load packages
# Install
if(!require("car")) install.packages("car")
if(!require("dplyr")) install.packages("dplyr")
if(!require("lmtest")) install.packages("lmtest")
# Load
library(car)
library(dplyr)
library(lmtest)
Prep/Read in Data
# Read in data
# Columns: Unit, Month, Site, Vegetation_Type, CPUE, av_temp, av_do, av_pH, av_turbidity, av_conductivity,
Fyke_EF_LR = read.csv('C:/Users/hayde/OneDrive/Desktop/UMichigan/Masters project/code and anlysis/Electrofishing/Linear/final version/ef_linear2_final.csv')
str(Fyke_EF_LR)
## 'data.frame': 30 obs. of 13 variables:
## $ site_ID : chr "MC106062022" "MC107192022" "MC108152022" "MC206072022" ...
## $ Site : int 1 1 1 2 2 2 3 3 3 1 ...
## $ Unit : chr "MC" "MC" "MC" "MC" ...
## $ month : int 6 7 8 6 7 8 6 7 8 6 ...
## $ Vegetation.Type : chr "Open Water" "Open Water" "Submerged Aquatic Vegetation" "Submerged Aquatic Vegetation" ...
## $ av_temp : num 18.9 25.6 20.9 19.9 26.9 ...
## $ av_do : num 9.39 4.15 3.55 10.57 5.94 ...
## $ av_pH : num 8.05 7.52 7.5 8.5 8.27 ...
## $ av_turbidity : num 20.86 35.34 9.34 24.65 119 ...
## $ av_conductivity : num 513 704 602 459 443 ...
## $ effort_min : num 3.93 10.02 8.48 10.05 10.17 ...
## $ SumOfSPECIES_COUNT: int 32 25 15 27 19 42 25 20 71 41 ...
## $ cpue : num 8.14 2.5 1.77 2.69 1.87 ...
Perform the Linear Regressions
# Regression Analyses - CPUE:Temp, CPUE:DO, CPUE:pH, CPUE:Turb, CPUE:Cond
FishLRtemp = lm(cpue ~ av_temp, data=Fyke_EF_LR)
summary(FishLRtemp)
##
## Call:
## lm(formula = cpue ~ av_temp, data = Fyke_EF_LR)
##
## Residuals:
## Min 1Q Median 3Q Max
## -2.5466 -0.6590 -0.1865 0.1991 4.7678
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 8.13788 2.01163 4.045 0.000372 ***
## av_temp -0.25228 0.08771 -2.876 0.007610 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.534 on 28 degrees of freedom
## Multiple R-squared: 0.2281, Adjusted R-squared: 0.2005
## F-statistic: 8.273 on 1 and 28 DF, p-value: 0.00761
FishLRDO = lm(cpue ~ av_do, data=Fyke_EF_LR)
summary(FishLRDO)
##
## Call:
## lm(formula = cpue ~ av_do, data = Fyke_EF_LR)
##
## Residuals:
## Min 1Q Median 3Q Max
## -2.2526 -0.7816 -0.3187 0.5417 5.7751
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 2.55615 0.95948 2.664 0.0127 *
## av_do -0.02085 0.12743 -0.164 0.8712
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.745 on 28 degrees of freedom
## Multiple R-squared: 0.0009551, Adjusted R-squared: -0.03473
## F-statistic: 0.02677 on 1 and 28 DF, p-value: 0.8712
FishLRpH = lm(cpue ~ av_pH, data=Fyke_EF_LR)
summary(FishLRpH)
##
## Call:
## lm(formula = cpue ~ av_pH, data = Fyke_EF_LR)
##
## Residuals:
## Min 1Q Median 3Q Max
## -2.0393 -0.7340 -0.3141 0.3974 5.7824
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 9.0394 6.8192 1.326 0.196
## av_pH -0.8306 0.8532 -0.973 0.339
##
## Residual standard error: 1.717 on 28 degrees of freedom
## Multiple R-squared: 0.03274, Adjusted R-squared: -0.001808
## F-statistic: 0.9477 on 1 and 28 DF, p-value: 0.3386
FishLRTurb = lm(cpue ~ av_turbidity, data=Fyke_EF_LR)
summary(FishLRTurb)
##
## Call:
## lm(formula = cpue ~ av_turbidity, data = Fyke_EF_LR)
##
## Residuals:
## Min 1Q Median 3Q Max
## -2.0600 -0.8537 -0.1779 0.4550 5.8003
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 2.06919 0.43583 4.748 5.53e-05 ***
## av_turbidity 0.01276 0.01146 1.113 0.275
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.708 on 28 degrees of freedom
## Multiple R-squared: 0.04239, Adjusted R-squared: 0.008187
## F-statistic: 1.239 on 1 and 28 DF, p-value: 0.2751
FishLRCond = lm(cpue ~ av_conductivity, data=Fyke_EF_LR)
summary(FishLRCond)
##
## Call:
## lm(formula = cpue ~ av_conductivity, data = Fyke_EF_LR)
##
## Residuals:
## Min 1Q Median 3Q Max
## -2.7053 -0.8482 -0.1219 0.3205 5.5926
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 3.854003 1.060064 3.636 0.00111 **
## av_conductivity -0.002556 0.001793 -1.425 0.16510
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 1.686 on 28 degrees of freedom
## Multiple R-squared: 0.06765, Adjusted R-squared: 0.03436
## F-statistic: 2.032 on 1 and 28 DF, p-value: 0.1651
Time to plot!
# Temp
FishLRTempplot = plot(Fyke_EF_LR$av_temp, Fyke_EF_LR$cpue,col = "black",
main = "Total Site CPUE & Average Temperature Regression",
abline(lm(Fyke_EF_LR$cpue ~ Fyke_EF_LR$av_temp)),
cex = 1.3,
pch = 16,
xlab = "Average Temperature (Celsius),
ylab = Total Site CPUE")
# DO
FishLR_DOplot = plot(Fyke_EF_LR$av_do,Fyke_EF_LR$cpue,col = "black",
main = "Total Site CPUE & Average Dissolved Oxygen Regression",
abline(lm(Fyke_EF_LR$cpue~Fyke_EF_LR$av_do)),
cex = 1.3,
pch = 16,
xlab = "Average Dissolved Oxygen (mg/L)",
ylab = "Total Site CPUE")
# PH
FishLR_pHplot = plot(Fyke_EF_LR$av_pH,Fyke_EF_LR$cpue,col = "black",
main = "Total Site CPUE & Average pH Regression",
abline(lm(Fyke_EF_LR$cpue~Fyke_EF_LR$av_pH)),
cex = 1.3,
pch = 16,
xlab = "Average pH",
ylab = "Total Site CPUE" )
# TURB
FishLR_Turbplot = plot(Fyke_EF_LR$av_turbidity,Fyke_EF_LR$cpue,col = "black",
main = "Total Site CPUE & Average Turbidity Regression",
abline(lm(Fyke_EF_LR$cpue~Fyke_EF_LR$av_turbidity)),
cex = 1.3,
pch = 16,
xlab = "Average Turbidity (FNU)",
ylab = "Total Site CPUE")
# COND
FishLR_Condplot = plot(Fyke_EF_LR$av_conductivity,Fyke_EF_LR$cpue,col = "black",
main = "Total Site CPUE & Average Conductivity Regression",
abline(lm(Fyke_EF_LR$cpue~Fyke_EF_LR$av_conductivity)),
cex = 1.3,
pch = 16,
xlab = "Average Conductivity (uS/cm2)",
ylab = "Total Site CPUE")
