extractHydroVars: Extract hydrodynamic variables from WeStCOMS meshes

In Sz-Tim/WeStCOMS: A set of functions for working with WeStCOMS data in R

Extract hydrodynamic variables from WeStCOMS meshes

Description

Given an input dataframe with site locations, dates, hours, and depths, this function extracts the corresponding WeStCOMS data. Output can be specific hours and depths, or summarised for the day or water column (surface to depth *d*) as given in 'daySummaryFn' and 'depthSummaryFn'.

Usage

extractHydroVars(
  sampling.df,
  westcoms.dir,
  hydroVars,
  daySummaryFn = NULL,
  depthSummaryFn = NULL,
  regional = F,
  sep = "/",
  cores = 1,
  progress = T,
  errorhandling = "remove",
  returnFullDf = FALSE
)

Arguments

sampling.df	Dataframe with a row for each sample. Columns must include 'site.id', 'obs.id', 'date' (YYYYMMDD), 'hour', 'depth', 'grid', 'site.elem', 'trinode_1', 'trinode_2', and 'trinode_3', which can be added through a spatial join with the mesh files (see vignette)
westcoms.dir	Character vector with directories for WeStCOMS v1 and WeStCOMS v2 hydrodynamic files
hydroVars	Character vector of hydrodynamic variables to extract
daySummaryFn	Vector of functions to summarise by day, one per var; if 'NULL' (default), single hour is extracted
depthSummaryFn	Vector of functions to summarise across depth, one per var; if 'NULL' (default), single hour is extracted
regional	Logical: does sampling.df include rows to calculate regional averages? Requires a row for each element to average for each site. For example, a row for each element within a 1km radius, with the results averaged
sep	Directory separation character (Windows: '\', Unix: '/')
cores	Number of cores for extracting in parallel; default is 1
progress	Logical: Show progress bar?
errorhandling	Passed to 'foreach': one of "stop", "remove", or "pass"
returnFullDf	Logical: return full dataframe or only obs.id + hydrovars?

Value

dataframe with site.id, date, and hydrodynamic variables

Sz-Tim/WeStCOMS documentation built on April 17, 2025, 3:10 p.m.