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Read FPOD data

fp_read.Rd

This function reads an FPOD or CPOD data file (FP1, FP3, CP1, CP3) into R.

Usage

fp_read(file, tz = "", simplify = TRUE, amp = "extended")

Arguments

file

a character string. The path to the FPOD (or CPOD) data file.

tz

a character string. The time zone specification to be used for calculating dates. Passed unchanged to as.POSIXct().

simplify

logical. If TRUE, simplifies the clicks data.table by stripping away some columns, such as clk_ipi_range, ipi_pre_max, amp_reversals, duration, and has_wav.

amp

a character string. With amp="extended", higher values are extrapolated from the duration of clipping and the IPI. For any other values of amp, the compressed SPL values recorded by the FPOD are used directly.

Value

A list, with one or more of the following data.frames (or data.tables, if available):

  • header: a list with pod name, coordinates, starting time, stopping time, user notes, etc.

  • clicks: A data.frame (or data.table) with data about each click. See details.

  • wav (only FPx files): pseudo-wav data - inter-peak-intervals and raw amplitudes for a subset of clicks

  • env: misc data, ambient temperature (in deg C) and battery voltage per stack (in units of 10 millivolts)

Details

The clicks data.frame contains the following columns:

  • time: The time and date of the click, at microsecond resolution. Note that R might only display dates and times to a second precision, but any date or time calculations will use the full precision.

  • minute: minutes elapsed, since starting the FPOD

  • microsec: microseconds elapsed, since the start of the minute.

  • click_no: an ID number that uniquely identifies the click.

  • train_id: an ID number from the KERNO classifier, reset for each minute.

  • species: the species classification from the KERNO classifier

  • quality_level: the quality level of the classification, 0 (?/echo), 1 (Lo), 2 (Mod) or 3 (Hi).

  • echo: TRUE if the KERNO classifier thinks this click might be an echo of another click that has already been classified.

  • ncyc: number of cycles in click. This is a proxy for the click duration.

  • pkat: the number of the cycle with the highest amplitude

  • clk_ipi_range: range of inter-peak-intervals (IPIs) among cycles in click

  • ipi_pre_max: the IPI before pkat, in 250 nanosecond units

  • ipi_at_max: the IPI at pkat, in 250 nanosecond units

  • khz: The frequency (in kHz) of the peak cycle.

  • amp_at_max: the peak amplitude (SPL) of the loudest cycle

  • amp_reversals: the number of amplitude reversals

  • duration: click duration

  • has_wav: TRUE if there is a pseudo-WAV recorded for this click.

See also

fp_find_buzzes(), fp_summarize()

Examples

# read a FP3 file
fn <- fp_example("gullars_period1.FP3")
dat <- fp_read(fn)

# show misc. information (pod number, deployment date, etc.)
dat$header
#> $pod_id
#> [1] 7660
#> 
#> $first_logged_min
#> [1] 65709000
#> 
#> $last_logged_min
#> [1] 65723400
#> 
#> $water_depth
#> [1] 30
#> 
#> $deployment_depth
#> [1] 0
#> 
#> $lat_text
#> [1] "70,03332"
#> 
#> $lon_text
#> [1] "18,9162"
#> 
#> $location_text
#> [1] ""
#> 
#> $notes_text
#> [1] ""
#> 
#> $gmt_text
#> [1] ""
#> 
#> $pic_ver
#> [1] 23
#> 
#> $fpga_ver
#> [1] 1034
#> 
#> $extended_amps
#> [1] TRUE
#> 
#> $clicks_in_fp1
#> [1] 48680158
#> 
#> $filename
#> [1] "/home/runner/work/_temp/Library/fpod/extdata/gullars_period1.FP3"
#> 

# show battery levels and recorded temperatures for each minute
dat$env
#>        minute  degC bat1v bat2v
#>         <int> <int> <int> <int>
#>     1:      1     6    79    70
#>     2:      2     6    79    69
#>     3:      3     6    79    69
#>     4:      4     6    79    70
#>     5:      5     6    79    70
#>    ---                         
#> 14396:  14396     5    79    67
#> 14397:  14397     5    79    67
#> 14398:  14398     5    79    66
#> 14399:  14399     5    79    67
#> 14400:  14400     5    79    67

# tally up the number of clicks in each species category
table(dat$clicks$species)
#> 
#>      NBHF     Sonar Unclassed 
#>     51590      7452     23595