Background

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)"


Reported Wash-Over Exposure

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:

Modeled Risk of Wave Wash-Over

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


Nest Productivity Assessments

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


Additional Nesting Analyses

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"