PAMscapes (version 0.11.3)

checkSoundscapeInput: Check Proper Formatting for Soundscape Inputs

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

checkSoundscapeInput(
  x,
  needCols = c("UTC"),
  skipCheck = FALSE,
  timeBin = NULL,
  binFunction = median,
  octave = c("original", "tol", "ol"),
  label = NULL,
  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

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

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