bccm_bottom_oxygen_full: Use BCCM model output for the full domain of the model (not...

In pbs-assess/PACea: An R package of Pacific ecosystem information to help facilitate an ecosystem approach to fisheries management

Use BCCM model output for the full domain of the model (not just within Canada's Exclusive Economic Zone).

Description

Loading and/or downloading British Columbia Continental Margin (BCCM) model outputs for the full domain of the model (down into US waters) to local drive. Use the functions without ‘_full' get only the values in Canada’s Exclusive Economic Zone. See the two BCCM vignettes.

To download all BCCM data for the full domain, use the function [bccm_all_variables_full()], and see that help for further details about the model.

Usage

bccm_bottom_oxygen_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_bottom_ph_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_bottom_salinity_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_bottom_temperature_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_surface_oxygen_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_surface_ph_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_surface_salinity_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_surface_temperature_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_avg0to40m_oxygen_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_avg0to40m_ph_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_avg0to40m_salinity_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_avg0to40m_temperature_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_avg40to100m_oxygen_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_avg40to100m_ph_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_avg40to100m_salinity_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_avg40to100m_temperature_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_avg100mtoBot_oxygen_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_avg100mtoBot_ph_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_avg100mtoBot_salinity_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_avg100mtoBot_temperature_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_phytoplankton_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

bccm_primaryproduction_full(
  update = FALSE,
  ask = interactive(),
  force = FALSE,
  version = "01",
  cache_subfolder = "bccm_full"
)

Arguments

update	Logical. Would you like to check for a newer version of the layer?
ask	Logical. Should the user be asked before downloading the data to local cache? Defaults to the value of interactive().
force	Logical. Should download of data be forced? Overrides 'ask' argument if TRUE.
version	character Version number of data as saved on Zenodo. Only currently works for "01" as that's all that is currently available.
cache_subfolder	character. Subfolder to put or look for the objects; defaults to 'hotssea' and it is best to stick with this. The objects will be put in your 'paste0(pacea::pacea_cache(), cache_subfolder)' directory.

Format

A simple features dataframe.

Details

The following 22 functions serve to download specific individual ocean variables of the BCCM model data over its full domain, on a 2 km x 2 km grid. Each file is around 120 Mb, but only takes a couple of minutes (on a home network, may be slower from a work network because of firewalls). If a variable has already been downloaded, the function will simply load data from your 'paste0(pacea_cache(), "/bccm_full"' folder into your local R environment.

The 22 objects available are desribed below as their respective functions; the equivalent functions without '_full' are for the BCCM outputs restricted to Canada's EEZ and on a coarser grid for the offshore. The objects obtained here are stored on Zenodo, with [get_zenodo_data()] automatically taking care of the DOI address for the one-time download.

If you get an error see [bccm_all_variables_full()].

Surface values represent values at the centre of the top BCCM grid cell. These top cells span depths that vary with the bathymetry, from 0.2 to 1.6 m.

bccm_*depth*_oxygen_full() Dissolved oxygen measured as mmol-oxygen m^-3
bccm_*depth*_salinity_full() Salinity in ppt
bccm_*depth*_temperature_full() Temperature in oC
bccm_*depth*_ph_full() pH
bccm_phytoplankton_full() Total phytoplankton biomass in mmol-nitrogen m^-2
bccm_primaryproduction_full() Total primary production in gC m^-2 d^-1

NOTE:
*depth* must be replaced by one of the following depth categories:

bottomsea bottom
0to40average between 0m and 40m depth
40to100average between 40m and 100m depth
100tobot : average between 100m depth and sea bottom
surfacesea surface

Value

'sf' data object requested.

Examples

## Not run: 
b <- bccm_bottom_temperature_full()
plot(b, months = 1:12)

plot(bccm_primaryproduction_full(), months = 1:12)

## End(Not run)

pbs-assess/PACea documentation built on April 17, 2025, 11:36 p.m.