Total mortality of tagged corals data analysis
Setup
Import data
Prevalence of total colony mortality
Total colony mortality was recorded using the condition code “DEAD”. Here, we summarize the number of corals at each site that died at any point.
| site | channel | reef | dir | n | dead | prop |
|---|---|---|---|---|---|---|
| HBN2 | channelside | HB | N | 15 | 2 | 0.1333333 |
| HBN3 | channelside | HB | N | 27 | 9 | 0.3333333 |
| HBNC1 | control | HB | N | 14 | 6 | 0.4285714 |
| HBS1 | channelside | HB | S | 18 | 1 | 0.0555556 |
| HBS2 | channelside | HB | S | 26 | 4 | 0.1538462 |
| HBS3 | channelside | HB | S | 29 | 17 | 0.5862069 |
| HBS4 | channelside | HB | S | 25 | 14 | 0.5600000 |
| HBSC1 | control | HB | S | 30 | 10 | 0.3333333 |
| R2N1 | channelside | R2 | N | 30 | 13 | 0.4333333 |
| R2N2 | channelside | R2 | N | 25 | 10 | 0.4000000 |
| R2NC1 | control | R2 | N | 30 | 6 | 0.2000000 |
| R2NC2 | control | R2 | N | 30 | 5 | 0.1666667 |
| R2NC3 | control | R2 | N | 30 | 8 | 0.2666667 |
| R2S1 | channelside | R2 | S | 28 | 8 | 0.2857143 |
| R2S2 | channelside | R2 | S | 24 | 13 | 0.5416667 |
| R2SC1 | control | R2 | S | 30 | 9 | 0.3000000 |
| R2SC2 | control | R2 | S | 25 | 16 | 0.6400000 |
| R3N1 | channelside | R3 | N | 24 | 4 | 0.1666667 |
| R3NC1 | control | R3 | N | 24 | 8 | 0.3333333 |
| R3S1 | channelside | R3 | S | 19 | 6 | 0.3157895 |
| R3S2 | channelside | R3 | S | 25 | 6 | 0.2400000 |
| R3S3 | channelside | R3 | S | 26 | 6 | 0.2307692 |
| R3SC1 | control | R3 | S | 25 | 4 | 0.1600000 |
| R3SC2 | control | R3 | S | 23 | 9 | 0.3913043 |
| R3SC3 | control | R3 | S | 25 | 10 | 0.4000000 |
Was total mortality more common at channelside sites?
| reef | dir | contrast | odds.ratio | SE | df | z.ratio | p.value |
|---|---|---|---|---|---|---|---|
| HB | N | channelside - control | 0.6785243 | 0.5648513 | NA | -0.4658845 | 0.6412982 |
| R2 | N | channelside - control | 2.2979078 | 1.1193767 | NA | 1.7079659 | 0.0876427 |
| R3 | N | channelside - control | 0.9812021 | 0.8612385 | NA | -0.0216201 | 0.9827510 |
| HB | S | channelside - control | 0.4320926 | 0.2713146 | NA | -1.3363659 | 0.1814297 |
| R2 | S | channelside - control | 1.0588835 | 0.6069665 | NA | 0.0998145 | 0.9204916 |
| R3 | S | channelside - control | 0.8488125 | 0.4439392 | NA | -0.3134095 | 0.7539696 |
There are no differences in total colony mortality between channelside and control sites at any reef location. However, total mortality overall is high, and the majority of this mortality may be attributable to white plague disease. Therefore, to assess mortality that may be associated with sedimentation, it may be more informative to analyze only disease-resistant corals.
Total mortality of disease-resistant corals
| reef | dir | contrast | odds.ratio | SE | df | z.ratio | p.value |
|---|---|---|---|---|---|---|---|
| HB | N | channelside - control | 6.653563e+08 | 1.860612e+13 | NA | 0.0007265 | 0.9994203 |
| R2 | N | channelside - control | 7.440165e+00 | 7.384066e+00 | NA | 2.0221402 | 0.0431619 |
| R3 | N | channelside - control | 3.317280e+08 | 4.611807e+12 | NA | 0.0014113 | 0.9988740 |
| HB | S | channelside - control | 8.347243e-01 | 1.561091e+04 | NA | -0.0000097 | 0.9999923 |
| R2 | S | channelside - control | 0.000000e+00 | 1.080000e-05 | NA | -0.0017284 | 0.9986209 |
| R3 | S | channelside - control | 3.776662e-01 | 4.537444e-01 | NA | -0.8104791 | 0.4176648 |
For disease-resistant corals, there was significantly higher total mortality at channelside sites (36%) relative to control sites (7%) on the northern middle reef. For the southern middle reef and the outer reef, there was no significant difference in total mortality of disease-resistant corals detected between channelside and control sites. This may also be due to low sample sizes of disease-resistant corals which reduced statistical power.