Appendix B: HGAM analysis of road survey counts

Road-effect mitigation promotes connectivity and reduces mortality at the population-level

Sean P Boyle, Matthew G Keevil, Jacqueline D Litzgus, Don Tyerman, David Lesbarrères

B.1 Analysis methods

B.1.1 Model selection
We created a set of negative binomial Hierarchical Generalized Additive Models (HGAMs;
Wood, 2017; Pedersen et al., 2019) for each taxon (turtles, snakes, amphibians) with smoothing
functions applied to Julian day-of-year (jday), which allowed us to model the effect of
seasonality and account for potential annual variation in survey effort, abundance, and movement
by including year effects. We chose a negative binomial error distribution because it fit the data
markedly better than Poisson or quasi-Poisson approaches as assessed using Q-Q plots (via
package mgcViz; Fasiolo et al., 2018) and hanging rootograms (via package countreg; Kleiber and
Zeileis, 2016) applied to saturated models for each taxon. Models were fitted by restricted
maximum likelihood and analyzed in R version 4.0.2 (R Development Core Team, 2020) using
package mgcv version 1.8-31 (Wood, 2017, 2011). For all estimates of uncertainty (standard
error, confidence intervals), we accounted for smoothing parameter uncertainty by setting the
option unconditional = TRUE in the predict.gam function of package mgcv (Wood, 2017).
For all models in the candidate sets (Table B.1), we included the BACI treatment effects of site
(Impact or Control) and period (Before, During, or After construction of mitigation) and their
interaction as parametric fixed effects. Models differed in whether year, site, or their interaction
were included as levels in the smoothing component and whether a random effect of date was
included. We did not include a separate random date effect in models having a year effect in the
smooth term(s) to avoid redundancy between date and the combinations of jday and year. We
varied the hierarchical relationship among effect levels according to the HGAM taxonomy
developed by Pedersen et al. (2019). Briefly, this approach expands on the view of smooth terms
as random effects by presenting models with smooth patterns among levels nested within a
global overall non-linear trend. This nesting can include either or both of the amount of
smoothing (the complexity or ‘wiggliness’, which is determined by the penalized number of
basis functions) as well as the shape of the non-linear trend itself. An outline of the Pedersen et
al. (2019) taxonomy is:
• Model G — Single, shared global trend.
• Model GS — Global trend with shared penalty: shapes among levels may deviate from the
global trend while having the same complexity (shared penalty matrix and global trend).
• Model S — Shared smooth: all levels have the same complexity but their shapes are
independent (shared penalty matrix; no global trend).
• Model GI — Levels have shapes that deviated from a shared global trend but wiggliness is
independent (the penalty matrix for each level is independent).
• Model I — All levels are independent in shape and complexity.
We ranked models by AIC (Burnham and Anderson, 2002) to choose the best supported
smoothing and random effects structure before examining the parametric BACI treatment effects
in the top model for each taxon (Tables B.3, B.4, B.5) . We assessed significance of these effects
using Wald χ 2 tests in the top models as well as competing models that had approximately
equivalent support ( ΔAIC <2 ; Burnham and Anderson, 2002) (Section B.2.6). These are
ANOVA-style tests (implemented using the anova.gam function from package mgcv) that assess
significance across all levels of each of site, period, and period × site interaction.

B.1.2 Planned comparisons, effect size, and interpretation of the After × Impact
effect
Typical BACI designs conceive of the control and impact sites as having an additive relationship
— meaning that they are expected to vary in parallel (on the linear predictor scale) after
accounting for stochastic variability — until the impact site response is potentially deflected by
the effect of the impact in question (Stewart-Oaten and Bence, 2001; Stewart-Oaten et al., 1986).
We specifically examined the significance of the site×period interaction level After × Impact
because this is the key effect in the BACI design (Stewart-Oaten et al., 1986): the change in the
relative response of the sites after the impact occurs (the impact being the implementation of
road mortality mitigation in our case). We also examined the During × Impact level, which
represents the effect of incomplete mitigation. We fitted the models using the (default) treatment
contrasts for fixed effects and specified Before and Control as the reference levels. Therefore, the
Control site during the Before period is the intercept. We treated the interaction levels After ×
Impact and During × Impact as planned comparisons (i.e. without adjusting the p-value as would
be necessary for unplanned, post-hoc comparisons among treatment levels). This further
comparison is necessary because our experimental design included a During period. Without
separating the interaction levels, we could not assess the possibility that any significant overall
period × site interaction might be attributed to the During level effect.
The BACI null hypothesis predicts no substantial impact effect, in which case the impact site
response is simply the additive effect of site and the additive effect of period with no interaction
term. Under the alternate hypothesis, the impact changes the response at the impact site but not at
the control site so that the sites’ responses are no longer parallel and this change is quantified by
the interaction term. Therefore, we quantified the effect size of the After level of the mitigation
as the magnitude of the After × Impact effect relative to the null expectation of no interaction.
Similarly, the magnitude of the During × Impact level effect quantifies the effect of incomplete
mitigation.
We used the default log link for the negative binomial generalized linear models, and therefore
the expected response, μ is an exponential function of the linear predictors:
(β0 +β 1 X i1 +...+ βq X iq )
μi=e

(e.g., Zuur et al., 2009; McDonald et al., 2000), where β values are model coefficients and X iq
are entries of the design matrix. Equivalently:
β0 β1 X i1 βq X iq
μi=e ×e ×... ×e

Therefore, each exponentiated coefficient represents a proportional change in the mean response
due to the corresponding effect.
The BACI treatment coefficients given the treatment contrasts and the factor levels that we
specified are:
β BC ¿ Intercept, given that Control site Before period is the reference level.
βI ¿ Coefficent for the additive Impact site effect in all periods.
βD ¿ Coefficent for the additive effect of the During period at both sites.
βA ¿ Coefficent for the additive effect of the After period at both sites.
βD × I ¿ Coefficent for the interaction effect of the During period at the Impact site.
β A × I ¿ Coefficent for the After period and Impact site interaction (i.e., mitigation effect).

Quantifying partial effects involves examining effects of interest on the response scale (i.e., daily
counts) while holding all other effects constant. (Marginal effects are similar except they are
quantified on the scale of the linear predictors, which is related to the response scale by log link).
We held smooth terms and random effects constant to focus on the BACI partial effects, which
are:

μBC ¿eβ BC
¿ Control site; Before period (i.e., intercept).
βBC βI
μ BI ¿e e ¿ Impact site; Before period.
βBC βD
μ DC ¿e e ¿ Control site; During period.
βBC βD βI β D× I
μDI ¿e e e e ¿ Impact site; During period.
βBC βD βI
μ H 0 DI ¿e e e ¿ Hypothetical Impact site During period under H 0 .
βBC βA
μ AC ¿e e ¿ Control site; After period.
βBC βA βI β A× I
μ AI ¿e e e e ¿ Impact site; After period.
βBC βA βI
μ H 0 AI ¿e e e ¿ Hypothetical Impact site After period under H 0 .

Therefore, the response of the Impact site in the After period, μ AI , is related to the null
β
expectation as μ AI =μ H 0 AI × e so that e β quantifies the proportional effect of the impact on
A× I A ×I

the response scale (daily counts), which we report as percent change, %=(e β −1)×100 . A× I

B.1.2.1Effect size as a ratio-of-ratios

Effect sizes for BACI designs are often calculated as a difference-of-differences (e.g. Stewart-
Oaten et al., 1986; Christie et al., 2019):
 ( Afte r Impact − After Control )−(Befor e Impact −Befor e Control)

However, generalized linear models with a log link, such as Poisson or negative binomial models
of count data, are multiplicative with effects that are proportional on the response scale, so it is
appropriate to compare effects as ratios (McDonald et al., 2000). Therefore, we considered effect
size as a ratio-of-ratios following the approach used by Conner et al. (2016) in the context of
Bayesian BACI analyses. Conner et al. (2016) denote effect size as R BACI and define it as R A /R B,
which is the ratio of mean response values at Impact and Control sites during the After period
divided by the equivalent ratio during the Before period. To illustrate this definition applied our
analysis, we set aside the During period to focus on comparing site proportional responses in the
Before vs. After periods and note that:
μ BI e β e β β
I BC

R B=¿ = β =e I

μBC e BC

μ AI e β e β e β e β
BC A I A ×I

R A =¿ = =e β e β I A× I

μ AC β
e e β BC A

and therefore effect size for this comparison is also equivalent to the exponential of the After ×
Before interaction coefficient:
βI β A× I
e e β A× I
R BACI = β
=e
e I

B.1.2.2Estimating predictions from the null hypothesis

Plotting hypothetical predictions based on null hypotheses can help to visualize the assumptions
and logic underlying analyses. This is relevant for our BACI approach because we discuss our
effects (percent change) in relation to null predictions. In typical analyses, the null hypothesis is
a fixed quantity. The BACI H 0 of no interaction implies predictions about the Impact site
relative to a Control site for which the responses are also estimated. Therefore, although H 0
predicts a fixed quantity at with respect to the linear model interaction coefficient(s) ( β interaction=0
), uncertainty in the other coefficients must be accounted for to quantify predictions on the
response scale based on H 0.

We generated predicted hypothetical partial effects under H 0 given estimated main effects by
adapting a procedure used with package mgcv to generate estimates and variances for sums of
predictions (in R, see help(predict.gam, package = "mgcv")). Given β as the vector of model
coefficients β q, we created vector x H 0 AI of indicator values ( x q) with the same length as β and set
all x q=0 except the three values corresponding to β BC , β A , and β I , which were set to 1. The
linear predictor for μ H 0 AI was then
T
ln (μ H 0 AI )=x H 0 AI β

and the standard error (on the linear predictor scale) was:

S E2H 0 AI =xTH 0 AI V x H 0 AI
where V is the variance-covariance matrix for the model. We used the same approach to obtain
hypothetical partial effects for μ H 0 DI . We also tested this approach by confirming that it could
recover the same estimates and standard errors for marginal effects available from a direct
application of the predict.gam function.
B.1.2.3Post hoc Before-After comparison
A strength of BACI analyses is that there is no prior assumption about temporal patterns in the
responses, which are instead inferred using observations of the Control site(s) to account for
shared trends that are independent of potential impact effects (Stewart-Oaten et al., 1986).
Therefore, temporal comparisons within-sites are not inherently meaningful for making
inferences about impact effects. Nevertheless, within-period comparisons can provide additional
context to evaluate conservation and management actions (e.g., Baxter-Gilbert et al., 2015).
Therefore, when we found an evidence of a significant After × Impact effect, we also estimated
the proportional change between Before and After periods at the Impact site. We calculated this
proportion as:
μ AI e β e β e β e β
BC A I A×I

= =e β e β A A× I

μBI eβ eβ
BC I

which we estimated with standard error using the same approach that we applied to make
hypothetical predictions for H 0. This comparison was not a focus of our analysis, and we did not
compute p-values, but we did calculate an approximate 95% CI as ± 1.96 ×SE on the linear scale.
After transforming into the response scale, CIs that do not overlap 1 suggest a potentially
significant change, which should be interpreted cautiously because the CIs are approximate and
were not adjusted for additional comparisons.
 Table B.1. HGAM candidate model specifications applied to road survey counts of turtles,
snakes, and amphibians. All models contain parametric terms for site and period and vary in
the smoothing model (Smooth) applied to Julian day-of-year and presence of random effects
(RE) of date. Smooth term abbreviations refer to the taxonomy of Pedersen et al. (2019) and
were applied across levels of the effect(s) within parentheses. The Formula column provides
the linear model formula used to construct each model.
Model Smooth RE Formula
GS(year:site count ~ period + site + period:site + s(jday, k=20,
1
) m=2) + s(jday, year:site, bs="fs", k=20, m=2)
count ~ period + site + period:site + s(jday,
2 GI(year:site) bs="tp", k=20, m=2) + s(jday, by=year:site,
bs="tp", k=20, m=1) + s(year, site, bs="re")
count ~ period + site + period:site + s(jday,
3 S(year:site)
year:site, bs="fs", k=20, m=2)
count ~ period + site + period:site + s(jday,
4 I(year:site)
by=year:site, bs="tp", k=20, m=2)
count ~ period + site + period:site + s(jday, k=20,
5 GS(year)
m=2) + s(jday, year, bs="fs", k=20, m=2)
count ~ period + site + period:site + s(jday,
6 GI(year) bs="tp", k=20, m=2) + s(jday, by=year, bs="tp",
k=20, m=1) + s(year, bs="re", k=6)
count ~ period + site + period:site + s(jday, year,
7 S(year)
bs="fs", k=20, m=2)
count ~ period + site + period:site + s(jday,
8 I(year)
by=year, bs="tp", k=20, m=2)
count ~ period + site + period:site + s(jday, site,
9 S(site) date
bs="fs", k=20, m=2) + s(date, bs="re")
count ~ period + site + period:site + s(jday, site,
10 S(site)
bs="fs", k=20, m=2)
count ~ period + site + period:site + s(jday,
11 I(site) date
by=site, bs="tp", k=20, m=2) + s(date, bs="re")
count ~ period + site + period:site + s(jday,
12 I(site)
by=site, bs="tp", k=20, m=2)
count ~ period + site + period:site + s(jday,
13 G date
bs="tp", k=20, m=2) + s(date, bs="re")
count ~ period + site + period:site + s(jday,
14 G
bs="tp", k=20, m=2)
count ~ period + site + period:site + s(date,
15 date
bs="re")
16 count ~ period + site + period:site
 B.2 Results
B.2.1 Data summary

Figure B.1. Histograms of road survey counts. Each observation is a daily total at one of two
sites site (Control and Impact) for A) turtles (range 0–7), B) snakes (range 0–6), and C)
amphibians (range 0–324). Plotted data include both sites and all years (2013–2018)
surveyed. Bars represent bins with widths = 1. The highest 1% amphibian counts are
indicated with circles for visibility.

Table B.2. Summary of daily road survey counts of turtles, snakes, and amphibians at
Impact and Control sites at Presqu’ile Provincial Park. Daily surveys in 2013–2017 were
simultaneous except during initial training at the start of each field season. In 2018, surveys
alternated between sites (one site-survey/day).
Mean daily count
Survey days
Turtles Snakes Amphibians
Year Period
Impac Contro Impac Contr Ratio Impac Contr Ratio Impac Contr Ratio
* * *
t l t ol t ol t ol
201 Befor
96 94 0.35 0.40 0.87 0.46 0.180 2.6 21.0 5.7 3.70
3 e
201 Befor
94 91 0.45 0.37 1.20 0.57 0.120 4.8 19.0 6.8 2.80
4 e
201 Befor
97 94 0.30 0.33 0.91 0.21 0.074 2.8 11.0 1.9 5.80
5 e
201 Durin
100 99 0.28 0.41 0.68 0.34 0.110 3.1 4.7 1.4 3.40
6 g
201
After 92 98 0.12 0.37 0.32 0.68 0.210 3.2 12.0 11.0 1.10
7
 Mean daily count
Survey days
Turtles Snakes Amphibians
Year Period
Impac Contro Impac Contr Ratio Impac Contr Ratio Impac Contr Ratio
* * *
t l t ol t ol t ol
201
After 57 55 0.07 0.36 0.19 0.07 0.036 1.9 4.1 5.9 0.69
8
*
Impact mean daily count / Control mean daily count
B.2.2 AIC model selection tables
B.2.2.1 Turtles

Table B.3. HGAMs of turtle counts ranked by AIC. Smooth and random effects terms varied
among models but the fixed effects components were period + site + period × site for all
models. Column RE indicates whether a random effect of date was included.
Model Smooth RE AIC AIC
11 I(site) date 1409.8 0.0
9 S(site) date 1410.0 0.2
6 GI(year) 1410.4 0.6
13 G date 1419.1 9.3
8 I(year) 1424.8 15.0
2 GI(year:site) 1431.1 21.2
1 GS(year:site) 1431.3 21.5
5 GS(year) 1435.8 26.0
4 I(year:site) 1436.1 26.3
7 S(year) 1448.0 38.2
10 S(site) 1448.4 38.6
12 I(site) 1448.4 38.6
14 G 1451.1 41.3
3 S(year:site) 1456.0 46.2
15 date 1477.8 68.0
16 1544.2 134.4
B.2.2.2Snakes

Table B.4. HGAMs of snake counts ranked by AIC. Smooth and random effects terms
varied among models but the fixed effects components were period + site + period × site
for all models. Column RE indicates whether a random effect of date was included.
Model Smooth RE AIC AIC
6 GI(year) 1292.6 0.0
5 GS(year) 1292.9 0.3
2 GI(year:site) 1295.8 3.2
7 S(year) 1295.9 3.3
3 S(year:site) 1297.9 5.3
1 GS(year:site) 1298.0 5.4
10 S(site) 1324.4 31.8
12 I(site) 1324.5 31.9
8 I(year) 1328.7 36.1
14 G 1330.3 37.7
4 I(year:site) 1332.3 39.7
11 I(site) date 1341.1 48.5
9 S(site) date 1341.3 48.7
16 1344.7 52.1
13 G date 1349.3 56.8
15 date 1360.6 68.0
B.2.2.3Amphibians

Table B.5. HGAMs of amphibian counts ranked by AIC. Smooth and random effects terms
varied among models but the fixed effects components were period + site + period × site
for all models. Column RE indicates whether a random effect of date was included.
Model Smooth RE AIC AIC
6 GI(year) 5595.8 0.0
13 G date 5622.1 26.3
11 I(site) date 5631.4 35.6
8 I(year) 5634.0 38.2
9 S(site) date 5639.1 43.3
7 S(year) 5643.3 47.5
15 date 5646.1 50.3
2 GI(year:site) 5658.3 62.6
1 GS(year:site) 5675.6 79.9
5 GS(year) 5685.6 89.8
4 I(year:site) 5688.0 92.2
3 S(year:site) 5704.9 109.1
12 I(site) 5725.8 130.0
10 S(site) 5727.4 131.6
14 G 5729.9 134.1
16 5907.9 312.2

B.2.3 Interaction effect estimates and interpretation

We examined the parameter estimates from the preferred model for each taxon. The After ×
Impact effect on turtle counts was a 69.4 % reduction ( z=−3.5 , P=0.00053, 95% CI: 40.1–84.4
%) at the Impact site relative to the expected response under the null prediction of no Impact
effect due to mitigation. The After × Impact effect on amphibian counts was a decrease of 69.8
% ( z=−5.6 , P=2.2e-08 , 95% CI: 54–80.2 %) at the Impact site. There was no significant After
× Impact effect for snakes (estimated change relative to the null prediction: 8.4 % decrease,
z=−0.24, P=0.81, 95% CI: 84.8 % increase–54.6 % decrease).
There were no significant effects of incomplete mitigation for any taxon as quantified by the
During × Impact level interaction. The During × Impact effect on turtle counts was a 22.5 %
decrease ( z=−0.84, P=0.4, 95% CI: 40.8 % increase–57.3 % decrease) at the Impact site
relative to the expected response under the null prediction of no impact effect of incomplete
mitigation. The During × Impact effect on amphibian counts was an increase of 7.0 % ( z=0.25 ,
P=0.8, 95% CI: 82.0 % increase–37.1 % decrease) at the Impact site. The During × Impact
effect for snakes was a 9.3 % decrease, z=−0.22, P=0.82, 95% CI: 113.0 % increase–61.4 %
decrease).
B.2.4 Before-After post hoc comparison at the Impact site
We compared Before and After periods at the Impact site for turtles and amphibians, which each
had significant effect of the After level of the period × site interaction. There was a 65.3 %
reduction (95% CI: 37.3–80.8 %) between the Before and After periods in mean daily turtle
counts at the Impact site. The proportional change in amphibian counts at the Impact site was a
less substantial reduction of 45.1 % (95% CI: 25.5 % increase–76.0 % decrease) and the
confidence interval for percent change overlapped 0%.
While the size of the BACI interaction effect was similarly large for both turtles and amphibians,
the proportional change between periods at the Impact site was obvious for turtles, for which
counts were comparatively stable at the Control site and within periods at the Impact site, but
ambiguous for amphibians. Amphibian counts were more variable and therefore the mitigation
Impact effect is obscured when assessed using the within-site, among-period comparison, which
does not leverage the BACI design’s ability to control for temporal variation.
Effect sizes, in general, are the difference between observed responses and predictions under the
null hypothesis (Unkittrick et al., 2009), and so their biological validity depends on whether the
null hypothesis represents a reasonable counterfactual scenario (Smith et al., 1993). The BACI
approach is predicated on a consistent, underlying association between responses at Control and
Impact sites, with the null hypothesis allowing for temporal variation but positing consistency in
the nature of this association after the impact event, which is not always a robust assumption
(Underwood, 1994). In some circumstances, within-site comparisons can be made to supplement
inferences drawn from the BACI interaction effect if researchers or managers are not completely
committed to the BACI assumptions (Baxter-Gilbert et al., 2015; Smith et al., 1993). However,
Before–After comparisons alone have much lower statistical power in the presence of temporal
variability (Christie et al., 2019; Smokorowski and Randall, 2017).
B.2.5
B.2.6 HGAM BACI plots

Figure B.2. Comparison of BACI partial effects on the response scale (mean daily counts; A,
B, C) with BACI marginal effects on the linear predictor scale (log mean daily counts; D, E,
F) for turtles (A,D), snakes (B,E), and amphibians (C,F) observed during road surveys of
Control and Impact sites. ‘ H 0 Impact’ indicates hypothetical main-effects-only predictions
of the null hypothesis of no BACI interaction effects. H 0 is the additive model with no
interaction. In our negative binomial model using a log link function an additive model
implies a consistent ratio between treatments, which are then parallel on a logarithmic scale.
Results are shown for the top AIC-ranked model for each taxon while holding random and
smoothing effects constant. Error bars indicate 95% CIs.
Figure B.3. Response-scale fitted values from negative binomial hierarchical generalized
additive models (HGAMs) of daily road survey counts fitted with a smoothing function on
Julian day with approximate 95% CI bands. The fitted values were calculated while holding
the random effect of date constant if present in the model. The top model chosen using AIC
 model selection was plotted for each taxon. Amphibian CI bands were cropped to visualize
means at an appropriate scale.

B.2.7 Summaries of models with ΔAIC < 2

B.2.7.1Turtles

B.2.7.1.1 Turtle model 11: I(site) RE(date)

Model rank: 1, ΔAIC =0, deviance explained = 53.6 %. Negative binomial size (dispersion)
^
parameter: θ=7.93 .

Turtle model 11 parametric fixed effects.

Effect df 2 Pa
period 2 0.4 0.83
site 1 0.0 0.88
period:site 2 12.0 0.0025 **
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05
a

Turtle model 11 planned comparisons examining both period × site interaction levels.
BA × CI level Est.a SE z Pb
During:Impact -0.254 0.304 -0.837 0.4
After:Impact -1.18 0.342 -3.47 0.00053 ***
a
coefficient value on the linear predictor (log link) scale
b
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05

Turtle model 11 smooth and random effects with approximate p-values.

Effect edfa 2 Pb
s(jday):siteControl 5.07 52.7 1.7e-09 ***
s(jday):siteImpact 5.53 38.7 2e-06 ***
s(date) 146.29 239.3 4.9e-15 ***
a
Estimated degrees of freedom
b
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05
 B.2.7.1.2 Turtle model 9: S(site) RE(date)
Model rank: 2, ΔAIC =0.2, deviance explained = 53.7 %. Negative binomial size (dispersion)
^
parameter: θ=8.06 .

Turtle model 9 parametric fixed effects

Effect df 2 Pa
period 2 0.4 0.81
site 1 0.0 0.84
period:site 2 12.5 0.002 **
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05
a

Turtle model 9 planned comparisons examining both period × site interaction levels.
BA × CI level Est.a SE z Pb
During:Impact -0.259 0.303 -0.854 0.39
After:Impact -1.2 0.341 -3.53 0.00042 ***
a
coefficient value on the linear predictor (log link) scale
b
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05

Turtle model 9 smooth and random effects with approximate p-values

Effect edfa 2 Pb
s(jday,site) 8.44 153.5 4.5e-17 ***
s(date) 150.04 248.8 6.3e-16 ***
a
Estimated degrees of freedom
b
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05
 B.2.7.1.3 Turtle model 6: GI(year)
Model rank: 3, ΔAIC =0.6, deviance explained = 30.3 %. Negative binomial size (dispersion)
^
parameter: θ=1.43 .

Turtle model 6 parametric fixed effects

Effect df 2 Pa
period 2 6.3 0.044 *
site 1 0.0 0.86
period:site 2 13.1 0.0015 **
a
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05

Turtle model 6 planned comparisons examining both period × site interaction levels.
BA × CI level Est.a SE z Pb
During:Impact -0.381 0.335 -1.14 0.26
After:Impact -1.27 0.351 -3.61 0.00031 ***
a
coefficient value on the linear predictor (log link) scale
b
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05

Turtle model 6 smooth and random effects with approximate p-values

Effect edfa 2 Pb
s(jday) 1.00 0.6 0.44
s(jday):year2013 9.62 46.8 6.7e-09 ***
s(jday):year2014 8.87 66.6 2.1e-14 ***
s(jday):year2015 6.20 36.0 1.4e-08 ***
s(jday):year2016 6.07 26.0 5.8e-06 ***
s(jday):year2017 1.03 1.5 0.18
s(jday):year2018 0.00 0.0 0.57
s(year) 0.00 0.0 0.7
Estimated degrees of freedom
a

Significance. codes: 0 *** 0.001 ** 0.01 * 0.05

b
B.2.7.2Snakes

B.2.7.2.1 Snake model 6: GI(year)

Model rank: 1, ΔAIC =0, deviance explained = 18.7 %. Negative binomial size (dispersion)
^
parameter: θ=0.89 .

Snake model 6 parametric fixed effects

Effect df 2 Pa
period 2 0.2 0.92
site 1 30.9 2.7e-08 ***
period:site 2 0.1 0.96
a
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05

Snake model 6 planned comparisons examining both period × site interaction levels.
BA × CI level Est.a SE z Pb
During:Impact -0.0977 0.435 -0.224 0.82
After:Impact -0.0872 0.357 -0.244 0.81
a
coefficient value on the linear predictor (log link) scale
b
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05

Snake model 6 smooth and random effects with approximate p-values

Effect edfa 2 Pb
s(jday) 2.34 14.3 0.0023 **
s(jday):year2013 0.00 0.0 0.35
s(jday):year2014 0.00 0.0 0.85
s(jday):year2015 0.00 0.0 0.67
s(jday):year2016 1.00 1.6 0.14
s(jday):year2017 0.83 1.2 0.19
s(jday):year2018 0.31 0.4 0.28
s(year) 2.83 34.0 7e-08 ***
a
Estimated degrees of freedom
b
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05
 B.2.7.2.2 Snake model 5: GS(year)
Model rank: 2, ΔAIC =0.3, deviance explained = 18.6 %. Negative binomial size (dispersion)
^
parameter: θ=0.89 .

Snake model 5 parametric fixed effects

Effect df 2 Pa
period 2 0.2 0.91
site 1 30.8 2.9e-08 ***
period:site 2 0.1 0.96
a
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05

Snake model 5 planned comparisons examining both period × site interaction levels.
BA × CI level Est.a SE z Pb
During:Impact -0.0934 0.435 -0.215 0.83
After:Impact -0.0858 0.357 -0.24 0.81
a
coefficient value on the linear predictor (log link) scale
b
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05

Snake model 5 smooth and random effects with approximate p-values

Effect edfa 2 Pb
s(jday) 2.36 10.7 0.012 *
s(jday,year) 4.88 38.2 1.1e-08 ***
Estimated degrees of freedom
a

Significance. codes: 0 *** 0.001 ** 0.01 * 0.05

b
B.2.7.3Amphibians

B.2.7.3.1 Amphibian model 6: GI(year)

Model rank: 1, ΔAIC =0, deviance explained = 41.7 %. Negative binomial size (dispersion)
^
parameter: θ=0.51 .

Amphibian model 6 parametric fixed effects

Effect df 2 Pa
period 2 11.7 0.0028 **
site 1 80.1 3.6e-19 ***
period:site 2 34.9 2.7e-08 ***
a
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05

Amphibian model 6 planned comparisons examining both period × site interaction levels.
BA × CI level Est.a SE z Pb
During:Impact 0.0673 0.27 0.249 0.8
After:Impact -1.2 0.214 -5.6 2.2e-08 ***
a
coefficient value on the linear predictor (log link) scale
b
Significance. codes: 0 *** 0.001 ** 0.01 * 0.05

Amphibian model 6 smooth and random effects with approximate p-values

Effect edfa 2 Pb
s(jday) 4.21 11.0 0.047 *
s(jday):year2013 7.59 25.4 1.5e-05 ***
s(jday):year2014 7.57 24.7 2.6e-05 ***
s(jday):year2015 11.57 54.0 7.4e-10 ***
s(jday):year2016 13.70 53.2 1.3e-08 ***
s(jday):year2017 9.74 42.2 1.9e-08 ***
s(jday):year2018 0.01 0.0 0.19
s(year) 2.74 32.3 3.6e-08 ***
Estimated degrees of freedom
a

Significance. codes: 0 *** 0.001 ** 0.01 * 0.05

b
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