Effort A Sequim Bay project final survival assay results

sequim-bay
hardening
experimental design
Final lab survival assay results for Effort A seed project from Sequim Bay outplants
Author

Ariana Huffmyer

Published

October 7, 2026

Overview

Over the last few weeks, students lab conducted final sampling and survival assays of outplanted oysters that were sampled from the field at Sequim Bay.

This post details the results from these assays.

All data will be stored on GitHub here for the hardening project and the script for today is located here.

Data overview

Data are recorded for individual oysters with a “status” column indicating mortality. Each oyster is recorded as either a “0” (alive) or a “1” (dead) at each assessed time point. While the exact hours for survival checks vary for each of the 2 rounds of trials for this project, in general oysters were checked twice per day for about 50-60 hours of total heat exposure.

Trials were conducted in 1 round with n=37-38 per treatment group (n=2 groups) in each round. The treatment groups are from original hardening treatments conducted in 2024 followed by outplanting through summer 2026:

  • Control
  • Daily exposure to 25°C for 2 weeks

For all analyses, we are interested in the effect hardening treatment.

Method overview

In the script linked above, I performed Kaplan-Meier survivorship curves with Cox Proportional Hazards survival models to initially explore the data. This revealed that rounds were significantly different from each other, as expected.

I therefore proceeded with binomial logistic regressions to allow me to account for round and oyster length as random effects while testing for the main effects of hardening treatment.

In this analysis that I describe below, I present the statistical results from the logistic regression and post hoc tests for each group I also show model-projected survivorship curves with calculations of LT50 (time to 50% mortality) to quantify the differences between hardening treatments.

Results

Temperatures from each round

I first plotted temperatures from each round, which were recorded in n=5 cups at each time point.

Survival model

I used a binomial logistic regression using the following code.

surv_model<-glmer(status ~ time * group + (1|length.mm), family = binomial(link = "logit"), data=data)

summary(surv_model)
Anova(surv_model)

The ANOVA results are:

Analysis of Deviance Table (Type II Wald chisquare tests)

Response: status
             Chisq Df Pr(>Chisq)    
time       88.2437  1    < 2e-16 ***
group       0.3021  1    0.58258    
time:group  4.9603  1    0.02594 *

There is a significant effect of treatment (P=0.026).

Random effects demonstrate no trend of length strongly affecting mortality.

I generated post hoc comparisons shown below.

Survival curve plotting

I then generated model predicted mortality probabilities and plotted them for each treatment group.

# Generate predicted probabilities
data$predicted_mortality <- predict(surv_model, type = "response")

# Plot
plot2<-ggplot(data, aes(x = time, y = predicted_mortality, color = group, fill = group, group=group)) +
  geom_point(aes(y = status), alpha = 0.6, position = position_jitter(height = 0.03)) +
  geom_smooth(method = "glm", method.args = list(family = "binomial"), se = FALSE) +
  #scale_color_manual(values=c("cyan3", "coral"))+
  labs(
    title = "",
    y = "Probability of Mortality",
  ) +
  theme_classic();plot2

I performed post hoc tests using emmeans.

emm<-emmeans(surv_model, ~group)
pairs(emm)

There was higher survival in the treated oysters, but only marginally significant (P=0.042).

 contrast                            estimate    SE  df z.ratio p.value
 Effort A Control - Effort A Treated     1.23 0.605 Inf   2.035  0.0419

LT50 calculations

I then calculated LT50’s for each treatment group. The LT50 is the time to estimated 50% mortality for each group. If this value is higher that indicates a longer time to reach 50% mortality and therefore more tolerance.

| LT50_treated| LT50_control|
|------------:|------------:|
|         56.1|         55.1|

Conclusions

Overall, this survival test suggests:

  • There is an effect of thermal hardening in Effort A, although the difference is small - the LT50 was slightly higher by about 1 hours in the treated group.