quo_an: Habitat selectivity through quotient analysis
In mhpob/TelemetryR: Handle VEMCO detection data.

Description Usage Arguments Details Value

quo_an executes the quotient approach defined in Overholtz et al. 2011. Proportion of fish incidence in a water quality bin is divided by the proportion of stations within that bin. Values greater than 1 indicate preference.

1	quo_an(wq, det, bin_width = 1, pres_abs = F, R = 999)

`wq`	Numeric. Water quality data at each station.
`det`	Numeric. Number of detections at each station.
`bin_width`	Numeric. Size of water quality bins. Default is 1.
`pres_abs`	Logical. Should the data be reduced to presence/absence? Default is false.
`R`	Numeric. Number of bootstrap replicates. Default is 999.

This approach was outlined in:

Van Der Lingen, CD, L Hutchings, D Merkle, JJ van der Westhuizen, and J Nelson. 2001. Comparative spawning habitats of anchovy (Engraulis capensis) and sardine (Sardinops sagax) in the southern Benguela upwelling ecosystem. 185-209. Spatial processes and management of marine populations. Alaska Sea Grant College Program, AK-SG-01-02, Fairbanks.

It was defined, as it appears here, in:

Overholtz, W.J., Hare, J.A. and Keith, C.M., 2011. Impacts of interannual environmental forcing and climate change on the distribution of Atlantic mackerel on the US Northeast continental shelf. Marine and Coastal Fisheries, 3(1), pp.219-232.

The proportion of sites in each water quality bin (pSe) is determined by dividing the number of stations within the bin by the total number of stations. The porportion of stations with fish (M) in each bin (pMe) is determined by dividing the number of stations in the bin with fish by the total number of stations with fish. The quotient value for the water quality bin (Qe) is calculated as pMe/pSe.

Values greater than 1 “indicate a greater number of positive (fish) stations than expected based on sampling effort”. Confidence intervals are calculated using boot.ci from the boot package. The type input to boot.ci is "perc"; all other inputs to boot and boot.ci are the function defaults.

Output is a data frame with bin labels, number of detections or number sites with detections (depending on pres_abs input) within each bin, number of sites within each bin, and pMe, pSe, and Qe as defined above. Confidence intervals at the 0.025 and 0.975 percentiles are also provided.

mhpob/TelemetryR documentation built on Sept. 28, 2020, 11:33 a.m.