer |
| plot.pacea_stanom | Plot anomaly of BCCM spatiotemporal data layer |
| plot.pacea_zooplankton | Plot the one of the zooplankton anomalies. |
| plot_red_blue | Plot the red/blue style of anomaly plot, linearly... |
| plot_red_blue_bar | Plot the red/blue style of anomaly plot as barplots without... |
| plot_with_uncertainty_discrete | Plot medians with uncertainty bars, such as for stock... |
| point2rast | Points to raster nearest neighbour interpolation |
| standardise | Standardise a vector of values to a mean of 0 and standard... |
| zooplankton_sog | Zooplankton anomalies in the Strait of Georgia |
| zooplankton_sog_axis_names | Zooplankton anomalies in the Strait of Georgia - long names... |
