estimateN: Abundance point estimates

Description Usage Arguments Details Value Author(s) See Also

Description

Estimate abundance given a distance function, detection data, site data, and area. This is called internally by abundEstim. Users should use abundEstim to estimate abundance.

Usage

1
estimateN(dfunc, detectionData, siteData, area = 1, bySite = FALSE)

Arguments

dfunc

An estimate distance function (see dfuncEstim).

detectionData

A data frame containing information on detections. The minimum amount of information is the detection distances and transect or point ID where each detection occurred. (see Input data frames in help for dfuncEstim).

siteData

A data frame containing information on the transects or points surveyed (see dfuncEstim).

area

Total area of inference, study area size, or unit conversion. See abundEstim.

bySite

A logical scalar indicating whether to compute site-level estimates of abundance. The default (bySite=FALSE) returns only one overall abundance estimate. See Value and Details.

Details

If x is the data frame returned when bySite = TRUE, the following is true:

  1. For line transects, sum(x$abundance)*area/(2*w*sum(x$length)) is the estimate of abundance on the study area or the abundance estimate when bySite = FALSE.

  2. area*sum(x$density)/nrow(x) is the estimate of abundance on the study area or the abundance estimate when bySite = FALSE.

Value

If bySite is FALSE, a list containing the following components:

dfunc

The input distance function.

abundance

Estimated abundance in the study area (if area > 1) or estimated density in the study area (if area = 1).

n

The number of detections (not individuals, unless all group sizes = 1) used in the estimate of abundance.

area

Total area of inference. Study area size

esw

Effective strip width for line-transects, effective radius for point-transects. Both derived from dfunc

.

n.sites

Total number of transects for line-transects, total number of points for point-transects.

tran.len

Total transect length. NULL for point-transects.

avg.group.size

Average group size

If bySite is TRUE, a data frame containing site-level estimated abundance. The data frame is an exact copy of siteData with the following columns tacked onto the end:

effDist

The effective sampling distance at the site. For line- transects, this is ESW at the site. For points, this is EDR.

pDetection

Average probability of detection at the site. If only site-level covariates appear in the distance function, pDetection is constant within a site. When detection-level covariates are present, pDetection is the average at the site.

observedCount

The total number of individuals detected at a site.

abundance

Estimated abundance at the site. This is the sum of inflated group sizes at the site. i.e., each group size at the site is divided by its pDetection, and then summed.

density

Estimated density at the site. This is abundance at the site divided by the sampled area at the site. E.g., for line transects, this is abundance divided by 2*w*length. For points, this is abundance divided by pi*w^2.

effArea

The effective area sampled at the site. This could be used as an offset in a subsequent linear model. For line transects, this is 2*ESW*length. For points, this is pi*EDR^2.

Author(s)

Trent McDonald, WEST Inc., tmcdonald@west-inc.com
Jason Carlisle, University of Wyoming and WEST Inc, jcarlisle@west-inc.com
Aidan McDonald, WEST Inc., aidan@mcdcentral.org

See Also

dfuncEstim, abundEstim


Rdistance documentation built on May 2, 2019, 3:49 a.m.