Call: dfuncEstim(data = sparrowDf, dist ~ groupsize(groupsize),
likelihood = "halfnorm")
Coefficients:
Estimate SE z p(>|z|)
(Intercept) 3.959313 0.03767961 105.0784 0
The dfunc output shows parameter estimates, convergence status, and effective strip width (i.e., 65.69518 [m]).
Plots
Plots of the estimated function are easy.
plot(dfunc)
Plots can be customized in a number of ways. For example, we can change the number of bars, color the bars, the titles, etc.
plot(dfunc , density =-1 , col.dfunc ="blue" , nbins =30 , col =c("darkgoldenrod1", "darkgoldenrod3") )
plot(dfunc , nbins =40 , col ="blue" , density =-1 , col.dfunc ="orange" , main ="Sparrow detection")rug(unnest(dfunc$data)$dist, col="red")
Abundance Estimates
Information on the transects (i.e., number and length of each) is contained in sparrowDf data frame.
Let’s assume the study area on which these transects were collected was 300 ha. Estimates of sparrow density on the sampled transects and sparrow abundance in the study area are obtained by calling the abundEstim function with an estimate distance function, transect data frame, and study area size. Measurement units must be applied to study area size so that Rdistance computes density correctly. By default, Rdistance computes 95% confidence intervals by bootstrap resampling individual transects in the transect information data frame. Setting showProgress to FALSE shuts off the progress bar. Outside of markup documents, the bootstrap progress bar can improve sanity of the analyst.
abund <-abundEstim(dfunc , area = units::set_units(300, "ha") , plot.bs =TRUE , R =100 , showProgress =FALSE)
summary(abund)
Call: dfuncEstim(data = sparrowDf, dist ~ groupsize(groupsize),
likelihood = "halfnorm")
Coefficients:
Estimate SE z p(>|z|)
(Intercept) 3.959313 0.03767961 105.0784 0
Convergence: Success
Function: HALFNORM
Strip: 0 [m] to 207 [m]
Effective strip width (ESW): 65.69518 [m]
Probability of detection: 0.317368
Scaling: g(0 [m]) = 1
Log likelihood: -1667.639
AICc: 3337.289
Surveyed Units: 36000 [m]
Individuals seen: 374 in 356 groups
Average group size: 1.050562
Group size range: 1 to 3
Density in sampled area: 7.906888e-05 [1/m^2]
95% CI: 6.152619e-05 [1/m^2] to 9.892083e-05 [1/m^2]
Abundance in 3e+06 [m^2] study area: 237.2066
95% CI: 184.5786 to 296.7625
In the summary output, density and abundance estimates along with boostrap confidence intervals appear below the distance function.
