Mackenzie stats update

Generating ‘Chance’ Dataset

For Y33, I generated n chance observations. Real data assigned ‘used’ (1) and chance data as ‘unused’ (0)

setwd("C:/Users/mgues/OneDrive - Concordia University - Canada/Desktop/GitHub Reps/Backyard-Birds-MG") 
library(tidyverse)
library(knitr)
library(kableExtra)
library(tibble)
library(lmtest)


Y33Trees <- read.csv("1-Input/Y33Trees.csv")
Y33Data<- read.csv("1-Input/Y33_data.csv")

n <- nrow(Y33Data)

l <- levels(as.factor((Y33Trees %>% 
                        unite(unitedY33, c("Tree.species","DBHClass")))$unitedY33))

set.seed(2901)
randompts <- tibble(unitedY33 = sample(l, n, replace = T), .rows = n) %>% 
  separate(unitedY33, c("Tree.species","DBHClass"), sep = "_")

randompts$Presence <- 0

model_data <- bind_rows(Y33Data, randompts)


knitr::kable(model_data, 
             caption = "Real and Chance Observations")

Real and Chance Observations
Tree.species	DBHClass	Presence
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACPA	Small	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
PHCO	Small	1
ANCE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACNE	Large	1
ACPA	Small	0
ACNE	Large	0
ACNE	Large	0
ACPA	Small	0
ACNE	Large	0
ACPA	Small	0
ACPA	Small	0
ACNE	Large	0
ACNE	Large	0
ACNE	Large	0
PHCO	Small	0
ACPA	Small	0
ACPA	Small	0
ACNE	Large	0
ACPA	Small	0
PHCO	Small	0
ACNE	Large	0
PHCO	Small	0
ACPA	Small	0
ACPA	Small	0
ACPA	Small	0
PHCO	Small	0
ACNE	Large	0
PHCO	Small	0
ACNE	Large	0
PHCO	Small	0
ACNE	Large	0

Modeling

With this data set we have: Presence (binomial dependent variable) and Tree species and DBH Class as independent variables (categorical factors)

It seems like a logistic regression works in this situation (run below)

model <- glm(Presence~Tree.species+DBHClass, family="binomial", data=model_data)
summary(model)


Call:
glm(formula = Presence ~ Tree.species + DBHClass, family = "binomial", 
    data = model_data)

Coefficients: (1 not defined because of singularities)
                  Estimate Std. Error z value Pr(>|z|)   
(Intercept)         0.7802     0.3641   2.143  0.03214 * 
Tree.speciesACPA   -3.0827     1.1102  -2.777  0.00549 **
Tree.speciesANCE   15.7859  2399.5447   0.007  0.99475   
Tree.speciesPHCO   -2.5719     1.1398  -2.256  0.02405 * 
DBHClassSmall           NA         NA      NA       NA   
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 74.860  on 53  degrees of freedom
Residual deviance: 56.018  on 50  degrees of freedom
AIC: 64.018

Number of Fisher Scoring iterations: 15

Issues I’m encountering at this point:

Interpretation of this (very rough) model output? (p-values?)
Tree species and DBH class are not independent from each other, not sure how to deal with this (ANCOVA?)

ARUs

Sites

Species breakdown by site

Parks: May 10-July 12

Residential: June 12-July 12

Trenholme (21)	WB (28, 34)	Loyola (28, 29)	Benny (24, 26)
Am. crow	Am. crow	Am. crow	Am. crow
Am. goldfinch	Am. goldfinch	Am. goldfinch	Am. goldfinch
Am. redstart	Am. robin	Am. robin	Am. robin
Am. robin	Bay-breasted warbler*	Chickadee	Bay-breasted warbler*
Bay-breasted warbler*	Black-throated blue warbler*	Black-throated blue warbler*	Chickadee
Chickadee	Black-throated green warbler*	Black-throated green warbler*	Black-throated blue warbler*
Black-throated blue warbler*	Blackpoll Warbler*	Blackpoll Warbler*	Black-throated green warbler*
Black-throated green warbler*	Blue jay	Blue Jay	Blackpoll Warbler
Blue jay	Cedar waxwing	Cedar waxwing	Blue Jay
Cedar waxwing	Chimney Swift	Chimney Swift	Cedar Waxwing
Chimney swift	Chipping Sparrow	Chipping Sparrow	Chimney Swift
Chipping sparrow	Common Grackle	Common Grackle	Chipping Sparrow
Common Grackle	Common Nighthawk	Canada Goose	Common Grackle
Downy Woodpecker	Dark-eyed Junco*	Downy Woodpecker	Downy Woodpecker
E. Wood-Pewee*	Downy Woodpecker	European Starling	European Starling
Euro. Starling	Euro. Starling	Hairy Woodpecker	Northern Cardinal
Least Flycatcher*	House Sparrow	House Sparrow	Red-breasted Nuthatch
Merlin	Least Flycatcher*	Least Flycatcher*	Red-eyed Vireo
N. Cardinal	Merlin	Merlin	Ring-billed Gull
N. Flicker	Nashville Warbler*	Mourning Dove	Song Sparrow
Ring-billed Gull	N. Cardinal	Nashville Warbler*	Tennessee Warbler
Tennessee Warbler*	N. Flicker	Northern Cardinal	Warbling Vireo
	Red-breasted Nuthatch	Northern Flicker	White-throated Sparrow
	Red-eyed Vireo	R.breasted Nuthatch	Yellow-bellied flycatcher
	Ring-billed Gull	Ring-billed Gull	Northern Parula?
	R.-breasted Grosbeak*	Swainson’s Thrush^	Myrtle?
	Swainson’s Thrush*	Tennessee Warbler^
	Tennessee Warbler*	W.throated Sparrow^
	Veery?	Veery?
	B.-gray Gnatcatcher?
	American Redstart?
	Northern Parula?
	Red-shouldered Hawk?
	G. Crested Flycatcher?

Noa (14)	Kathy (14)	Dom (10)	Deanne (20)
Am. crow	Am. crow	Am. crow	Am. crow
Am. robin	Am. goldfinch	Cedar Waxwing	Am. goldfinch
Black-capped Chickadee	Am. robin	Chimney Swift	Am. robin
Cedar Waxwing	Black-capped Chickadee	European Starling	Black-capped Chickadee
Chimney Swift	Cedar Waxwing	House Sparrow	Cedar Waxwing
Chipping Sparrow	Chipping Sparrow	Harry woodpecker	Chimney swift
Common Grackle	Common Grackle	Northern Cardinal	Chipping Sparrow
European Starling	Chimney swift	Ring-billed Gull	Common Grackle
House Finch	Downy Woodpecker	White-breasted Nuthatch	Common Raven
House Sparrow	European Starling	Common Nighthawk?	Downy Woodpecker
Northern Cardinal	Northern Cardinal		European Starling
Northern Flicker	Ring-billed Gull		House Finch
Red-breasted Nuthatch	Song Sparrow		House sparrow
Ring-billed Gull	White-breasted Nuthatch		Northern Cardinal
			Northern Flicker
			Red-breasted Nuthatch
			Red-eyed Vireo
			Ring-billed Gull
			Song sparrow
			White-breasted nuthatch

ARU Sites