1. Load libaries
library(tidyverse)
library(plyr)
library(kableExtra)
library(ggplot2)
library(dplyr)
library(lubridate)
2. Load data
file_path <- "C:/Users/oelle/Documents/Meine Dokumente/Research/Projects/Project_RockLobster/Temperature acclimation/Aerobic scope/Statistics/"
save_path <- "C:/Users/oelle/Documents/Meine Dokumente/Research/Projects/Project_RockLobster/Temperature acclimation/Aerobic scope/Statistics/Q10/"
# Read combined data file
mo2_data <- read.csv(paste(file_path, "MO2_Escape_Data_long.csv", sep = ""))
# Read combined data as means
mo2_data_means <- read.csv(paste(file_path, "MO2_Escape_Data_means_long.csv", sep = ""))
3. Define Q10 function
# df_data <- sub_trait
# species_var <- "Species"
# group_var <- ""
# level_var <- "AcclimationTemperature_C"
# temp_var <- "ExperimentalTemperature_C"
# data_var <- "mean"
# Function to calculate Q10
get_q10 <- function(df_data, group_var, species_var, level_var, temp_var, data_var) {
# Convert to data frame
df_data <- as.data.frame(df_data)
# Find columns for variables
species_var_index <- grep(species_var, names(df_data))
group_var_index <- grep(group_var, names(df_data))
temp_var_index <- grep(temp_var, names(df_data))
data_var_index <- grep(data_var, names(df_data))
level_var_index <- grep(level_var, names(df_data))
# Extract animal IDs
group_ID <- unique(df_data[ ,group_var_index])
# Create data vectors
Q10 <- data.frame()
i <- 3
# Loop over each group ID
for (i in seq_along(group_ID)){
# Subset by animal ID
data_sub <- df_data[df_data[,group_var_index]==group_ID[i],]
# only calculate Q10 if there are more than two data points
if(nrow(data_sub)>1) {
# Order by temperature
data_sub <- data_sub[order(data_sub[,temp_var_index]),]
# Define row indices
r1 <- c(1:(nrow(data_sub)-1))
r2 <- c(2:nrow(data_sub))
# Calculate Q10= (R2/R1)^(10/(T2 - T1)) and attach to vector variable
rate1 <- data_sub[,data_var_index][r1]
rate2 <- data_sub[,data_var_index][r2]
temp1 <- data_sub[,temp_var_index][r1]
temp2 <- data_sub[,temp_var_index][r2]
q10 <- (rate2/rate1)^(10/(temp2-temp1))
# Create results table
Q10 <- rbind(Q10, data.frame("Species" = data_sub[,species_var_index][r1],
"Group_ID" = data_sub[,group_var_index][r1],
"AcclimationTemperature_C" = data_sub[,level_var_index][r1],
"Q10" = round(q10, 3),
"Temp1" = round(temp1, 1),
"Temp2" = round(temp2, 1)))
}
# End loop
}
# Return Q10 results
return(Q10)
# End function
}
4A. Calculate thermal coefficients for all traits and temperatures
# Remove unneeded columns
sub_data <- mo2_data[,c(2:3, 5:6,11:12)]
# Create data frame for Q10 calculations
q10_all <- data.frame()
# Loop over traits and calculate q10
i <- 1
for(i in seq_along(unique(sub_data$Trait))){
# Select animal ID
trait <- unique(sub_data$Trait)[i]
sub_trait <- filter(sub_data, Trait == trait)
# Q10 function
q10 <- get_q10(sub_trait, group_var = "AntTag",
species_var = "Species",
temp_var = "ExperimentalTemperature_C",
level_var = "AcclimationTemperature_C",
data_var = "value")
# Attach trait column
q10$Trait <- trait
# Attach to q10 data frame
q10_all <- rbind(q10_all, q10)
}
4B. Calculate thermal coefficients for all traits but only for 14 and 21.5°C experimental temperature
# Remove data for 17.5°C experimental temperature
sub_no17 <- filter(sub_data, ExperimentalTemperature_C != 17.5)
# Create data frame for Q10 calculations
q10_all_no17 <- data.frame()
# Loop over traits and calculate q10
i <- 1
for(i in seq_along(unique(sub_data$Trait))){
# Select animal ID
trait <- unique(sub_no17$Trait)[i]
sub_trait <- filter(sub_no17, Trait == trait)
# Q10 function
q10 <- get_q10(sub_trait, group_var = "AntTag",
species_var = "Species",
temp_var = "ExperimentalTemperature_C",
level_var = "AcclimationTemperature_C",
data_var = "value")
# Attach trait column
q10$Trait <- trait
# Attach to q10 data frame
q10_all_no17 <- rbind(q10_all_no17, q10)
}
4C Calculate Q10 for means of data without 17.5°C experimental temperature
# Remove unneeded columns
sub_data_means <- mo2_data_means[,c(2:5, 7)]
# Remove data for 17.5°C experimental temperature
sub_means_no17 <- filter(sub_data_means, ExperimentalTemperature_C != 17.5)
# Create data frame for Q10 calculations
q10_means_all <- data.frame()
# Loop over traits and calculate q10
i <- 1
for(i in seq_along(unique(sub_means_no17$Trait))){
# Subset by trait
trait <- unique(sub_means_no17$Trait)[i]
sub_trait <- filter(sub_means_no17, Trait == trait)
# Loop for each species
Q10_species <- data.frame()
z <- 1
for(z in seq_along(unique(sub_trait$Species))){
# Subset by species
species <- unique(sub_trait$Species)[z]
sub_species <- filter(sub_trait, Species == species)
# Loop for each acclimation temperature
# Create data vectors
Q10 <- data.frame()
x <- 1
for(x in seq_along(unique(sub_species$AcclimationTemperature_C))){
# Subset by acclimation temperature
AcclimationTemp <- unique(sub_species$AcclimationTemperature_C)[x]
sub_AcclimationTemp <- filter(sub_species, AcclimationTemperature_C == AcclimationTemp)
# Order by temperature
sub_AcclimationTemp <- sub_AcclimationTemp[order(sub_AcclimationTemp$ExperimentalTemperature_C),]
# Define row indices
r1 <- c(1:(nrow(sub_AcclimationTemp)-1))
r2 <- c(2:nrow(sub_AcclimationTemp))
# Calculate Q10= (R2/R1)^(10/(T2 - T1)) and attach to vector variable
rate1 <- sub_AcclimationTemp$mean[r1]
rate2 <- sub_AcclimationTemp$mean[r2]
temp1 <- sub_AcclimationTemp$ExperimentalTemperature_C[r1]
temp2 <- sub_AcclimationTemp$ExperimentalTemperature_C[r2]
q10 <- (rate2/rate1)^(10/(temp2-temp1))
# Create results table
Q10 <- rbind(Q10, data.frame("Species" = sub_AcclimationTemp$Species[1],
"AcclimationTemperature_C" = sub_AcclimationTemp$AcclimationTemperature_C[1],
"Trait" = sub_AcclimationTemp$Trait[1],
"Q10" = round(q10, 3),
"Temp1" = round(temp1, 1),
"Temp2" = round(temp2, 1)))
# Close loop x
}
# Attach to data frame
Q10_species <- rbind(Q10_species, Q10)
# Close loop z
}
# Attach to overall q10 data frame
q10_means_all <- rbind(q10_means_all, Q10_species)
# Close loop i
}
5A. Calculate descriptive statistics for all Q10
# Remove outliers
outliers <- boxplot(q10_all$Q10, plot = FALSE)$out
q10_all_noOutliers <- q10_all[-which(q10_all$Q10 %in% outliers),]
# Calculate summary statistics
q10_means <- ddply(q10_all_noOutliers, c("Species", "Trait", "AcclimationTemperature_C", "Temp1"), summarise,
mean = mean(Q10, na.rm = TRUE),
n = length(Q10),
sd = sd(Q10, na.rm = TRUE),
ci = qt(0.975, n) * sd / sqrt(n),
lower_ci = mean-ci,
upper_ci = mean+ci,
min = min(Q10),
max = max(Q10))
# Round values
q10_means <- q10_means %>% mutate_if(is.numeric, round, digit = 3)
# Display results
q10_means %>% kbl(digits = 1, caption = "Thermal coefficent Q10") %>% kable_classic()
Thermal coefficent Q10
Species
|
Trait
|
AcclimationTemperature_C
|
Temp1
|
mean
|
n
|
sd
|
ci
|
lower_ci
|
upper_ci
|
min
|
max
|
Jasus edwardsii
|
AerobicScope
|
14.0
|
14.0
|
1.3
|
6
|
1.0
|
1.0
|
0.3
|
2.3
|
0.3
|
3.2
|
Jasus edwardsii
|
AerobicScope
|
14.0
|
17.5
|
0.6
|
5
|
0.3
|
0.3
|
0.3
|
0.9
|
0.2
|
0.9
|
Jasus edwardsii
|
AerobicScope
|
17.5
|
14.0
|
1.0
|
6
|
0.8
|
0.8
|
0.2
|
1.8
|
0.0
|
2.2
|
Jasus edwardsii
|
AerobicScope
|
17.5
|
17.5
|
1.2
|
5
|
1.1
|
1.2
|
0.0
|
2.4
|
0.6
|
3.1
|
Jasus edwardsii
|
AerobicScope
|
21.5
|
14.0
|
1.6
|
6
|
0.5
|
0.5
|
1.1
|
2.1
|
1.0
|
2.2
|
Jasus edwardsii
|
AerobicScope
|
21.5
|
17.5
|
1.2
|
6
|
0.6
|
0.6
|
0.6
|
1.9
|
0.7
|
2.4
|
Jasus edwardsii
|
AerobicScopeFactorial
|
14.0
|
14.0
|
0.7
|
6
|
0.6
|
0.6
|
0.1
|
1.2
|
0.1
|
1.4
|
Jasus edwardsii
|
AerobicScopeFactorial
|
14.0
|
17.5
|
0.3
|
5
|
0.2
|
0.2
|
0.1
|
0.5
|
0.1
|
0.5
|
Jasus edwardsii
|
AerobicScopeFactorial
|
17.5
|
14.0
|
0.6
|
6
|
0.7
|
0.7
|
-0.1
|
1.4
|
0.0
|
2.0
|
Jasus edwardsii
|
AerobicScopeFactorial
|
17.5
|
17.5
|
0.5
|
5
|
0.5
|
0.5
|
-0.1
|
1.0
|
0.1
|
1.3
|
Jasus edwardsii
|
AerobicScopeFactorial
|
21.5
|
14.0
|
0.8
|
6
|
0.8
|
0.8
|
0.0
|
1.6
|
0.0
|
1.9
|
Jasus edwardsii
|
AerobicScopeFactorial
|
21.5
|
17.5
|
0.9
|
6
|
0.9
|
0.9
|
0.0
|
1.7
|
0.2
|
2.6
|
Jasus edwardsii
|
as_50_recovery_time
|
14.0
|
14.0
|
2.0
|
2
|
2.6
|
7.9
|
-5.9
|
9.9
|
0.1
|
3.8
|
Jasus edwardsii
|
as_50_recovery_time
|
14.0
|
17.5
|
0.9
|
4
|
0.6
|
0.8
|
0.1
|
1.7
|
0.6
|
1.8
|
Jasus edwardsii
|
as_50_recovery_time
|
17.5
|
14.0
|
0.6
|
4
|
0.9
|
1.2
|
-0.6
|
1.8
|
0.1
|
1.9
|
Jasus edwardsii
|
as_50_recovery_time
|
17.5
|
17.5
|
0.7
|
2
|
1.0
|
3.1
|
-2.4
|
3.8
|
0.0
|
1.4
|
Jasus edwardsii
|
as_50_recovery_time
|
21.5
|
14.0
|
1.6
|
3
|
1.0
|
1.9
|
-0.3
|
3.5
|
1.0
|
2.8
|
Jasus edwardsii
|
as_50_recovery_time
|
21.5
|
17.5
|
1.3
|
6
|
1.0
|
1.0
|
0.3
|
2.4
|
0.0
|
2.7
|
Jasus edwardsii
|
EPOC
|
14.0
|
14.0
|
2.1
|
4
|
0.4
|
0.6
|
1.5
|
2.7
|
1.8
|
2.7
|
Jasus edwardsii
|
EPOC
|
14.0
|
17.5
|
1.4
|
5
|
2.0
|
2.3
|
-0.9
|
3.7
|
0.4
|
4.9
|
Jasus edwardsii
|
EPOC
|
17.5
|
14.0
|
1.0
|
6
|
1.4
|
1.4
|
-0.4
|
2.4
|
0.0
|
3.7
|
Jasus edwardsii
|
EPOC
|
17.5
|
17.5
|
3.2
|
2
|
2.1
|
6.3
|
-3.0
|
9.5
|
1.8
|
4.7
|
Jasus edwardsii
|
EPOC
|
21.5
|
14.0
|
4.1
|
2
|
0.7
|
2.0
|
2.0
|
6.1
|
3.6
|
4.5
|
Jasus edwardsii
|
EPOC
|
21.5
|
17.5
|
0.7
|
6
|
0.3
|
0.3
|
0.4
|
1.1
|
0.1
|
1.0
|
Jasus edwardsii
|
escape_speed_CLSec
|
14.0
|
14.0
|
1.2
|
6
|
0.6
|
0.6
|
0.5
|
1.8
|
0.5
|
2.0
|
Jasus edwardsii
|
escape_speed_CLSec
|
14.0
|
17.5
|
1.0
|
5
|
0.4
|
0.5
|
0.5
|
1.5
|
0.6
|
1.4
|
Jasus edwardsii
|
escape_speed_CLSec
|
17.5
|
14.0
|
1.3
|
6
|
0.9
|
0.9
|
0.4
|
2.2
|
0.3
|
2.8
|
Jasus edwardsii
|
escape_speed_CLSec
|
17.5
|
17.5
|
1.4
|
6
|
0.8
|
0.8
|
0.7
|
2.2
|
NA
|
NA
|
Jasus edwardsii
|
escape_speed_CLSec
|
21.5
|
14.0
|
1.2
|
6
|
0.5
|
0.5
|
0.7
|
1.7
|
0.7
|
2.1
|
Jasus edwardsii
|
escape_speed_CLSec
|
21.5
|
17.5
|
1.7
|
5
|
0.9
|
1.0
|
0.6
|
2.7
|
0.9
|
3.1
|
Jasus edwardsii
|
escape_speed_CLSec_top10
|
14.0
|
14.0
|
1.1
|
6
|
0.7
|
0.7
|
0.4
|
1.8
|
0.4
|
2.2
|
Jasus edwardsii
|
escape_speed_CLSec_top10
|
14.0
|
17.5
|
1.0
|
5
|
0.5
|
0.6
|
0.4
|
1.6
|
0.5
|
1.7
|
Jasus edwardsii
|
escape_speed_CLSec_top10
|
17.5
|
14.0
|
1.3
|
6
|
0.8
|
0.8
|
0.5
|
2.1
|
0.5
|
2.5
|
Jasus edwardsii
|
escape_speed_CLSec_top10
|
17.5
|
17.5
|
1.6
|
6
|
0.8
|
0.8
|
0.8
|
2.4
|
NA
|
NA
|
Jasus edwardsii
|
escape_speed_CLSec_top10
|
21.5
|
14.0
|
1.4
|
6
|
0.5
|
0.5
|
0.8
|
1.9
|
0.7
|
2.2
|
Jasus edwardsii
|
escape_speed_CLSec_top10
|
21.5
|
17.5
|
1.4
|
5
|
0.8
|
0.9
|
0.5
|
2.3
|
0.6
|
2.6
|
Jasus edwardsii
|
escape_speed_cmSec
|
14.0
|
14.0
|
1.2
|
6
|
0.6
|
0.6
|
0.5
|
1.8
|
0.5
|
2.0
|
Jasus edwardsii
|
escape_speed_cmSec
|
14.0
|
17.5
|
1.0
|
5
|
0.4
|
0.5
|
0.5
|
1.5
|
0.6
|
1.4
|
Jasus edwardsii
|
escape_speed_cmSec
|
17.5
|
14.0
|
1.3
|
6
|
0.9
|
0.9
|
0.4
|
2.2
|
0.3
|
2.8
|
Jasus edwardsii
|
escape_speed_cmSec
|
17.5
|
17.5
|
1.4
|
6
|
0.8
|
0.8
|
0.7
|
2.2
|
NA
|
NA
|
Jasus edwardsii
|
escape_speed_cmSec
|
21.5
|
14.0
|
1.2
|
6
|
0.5
|
0.5
|
0.7
|
1.7
|
0.7
|
2.1
|
Jasus edwardsii
|
escape_speed_cmSec
|
21.5
|
17.5
|
1.7
|
5
|
0.9
|
1.0
|
0.6
|
2.7
|
0.9
|
3.1
|
Jasus edwardsii
|
escape_speed_cmSec_top10
|
14.0
|
14.0
|
1.1
|
6
|
0.7
|
0.7
|
0.4
|
1.8
|
0.4
|
2.2
|
Jasus edwardsii
|
escape_speed_cmSec_top10
|
14.0
|
17.5
|
1.0
|
5
|
0.5
|
0.6
|
0.4
|
1.6
|
0.5
|
1.7
|
Jasus edwardsii
|
escape_speed_cmSec_top10
|
17.5
|
14.0
|
1.3
|
6
|
0.8
|
0.8
|
0.5
|
2.1
|
0.5
|
2.5
|
Jasus edwardsii
|
escape_speed_cmSec_top10
|
17.5
|
17.5
|
1.6
|
6
|
0.8
|
0.8
|
0.8
|
2.5
|
NA
|
NA
|
Jasus edwardsii
|
escape_speed_cmSec_top10
|
21.5
|
14.0
|
1.4
|
6
|
0.5
|
0.5
|
0.8
|
1.9
|
0.7
|
2.2
|
Jasus edwardsii
|
escape_speed_cmSec_top10
|
21.5
|
17.5
|
1.4
|
5
|
0.8
|
0.9
|
0.5
|
2.3
|
0.6
|
2.6
|
Jasus edwardsii
|
escape_total
|
14.0
|
14.0
|
1.0
|
4
|
0.7
|
1.0
|
0.1
|
2.0
|
0.3
|
1.8
|
Jasus edwardsii
|
escape_total
|
14.0
|
17.5
|
0.5
|
5
|
0.4
|
0.5
|
0.0
|
1.0
|
0.0
|
1.2
|
Jasus edwardsii
|
escape_total
|
17.5
|
14.0
|
0.5
|
5
|
0.5
|
0.6
|
-0.1
|
1.0
|
0.0
|
1.2
|
Jasus edwardsii
|
escape_total
|
17.5
|
17.5
|
1.6
|
4
|
1.3
|
1.9
|
-0.2
|
3.5
|
0.4
|
3.4
|
Jasus edwardsii
|
escape_total
|
21.5
|
14.0
|
1.5
|
3
|
0.4
|
0.8
|
0.8
|
2.3
|
1.2
|
2.0
|
Jasus edwardsii
|
escape_total
|
21.5
|
17.5
|
1.1
|
5
|
0.9
|
1.1
|
0.1
|
2.2
|
0.4
|
2.6
|
Jasus edwardsii
|
MMR
|
14.0
|
14.0
|
1.5
|
6
|
0.8
|
0.8
|
0.7
|
2.3
|
0.8
|
3.0
|
Jasus edwardsii
|
MMR
|
14.0
|
17.5
|
1.0
|
5
|
0.3
|
0.3
|
0.7
|
1.3
|
0.7
|
1.3
|
Jasus edwardsii
|
MMR
|
17.5
|
14.0
|
1.1
|
6
|
0.7
|
0.7
|
0.4
|
1.9
|
0.3
|
2.3
|
Jasus edwardsii
|
MMR
|
17.5
|
17.5
|
1.8
|
6
|
1.0
|
1.0
|
0.8
|
2.9
|
0.9
|
3.4
|
Jasus edwardsii
|
MMR
|
21.5
|
14.0
|
1.9
|
6
|
0.4
|
0.4
|
1.5
|
2.2
|
1.3
|
2.4
|
Jasus edwardsii
|
MMR
|
21.5
|
17.5
|
1.4
|
6
|
0.3
|
0.3
|
1.1
|
1.6
|
1.0
|
1.7
|
Jasus edwardsii
|
Recovery_Rate
|
14.0
|
14.0
|
1.6
|
6
|
0.6
|
0.6
|
1.0
|
2.1
|
0.6
|
2.1
|
Jasus edwardsii
|
Recovery_Rate
|
14.0
|
17.5
|
0.8
|
5
|
0.4
|
0.4
|
0.3
|
1.2
|
0.2
|
1.3
|
Jasus edwardsii
|
Recovery_Rate
|
17.5
|
14.0
|
0.8
|
6
|
0.5
|
0.5
|
0.3
|
1.3
|
0.2
|
1.6
|
Jasus edwardsii
|
Recovery_Rate
|
17.5
|
17.5
|
2.3
|
4
|
1.3
|
1.8
|
0.5
|
4.1
|
0.9
|
3.6
|
Jasus edwardsii
|
Recovery_Rate
|
21.5
|
14.0
|
2.5
|
5
|
1.3
|
1.5
|
1.0
|
3.9
|
0.8
|
4.1
|
Jasus edwardsii
|
Recovery_Rate
|
21.5
|
17.5
|
1.8
|
6
|
1.6
|
1.6
|
0.2
|
3.4
|
0.5
|
4.8
|
Jasus edwardsii
|
recovery_time
|
14.0
|
14.0
|
1.8
|
4
|
0.9
|
1.2
|
0.6
|
3.0
|
1.0
|
3.1
|
Jasus edwardsii
|
recovery_time
|
14.0
|
17.5
|
1.5
|
5
|
1.4
|
1.6
|
-0.1
|
3.1
|
0.5
|
3.9
|
Jasus edwardsii
|
recovery_time
|
17.5
|
14.0
|
0.7
|
5
|
0.8
|
0.9
|
-0.2
|
1.6
|
0.0
|
1.5
|
Jasus edwardsii
|
recovery_time
|
17.5
|
17.5
|
1.6
|
4
|
1.2
|
1.7
|
-0.1
|
3.2
|
0.3
|
3.0
|
Jasus edwardsii
|
recovery_time
|
21.5
|
14.0
|
2.9
|
3
|
1.5
|
2.8
|
0.1
|
5.6
|
1.8
|
4.6
|
Jasus edwardsii
|
recovery_time
|
21.5
|
17.5
|
0.7
|
6
|
0.6
|
0.6
|
0.1
|
1.3
|
0.1
|
1.7
|
Jasus edwardsii
|
RMR
|
14.0
|
14.0
|
2.3
|
5
|
1.3
|
1.5
|
0.8
|
3.8
|
1.0
|
4.4
|
Jasus edwardsii
|
RMR
|
14.0
|
17.5
|
2.5
|
5
|
1.0
|
1.2
|
1.3
|
3.7
|
1.9
|
4.3
|
Jasus edwardsii
|
RMR
|
17.5
|
14.0
|
2.7
|
6
|
1.1
|
1.1
|
1.6
|
3.9
|
1.3
|
4.6
|
Jasus edwardsii
|
RMR
|
17.5
|
17.5
|
1.8
|
5
|
0.8
|
0.9
|
0.9
|
2.7
|
0.9
|
2.6
|
Jasus edwardsii
|
RMR
|
21.5
|
14.0
|
2.0
|
5
|
0.6
|
0.7
|
1.3
|
2.7
|
1.4
|
2.8
|
Jasus edwardsii
|
RMR
|
21.5
|
17.5
|
2.4
|
6
|
0.8
|
0.8
|
1.6
|
3.2
|
1.4
|
3.5
|
Jasus edwardsii
|
SMR
|
14.0
|
14.0
|
2.2
|
4
|
1.3
|
1.8
|
0.4
|
4.1
|
1.2
|
4.1
|
Jasus edwardsii
|
SMR
|
14.0
|
17.5
|
2.6
|
3
|
0.3
|
0.6
|
2.0
|
3.2
|
2.3
|
2.9
|
Jasus edwardsii
|
SMR
|
17.5
|
14.0
|
2.5
|
4
|
1.9
|
2.6
|
-0.1
|
5.1
|
0.5
|
4.9
|
Jasus edwardsii
|
SMR
|
17.5
|
17.5
|
2.5
|
5
|
1.4
|
1.6
|
1.0
|
4.1
|
0.7
|
3.9
|
Jasus edwardsii
|
SMR
|
21.5
|
14.0
|
1.2
|
3
|
0.4
|
0.6
|
0.6
|
1.9
|
1.0
|
1.6
|
Jasus edwardsii
|
SMR
|
21.5
|
17.5
|
2.2
|
5
|
1.2
|
1.4
|
0.8
|
3.5
|
0.7
|
3.4
|
Jasus edwardsii
|
SMR_fraction
|
14.0
|
14.0
|
2.5
|
5
|
2.2
|
2.5
|
0.0
|
4.9
|
0.7
|
4.8
|
Jasus edwardsii
|
SMR_fraction
|
14.0
|
17.5
|
2.4
|
3
|
0.4
|
0.8
|
1.6
|
3.2
|
2.1
|
2.9
|
Jasus edwardsii
|
SMR_fraction
|
17.5
|
14.0
|
1.6
|
4
|
1.0
|
1.4
|
0.2
|
3.0
|
0.5
|
2.9
|
Jasus edwardsii
|
SMR_fraction
|
17.5
|
17.5
|
2.2
|
5
|
1.8
|
2.1
|
0.1
|
4.3
|
0.2
|
4.4
|
Jasus edwardsii
|
SMR_fraction
|
21.5
|
14.0
|
2.0
|
5
|
1.8
|
2.0
|
0.0
|
4.1
|
0.5
|
4.5
|
Jasus edwardsii
|
SMR_fraction
|
21.5
|
17.5
|
1.5
|
5
|
0.8
|
0.9
|
0.6
|
2.5
|
0.4
|
2.4
|
Sagmariasus verreauxi
|
AerobicScope
|
14.0
|
14.0
|
1.1
|
5
|
0.7
|
0.8
|
0.3
|
1.9
|
0.3
|
2.1
|
Sagmariasus verreauxi
|
AerobicScope
|
14.0
|
17.5
|
0.8
|
6
|
0.4
|
0.4
|
0.4
|
1.2
|
0.1
|
1.3
|
Sagmariasus verreauxi
|
AerobicScope
|
17.5
|
14.0
|
1.4
|
5
|
0.7
|
0.8
|
0.6
|
2.1
|
0.5
|
2.1
|
Sagmariasus verreauxi
|
AerobicScope
|
17.5
|
17.5
|
1.2
|
6
|
0.5
|
0.5
|
0.7
|
1.7
|
0.7
|
2.1
|
Sagmariasus verreauxi
|
AerobicScope
|
21.5
|
14.0
|
1.8
|
6
|
0.7
|
0.7
|
1.2
|
2.5
|
1.1
|
2.7
|
Sagmariasus verreauxi
|
AerobicScope
|
21.5
|
17.5
|
1.3
|
6
|
0.5
|
0.5
|
0.9
|
1.8
|
0.9
|
1.8
|
Sagmariasus verreauxi
|
AerobicScopeFactorial
|
14.0
|
14.0
|
0.3
|
5
|
0.1
|
0.1
|
0.2
|
0.4
|
0.1
|
0.4
|
Sagmariasus verreauxi
|
AerobicScopeFactorial
|
14.0
|
17.5
|
0.6
|
6
|
0.4
|
0.4
|
0.2
|
0.9
|
0.2
|
1.1
|
Sagmariasus verreauxi
|
AerobicScopeFactorial
|
17.5
|
14.0
|
0.7
|
5
|
0.5
|
0.6
|
0.0
|
1.3
|
0.1
|
1.3
|
Sagmariasus verreauxi
|
AerobicScopeFactorial
|
17.5
|
17.5
|
0.6
|
6
|
0.6
|
0.6
|
0.0
|
1.2
|
0.2
|
1.8
|
Sagmariasus verreauxi
|
AerobicScopeFactorial
|
21.5
|
14.0
|
0.8
|
6
|
0.4
|
0.4
|
0.4
|
1.2
|
0.5
|
1.4
|
Sagmariasus verreauxi
|
AerobicScopeFactorial
|
21.5
|
17.5
|
0.5
|
6
|
0.3
|
0.3
|
0.2
|
0.7
|
0.2
|
0.9
|
Sagmariasus verreauxi
|
as_50_recovery_time
|
14.0
|
14.0
|
1.4
|
2
|
1.9
|
5.7
|
-4.3
|
7.1
|
0.1
|
2.7
|
Sagmariasus verreauxi
|
as_50_recovery_time
|
14.0
|
17.5
|
0.7
|
5
|
0.6
|
0.7
|
0.0
|
1.4
|
0.1
|
1.6
|
Sagmariasus verreauxi
|
as_50_recovery_time
|
17.5
|
14.0
|
1.2
|
4
|
1.4
|
1.9
|
-0.7
|
3.1
|
0.1
|
3.2
|
Sagmariasus verreauxi
|
as_50_recovery_time
|
17.5
|
17.5
|
0.5
|
2
|
0.5
|
1.6
|
-1.1
|
2.1
|
0.1
|
0.9
|
Sagmariasus verreauxi
|
as_50_recovery_time
|
21.5
|
14.0
|
1.6
|
5
|
1.5
|
1.7
|
0.0
|
3.3
|
0.4
|
4.1
|
Sagmariasus verreauxi
|
as_50_recovery_time
|
21.5
|
17.5
|
1.5
|
2
|
0.1
|
0.2
|
1.3
|
1.7
|
1.5
|
1.6
|
Sagmariasus verreauxi
|
EPOC
|
14.0
|
14.0
|
2.1
|
4
|
1.9
|
2.6
|
-0.5
|
4.7
|
0.8
|
4.8
|
Sagmariasus verreauxi
|
EPOC
|
14.0
|
17.5
|
1.9
|
6
|
1.6
|
1.6
|
0.3
|
3.4
|
0.3
|
4.0
|
Sagmariasus verreauxi
|
EPOC
|
17.5
|
14.0
|
0.9
|
3
|
0.4
|
0.8
|
0.1
|
1.6
|
0.6
|
1.3
|
Sagmariasus verreauxi
|
EPOC
|
17.5
|
17.5
|
1.9
|
6
|
1.1
|
1.1
|
0.8
|
3.1
|
0.1
|
3.3
|
Sagmariasus verreauxi
|
EPOC
|
21.5
|
14.0
|
0.7
|
3
|
0.4
|
0.7
|
0.0
|
1.4
|
0.3
|
1.0
|
Sagmariasus verreauxi
|
EPOC
|
21.5
|
17.5
|
2.5
|
5
|
1.5
|
1.7
|
0.8
|
4.2
|
0.5
|
4.3
|
Sagmariasus verreauxi
|
escape_speed_CLSec
|
14.0
|
14.0
|
0.7
|
5
|
0.4
|
0.4
|
0.3
|
1.2
|
0.4
|
1.3
|
Sagmariasus verreauxi
|
escape_speed_CLSec
|
14.0
|
17.5
|
1.5
|
4
|
0.3
|
0.4
|
1.0
|
1.9
|
1.1
|
1.9
|
Sagmariasus verreauxi
|
escape_speed_CLSec
|
17.5
|
14.0
|
1.5
|
5
|
0.6
|
0.6
|
0.9
|
2.1
|
NA
|
NA
|
Sagmariasus verreauxi
|
escape_speed_CLSec
|
17.5
|
17.5
|
1.2
|
6
|
0.4
|
0.4
|
0.7
|
1.6
|
NA
|
NA
|
Sagmariasus verreauxi
|
escape_speed_CLSec
|
21.5
|
14.0
|
1.3
|
5
|
0.5
|
0.5
|
0.8
|
1.9
|
0.8
|
2.0
|
Sagmariasus verreauxi
|
escape_speed_CLSec
|
21.5
|
17.5
|
1.4
|
6
|
0.5
|
0.5
|
0.9
|
1.9
|
0.9
|
2.3
|
Sagmariasus verreauxi
|
escape_speed_CLSec_top10
|
14.0
|
14.0
|
0.7
|
5
|
0.3
|
0.4
|
0.3
|
1.1
|
0.3
|
1.3
|
Sagmariasus verreauxi
|
escape_speed_CLSec_top10
|
14.0
|
17.5
|
1.6
|
4
|
0.5
|
0.6
|
0.9
|
2.2
|
1.2
|
2.2
|
Sagmariasus verreauxi
|
escape_speed_CLSec_top10
|
17.5
|
14.0
|
1.9
|
5
|
0.9
|
1.0
|
0.9
|
2.8
|
NA
|
NA
|
Sagmariasus verreauxi
|
escape_speed_CLSec_top10
|
17.5
|
17.5
|
1.1
|
6
|
0.5
|
0.5
|
0.6
|
1.6
|
NA
|
NA
|
Sagmariasus verreauxi
|
escape_speed_CLSec_top10
|
21.5
|
14.0
|
1.4
|
5
|
0.6
|
0.7
|
0.7
|
2.0
|
0.6
|
1.9
|
Sagmariasus verreauxi
|
escape_speed_CLSec_top10
|
21.5
|
17.5
|
1.4
|
6
|
0.4
|
0.4
|
1.0
|
1.8
|
1.0
|
2.1
|
Sagmariasus verreauxi
|
escape_speed_cmSec
|
14.0
|
14.0
|
0.8
|
5
|
0.4
|
0.4
|
0.3
|
1.2
|
0.4
|
1.4
|
Sagmariasus verreauxi
|
escape_speed_cmSec
|
14.0
|
17.5
|
1.5
|
4
|
0.3
|
0.4
|
1.0
|
1.9
|
1.1
|
1.9
|
Sagmariasus verreauxi
|
escape_speed_cmSec
|
17.5
|
14.0
|
1.5
|
5
|
0.6
|
0.6
|
0.9
|
2.1
|
NA
|
NA
|
Sagmariasus verreauxi
|
escape_speed_cmSec
|
17.5
|
17.5
|
1.2
|
6
|
0.4
|
0.4
|
0.7
|
1.6
|
NA
|
NA
|
Sagmariasus verreauxi
|
escape_speed_cmSec
|
21.5
|
14.0
|
1.3
|
5
|
0.5
|
0.5
|
0.8
|
1.9
|
0.8
|
2.0
|
Sagmariasus verreauxi
|
escape_speed_cmSec
|
21.5
|
17.5
|
1.4
|
6
|
0.5
|
0.5
|
0.9
|
1.9
|
0.9
|
2.3
|
Sagmariasus verreauxi
|
escape_speed_cmSec_top10
|
14.0
|
14.0
|
0.7
|
5
|
0.4
|
0.4
|
0.3
|
1.1
|
0.3
|
1.3
|
Sagmariasus verreauxi
|
escape_speed_cmSec_top10
|
14.0
|
17.5
|
1.6
|
4
|
0.5
|
0.6
|
0.9
|
2.2
|
1.2
|
2.2
|
Sagmariasus verreauxi
|
escape_speed_cmSec_top10
|
17.5
|
14.0
|
1.9
|
5
|
0.9
|
1.0
|
0.9
|
2.8
|
NA
|
NA
|
Sagmariasus verreauxi
|
escape_speed_cmSec_top10
|
17.5
|
17.5
|
1.1
|
6
|
0.5
|
0.5
|
0.6
|
1.6
|
NA
|
NA
|
Sagmariasus verreauxi
|
escape_speed_cmSec_top10
|
21.5
|
14.0
|
1.4
|
5
|
0.6
|
0.7
|
0.7
|
2.0
|
0.6
|
1.9
|
Sagmariasus verreauxi
|
escape_speed_cmSec_top10
|
21.5
|
17.5
|
1.4
|
6
|
0.4
|
0.4
|
1.0
|
1.8
|
1.0
|
2.1
|
Sagmariasus verreauxi
|
escape_total
|
14.0
|
14.0
|
1.7
|
5
|
1.5
|
1.8
|
-0.1
|
3.4
|
0.2
|
3.9
|
Sagmariasus verreauxi
|
escape_total
|
14.0
|
17.5
|
0.4
|
4
|
0.2
|
0.3
|
0.1
|
0.6
|
0.1
|
0.5
|
Sagmariasus verreauxi
|
escape_total
|
17.5
|
14.0
|
1.5
|
5
|
0.7
|
0.8
|
0.7
|
2.3
|
0.6
|
2.3
|
Sagmariasus verreauxi
|
escape_total
|
17.5
|
17.5
|
0.6
|
6
|
0.4
|
0.4
|
0.3
|
1.0
|
0.1
|
1.1
|
Sagmariasus verreauxi
|
escape_total
|
21.5
|
14.0
|
1.9
|
5
|
1.4
|
1.6
|
0.3
|
3.4
|
0.5
|
3.7
|
Sagmariasus verreauxi
|
escape_total
|
21.5
|
17.5
|
1.4
|
6
|
1.4
|
1.4
|
0.0
|
2.7
|
0.3
|
3.6
|
Sagmariasus verreauxi
|
MMR
|
14.0
|
14.0
|
1.6
|
5
|
0.8
|
0.9
|
0.7
|
2.5
|
1.0
|
3.0
|
Sagmariasus verreauxi
|
MMR
|
14.0
|
17.5
|
1.2
|
6
|
0.1
|
0.1
|
1.1
|
1.3
|
1.1
|
1.3
|
Sagmariasus verreauxi
|
MMR
|
17.5
|
14.0
|
1.5
|
5
|
0.5
|
0.5
|
1.0
|
2.1
|
1.1
|
2.2
|
Sagmariasus verreauxi
|
MMR
|
17.5
|
17.5
|
1.4
|
6
|
0.3
|
0.3
|
1.1
|
1.7
|
1.0
|
1.7
|
Sagmariasus verreauxi
|
MMR
|
21.5
|
14.0
|
1.9
|
6
|
0.5
|
0.5
|
1.3
|
2.4
|
1.2
|
2.5
|
Sagmariasus verreauxi
|
MMR
|
21.5
|
17.5
|
1.6
|
6
|
0.4
|
0.4
|
1.2
|
2.0
|
1.2
|
2.1
|
Sagmariasus verreauxi
|
Recovery_Rate
|
14.0
|
14.0
|
1.7
|
5
|
1.4
|
1.6
|
0.1
|
3.3
|
0.2
|
3.9
|
Sagmariasus verreauxi
|
Recovery_Rate
|
14.0
|
17.5
|
0.7
|
6
|
0.5
|
0.5
|
0.2
|
1.3
|
0.1
|
1.5
|
Sagmariasus verreauxi
|
Recovery_Rate
|
17.5
|
14.0
|
2.0
|
5
|
1.2
|
1.3
|
0.6
|
3.3
|
0.5
|
3.0
|
Sagmariasus verreauxi
|
Recovery_Rate
|
17.5
|
17.5
|
1.5
|
6
|
0.8
|
0.8
|
0.7
|
2.4
|
0.4
|
2.9
|
Sagmariasus verreauxi
|
Recovery_Rate
|
21.5
|
14.0
|
2.4
|
6
|
1.0
|
1.0
|
1.4
|
3.4
|
1.1
|
3.6
|
Sagmariasus verreauxi
|
Recovery_Rate
|
21.5
|
17.5
|
1.9
|
6
|
0.4
|
0.4
|
1.5
|
2.2
|
1.4
|
2.3
|
Sagmariasus verreauxi
|
recovery_time
|
14.0
|
14.0
|
2.1
|
4
|
1.4
|
1.9
|
0.2
|
4.0
|
0.7
|
3.9
|
Sagmariasus verreauxi
|
recovery_time
|
14.0
|
17.5
|
1.5
|
4
|
0.9
|
1.3
|
0.2
|
2.8
|
0.7
|
2.7
|
Sagmariasus verreauxi
|
recovery_time
|
17.5
|
14.0
|
0.9
|
4
|
0.9
|
1.3
|
-0.4
|
2.2
|
0.2
|
2.3
|
Sagmariasus verreauxi
|
recovery_time
|
17.5
|
17.5
|
1.1
|
5
|
0.8
|
0.9
|
0.2
|
1.9
|
0.1
|
2.2
|
Sagmariasus verreauxi
|
recovery_time
|
21.5
|
14.0
|
1.1
|
5
|
1.2
|
1.4
|
-0.3
|
2.6
|
0.2
|
3.2
|
Sagmariasus verreauxi
|
recovery_time
|
21.5
|
17.5
|
1.4
|
5
|
0.9
|
1.0
|
0.4
|
2.4
|
0.3
|
2.4
|
Sagmariasus verreauxi
|
RMR
|
14.0
|
14.0
|
2.9
|
4
|
1.3
|
1.8
|
1.1
|
4.7
|
1.7
|
4.1
|
Sagmariasus verreauxi
|
RMR
|
14.0
|
17.5
|
1.7
|
5
|
0.7
|
0.8
|
0.9
|
2.4
|
1.3
|
2.8
|
Sagmariasus verreauxi
|
RMR
|
17.5
|
14.0
|
2.6
|
4
|
0.9
|
1.3
|
1.3
|
3.9
|
1.3
|
3.5
|
Sagmariasus verreauxi
|
RMR
|
17.5
|
17.5
|
2.2
|
6
|
0.2
|
0.2
|
1.9
|
2.4
|
1.8
|
2.3
|
Sagmariasus verreauxi
|
RMR
|
21.5
|
14.0
|
2.3
|
6
|
1.0
|
1.0
|
1.3
|
3.2
|
0.9
|
3.5
|
Sagmariasus verreauxi
|
RMR
|
21.5
|
17.5
|
2.7
|
5
|
1.3
|
1.5
|
1.2
|
4.1
|
1.6
|
4.5
|
Sagmariasus verreauxi
|
SMR
|
14.0
|
14.0
|
3.8
|
3
|
0.3
|
0.6
|
3.2
|
4.4
|
3.5
|
4.2
|
Sagmariasus verreauxi
|
SMR
|
14.0
|
17.5
|
2.3
|
5
|
1.3
|
1.5
|
0.9
|
3.8
|
1.2
|
4.1
|
Sagmariasus verreauxi
|
SMR
|
17.5
|
14.0
|
2.1
|
3
|
1.3
|
2.4
|
-0.4
|
4.5
|
1.2
|
3.6
|
Sagmariasus verreauxi
|
SMR
|
17.5
|
17.5
|
2.9
|
5
|
1.6
|
1.9
|
1.1
|
4.8
|
0.9
|
4.8
|
Sagmariasus verreauxi
|
SMR
|
21.5
|
14.0
|
2.5
|
6
|
0.7
|
0.7
|
1.8
|
3.2
|
1.7
|
3.5
|
Sagmariasus verreauxi
|
SMR
|
21.5
|
17.5
|
3.2
|
4
|
1.0
|
1.3
|
1.9
|
4.5
|
2.1
|
4.3
|
Sagmariasus verreauxi
|
SMR_fraction
|
14.0
|
14.0
|
3.5
|
4
|
1.0
|
1.3
|
2.1
|
4.8
|
2.8
|
4.8
|
Sagmariasus verreauxi
|
SMR_fraction
|
14.0
|
17.5
|
2.0
|
5
|
1.1
|
1.2
|
0.7
|
3.2
|
0.9
|
3.3
|
Sagmariasus verreauxi
|
SMR_fraction
|
17.5
|
14.0
|
1.1
|
3
|
0.4
|
0.8
|
0.3
|
1.9
|
0.8
|
1.6
|
Sagmariasus verreauxi
|
SMR_fraction
|
17.5
|
17.5
|
2.3
|
5
|
1.4
|
1.6
|
0.7
|
3.9
|
0.6
|
4.3
|
Sagmariasus verreauxi
|
SMR_fraction
|
21.5
|
14.0
|
1.5
|
6
|
0.6
|
0.6
|
0.8
|
2.1
|
0.7
|
2.2
|
Sagmariasus verreauxi
|
SMR_fraction
|
21.5
|
17.5
|
2.4
|
5
|
1.3
|
1.5
|
0.9
|
4.0
|
1.1
|
4.4
|
5B. Calculate descriptive statistics for Q10 without 17.5 experimental temperature
# Remove outliers
outliers <- boxplot(q10_all_no17$Q10, plot = FALSE)$out
q10_all_no17_noOutliers <- q10_all_no17[-which(q10_all_no17$Q10 %in% outliers),]
# Calculate summary statistics
q10_means_no17 <- ddply(q10_all_no17_noOutliers, c("Species", "Trait", "AcclimationTemperature_C", "Temp1"), summarise,
mean = mean(Q10, na.rm = TRUE),
n = length(Q10),
sd = sd(Q10, na.rm = TRUE),
ci = qt(0.975, n) * sd / sqrt(n),
lower_ci = mean-ci,
upper_ci = mean+ci,
min = min(Q10),
max = max(Q10))
# Round values
q10_means_no17 <- q10_means_no17 %>% mutate_if(is.numeric, round, digit = 3)
# Display results
q10_means_no17 %>% kbl(digits = 1, caption = "Thermal coefficent Q10") %>% kable_classic()
Thermal coefficent Q10
Species
|
Trait
|
AcclimationTemperature_C
|
Temp1
|
mean
|
n
|
sd
|
ci
|
lower_ci
|
upper_ci
|
min
|
max
|
Jasus edwardsii
|
AerobicScope
|
14.0
|
14
|
0.8
|
5
|
0.3
|
0.4
|
0.4
|
1.2
|
0.4
|
1.4
|
Jasus edwardsii
|
AerobicScope
|
17.5
|
14
|
0.9
|
6
|
0.2
|
0.2
|
0.8
|
1.1
|
0.7
|
1.1
|
Jasus edwardsii
|
AerobicScope
|
21.5
|
14
|
1.3
|
6
|
0.3
|
0.3
|
1.0
|
1.6
|
0.9
|
1.7
|
Jasus edwardsii
|
AerobicScopeFactorial
|
14.0
|
14
|
0.4
|
5
|
0.2
|
0.2
|
0.2
|
0.6
|
0.3
|
0.7
|
Jasus edwardsii
|
AerobicScopeFactorial
|
17.5
|
14
|
0.4
|
6
|
0.0
|
0.0
|
0.3
|
0.4
|
0.3
|
0.4
|
Jasus edwardsii
|
AerobicScopeFactorial
|
21.5
|
14
|
0.6
|
6
|
0.3
|
0.3
|
0.3
|
0.9
|
0.2
|
1.0
|
Jasus edwardsii
|
as_50_recovery_time
|
14.0
|
14
|
1.9
|
3
|
0.9
|
1.6
|
0.3
|
3.5
|
1.3
|
2.9
|
Jasus edwardsii
|
as_50_recovery_time
|
17.5
|
14
|
1.4
|
3
|
1.2
|
2.3
|
-0.9
|
3.7
|
0.0
|
2.3
|
Jasus edwardsii
|
as_50_recovery_time
|
21.5
|
14
|
2.2
|
4
|
1.2
|
1.7
|
0.5
|
3.9
|
1.0
|
3.6
|
Jasus edwardsii
|
EPOC
|
14.0
|
14
|
2.0
|
5
|
1.0
|
1.2
|
0.8
|
3.2
|
0.9
|
3.3
|
Jasus edwardsii
|
EPOC
|
17.5
|
14
|
1.7
|
5
|
0.5
|
0.6
|
1.1
|
2.3
|
0.9
|
2.3
|
Jasus edwardsii
|
EPOC
|
21.5
|
14
|
2.5
|
4
|
1.0
|
1.4
|
1.1
|
3.9
|
1.8
|
4.0
|
Jasus edwardsii
|
escape_speed_CLSec
|
14.0
|
14
|
1.0
|
5
|
0.4
|
0.5
|
0.5
|
1.5
|
0.6
|
1.7
|
Jasus edwardsii
|
escape_speed_CLSec
|
17.5
|
14
|
1.3
|
6
|
0.1
|
0.1
|
1.2
|
1.4
|
NA
|
NA
|
Jasus edwardsii
|
escape_speed_CLSec
|
21.5
|
14
|
1.3
|
6
|
0.3
|
0.3
|
1.0
|
1.6
|
0.9
|
1.8
|
Jasus edwardsii
|
escape_speed_CLSec_top10
|
14.0
|
14
|
0.9
|
5
|
0.4
|
0.5
|
0.4
|
1.4
|
0.5
|
1.5
|
Jasus edwardsii
|
escape_speed_CLSec_top10
|
17.5
|
14
|
1.4
|
6
|
0.1
|
0.1
|
1.3
|
1.5
|
NA
|
NA
|
Jasus edwardsii
|
escape_speed_CLSec_top10
|
21.5
|
14
|
1.3
|
6
|
0.3
|
0.3
|
1.0
|
1.6
|
0.9
|
1.8
|
Jasus edwardsii
|
escape_speed_cmSec
|
14.0
|
14
|
1.0
|
5
|
0.4
|
0.5
|
0.5
|
1.5
|
0.6
|
1.7
|
Jasus edwardsii
|
escape_speed_cmSec
|
17.5
|
14
|
1.3
|
6
|
0.1
|
0.1
|
1.2
|
1.4
|
NA
|
NA
|
Jasus edwardsii
|
escape_speed_cmSec
|
21.5
|
14
|
1.3
|
6
|
0.3
|
0.3
|
1.0
|
1.6
|
0.9
|
1.8
|
Jasus edwardsii
|
escape_speed_cmSec_top10
|
14.0
|
14
|
0.9
|
5
|
0.4
|
0.5
|
0.4
|
1.4
|
0.5
|
1.5
|
Jasus edwardsii
|
escape_speed_cmSec_top10
|
17.5
|
14
|
1.4
|
6
|
0.1
|
0.1
|
1.3
|
1.5
|
NA
|
NA
|
Jasus edwardsii
|
escape_speed_cmSec_top10
|
21.5
|
14
|
1.3
|
6
|
0.3
|
0.3
|
1.0
|
1.6
|
0.9
|
1.8
|
Jasus edwardsii
|
escape_total
|
14.0
|
14
|
1.5
|
5
|
1.4
|
1.6
|
-0.1
|
3.1
|
0.1
|
3.6
|
Jasus edwardsii
|
escape_total
|
17.5
|
14
|
1.2
|
6
|
0.2
|
0.2
|
1.0
|
1.4
|
1.0
|
1.5
|
Jasus edwardsii
|
escape_total
|
21.5
|
14
|
2.1
|
6
|
1.2
|
1.2
|
0.9
|
3.3
|
0.7
|
3.7
|
Jasus edwardsii
|
MMR
|
14.0
|
14
|
1.2
|
5
|
0.2
|
0.3
|
1.0
|
1.5
|
0.9
|
1.6
|
Jasus edwardsii
|
MMR
|
17.5
|
14
|
1.3
|
6
|
0.2
|
0.2
|
1.1
|
1.4
|
1.0
|
1.4
|
Jasus edwardsii
|
MMR
|
21.5
|
14
|
1.6
|
6
|
0.2
|
0.2
|
1.3
|
1.8
|
1.4
|
2.0
|
Jasus edwardsii
|
Recovery_Rate
|
14.0
|
14
|
1.1
|
5
|
0.4
|
0.4
|
0.7
|
1.5
|
0.6
|
1.6
|
Jasus edwardsii
|
Recovery_Rate
|
17.5
|
14
|
1.6
|
6
|
0.4
|
0.4
|
1.2
|
1.9
|
0.9
|
2.0
|
Jasus edwardsii
|
Recovery_Rate
|
21.5
|
14
|
2.0
|
6
|
0.8
|
0.8
|
1.2
|
2.8
|
1.1
|
3.1
|
Jasus edwardsii
|
recovery_time
|
14.0
|
14
|
1.7
|
5
|
0.5
|
0.6
|
1.2
|
2.3
|
1.1
|
2.3
|
Jasus edwardsii
|
recovery_time
|
17.5
|
14
|
1.4
|
6
|
0.5
|
0.5
|
0.8
|
1.9
|
0.6
|
2.1
|
Jasus edwardsii
|
recovery_time
|
21.5
|
14
|
1.7
|
6
|
0.7
|
0.7
|
1.0
|
2.3
|
0.8
|
2.9
|
Jasus edwardsii
|
RMR
|
14.0
|
14
|
2.3
|
5
|
0.4
|
0.5
|
1.8
|
2.8
|
1.9
|
3.0
|
Jasus edwardsii
|
RMR
|
17.5
|
14
|
2.3
|
6
|
0.5
|
0.5
|
1.8
|
2.8
|
1.9
|
3.2
|
Jasus edwardsii
|
RMR
|
21.5
|
14
|
2.4
|
6
|
0.5
|
0.5
|
1.8
|
2.9
|
1.9
|
3.2
|
Jasus edwardsii
|
SMR
|
14.0
|
14
|
2.8
|
3
|
0.6
|
1.0
|
1.8
|
3.8
|
2.4
|
3.4
|
Jasus edwardsii
|
SMR
|
17.5
|
14
|
3.1
|
5
|
0.3
|
0.4
|
2.8
|
3.5
|
2.8
|
3.6
|
Jasus edwardsii
|
SMR
|
21.5
|
14
|
2.1
|
4
|
0.4
|
0.6
|
1.5
|
2.7
|
1.7
|
2.6
|
Jasus edwardsii
|
SMR_fraction
|
14.0
|
14
|
2.8
|
5
|
0.8
|
0.9
|
1.9
|
3.7
|
1.5
|
3.6
|
Jasus edwardsii
|
SMR_fraction
|
17.5
|
14
|
2.6
|
6
|
0.3
|
0.3
|
2.4
|
2.9
|
2.3
|
3.1
|
Jasus edwardsii
|
SMR_fraction
|
21.5
|
14
|
1.8
|
5
|
0.8
|
0.9
|
0.9
|
2.7
|
1.1
|
3.0
|
Sagmariasus verreauxi
|
AerobicScope
|
14.0
|
14
|
0.9
|
5
|
0.5
|
0.6
|
0.3
|
1.5
|
0.2
|
1.5
|
Sagmariasus verreauxi
|
AerobicScope
|
17.5
|
14
|
1.2
|
5
|
0.2
|
0.3
|
0.9
|
1.5
|
0.9
|
1.5
|
Sagmariasus verreauxi
|
AerobicScope
|
21.5
|
14
|
1.5
|
6
|
0.4
|
0.4
|
1.1
|
1.9
|
1.0
|
2.1
|
Sagmariasus verreauxi
|
AerobicScopeFactorial
|
14.0
|
14
|
0.4
|
5
|
0.2
|
0.2
|
0.2
|
0.6
|
0.2
|
0.6
|
Sagmariasus verreauxi
|
AerobicScopeFactorial
|
17.5
|
14
|
0.5
|
5
|
0.2
|
0.3
|
0.2
|
0.8
|
0.3
|
0.8
|
Sagmariasus verreauxi
|
AerobicScopeFactorial
|
21.5
|
14
|
0.6
|
6
|
0.2
|
0.2
|
0.4
|
0.8
|
0.3
|
0.8
|
Sagmariasus verreauxi
|
as_50_recovery_time
|
14.0
|
14
|
1.6
|
3
|
2.1
|
3.8
|
-2.1
|
5.4
|
0.3
|
4.0
|
Sagmariasus verreauxi
|
as_50_recovery_time
|
17.5
|
14
|
2.6
|
4
|
0.3
|
0.4
|
2.2
|
3.1
|
2.2
|
2.8
|
Sagmariasus verreauxi
|
as_50_recovery_time
|
21.5
|
14
|
1.7
|
3
|
1.3
|
2.4
|
-0.7
|
4.1
|
0.8
|
3.2
|
Sagmariasus verreauxi
|
EPOC
|
14.0
|
14
|
1.4
|
4
|
0.4
|
0.6
|
0.7
|
2.0
|
1.0
|
1.9
|
Sagmariasus verreauxi
|
EPOC
|
17.5
|
14
|
1.6
|
5
|
0.7
|
0.8
|
0.8
|
2.4
|
0.7
|
2.6
|
Sagmariasus verreauxi
|
EPOC
|
21.5
|
14
|
2.4
|
4
|
1.7
|
2.3
|
0.0
|
4.7
|
0.6
|
3.8
|
Sagmariasus verreauxi
|
escape_speed_CLSec
|
14.0
|
14
|
1.0
|
5
|
0.2
|
0.3
|
0.8
|
1.3
|
0.7
|
1.3
|
Sagmariasus verreauxi
|
escape_speed_CLSec
|
17.5
|
14
|
1.1
|
5
|
0.2
|
0.3
|
0.8
|
1.3
|
0.7
|
1.3
|
Sagmariasus verreauxi
|
escape_speed_CLSec
|
21.5
|
14
|
1.3
|
5
|
0.3
|
0.4
|
1.0
|
1.7
|
1.0
|
1.7
|
Sagmariasus verreauxi
|
escape_speed_CLSec_top10
|
14.0
|
14
|
1.0
|
5
|
0.2
|
0.3
|
0.7
|
1.3
|
0.7
|
1.3
|
Sagmariasus verreauxi
|
escape_speed_CLSec_top10
|
17.5
|
14
|
1.1
|
5
|
0.2
|
0.2
|
0.9
|
1.4
|
0.8
|
1.4
|
Sagmariasus verreauxi
|
escape_speed_CLSec_top10
|
21.5
|
14
|
1.4
|
5
|
0.4
|
0.5
|
0.9
|
1.9
|
0.9
|
2.0
|
Sagmariasus verreauxi
|
escape_speed_cmSec
|
14.0
|
14
|
1.0
|
5
|
0.3
|
0.3
|
0.8
|
1.3
|
0.7
|
1.4
|
Sagmariasus verreauxi
|
escape_speed_cmSec
|
17.5
|
14
|
1.1
|
5
|
0.2
|
0.3
|
0.8
|
1.3
|
0.7
|
1.3
|
Sagmariasus verreauxi
|
escape_speed_cmSec
|
21.5
|
14
|
1.3
|
5
|
0.3
|
0.4
|
1.0
|
1.7
|
1.0
|
1.7
|
Sagmariasus verreauxi
|
escape_speed_cmSec_top10
|
14.0
|
14
|
1.0
|
5
|
0.3
|
0.3
|
0.7
|
1.3
|
0.7
|
1.3
|
Sagmariasus verreauxi
|
escape_speed_cmSec_top10
|
17.5
|
14
|
1.1
|
5
|
0.2
|
0.2
|
0.9
|
1.4
|
0.8
|
1.4
|
Sagmariasus verreauxi
|
escape_speed_cmSec_top10
|
21.5
|
14
|
1.4
|
5
|
0.4
|
0.5
|
0.9
|
1.9
|
0.9
|
2.0
|
Sagmariasus verreauxi
|
escape_total
|
14.0
|
14
|
0.7
|
5
|
0.5
|
0.6
|
0.1
|
1.3
|
0.2
|
1.3
|
Sagmariasus verreauxi
|
escape_total
|
17.5
|
14
|
0.8
|
5
|
0.3
|
0.4
|
0.5
|
1.2
|
0.4
|
1.2
|
Sagmariasus verreauxi
|
escape_total
|
21.5
|
14
|
1.0
|
5
|
0.3
|
0.4
|
0.7
|
1.4
|
0.7
|
1.4
|
Sagmariasus verreauxi
|
MMR
|
14.0
|
14
|
1.3
|
5
|
0.3
|
0.4
|
0.9
|
1.7
|
1.1
|
1.9
|
Sagmariasus verreauxi
|
MMR
|
17.5
|
14
|
1.4
|
5
|
0.2
|
0.2
|
1.2
|
1.6
|
1.1
|
1.6
|
Sagmariasus verreauxi
|
MMR
|
21.5
|
14
|
1.7
|
6
|
0.4
|
0.4
|
1.4
|
2.1
|
1.3
|
2.2
|
Sagmariasus verreauxi
|
Recovery_Rate
|
14.0
|
14
|
1.0
|
5
|
0.7
|
0.8
|
0.2
|
1.8
|
0.3
|
2.0
|
Sagmariasus verreauxi
|
Recovery_Rate
|
17.5
|
14
|
1.8
|
5
|
0.8
|
0.9
|
0.9
|
2.7
|
0.9
|
2.9
|
Sagmariasus verreauxi
|
Recovery_Rate
|
21.5
|
14
|
2.1
|
6
|
0.5
|
0.5
|
1.5
|
2.6
|
1.5
|
2.8
|
Sagmariasus verreauxi
|
recovery_time
|
14.0
|
14
|
1.6
|
3
|
0.8
|
1.5
|
0.1
|
3.1
|
1.1
|
2.6
|
Sagmariasus verreauxi
|
recovery_time
|
17.5
|
14
|
0.9
|
5
|
0.3
|
0.3
|
0.6
|
1.2
|
0.5
|
1.2
|
Sagmariasus verreauxi
|
recovery_time
|
21.5
|
14
|
1.8
|
6
|
1.1
|
1.1
|
0.7
|
2.8
|
0.3
|
3.2
|
Sagmariasus verreauxi
|
RMR
|
14.0
|
14
|
2.2
|
5
|
0.4
|
0.5
|
1.7
|
2.7
|
1.5
|
2.6
|
Sagmariasus verreauxi
|
RMR
|
17.5
|
14
|
2.6
|
5
|
0.6
|
0.7
|
1.9
|
3.3
|
1.8
|
3.5
|
Sagmariasus verreauxi
|
RMR
|
21.5
|
14
|
2.6
|
6
|
0.9
|
0.9
|
1.6
|
3.5
|
1.2
|
3.8
|
Sagmariasus verreauxi
|
SMR
|
14.0
|
14
|
2.1
|
2
|
0.2
|
0.5
|
1.6
|
2.6
|
2.0
|
2.2
|
Sagmariasus verreauxi
|
SMR
|
17.5
|
14
|
2.9
|
4
|
0.9
|
1.3
|
1.6
|
4.1
|
1.9
|
4.0
|
Sagmariasus verreauxi
|
SMR
|
21.5
|
14
|
2.9
|
5
|
0.3
|
0.3
|
2.6
|
3.3
|
2.5
|
3.2
|
Sagmariasus verreauxi
|
SMR_fraction
|
14.0
|
14
|
2.0
|
3
|
0.4
|
0.8
|
1.2
|
2.8
|
1.7
|
2.5
|
Sagmariasus verreauxi
|
SMR_fraction
|
17.5
|
14
|
2.3
|
5
|
1.0
|
1.2
|
1.1
|
3.5
|
1.2
|
3.9
|
Sagmariasus verreauxi
|
SMR_fraction
|
21.5
|
14
|
2.0
|
6
|
0.9
|
0.9
|
1.1
|
3.0
|
1.3
|
3.8
|
6. Save results
# All q10
write.csv(q10_all, paste(save_path, "Q10.csv", sep = ""))
# Q10 without outliers
write.csv(q10_all_noOutliers, paste(save_path, "Q10_outliers.csv", sep = ""))
# Q10 means
write.csv(q10_means, paste(save_path, "Q10_means.csv", sep = ""))
# All q10 without 17.5 experimental temperature
write.csv(q10_all_no17, paste(save_path, "Q10_no17C.csv", sep = ""))
# Q10 without outliers without 17.5 experimental temperature
write.csv(q10_all_no17_noOutliers, paste(save_path, "Q10_outliers_no17C.csv", sep = ""))
# Q10 means without 17.5 experimental temperature
write.csv(q10_means_no17, paste(save_path, "Q10_means.csv_no17C.csv", sep = ""))
# Q10 values based on data means
write.csv(q10_means_all, paste(save_path, "Q10_data_means_no17C.csv", sep = ""))
7A. Display results for MMR, SMR and Aerobic scope only
# Select traits for display
trait_display <- c("SMR", "MMR", "AerobicScope")
# Filter traits
sub_q10 <- q10_means_no17 %>% filter(Trait %in% trait_display)
# Remove unneeded columns
sub_q10 <- sub_q10[, c(1:3,5,9:10)]
# Display table
sub_q10 %>% kbl(digits = 1, caption = "Thermal coefficent Q10") %>% kable_classic()
Thermal coefficent Q10
Species
|
Trait
|
AcclimationTemperature_C
|
mean
|
lower_ci
|
upper_ci
|
Jasus edwardsii
|
AerobicScope
|
14.0
|
0.8
|
0.4
|
1.2
|
Jasus edwardsii
|
AerobicScope
|
17.5
|
0.9
|
0.8
|
1.1
|
Jasus edwardsii
|
AerobicScope
|
21.5
|
1.3
|
1.0
|
1.6
|
Jasus edwardsii
|
MMR
|
14.0
|
1.2
|
1.0
|
1.5
|
Jasus edwardsii
|
MMR
|
17.5
|
1.3
|
1.1
|
1.4
|
Jasus edwardsii
|
MMR
|
21.5
|
1.6
|
1.3
|
1.8
|
Jasus edwardsii
|
SMR
|
14.0
|
2.8
|
1.8
|
3.8
|
Jasus edwardsii
|
SMR
|
17.5
|
3.1
|
2.8
|
3.5
|
Jasus edwardsii
|
SMR
|
21.5
|
2.1
|
1.5
|
2.7
|
Sagmariasus verreauxi
|
AerobicScope
|
14.0
|
0.9
|
0.3
|
1.5
|
Sagmariasus verreauxi
|
AerobicScope
|
17.5
|
1.2
|
0.9
|
1.5
|
Sagmariasus verreauxi
|
AerobicScope
|
21.5
|
1.5
|
1.1
|
1.9
|
Sagmariasus verreauxi
|
MMR
|
14.0
|
1.3
|
0.9
|
1.7
|
Sagmariasus verreauxi
|
MMR
|
17.5
|
1.4
|
1.2
|
1.6
|
Sagmariasus verreauxi
|
MMR
|
21.5
|
1.7
|
1.4
|
2.1
|
Sagmariasus verreauxi
|
SMR
|
14.0
|
2.1
|
1.6
|
2.6
|
Sagmariasus verreauxi
|
SMR
|
17.5
|
2.9
|
1.6
|
4.1
|
Sagmariasus verreauxi
|
SMR
|
21.5
|
2.9
|
2.6
|
3.3
|
7B. Display results for MMR, SMR and Aerobic scope only based on data means
# Select traits for display
trait_display <- c("SMR", "MMR", "AerobicScope")
# Filter traits
sub_q10 <- q10_means_all %>% filter(Trait %in% trait_display)
# Remove unneeded columns
sub_q10 <- sub_q10[, c(1:4)]
names(sub_q10)
## [1] "Species" "AcclimationTemperature_C"
## [3] "Trait" "Q10"
# Transform to wide format
sub_q10 <- spread(sub_q10, AcclimationTemperature_C, Q10)
# Re-order
sub_q10 <- sub_q10[with(sub_q10, order(Species, Trait, decreasing = TRUE)),]
# Display table
sub_q10 %>% kbl(digits = 1, caption = "Thermal coefficent Q10") %>% kable_classic()
Thermal coefficent Q10
|
Species
|
Trait
|
14
|
17.5
|
21.5
|
6
|
Sagmariasus verreauxi
|
SMR
|
3.7
|
3.1
|
3.2
|
5
|
Sagmariasus verreauxi
|
MMR
|
1.4
|
1.5
|
1.7
|
4
|
Sagmariasus verreauxi
|
AerobicScope
|
1.0
|
1.2
|
1.4
|
3
|
Jasus edwardsii
|
SMR
|
3.3
|
3.3
|
2.7
|
2
|
Jasus edwardsii
|
MMR
|
1.3
|
1.2
|
1.6
|
1
|
Jasus edwardsii
|
AerobicScope
|
0.9
|
0.9
|
1.3
|