PAMscapes (version 0.11.3)

loadSoundscapeData: Load Soundscape Data

Description

Reads and checks data to ensure formatting will work for other PAMscapes functions. Will read and check the formatting of CSV files, or check the formatting of dataframes. Can also read in MANTA NetCDF files and format the data appropriately.

Usage

loadSoundscapeData(
  x,
  needCols = c("UTC"),
  skipCheck = FALSE,
  timeBin = NULL,
  binFunction = "median",
  binCount = FALSE,
  octave = c("original", "tol", "ol"),
  label = NULL,
  keepQuals = c(1),
  keepEffort = TRUE,
  dropNonHmd = TRUE,
  tz = "UTC",
  extension = c("nc", "csv")
)

Value

a dataframe

Arguments

x

a dataframe, path to a CSV file, or path to a MANTA NetCDF file, or folder containing these. If x is a vector of file paths then all will be read in and combined. If x is a folder, then all files with extension extension will be loaded. Note this will not load files within subfolders, only the main folder.

needCols

names of columns that must be present in x, if any are missing will trigger an error

skipCheck

logical flag to skip some data checking, recommended to keep as FALSE

timeBin

amount of time to bin data by, format can be "#Unit" e.g. '2hour' or '1day'

binFunction

summary function to apply to data in each time bin, default is "median"

binCount

logical flag to return the number of times in each time bin as column "binCount"

octave

one of "original", "tol", or "ol". If "original" then nothing happens, otherwise data are converted to Octave-leve ("ol") or Third-Octave-Level ("tol") measurements using createOctaveLevel

label

optional, if not NULL then this value will be added as an additional column "label" to the output

keepQuals

quality flag values to keep. Accepts vector of integers from (1, 2, 3, 4) corresponding to flag labels "Good", "Not evaluated/Unknown", "Compromised/Questionable", and "Unusable/Bad". HMD levels for points with data quality flags outside of keepQuals will be marked as NA.

keepEffort

if TRUE or FALSE, a logical flag whether or not to keep the effort information with the outputs (number of seconds per minute). If a numeric value, then any minutes with an effort value less than keepEffort will be removed (e.g. 50 will remove minutes with less than 50 seconds of effort)

dropNonHmd

logical flag to drop non-standard hybrid millidecade bands, only applies to HMD type data. Some datasets have frequency values that are not part of the standard HMD bands (e.g. at exactly the Nyquist rate), if TRUE these will be removed.

tz

timezone of the data being loaded, will be converted to UTC after load

extension

only used if x is a folder, the file extension to load. Must be one of "nc" or "csv"

Author

Taiki Sakai

Details

Files created by MANTA and Triton software will be reformatted to have consisitent formatting. The first column will be renamed to "UTC", and columns containing soundscape metrics will be named using the convention "TYPE_FREQUENCY", e.g. "HMD_1", "HMD_2" for Manta hybrid millidecade mesaurements.

Inputs from sources other than MANTA or Triton can be accepted in either "wide" or "long" format. Wide format must follow the conventions above - first column "UTC", other columns named by "TYPE_FREQUENCY" where TYPE is consistent across all columns and FREQUENCY is in Hertz. Long format data must have the following columns:

"UTC"

- time of the measurement, in UTC timezone

"type"

- the type of soundscape measurement e.g. PSD or OL, must be the same for all

"frequency"

- the frequency of the measurement, in Hertz

"value"

- the soundscape measurement value, usually dB

Examples

manta <- loadSoundscapeData(system.file('extdata/MANTAExampleSmall1.csv', package='PAMscapes'))
str(manta)
ol <- loadSoundscapeData(system.file('extdata/OLSmall.csv', package='PAMscapes'))
str(ol)
psd <- loadSoundscapeData(system.file('extdata/PSDSmall.csv', package='PAMscapes'))
str(psd)