matchEnvData: Match Data From an Existing Netcdf File or Download and Match

In PAMmisc: Miscellaneous Functions for Passive Acoustic Analysis

Match Data From an Existing Netcdf File or Download and Match

Description

Extracts all variables from a netcdf file matching Longitude, Latitude, and UTC coordinates in given dataframe

Usage

matchEnvData(
  data,
  nc = NULL,
  var = NULL,
  buffer = c(0, 0, 0),
  FUN = c(mean),
  fileName = NULL,
  progress = TRUE,
  depth = 0,
  ...
)

## S4 method for signature 'data.frame'
matchEnvData(
  data,
  nc = NULL,
  var = NULL,
  buffer = c(0, 0, 0),
  FUN = c(mean),
  fileName = NULL,
  progress = TRUE,
  depth = 0,
  ...
)

Arguments

data	dataframe containing Longitude, Latitude, and UTC to extract matching variables from the netcdf file
nc	name of a netcdf file, ERDDAP dataset id, or an edinfo object
var	(optional) vector of variable names
buffer	vector of Longitude, Latitude, and Time (seconds) to buffer around each datapoint. All values within the buffer will be used to report the mean, median, and standard deviation
FUN	a vector or list of functions to apply to the data. Default is to apply mean, median, and standard deviation calculations
fileName	(optional) file name to save downloaded nc file to. If not provided, then no nc files will be stored, instead small temporary files will be downloaded and then deleted. This can be much faster, but means that the data will need to be downloaded again in the future. If fileName is provided, then the function will attempt to download a single nc file covering the entire range of your data. If your data spans a large amount of time and space this can be problematic.
progress	logical flag to show progress bar
depth	depth values (meters) to use for matching, overrides any Depth column in the data or can be used to specify desired depth range when not present in data. Variables will be summarised over the range of these depth values. NULL uses all available depth values
...	other parameters to pass to ncToData

Value

original dataframe with three attached columns for each variable in the netcdf file, one for each of mean, median, and standard deviation of all values within the buffer

Author(s)

Taiki Sakai [e-mail]

Examples

data <- data.frame(Latitude = 32, Longitude = -117,
                   UTC = as.POSIXct('2004-12-31 09:00:00', tz='UTC'))
## Not run: 
# Not run because downloads files
# default calculates mean, median, and standard deviation
matchEnvData(data, nc='jplMURSST41', var=c('analysed_sst', 'analysis_error'))
# get just mean within a buffer around coordinates
matchEnvData(data, nc='jplMURSST41', var=c('analysed_sst', 'analysis_error'),
             FUN = mean, buffer = c(.01, .01, 86400))

## End(Not run)
# Can also work from an existing nc file
nc <- system.file('extdata', 'sst.nc', package='PAMmisc')
matchEnvData(data, nc = nc)
# Using a custom function
meanPlusOne <- function(x) {
  mean(x, na.rm=TRUE) + 1
}
matchEnvData(data, nc=nc, FUN=c(mean, meanPlusOne))

PAMmisc documentation built on Aug. 17, 2023, 1:06 a.m.