README.md

Bird detectability offsets using QPAD v3

This approach supsersedes the functionality of the QPAD package (but estimates are still stored in the package).

This repository contains geospatial layers that are consistent with QPAD v3 estimates.

Installation

Install R then get the R dependencies:

if (!requireNamespace("QPAD")) {
  if (!requireNamespace("remotes"))
    install.packages("remotes")
  remotes::install_github("psolymos/QPAD")
}
if (!requireNamespace("sp"))
  install.packages("sp")
if (!requireNamespace("maptools"))
  install.packages("maptools")
if (!requireNamespace("raster"))
  install.packages("raster")
if (!requireNamespace("intrval"))
  install.packages("intrval")

Download or clone this GitHub repository:

git clone https://github.com/ABbiodiversity/recurring.git

Then set your working directory to the /offset directory of the project. Easiest, if using RStudio, is to double click on the offset.Rproj file which will open up the project and set the working directory.

Usage

An example can be found in the index.R file.

Step 1. Load required packages and objects

## load packages
library(QPAD)
library(maptools)
library(intrval)
library(raster)

## load v3 estimates
load_BAM_QPAD(version = 3)
if (getBAMversion() != "3")
  stop("This script requires BAM version 3")

## read raster data
rlcc <- raster("./data/lcc.tif")
rtree <- raster("./data/tree.tif")
rtz <- raster("./data/utcoffset.tif")
rd1 <- raster("./data/seedgrow.tif")
crs <- proj4string(rtree)

## source functions
source("functions.R")

Step 2. Define variables for your project

The date/time and coordinate specifications will make sure that required predictors are extracted in the way that match the estimates.

• the species ID need to be a single 4-letter AOU code (see getBAMspecieslist() for a full list)
• coordinates and time: can be single values or vectors (shorter objects recycled)
  • dt: date, ISO 8601 in YYYY-MM-DD (0-padded)
  • tm: time, ISO 8601 in hh:mm (24 hr clock, 0-padded)
  • lat: latitude [WGS84 (EPSG: 4326)]
  • lon: longitude [WGS84 (EPSG: 4326)]
• methods descriptors: can be single value or vector (recycled as needed)
  • dur: duration in minutes
  • dis: distance in meters

## species of interest
spp <- "OVEN"

## date and time
## https://en.wikipedia.org/wiki/ISO_8601
dt <- "2019-06-07" # ISO 8601 in YYYY-MM-DD (0-padded)
tm <- "05:20" # ISO 8601 in hh:mm (24 hr clock, 0-padded)

## spatial coordinates
lon <- -113.4938 # longitude WGS84 (EPSG: 4326)
lat <- 53.5461 # latitude WGS84 (EPSG: 4326)

## point count duration 
## and truncation distance (Inf for unlimited)
dur <- 10 # minutes
dis <- 100 # meters

Step 3. Organize predictors

This object can be reused for multiple species:

x <- make_x(dt, tm, lon, lat, dur, dis)
str(x)
##'data.frame':	1 obs. of  8 variables:
## $ TSSR  : num 0.0089
## $ JDAY  : num 0.43
## $ DSLS  : num 0.14
## $ LCC2  : Factor w/ 2 levels "Forest","OpenWet": 2
## $ LCC4  : Factor w/ 4 levels "DecidMixed","Conif",..: 3
## $ TREE  : num 2.55
## $ MAXDUR: num 10
## $ MAXDIS: num 1

NOTE: CRS related warnings are due to PROJ4 vs PROJ6 discrepancies when using GDAL > 3 because the +datum= part is deprecated.

Step 4. Calculate offsets

A is the known or estimated area of survey, p is availability given presence, q is detectability given avaibalility.

o <- make_off(spp, x)
str(o)
##'data.frame':	1 obs. of  5 variables:
## $ p         : num 0.991
## $ q         : num 0.562
## $ A         : num 3.14
## $ correction: num 1.75
## $ offset    : num 0.559

NOTE: offset is log(correction), correction = A*p*q, thus offset=log(A) + log(p) + log(q).

Use a loop over multiple species:

SPP <- getBAMspecieslist()
OFF <- matrix(0, nrow(x), length(SPP))
rownames(OFF) <- rownames(x) # your survey IDs here
colnames(OFF) <- SPP

for (spp in SPP) {
  cat(spp, "\n")
  flush.console()
  o <- make_off(spp, x)
  OFF[,spp] <- o$offset
}
str(OFF)
##num [1, 1:151] 0.1365 0.9699 0.0643 0.5917 -0.3132 ...
## - attr(*, "dimnames")=List of 2
##  ..$ : chr "17"
##  ..$ : chr [1:151] "ALFL" "AMCR" "AMGO" "AMPI" ...