Function reference • MiMeMo.tools

NEMO-MEDUSA

Summarising extracted model output.

NM_boundary_summary(): Summarise NEMO-MEDUSA Output into Time Series Along Transects

NM_decadal_summary(): Summarise NEMO-MEDUSA Output into Decadal Grids This function averages cleaned NEMO-MEDUSA monthly summaries into decadal grids.

NM_volume_summary(): Summarise NEMO-MEDUSA Output into Time Series Within Model Compartments This function averages NEMO-MEDUSA monthly summaries into time series for each model compartment.

boundaries(): Create a series of transects along the boundaries of model compartments

to_segments(): Interpolate vertical water movements to the boundary depth between shallow and deep compartments

characterise_flows(): Check if a segment runs parallel to latitude or longitude

decadal(): Prepare for Averaging by Decade

strip_ice(): Strip Snow and Ice Variables at Depth

point_plot(): Map Spatial Summaries

ts_plot(): Plot Temporal Summaries

stick_plot(): Create Stick Plots to Show Currents

Misc

Other assorted utilities.

execute(): Run an R Script in it's own Session Informatively

fill_in(): Fill missing values in a vector

sfc_as_cols(): Pull Coordinates from a Simple Feature Geometry Column

box_zoom(): Zoom a ggplot to the bounding box of an sf object

Window(): Get Indices to Use When Clipping netcdf Files at Import

get_SPM(): Extract Suspended Particulate Matter data from Globcolour

get_air(): Get Surface Irradiance & Air Temperature

get_air_dt(): Get Surface Irradiance & Air Temperature

get_cropped_fishing(): Import Fishing Effort Within Specified Areas

get_rivers(): Get Rivers

update_boundary_period() update_physics_period(): Reproject from Latitude and Longitude to Project CRS

Unit conversions

Helper functions to avoid introducing bugs when switching between scales

micro_to_full() full_to_micro() micro_to_milli() milli_to_micro() milli_to_full() full_to_milli() l_to_m3() m3_to_l() sec_to_day() day_to_sec() shortwave_to_einstein(): Helper functions for common unit conversions

Sediment

Water movements

Align tidal and wave data from different sources.

reshape_SINMOD(): Subset a SINMOD file to depth-averaged water velocities in an area.

get_tides_ts(): Calculate bed shear stress at a location

get_waves_ts(): Calculate bed shear stress at a location

get_bed_shear_stress(): Calculate bed shear stress at a location

sample_tides_year(): Calculate bed shear stress at a location

sample_waves(): Calculate bed shear stress at a location

vectors_2_direction(): Convert a U-V velocity field to speed and direction in degrees

Sediment properties

Calculate derived properties from sediment fractions.

mud_to_permeability(): Calculate sediment permeability

D50_to_porosity(): Calculate sediment porosity