Package index • callDensity

Call density estimation

The main entry points – the functions most users will call directly.

cde(): Call Density Estimate using auxiliary information from sonar equation
cdeFromParamFile(): Call density estimate from a parameter file (deprecated)
callDensity callDensity-package: callDensity: Analysis for bioacoustic call density estimation (ABCDE)

Uncertainty and coefficients of variation

Propagating and combining error terms into CV.Nc, CV.c, CV.pa, CV.Dc.

Dc_CV(): Coefficient of Variation (CV) for call density (Dc)
Nc_CV(): Nc_CV: Coefficient of Variation (CV) of the number of detected calls (Nc).
c_CV(): c_CV: Coefficient of Variation (CV) of false discovery rate (c).
pa_CV(): pa_CV: Coefficient of Variation (CV) of the probability of detection (pa).
ciFromCV(): Confidence interval from density and it's CV
falseDiscoveryCV(): WARNING: This function is not supported, and probably does not do what whatever you were hoping it might do. Perhaps consider function c_CV instead. CV of false discovery rate using Cochran approximation
var.wtd.mean.cochran(): Variance of a weighted mean following Chochran 1977 definition
jackknifeDetectors(): Leave-one-detector-out jackknife for a union call density estimate

Detection functions

Fitting, predicting, and displaying SNR-based detection curves – glm/gam/scam for observer-ground designs, vglm for adjudicated capture-recapture.

fitDetFun(): Fit an SNR detection function
checkDetFun(): Diagnose a fitted detection function
predictDetFun(): Predict detection function from fitted SNR models
predictDetFunList(): Predict detection functions for multiple models
predict(<detFun>): predict method for detFun objects
showDetFun(): Plot SNR detection function with observed SNR distributions
fitSNRdetectionFunc(): Fit an SNR-detection function
fitSNRvgam(): Fit an SNR-detection function with a closed population capture-recapture gam
fitSNRvglm(): Fit an SNR-detection function with a closed population capture-recapture glm
fitSNRbySeason(): Model SNR-detection function with season as a factor (deprecated?)
predVglmPDet(): Predict probability of detection from a VGLM SNR-detection function
showSNRdetectionFunc(): Plot an SNR detection function with mirrored SNR distributions
plotPDetRadials(): Plot probability of detection as a directional range footprint

Probability of detection and the sonar equation

pDetInArea(): Monte-Carlo simulation to predict average probability of detection in area
pDetGivenNL(): Probability of detection in the study area at a fixed noise level
studyArea(): Calculate study area for call density estimate.

Noise level estimation

nlFromDetections(): Estimate the noise level distribution from noise measured at detections
nlFromSnrInfo(): Estimate noise level distribution for MC simulation from the noise measurements included in the snrInfo file, plus the SNR detection function.
noiseLevelDistribution(): Mean and standard deviation of noise levels by month, season, or year.
predictSampledNL(): Predict the mean noise level you would measure at detections
kerguelen2015TL: pyRAM transmission loss, Kerguelen2015 summer, 25 Hz
kerguelen2015TLmeta: Transect metadata for the Kerguelen2015 pyRAM transmission loss table

Capture history construction

Building and reshaping the tables cde() and the detection-function functions expect, including the adjudicated-verdict convention CR analyses require.

chtToSNRinfo(): Convert a capture history table to SNRinfo format
capHist2snrInfo(): Convert a capture history table into an SNRinfo data.frame
capHistTosnrInfo(): Convert capture history DATA.FRAME into the 'SNRinfo' format used by the callDensity package
readCapHist(): Read a capture history csv file (e.g. created in Matlab)
simsTocaptureHistoryTable(): Merge N simulated detectors into a matchbox-native capture history table
mchToCR(): Convert a multi-observer capture history table to a two-observer CR table
resolveColumns(): Resolve column names from a prefix pattern or explicit vector
pivotSNR(): Pivot SNR observer columns to long format
addObserverMeans(): Compute row-wise mean across observer columns
multiObserverDetectionCount(): Multi-Observer Detection Count

False discovery rate

falseDiscoveryRate(): Estimate $c$ (False discovery rate)
falseDiscoveryRateFromNth(): WARNING: This function is not supported, and probably does not do what whatever you were hoping it might do. Use functions falseDiscoverRate and c_CV instead. False discovery rate from inspection of every Nth detection

Simulation

Generating synthetic calls, detectors, and detections – used throughout the vignettes and test suite.

simCallLocation(): Simulate animals calls using a uniform distribution time and space
simCallAcoustics(): Simulate acoustic properties of calls
simulateDetector(): Simulate a detector for a callDensity simulation.
simTLradials_20logR(): Simulate transmission loss (TL) radials following geometric (spherical) spreading law.
subsampleSimInTime(): Subsample from a capture history table or simulation at evenly spaced time intervals

Time and season utilities

capHistTimeSeason(): Add R datetime, season, and month codes to a capture history table
capHistTimeSeason2(): Add R datetime and season to a capture history table (version 2)
mat2Rdate(): Convert matlab datenum to R POSIXct
Rdate2mat(): Convert R POSIXct to matlab datenum
time2monthCode(): Lookup month codes from a POSIXct
time2season(): Lookup the season for a given POSIXct, x.
subsetByTimeCode(): Subset a data.frame by by months or season
deploymentDuration(): Calculate deployment duration from recording start times and durations
deploymentDurationFromsoundFolderCsv(): Calculate deployment duration from a Matlab soundFolder csv file.

Workflow and file helpers

defaultOutputFileNames(): Default names of output files for call density estimation
listTLFiles(): Return a list of existing TL files associated with the call density
updateDetectionFolder(): Change path to detection csv files
countDetections(): Title
unionDetections(): Count of events flagged positive by at least one of several detectors
densityInputTable(): Show table of inputs into call density estimate
densityResultsTable(): Table of call densities including CVs (ggplot2)
collectDensityResults(): Load specified density results text files in a directory

Plotting

densityPlot(): Bar-plot of call density by timeCodes (ggplot2)
detectionRateCorrectedPlot(): Bar-plot of detection rates by timeCodes and scaled (corrected) by precision (ggplot2)
detectionRatePlot(): Bar-plot of detection rates by timeCodes (ggplot2)
plotDetectionDistribution(): SNR histogram of true & false positives, and false negatives for callDensity simulation
plotSNRHistogram(): Plot SNR histogram by observer
plotSNRTimeSeries(): Plot SNR time series for the adjudicated subset
plotSpatialDetections(): Plot the spatial detection density for a callDensity simulation
computeSNRLims(): Compute pretty SNR limits across observer columns

Internal utilities

tidyeval enquo enquos .data := as_name as_label: Tidy eval helpers