NE_Physics: A class for navigating FVCOM datasets

In BigelowLab/necofs: FVCOM for NECOFS

Description

R6 base class

Public fields

filename

character, path or URL

NC

ncdf4 object

M

sf table of mesh

t0

POSIXct timestamp identifying the start time

verbose

logical for helpful messaging

Active bindings

open_bounds

provides the indices for open boundary elements (open water)

closed_bounds

provides the indices for closed boundary elements (shore)

Methods

Public methods

• NE_Physics$new()

• NE_Physics$print()

• NE_Physics$get_crs()

• NE_Physics$get_time()

• NE_Physics$random_points()

• NE_Physics$char_size()

• NE_Physics$mesh_metrics()

• NE_Physics$append_bounds()

• NE_Physics$clone()

---

Method new()

Usage

NE_Physics$new(
  filename,
  origin = as.POSIXct("1858-11-17 00:00:00", tz = "UTC"),
  verbose = FALSE
)

Arguments

filename

character either a filename or OpenDAP URL

origin

POSIXct timestamp indicating the start of the experiment

verbose

logical for helpful messaging

crs

---

Method print()

Pretty print

Usage

NE_Physics$print()

---

Method get_crs()

Retrieve the CRS

Usage

NE_Physics$get_crs(form = c("proj", "wkt")[1])

Arguments

form

character, one of 'proj', 'wkt'

Returns

CRS in the specified form

---

Method get_time()

retrieve the time relative to some epoch/origin

Usage

NE_Physics$get_time(origin = self$t0, ...)

Arguments

origin

POSIXct the orogin of relative timestamps

...

other arguments for fvcom_time

---

Method random_points()

Retriev one or more random points

Usage

NE_Physics$random_points(n = 1, select_time = c("first", "last", "random")[1])

Arguments

n

numeric, the number of points to generate

select_time

character, one of 'first' (default), 'last' or 'random'

Returns

sf object of class POINT

---

Method char_size()

find proxy for characteristic size based upon element size

NOTE if we update GEOS we could get size of inscribed circle

Usage

NE_Physics$char_size(what = c("min", "max", "square", "circle")[4])

Arguments

what

character

• min or square - side length of sqaure with equivalent area

• max - side of square with double the area (or 1.4*sqrt(area))

• circle - radius of circle with equivalent area

x

element mesh as sf

Returns

numeric characteristic size

---

Method mesh_metrics()

generate kinematics metrics for a given mesh

Usage

NE_Physics$mesh_metrics(
  ofile = file.path(dirname(self$filename), "mesh-elem-metrics.csv.gz")
)

Arguments

ofile

optional file to save to (as non-spatial CSV)

Returns

mesh (invisibly) with variables added including

• max_u, max_v, max_w maximum velocity by element over all sigma in m/s

• area element area in m^2

• char_dim characteristic dimension, for now the radius of the circle with equivalent area in m

---

Method append_bounds()

append the boundary info to the mesh table

Usage

NE_Physics$append_bounds()

Returns

mesh invisibly with appended boundary variable where

• open indicates the element is boundaed on at least one side by open water

• closed indicates the element is bounded on at least one side by shoreline

• internal indicated the element is not on the boundary

---

Method clone()

The objects of this class are cloneable with this method.

Usage

NE_Physics$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

BigelowLab/necofs documentation built on Jan. 7, 2022, 11:59 a.m.