Jo.plots: Joint occupancy parametric and null model plots

In vitaliskim/msco: Multi-Species Co-Occurrence Analyses

Joint occupancy parametric and null model plots

Description

Plots the null model and joint occupancy decline with order (number of species) and fits the decline to exponential, power law and exponential-power law parametric models, respectively.

Usage

Jo.plots(jo_Obj)

Arguments

jo_Obj

A joint occupancy model object returned by the function Jo.eng.

Details

This function provides a visualization of the forms of joint occupancy decline and null model test. It offers information on:

• the outcomes of the null model test (through the appended archetype value on (e) plot) and

• the comparisons between the forms of joint occupancy decline (through the affixed AIC and rsq values on (b), (c) and (d) plots, respectively).

Value

Produces a figure consisting of the following plots:

(a)	Joint occupancy decline.
(b)	Exponential regression of the joint occupancy decline.
(c)	Power law regression of the joint occupancy decline.
(d)	Exponential-power law regression of the joint occupancy decline.
(e)	Null model test.

References

Lagat, V. K., Latombe, G. and Hui, C. (2021a). A multi-species co-occurrence index to avoid type II errors in null model testing. DOI: ⁠<To be added>⁠.

Examples

## Not run: 

ex.data <- read.csv(system.file("extdata", "274.csv", package = "msco"))
jo_Obj <- msco::Jo.eng(ex.data, nReps = 999, All.plots = TRUE, s.dplot = FALSE, dig = 3)
jplots <- msco::Jo.plots(jo_Obj)
jplots

ex.data2 <- read.csv(system.file("extdata", "22.csv", package = "msco"))
jo_Obj2 <- msco::Jo.eng(ex.data2, nReps = 999, All.plots = TRUE, s.dplot = FALSE, dig = 3)
jplots2 <- msco::Jo.plots(jo_Obj2)
jplots2

ex.data3 <- read.csv(system.file("extdata", "78.csv", package = "msco"))
jo_Obj3 <- msco::Jo.eng(ex.data3, nReps = 999, All.plots = TRUE, s.dplot = FALSE, dig = 3)
jplots3 <- msco::Jo.plots(jo_Obj3)
jplots3

ex.data4 <- read.csv(system.file("extdata", "65.csv", package = "msco"))
jo_Obj4 <- msco::Jo.eng(ex.data4, nReps = 999, All.plots = TRUE, s.dplot = FALSE, dig = 3)
jplots4 <- msco::Jo.plots(jo_Obj4)
jplots4


## End(Not run)

vitaliskim/msco documentation built on Sept. 29, 2023, 9:22 p.m.