This R Markdown documents the analysis of 4 years of sea turtle nesting data in the Florida Panhandle. This data was collected by field surveyors permitted by the Florida Fish and Wildlife Conservation Commission (FWC) and/or the U.S. Fish and Wildlife Service (USFWS) and reported to FWC. It includes:
The Excel file was quality checked to identify potential errors and to standardize reporting terminology. This file was then brought into ArcMap 10.6 for visualization. Any points falling outside of the maximum nesting area polygon or on beaches other than their reported beach monitoring unit were removed from further analyses.
This analysis uses the following libraries:
library(dplyr)
library(knitr)
library(plotrix)
## [1] "This RMarkdown and the included analyses were built using R version 4.0.4 (2021-02-15)"
From 2016 to 2019, data on 7040 nests were provided by FWC with valid GPS coordinates - of which, 6773 (96.21%) corresponded to loggerhead sea turtles.
2865 loggerhead nests (42.30%) within the dataset were reported to have wave exposure:
Washed over nests had a significantly higher probability of wave exposure (13.6%) than their undisturbed counterparts (9.9%, p < 0.001). Completely washed out nests had an even higher probability of exposure (17.3%) while partially washed out nests were the highest (25.1%). All combination are statistically significant.
## Treatment
## Complete Wash-Out Partial Wash-Out Undisturbed Washed Over
## 1121 79 3908 1665
## [1] "Mean probability of wave exposure for completely washed out nest GPS locations: 0.173 (+/- 0.29, n = 1121)"
## [1] "Mean probability of wave exposure for partially washed out nest GPS locations: 0.251 (+/- 0.344, n = 79)"
## [1] "Mean probability of wave exposure for washed over nest GPS locations: 0.136 (+/- 0.25, n = 1665)"
## [1] "Mean probability of wave exposure for undisturbed nest GPS locations: 0.099 (+/- 0.219, n = 3908)"
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Wave.Exposure.Proportion..Dis.Eq. ~ Treatment, data = Loggerheads_Adjusted)
##
## $Treatment
## diff lwr upr
## Partial Wash-Out-Complete Wash-Out 0.07842017 0.006258087 0.15058225
## Undisturbed-Complete Wash-Out -0.07362367 -0.094627352 -0.05261998
## Washed Over-Complete Wash-Out -0.03643367 -0.060384214 -0.01248312
## Undisturbed-Partial Wash-Out -0.15204383 -0.222491574 -0.08159609
## Washed Over-Partial Wash-Out -0.11485384 -0.186235613 -0.04347206
## Washed Over-Undisturbed 0.03719000 0.019047591 0.05533240
## p adj
## Partial Wash-Out-Complete Wash-Out 0.0269260
## Undisturbed-Complete Wash-Out 0.0000000
## Washed Over-Complete Wash-Out 0.0005422
## Undisturbed-Partial Wash-Out 0.0000002
## Washed Over-Partial Wash-Out 0.0002106
## Washed Over-Undisturbed 0.0000009
Hatching success was significantly lower (p << 0.001) in washed over nests (32.7%) versus undisturbed nests (78.1%).
## [1] "Mean hatch success for washed over nest GPS locations: 0.327 (+/- 0.386, n = 843)"
## [1] "Mean hatch success for undisturbed nest GPS locations: 0.781 (+/- 0.297, n = 2104)"
##
## Call:
## glm(formula = hatch_Binom ~ Washed.Over, family = "binomial",
## data = loggerheadNestsForWashComparison)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -23.753 -5.728 2.962 5.039 15.922
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.311395 0.005389 243.4 <2e-16 ***
## Washed.OverYes -2.008434 0.009202 -218.3 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 216854 on 2946 degrees of freedom
## Residual deviance: 164615 on 2945 degrees of freedom
## AIC: 173605
##
## Number of Fisher Scoring iterations: 4
A similar trend was seen for emergence success (30.5% vs. 76.3%, p << 0.001).
## [1] "Mean emergence success for washed over nest GPS locations: 0.305 (+/- 0.375, n = 843)"
## [1] "Mean emergence success for undisturbed nest GPS locations: 0.763 (+/- 0.302, n = 2104)"
##
## Call:
## glm(formula = emerge_Binom ~ Washed.Over, family = "binomial",
## data = loggerheadNestsForWashComparison)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -23.132 -6.091 2.771 5.082 16.154
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.208755 0.005237 230.8 <2e-16 ***
## Washed.OverYes -2.008944 0.009227 -217.7 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 215543 on 2946 degrees of freedom
## Residual deviance: 162998 on 2945 degrees of freedom
## AIC: 172182
##
## Number of Fisher Scoring iterations: 4
By comparison, the typical predated (but not washed over) nest has a hatching success of 49.9% and an emergence success of 48.8%.
## [1] "Mean hatch success for washed over nest GPS locations: 0.327 (+/- 0.386, n = 843)"
## [1] "Mean hatch success for predated nest GPS locations: 0.499 (+/- 0.386, n = 721)"
##
## Call:
## glm(formula = hatch_Binom_Pred ~ Washed.Over * Predated, family = "binomial",
## data = Predation_Comparison)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -23.753 -5.925 2.229 5.073 15.922
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.311395 0.005389 243.36 <2e-16 ***
## Washed.OverYes -2.008434 0.009202 -218.27 <2e-16 ***
## PredatedYes -0.838836 0.010329 -81.22 <2e-16 ***
## Washed.OverYes:PredatedYes 0.679861 0.019439 34.97 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 274090 on 3817 degrees of freedom
## Residual deviance: 210711 on 3814 degrees of freedom
## AIC: 222539
##
## Number of Fisher Scoring iterations: 4
## [1] "Mean emergence success for washed over nest GPS locations: 0.305 (+/- 0.375, n = 843)"
## [1] "Mean emergence success for predated nest GPS locations: 0.488 (+/- 0.384, n = 721)"
##
## Call:
## glm(formula = emerge_Binom_Pred ~ Washed.Over * Predated, family = "binomial",
## data = Predation_Comparison)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -23.132 -6.190 2.013 5.116 16.154
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.208755 0.005237 230.83 <2e-16 ***
## Washed.OverYes -2.008944 0.009227 -217.71 <2e-16 ***
## PredatedYes -0.800488 0.010197 -78.50 <2e-16 ***
## Washed.OverYes:PredatedYes 0.670004 0.019600 34.18 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 272327 on 3817 degrees of freedom
## Residual deviance: 208926 on 3814 degrees of freedom
## AIC: 220947
##
## Number of Fisher Scoring iterations: 5
A nest was reported as “inundated” if standing water was found in the nest chamber during the nest excavation/productivity assessment. However, this data does not provide details regarding how long the inundation has been present nor how many times the nest may have been inundated prior to the excavation. Given this limitation, hatching success for inundated (but otherwise undisturbed) nests was 17.1% and emergence success was 15.3%.
## [1] "Mean hatch success for inundated nest GPS locations: 0.171 (+/- 0.294, n = 48)"
## [1] "Mean hatch success for undisturbed nest GPS locations: 0.781 (+/- 0.297, n = 2104)"
##
## Call:
## glm(formula = hatch_Binom_Inund ~ Inundated, family = "binomial",
## data = Inundated_Comparison)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -23.7527 -0.9608 3.4364 4.9104 19.4510
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.311395 0.005389 243.36 <2e-16 ***
## InundatedYes -2.940687 0.039829 -73.83 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 109124 on 2151 degrees of freedom
## Residual deviance: 101034 on 2150 degrees of freedom
## AIC: 108204
##
## Number of Fisher Scoring iterations: 5
## [1] "Mean emergence success for inundated nest GPS locations: 0.153 (+/- 0.266, n = 48)"
## [1] "Mean emergence success for undisturbed nest GPS locations: 0.763 (+/- 0.302, n = 2104)"
##
## Call:
## glm(formula = emerge_Binom_Inund ~ Inundated, family = "binomial",
## data = Inundated_Comparison)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -23.132 -1.443 3.364 4.981 19.999
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 1.208755 0.005237 230.83 <2e-16 ***
## InundatedYes -2.953015 0.041386 -71.35 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 109996 on 2151 degrees of freedom
## Residual deviance: 102072 on 2150 degrees of freedom
## AIC: 109454
##
## Number of Fisher Scoring iterations: 5
Below is a breakdown of the number of loggerhead nests included in the analyses by beach monitoring unit and year. Most of the nests come from Saint George Island (n = 1491, 22.05%), Cape Saint George Island (n = 992, 14.67%), and the Saint Joseph Peninsula (n = 777, 11.49%).
GINS - Gulf Islands National Seashore. AFB - Air Force Base. NWR - National Wildlife Refuge.
## 2016 2017 2018 2019 Total
## Bald Point State Park 1 2 2 1 6
## Cape Saint George Island 316 336 138 202 992
## Cape San Blas 60 78 39 79 256
## Cape San Blas AFB 123 55 42 51 271
## Deer Lake State Park 2 0 1 1 4
## Eglin AFB East 0 25 16 16 57
## Eglin AFB West 0 27 18 32 77
## Eglin Air Force Base 13 13 0 7 33
## GINS - Fort Pickens 26 21 23 29 99
## GINS - Perdido Key 13 74 20 25 132
## GINS - Santa Rosa 28 23 16 17 84
## Grayton Beach State Park 6 8 3 2 19
## Henderson Beach State Park 1 4 0 3 8
## Mexico Beach 14 19 12 19 64
## Miramar Beach 2 13 10 0 25
## Navarre Beach 0 7 3 5 15
## Okaloosa East 1 3 5 3 12
## Okaloosa Mid 7 7 5 4 23
## Okaloosa West 5 3 0 4 12
## Panama City Beach 55 47 46 39 187
## Pensacola Beach 35 31 21 22 109
## Perdido Key 8 18 0 9 35
## Perdido Key State Park 4 6 4 6 20
## Saint Andrews State Park 19 15 8 12 54
## Saint George Island 438 433 206 414 1491
## Saint George Island State Park 129 107 44 47 327
## Saint Joe Beach 21 14 15 7 57
## Saint Joseph Peninsula 263 195 129 190 777
## Saint Joseph Peninsula State Park 177 175 134 148 634
## Saint Vincent NWR 126 126 37 78 367
## Topsail Hill State Park 8 8 0 14 30
## Tyndall Air Force Base 67 98 77 81 323
## Walton East 23 34 26 11 94
## Walton Mid 8 12 12 4 36
## Walton West 4 23 9 7 43
## Total 2003 2060 1121 1589 6773
From 2016 to 2019, loggerhead nesting typically peaked between 20 June and 08 July, while hatchling emergence peaked between 09 August and 21 August. Slight fluctuations between years was common. The average incubation period was 58.5 days with an average clutch size of 95.2 eggs. Overall mean hatching success was 46.1% while emergence success was 44.7%.
Of the 6773 loggerhead nests with valid GPS coordinates:
* 1530 nests (22.59%) were reported to receive some level of predation
* 2961 nests (43.72%) were washed over or inundated at some point during their incubation or after hatchling emergence while 1217 nests (17.97% total, 41.10% washed over/inundated) experienced partial or complete erosion.
These counts are not mutually exclusive as a nest could experience multiple disturbances throughout its incubation.
## [1] "Mean incubation duration: 58.5 days"
## [1] "Mean clutch size: 95.2 eggs"
## [1] "Mean hatching success: 46.1%"
## [1] "Mean emergence success: 44.7%"
## [1] "N Predated: 1530 nests"
## [1] "N Washed Over/Inundated: 2961 nests"
## [1] "N Complete/Partial Erosion: 1217 nests"