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Chapter 3 — Supplementary information

In [1]:
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.ch3_out <- if (exists("ch3_out_dir")) ch3_out_dir else file.path(normalizePath("."), "outputs")
EnvBio_summary_table <- read.csv(file.path(.ch3_out, "tbl-env-fish-summary.csv"), check.names = FALSE)
Length–weight relationship used to estimate missing kōura weights. Observed (measured) and model-predicted body weights are shown in relation to orbital carapace length (OCL). The log₁₀–log₁₀ regression was fitted to individuals with both length and weight measurements (n = 240) and used to estimate missing weights (n = 81). Predicted values were back-transformed using a lognormal bias correction factor. The fitted regression equation is shown on the plot.
Raw relationships between all environmental predictors examined and kōura occurrence, CPUE, and BPUE across all 60 surveyed littoral sites. Each panel shows observed values at individual sites (n = 60 for occurrence; n = 33 for CPUE and BPUE). Points are jittered slightly for occurrence data to reduce overplotting. Predictors highlighted in bold were retained in final GAM models. 
In [2]:
View Code 
col_nms_env <- c("Lake","Variable","Unit","n","Mean","Median","Min","Max","CI low","CI high")
if (isTRUE(getOption("thesis.is.html")) && knitr::is_html_output()) {
  DT::datatable(EnvBio_summary_table, colnames = col_nms_env, filter = "top", rownames = FALSE,
                options = list(pageLength = 20, dom = 'Bfrtip', buttons = c('csv', 'excel')),
                extensions = 'Buttons') |>
    DT::formatRound(columns = c("Mean","Median","Min","Max","CI_low","CI_high"), digits = 2)
} else if (knitr::is_latex_output()) {
  knitr::kable(EnvBio_summary_table, digits = 2, escape = FALSE, booktabs = TRUE,
               align = c("l","l","l","r","r","r","r","r","r","r"),
               col.names = col_nms_env) |>
    kableExtra::kable_styling(
      latex_options = c("scale_down", "repeat_header", "striped"),
      font_size     = 8,
      stripe_color  = "gray!8"
    )
} else {
  knitr::kable(EnvBio_summary_table, digits = 2,
               align = c("l","l","l","r","r","r","r","r","r","r"),
               col.names = col_nms_env)
}
In [3]:
Distribution of environmental and biotic variables measured at littoral sampling sites across five Te Arawa lakes in the Rotorua region of Aotearoa New Zealand.
Lake Variable Unit n Mean Median Min Max CI low CI high
Rotorua Substrate index 12 3.66 3.30 2.80 6.30 3.01 4.31
Rotoiti Substrate index 12 3.92 3.20 2.00 8.00 2.73 5.11
Rotoehu Substrate index 12 2.77 2.45 2.00 4.90 2.15 3.39
Rotomā Substrate index 12 3.50 3.02 2.00 6.20 2.64 4.36
Ōkāreka Substrate index 12 2.86 2.70 1.00 6.20 1.92 3.79
All lakes Substrate index 60 3.34 3.00 1.00 8.00 2.98 3.71
Rotorua Slope 5m 12 0.02 0.01 0.01 0.16 0.00 0.05
Rotoiti Slope 5m 12 0.09 0.07 0.04 0.30 0.04 0.14
Rotoehu Slope 5m 12 0.08 0.06 0.02 0.27 0.03 0.12
Rotomā Slope 5m 12 0.07 0.06 0.01 0.23 0.03 0.11
Ōkāreka Slope 5m 12 0.11 0.13 0.01 0.20 0.07 0.15
All lakes Slope 5m 60 0.08 0.06 0.01 0.30 0.06 0.09
Rotorua Riparian vegetation % 12 67.50 100.00 0.00 100.00 40.12 94.88
Rotoiti Riparian vegetation % 12 92.50 100.00 20.00 100.00 77.88 107.12
Rotoehu Riparian vegetation % 12 67.50 100.00 0.00 100.00 36.95 98.05
Rotomā Riparian vegetation % 12 63.33 90.00 0.00 100.00 35.13 91.53
Ōkāreka Riparian vegetation % 12 75.83 100.00 0.00 100.00 48.01 103.66
All lakes Riparian vegetation % 60 73.33 100.00 0.00 100.00 62.65 84.02
Rotorua Overhanging trees % 12 46.67 30.00 0.00 100.00 15.50 77.83
Rotoiti Overhanging trees % 12 54.17 65.00 0.00 100.00 23.22 85.11
Rotoehu Overhanging trees % 12 35.83 0.00 0.00 100.00 5.25 66.42
Rotomā Overhanging trees % 12 52.50 55.00 0.00 100.00 22.44 82.56
Ōkāreka Overhanging trees % 12 52.50 65.00 0.00 100.00 21.71 83.29
All lakes Overhanging trees % 60 48.33 30.00 0.00 100.00 36.15 60.52
Rotorua Wood cover % 12 8.33 3.50 0.00 30.00 1.98 14.69
Rotoiti Wood cover % 12 4.25 1.50 0.00 20.00 0.31 8.19
Rotoehu Wood cover % 12 14.92 10.00 3.00 40.00 7.24 22.60
Rotomā Wood cover % 12 10.00 10.00 0.00 30.00 4.13 15.87
Ōkāreka Wood cover % 12 11.25 7.50 0.00 40.00 2.56 19.94
All lakes Wood cover % 60 9.75 5.00 0.00 40.00 6.96 12.54
Rotorua Emergent macrophytes % 12 0.00 0.00 0.00 0.00 0.00 0.00
Rotoiti Emergent macrophytes % 12 9.50 0.00 0.00 100.00 -8.71 27.71
Rotoehu Emergent macrophytes % 12 8.75 0.00 0.00 35.00 -0.74 18.24
Rotomā Emergent macrophytes % 12 10.83 0.00 0.00 80.00 -4.78 26.45
Ōkāreka Emergent macrophytes % 12 22.50 0.00 0.00 90.00 -0.35 45.35
All lakes Emergent macrophytes % 60 10.32 0.00 0.00 100.00 3.98 16.65
Rotorua Submerged macrophytes % 12 0.83 0.00 0.00 10.00 -1.00 2.67
Rotoiti Submerged macrophytes % 12 0.83 0.00 0.00 10.00 -1.00 2.67
Rotoehu Submerged macrophytes % 12 51.42 52.50 0.00 100.00 20.51 82.33
Rotomā Submerged macrophytes % 12 21.67 10.00 0.00 85.00 2.21 41.12
Ōkāreka Submerged macrophytes % 12 10.83 0.00 0.00 100.00 -7.43 29.10
All lakes Submerged macrophytes % 60 17.12 0.00 0.00 100.00 8.42 25.81
Rotorua Temperature Degree C 12 23.15 23.25 21.80 25.30 22.52 23.78
Rotoiti Temperature Degree C 12 21.62 21.50 20.60 23.80 21.03 22.22
Rotoehu Temperature Degree C 12 22.11 22.05 21.20 23.00 21.72 22.49
Rotomā Temperature Degree C 12 17.02 16.85 16.30 18.10 16.64 17.39
Ōkāreka Temperature Degree C 12 16.98 16.30 16.00 20.70 15.93 18.04
All lakes Temperature Degree C 60 20.18 21.25 16.00 25.30 19.44 20.91
Rotorua Dissolved oxygen mg/l 12 8.49 7.92 5.25 11.05 7.39 9.59
Rotoiti Dissolved oxygen mg/l 12 9.59 9.76 6.80 10.64 8.92 10.25
Rotoehu Dissolved oxygen mg/l 12 10.36 10.77 8.85 11.79 9.67 11.05
Rotomā Dissolved oxygen mg/l 12 9.72 9.76 8.66 10.31 9.45 9.98
Ōkāreka Dissolved oxygen mg/l 12 9.37 9.38 8.83 9.74 9.20 9.53
All lakes Dissolved oxygen mg/l 60 9.50 9.62 5.25 11.79 9.20 9.81
Rotorua Specific conductivity µS/cm 12 205.36 188.27 156.20 443.01 156.39 254.33
Rotoiti Specific conductivity µS/cm 12 163.11 158.70 155.79 196.01 156.22 170.00
Rotoehu Specific conductivity µS/cm 12 458.89 458.22 455.44 464.72 456.91 460.87
Rotomā Specific conductivity µS/cm 12 162.90 161.79 156.73 174.96 159.94 165.85
Ōkāreka Specific conductivity µS/cm 12 76.34 76.15 75.62 78.59 75.82 76.86
All lakes Specific conductivity µS/cm 60 213.32 162.55 75.62 464.72 178.41 248.23
Rotorua pH 12 6.94 7.04 3.78 7.69 6.29 7.60
Rotoiti pH 12 8.67 8.72 8.08 9.02 8.46 8.87
Rotoehu pH 12 8.83 8.90 8.46 9.21 8.68 8.99
Rotomā pH 12 7.80 7.92 6.44 8.56 7.47 8.13
Ōkāreka pH 12 8.32 8.29 7.77 9.00 8.15 8.50
All lakes pH 60 8.11 8.28 3.78 9.21 7.89 8.34
Rotorua Presence Catfish 12 0.08 0.00 0.00 1.00 0.00 0.38
Rotoiti Presence Catfish 12 0.42 0.00 0.00 1.00 0.15 0.72
Rotoehu Presence Catfish 12 0.00 0.00 0.00 0.00 0.00 0.26
Rotomā Presence Catfish 12 0.00 0.00 0.00 0.00 0.00 0.26
Ōkāreka Presence Catfish 12 0.00 0.00 0.00 0.00 0.00 0.26
All lakes Presence Catfish 60 0.10 0.00 0.00 1.00 0.04 0.21
Rotorua Presence Eel 12 0.33 0.00 0.00 1.00 0.10 0.65
Rotoiti Presence Eel 12 0.08 0.00 0.00 1.00 0.00 0.38
Rotoehu Presence Eel 12 0.00 0.00 0.00 0.00 0.00 0.26
Rotomā Presence Eel 12 0.25 0.00 0.00 1.00 0.05 0.57
Ōkāreka Presence Eel 12 0.00 0.00 0.00 0.00 0.00 0.26
All lakes Presence Eel 60 0.13 0.00 0.00 1.00 0.06 0.25
Rotorua Presence Goldfish 12 0.08 0.00 0.00 1.00 0.00 0.38
Rotoiti Presence Goldfish 12 0.67 1.00 0.00 1.00 0.35 0.90
Rotoehu Presence Goldfish 12 1.00 1.00 1.00 1.00 0.74 1.00
Rotomā Presence Goldfish 12 0.50 0.50 0.00 1.00 0.21 0.79
Ōkāreka Presence Goldfish 12 0.25 0.00 0.00 1.00 0.05 0.57
All lakes Presence Goldfish 60 0.50 0.50 0.00 1.00 0.37 0.63
Rotorua Presence Common smelt 12 0.25 0.00 0.00 1.00 0.05 0.57
Rotoiti Presence Common smelt 12 0.67 1.00 0.00 1.00 0.35 0.90
Rotoehu Presence Common smelt 12 0.50 0.50 0.00 1.00 0.21 0.79
Rotomā Presence Common smelt 12 0.42 0.00 0.00 1.00 0.15 0.72
Ōkāreka Presence Common smelt 12 0.58 1.00 0.00 1.00 0.28 0.85
All lakes Presence Common smelt 60 0.48 0.00 0.00 1.00 0.35 0.62
Rotorua Presence Kōaro 12 0.00 0.00 0.00 0.00 0.00 0.26
Rotoiti Presence Kōaro 12 0.00 0.00 0.00 0.00 0.00 0.26
Rotoehu Presence Kōaro 12 0.00 0.00 0.00 0.00 0.00 0.26
Rotomā Presence Kōaro 12 0.00 0.00 0.00 0.00 0.00 0.26
Ōkāreka Presence Kōaro 12 0.67 1.00 0.00 1.00 0.35 0.90
All lakes Presence Kōaro 60 0.13 0.00 0.00 1.00 0.06 0.25
Rotorua Presence Trout 12 0.17 0.00 0.00 1.00 0.02 0.48
Rotoiti Presence Trout 12 0.17 0.00 0.00 1.00 0.02 0.48
Rotoehu Presence Trout 12 0.00 0.00 0.00 0.00 0.00 0.26
Rotomā Presence Trout 12 0.00 0.00 0.00 0.00 0.00 0.26
Ōkāreka Presence Trout 12 0.17 0.00 0.00 1.00 0.02 0.48
All lakes Presence Trout 60 0.10 0.00 0.00 1.00 0.04 0.21