## This is the master R file for running stats for opsin expression from the Trinidad 2011 trip. Followed by environmetnal analyses. The stats are done in a step wise approach following the general outline of: (Step 1) MANOVA of all the opsins with all terms, (Step 2) Reducing the model by taking out non-significant terms and running updated MANOVA, (Step 3) Running individual ANOVAs on each of the opsins, (Step 4) Reducing the model for each opsin by removing non-signficant terms and running updated ANOVAs. ## ## This step wise approach is applied to the two data formats: Relative Opsin and Relative Housekeeping. Relative Opsin has measure for each of the 9 opsin genes and is the amount of total opsin gene expression that is made up of each gene (see equation in Sandkam et al) - this is the perferred measure of opsin expression when asking questions regarding color vision. Relative Housekeeping has measures for each of the 9 opsins in addition to rhodopsin (RH1) - the measure for each opsin is the Ct of that opsin compared to the average of 3 housekeeping genes (see equation in Sandkam and et al). Relative Housekeeping allows us to ask if particular opsins are driving differences to total opsin expression. ## ## NOTE: To increase sample sizes, days were pooled for each site/timepoint. Also, "Population" was not used as it is simply a function of the two terms "Watershed" and "Predation" which were both used instead. ## ####################################################### #/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\## ####################################################### ########________RELATIVE OPSIN ANALYSES________######## ####################################################### #/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\## ####################################################### RelOpsinAll <- read.table("/.../RelOpsinFinal.txt", header=T) summary(RelOpsinAll) ########________MANOVAs________######## ## Running MANOVA with all factors of interest ** NOTE: Predation is nested within Watershed ** (For non-nested code see 'unused code' section at bottom. ## BoundOpsins <- cbind (RelOpsinAll$LWS1, RelOpsinAll$LWS2, RelOpsinAll$LWS3, RelOpsinAll$LWSR, RelOpsinAll$RH21, RelOpsinAll$RH22, RelOpsinAll$SWS1, RelOpsinAll$SWS2A, RelOpsinAll$SWS2B) ## __ Binding all factors for MANOVA run __ ## OpsinAllMANOVAnested <- manova (log(BoundOpsins) ~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Sex * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) ## __ Log tranformed the data to meet assumptions of test and running MANOVA with factors: Predation(nested in watershed0), Sex, Watershed, and Time __ ## ## NOTE: Time is being run as a factor rather than a continous variable. ## summary(OpsinAllMANOVAnested) ## __ Shows sex is never significant (p=0.6568) or involved in any interactions that are significant __ ## ### __ Removing 'Sex' from the MANOVA and rerunning __ ### OpsinNoSexMANOVAnested <- manova (log(BoundOpsins) ~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) ## __ Log tranformed the data and running MANOVA with factors: Predation(nested in watershed), Watershed, and Time __ ## summary(OpsinNoSexMANOVAnested) ## __ Shows all factors (Watershed (p= 7.754e-09), Time (p<2.2e-16)), Watershed*Time(p<2.2e-16) and all interactions are highly signficant (Watershed*Time: p<2.2e-16) (Watershed*Predation*Time: p=<2.2e-16) __ ## ### __ Simple Main Effects: Subsetting the data by watershed __ ### OpsinAripo <- subset(RelOpsinAll, Watershed == "Aripo") OpsinMarianne <- subset(RelOpsinAll, Watershed == "Marianne") ## __ Binding the opsins within Watershed __ ## OpsinBoundAripo <- cbind(OpsinAripo$LWS1, OpsinAripo$LWS2, OpsinAripo$LWS3, OpsinAripo$LWSR, OpsinAripo$RH21, OpsinAripo$RH22, OpsinAripo$SWS1, OpsinAripo$SWS2A, OpsinAripo$SWS2B) OpsinBoundMarianne <- cbind(OpsinMarianne$LWS1, OpsinMarianne$LWS2, OpsinMarianne$LWS3, OpsinMarianne$LWSR, OpsinMarianne$RH21, OpsinMarianne$RH22, OpsinMarianne$SWS1, OpsinMarianne$SWS2A, OpsinMarianne$SWS2B) ### __ Running MANOVA on Aripo with factors Predation and Time __ ### AripoOpsinMANOVA <- manova(log(OpsinBoundAripo) ~ OpsinAripo$Predation * OpsinAripo$Time, as.factor(OpsinAripo$Time)) summary(AripoOpsinMANOVA) ## __ Shows highly significant effect of Predation (p=7.038e-09), Time (p<2.2e-16) and Predation*Time (p=1.176e-11) __ ## ### __ Running MANOVA on Marianne with factors Predation and Time __ ### MarianneOpsinMANOVA <- manova(log(OpsinBoundMarianne) ~ OpsinMarianne$Predation * OpsinMarianne$Time, as.factor(OpsinMarianne$Time)) summary(MarianneOpsinMANOVA) ## __ Shows highly significant effect of Predation (p<2.2e-16), Time (p<2.2e-16) and Predation*Time (p=4.813e-15) __ ## ### Subsetting by timepoint AripoTime1 <- subset(OpsinAripo, Time == "1") AripoTime2 <- subset(OpsinAripo, Time == "2") AripoTime3 <- subset(OpsinAripo, Time == "3") AripoTime4 <- subset(OpsinAripo, Time == "4") MarianneTime1 <- subset(OpsinMarianne, Time == "1") MarianneTime2 <- subset(OpsinMarianne, Time == "2") MarianneTime3 <- subset(OpsinMarianne, Time == "3") MarianneTime4 <- subset(OpsinMarianne, Time == "4") ## __ Binding the opsins within Watershed & Timepoint __ ## OpsinBoundAripoTime1 <- cbind(AripoTime1$LWS1, AripoTime1$LWS2, AripoTime1$LWS3, AripoTime1$LWSR, AripoTime1$RH21, AripoTime1$RH22, AripoTime1$SWS1, AripoTime1$SWS2A, AripoTime1$SWS2B) OpsinBoundAripoTime2 <- cbind(AripoTime2$LWS1, AripoTime2$LWS2, AripoTime2$LWS3, AripoTime2$LWSR, AripoTime2$RH21, AripoTime2$RH22, AripoTime2$SWS1, AripoTime2$SWS2A, AripoTime2$SWS2B) OpsinBoundAripoTime3 <- cbind(AripoTime3$LWS1, AripoTime3$LWS2, AripoTime3$LWS3, AripoTime3$LWSR, AripoTime3$RH21, AripoTime3$RH22, AripoTime3$SWS1, AripoTime3$SWS2A, AripoTime3$SWS2B) OpsinBoundAripoTime4 <- cbind(AripoTime4$LWS1, AripoTime4$LWS2, AripoTime4$LWS3, AripoTime4$LWSR, AripoTime4$RH21, AripoTime4$RH22, AripoTime4$SWS1, AripoTime4$SWS2A, AripoTime4$SWS2B) OpsinBoundMarianneTime1 <- cbind(MarianneTime1$LWS1, MarianneTime1$LWS2, MarianneTime1$LWS3, MarianneTime1$LWSR, MarianneTime1$RH21, MarianneTime1$RH22, MarianneTime1$SWS1, MarianneTime1$SWS2A, MarianneTime1$SWS2B) OpsinBoundMarianneTime2 <- cbind(MarianneTime2$LWS1, MarianneTime2$LWS2, MarianneTime2$LWS3, MarianneTime2$LWSR, MarianneTime2$RH21, MarianneTime2$RH22, MarianneTime2$SWS1, MarianneTime2$SWS2A, MarianneTime2$SWS2B) OpsinBoundMarianneTime3 <- cbind(MarianneTime3$LWS1, MarianneTime3$LWS2, MarianneTime3$LWS3, MarianneTime3$LWSR, MarianneTime3$RH21, MarianneTime3$RH22, MarianneTime3$SWS1, MarianneTime3$SWS2A, MarianneTime3$SWS2B) OpsinBoundMarianneTime4 <- cbind(MarianneTime4$LWS1, MarianneTime4$LWS2, MarianneTime4$LWS3, MarianneTime4$LWSR, MarianneTime4$RH21, MarianneTime4$RH22, MarianneTime4$SWS1, MarianneTime4$SWS2A, MarianneTime4$SWS2B) ### __ Running MANOVA on Aripo by Timepoint with factor Predation __ ### AripoOpsinMANOVATime1 <- manova(log(OpsinBoundAripoTime1) ~ AripoTime1$Predation) summary(AripoOpsinMANOVATime1) ## __ Shows highly significant effect of Predation (p=2.13e-08) ## AripoOpsinMANOVATime2 <- manova(log(OpsinBoundAripoTime2) ~ AripoTime2$Predation) summary(AripoOpsinMANOVATime2) ## __ Shows highly significant effect of Predation (p=2.429e-09) ## AripoOpsinMANOVATime3 <- manova(log(OpsinBoundAripoTime3) ~ AripoTime3$Predation) summary(AripoOpsinMANOVATime3) ## __ Shows highly significant effect of Predation (p=6.011e-07) ## AripoOpsinMANOVATime4 <- manova(log(OpsinBoundAripoTime4) ~ AripoTime4$Predation) summary(AripoOpsinMANOVATime4) ## __ Shows highly significant effect of Predation (p=1.283e-09) ## ### __ Running MANOVA on Marianne by Timepoint with factor Predation __ ### MarianneOpsinMANOVATime1 <- manova(log(OpsinBoundMarianneTime1) ~ MarianneTime1$Predation) summary(MarianneOpsinMANOVATime1) ## __ Shows highly significant effect of Predation (p=7.92e-14) ## MarianneOpsinMANOVATime2 <- manova(log(OpsinBoundMarianneTime2) ~ MarianneTime2$Predation) summary(MarianneOpsinMANOVATime2) ## __ Shows highly significant effect of Predation (p=6.005e-16) ## MarianneOpsinMANOVATime3 <- manova(log(OpsinBoundMarianneTime3) ~ MarianneTime3$Predation) summary(MarianneOpsinMANOVATime3) ## __ Shows highly significant effect of Predation (p=< 2.2e-16) ## MarianneOpsinMANOVATime4 <- manova(log(OpsinBoundMarianneTime4) ~ MarianneTime4$Predation) summary(MarianneOpsinMANOVATime4) ## __ Shows highly significant effect of Predation (p=< 2.2e-16) ## # # #/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\## # # ## _ CONCLUSIONS TO THIS POINT: Relative Opsin expression profiles differ by watershed, time, predation and interactions but not by sex. Time of day is expected as it's seen in many other studies. Watershed could be interesting but focus will stay on predation as that difference is likely more interesting in light of previous work and can comment on behavioral differences more easily. No sex differences is both not suprising (as it lines up with nearly all other studies of opsin expression in fish) and interesting since it goes against Laver and Taylor 2011. _ ## # # #/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\## ########________ANOVAs on each gene followed by removal of non-significant terms________######## ## LWS1 ## LWS1AllNest <- lm(RelOpsinAll$LWS1~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Sex * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(LWS1AllNest) ## Significant terms: Predation*Watershed, Predation*Watershed*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # LWS1SigFactorNest <- lm(RelOpsinAll$LWS1~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(LWS1SigFactorNest) ## Significant terms: Watershed*Predation, Watershed*Predation*Time. ## ## LWS2 ## LWS2AllNest <- lm(RelOpsinAll$LWS2~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Sex * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(LWS2AllNest) ## Significant terms: Watershed, Predation*Watershed, Watershed*Time, Predation*Watershed*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # LWS2SigFactorNest <- lm(RelOpsinAll$LWS2~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(LWS2SigFactorNest) ## Significant terms: Watershed, Watershed*Predation, Watershed*Time, Watershed*Predation*Time. ## ## LWS3 ## LWS3AllNest <- lm(RelOpsinAll$LWS3~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Sex * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(LWS3AllNest) ## Significant terms: Time, Watershed*Predation, Watershed*Predation*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # LWS3SigFactorNest <- lm(RelOpsinAll$LWS3~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(LWS3SigFactorNest) ## Significant terms: Time, Watershed*Predation, Watershed*Predation*Time. ## ## LWSR ## LWSRAllNest <- lm(RelOpsinAll$LWSR~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Sex * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(LWSRAllNest) ## Significant terms: Time, Watershed*Predation, Watershed*Time, Watershed*Predation*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # LWSRSigFactorNest <- lm(RelOpsinAll$LWSR~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(LWSRSigFactorNest) ## Significant terms: Time, Watershed*Predation, Watershed*Time, Watershed*Predation*Time. ## ## RH21 ## RH21AllNest <- lm(RelOpsinAll$RH21~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Sex * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(RH21AllNest) ## Significant terms: Watershed*Time. Non-significant terms for removal: Sex, Predation. ## # Removing non-significant terms # RH21SigFactorNest <- lm(RelOpsinAll$RH21~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Time * RelOpsinAll$Watershed, as.factor(RelOpsinAll$Time)) summary.aov(RH21SigFactorNest) ## Significant terms: Time*Watershed. ## ## RH22 ## RH22AllNest <- lm(RelOpsinAll$RH22~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Sex * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(RH22AllNest) ## Significant terms: Watershed, Watershed*Predation, Watershed*Predation*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # RH22SigFactorNest <- lm(RelOpsinAll$RH22~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(RH22SigFactorNest) ## Significant terms: Watershed, Predation*Watershed, Watershed*Predation*Time. ## ## SWS1 ## SWS1AllNest <- lm(RelOpsinAll$SWS1~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Sex * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(SWS1AllNest) ## Significant terms: Watershed, Watershed*Time, Watershed*Predation*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # SWS1SigFactorNest <- lm(RelOpsinAll$SWS1~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(SWS1SigFactorNest) ## Significant terms: Watershed, Watershed*Time, Watershed*Predation*Time. ## ## SWS2A ## SWS2AAllNest <- lm(RelOpsinAll$SWS2A~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Sex * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(SWS2AAllNest) ## Significant terms: Time, Watershed*Predation, Watershed*Time, Watershed*Predation*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # SWS2ASigFactorNest <- lm(RelOpsinAll$SWS2A~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(SWS2ASigFactorNest) ## Significant terms: Time, Watershed*Predation, Watershed*Time, Watershed*Predation*Time. ## ## SWS2B ## SWS2BAllNest <- lm(RelOpsinAll$SWS2B~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Sex * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(SWS2BAllNest) ## Significant terms: Watershed*Predation*Time. Non-significant terms for removal: Sex, Watershed. ## # Removing non-significant terms # SWS2BSigFactorNest <- lm(RelOpsinAll$SWS2B~ RelOpsinAll$Watershed/RelOpsinAll$Predation * RelOpsinAll$Time, as.factor(RelOpsinAll$Time)) summary.aov(SWS2BSigFactorNest) ## Significant terms: Watershed*Predation*Time. ## ## Running ANOVA's of Predation*Watershed for each Timepoint (pooled across days) for Relative Opsin Expression ## ### Subsetting by timepoint Time1 <- subset(RelOpsinAll, Time == "1") Time2 <- subset(RelOpsinAll, Time == "2") Time3 <- subset(RelOpsinAll, Time == "3") Time4 <- subset(RelOpsinAll, Time == "4") ## LWS1 ## LWS1OpsinTime1Nest <- lm(Time1$LWS1~ Time1$Watershed/Time1$Predation) LWS1OpsinTime2Nest <- lm(Time2$LWS1~ Time2$Watershed/Time2$Predation) LWS1OpsinTime3Nest <- lm(Time3$LWS1~ Time3$Watershed/Time3$Predation) LWS1OpsinTime4Nest <- lm(Time4$LWS1~ Time4$Watershed/Time4$Predation) summary.aov(LWS1OpsinTime1Nest) summary.aov(LWS1OpsinTime2Nest) summary.aov(LWS1OpsinTime3Nest) summary.aov(LWS1OpsinTime4Nest) ## LWS2 ## LWS2OpsinTime1Nest <- lm(Time1$LWS2~ Time1$Watershed/Time1$Predation) LWS2OpsinTime2Nest <- lm(Time2$LWS2~ Time2$Watershed/Time2$Predation) LWS2OpsinTime3Nest <- lm(Time3$LWS2~ Time3$Watershed/Time3$Predation) LWS2OpsinTime4Nest <- lm(Time4$LWS2~ Time4$Watershed/Time4$Predation) summary.aov(LWS2OpsinTime1Nest) summary.aov(LWS2OpsinTime2Nest) summary.aov(LWS2OpsinTime3Nest) summary.aov(LWS2OpsinTime4Nest) ## LWS3 ## LWS3OpsinTime1Nest <- lm(Time1$LWS3~ Time1$Watershed/Time1$Predation) LWS3OpsinTime2Nest <- lm(Time2$LWS3~ Time2$Watershed/Time2$Predation) LWS3OpsinTime3Nest <- lm(Time3$LWS3~ Time3$Watershed/Time3$Predation) LWS3OpsinTime4Nest <- lm(Time4$LWS3~ Time4$Watershed/Time4$Predation) summary.aov(LWS3OpsinTime1Nest) summary.aov(LWS3OpsinTime2Nest) summary.aov(LWS3OpsinTime3Nest) summary.aov(LWS3OpsinTime4Nest) ## LWSR ## LWSROpsinTime1Nest <- lm(Time1$LWSR~ Time1$Watershed/Time1$Predation) LWSROpsinTime2Nest <- lm(Time2$LWSR~ Time2$Watershed/Time2$Predation) LWSROpsinTime3Nest <- lm(Time3$LWSR~ Time3$Watershed/Time3$Predation) LWSROpsinTime4Nest <- lm(Time4$LWSR~ Time4$Watershed/Time4$Predation) summary.aov(LWSROpsinTime1Nest) summary.aov(LWSROpsinTime2Nest) summary.aov(LWSROpsinTime3Nest) summary.aov(LWSROpsinTime4Nest) ## RH21 ## RH21OpsinTime1Nest <- lm(Time1$RH21~ Time1$Watershed/Time1$Predation) RH21OpsinTime2Nest <- lm(Time2$RH21~ Time2$Watershed/Time2$Predation) RH21OpsinTime3Nest <- lm(Time3$RH21~ Time3$Watershed/Time3$Predation) RH21OpsinTime4Nest <- lm(Time4$RH21~ Time4$Watershed/Time4$Predation) summary.aov(RH21OpsinTime1Nest) summary.aov(RH21OpsinTime2Nest) summary.aov(RH21OpsinTime3Nest) summary.aov(RH21OpsinTime4Nest) ## RH22 ## RH22OpsinTime1Nest <- lm(Time1$RH22~ Time1$Watershed/Time1$Predation) RH22OpsinTime2Nest <- lm(Time2$RH22~ Time2$Watershed/Time2$Predation) RH22OpsinTime3Nest <- lm(Time3$RH22~ Time3$Watershed/Time3$Predation) RH22OpsinTime4Nest <- lm(Time4$RH22~ Time4$Watershed/Time4$Predation) summary.aov(RH22OpsinTime1Nest) summary.aov(RH22OpsinTime2Nest) summary.aov(RH22OpsinTime3Nest) summary.aov(RH22OpsinTime4Nest) ## SWS1 ## SWS1OpsinTime1Nest <- lm(Time1$SWS1~ Time1$Watershed/Time1$Predation) SWS1OpsinTime2Nest <- lm(Time2$SWS1~ Time2$Watershed/Time2$Predation) SWS1OpsinTime3Nest <- lm(Time3$SWS1~ Time3$Watershed/Time3$Predation) SWS1OpsinTime4Nest <- lm(Time4$SWS1~ Time4$Watershed/Time4$Predation) summary.aov(SWS1OpsinTime1Nest) summary.aov(SWS1OpsinTime2Nest) summary.aov(SWS1OpsinTime3Nest) summary.aov(SWS1OpsinTime4Nest) ## SWS2A ## SWS2AOpsinTime1Nest <- lm(Time1$SWS2A~ Time1$Watershed/Time1$Predation) SWS2AOpsinTime2Nest <- lm(Time2$SWS2A~ Time2$Watershed/Time2$Predation) SWS2AOpsinTime3Nest <- lm(Time3$SWS2A~ Time3$Watershed/Time3$Predation) SWS2AOpsinTime4Nest <- lm(Time4$SWS2A~ Time4$Watershed/Time4$Predation) summary.aov(SWS2AOpsinTime1Nest) summary.aov(SWS2AOpsinTime2Nest) summary.aov(SWS2AOpsinTime3Nest) summary.aov(SWS2AOpsinTime4Nest) ## SWS2B ## SWS2BOpsinTime1Nest <- lm(Time1$SWS2B~ Time1$Watershed/Time1$Predation) SWS2BOpsinTime2Nest <- lm(Time2$SWS2B~ Time2$Watershed/Time2$Predation) SWS2BOpsinTime3Nest <- lm(Time3$SWS2B~ Time3$Watershed/Time3$Predation) SWS2BOpsinTime4Nest <- lm(Time4$SWS2B~ Time4$Watershed/Time4$Predation) summary.aov(SWS2BOpsinTime1Nest) summary.aov(SWS2BOpsinTime2Nest) summary.aov(SWS2BOpsinTime3Nest) summary.aov(SWS2BOpsinTime4Nest) ## Running ANOVA's of Predation within each Watershed for each Timepoint (pooled across days) Relative to total Opsin expression ## ### Subsetting timepoint by Watershed AripoOpsinTime1 <- subset(Time1, Watershed == "Aripo") AripoOpsinTime2 <- subset(Time2, Watershed == "Aripo") AripoOpsinTime3 <- subset(Time3, Watershed == "Aripo") AripoOpsinTime4 <- subset(Time4, Watershed == "Aripo") MarianneOpsinTime1 <- subset(Time1, Watershed == "Marianne") MarianneOpsinTime2 <- subset(Time2, Watershed == "Marianne") MarianneOpsinTime3 <- subset(Time3, Watershed == "Marianne") MarianneOpsinTime4 <- subset(Time4, Watershed == "Marianne") ## ** Commented out are gene/timepoints that did not show a Watershed*Predation interaction FROM NESTED ANALYSIS ** ## ### Aripo Proportional Opsin by time running by Predation ## ## LWS1 ## LWS1AripoOpsinTime1 <- lm(AripoOpsinTime1$LWS1~ AripoOpsinTime1$Predation) LWS1AripoOpsinTime2 <- lm(AripoOpsinTime2$LWS1~ AripoOpsinTime2$Predation) LWS1AripoOpsinTime3 <- lm(AripoOpsinTime3$LWS1~ AripoOpsinTime3$Predation) LWS1AripoOpsinTime4 <- lm(AripoOpsinTime4$LWS1~ AripoOpsinTime4$Predation) summary.aov(LWS1AripoOpsinTime1) summary.aov(LWS1AripoOpsinTime2) summary.aov(LWS1AripoOpsinTime3) summary.aov(LWS1AripoOpsinTime4) ## LWS2 ## # LWS2AripoOpsinTime1 <- lm(AripoOpsinTime1$LWS2~ AripoOpsinTime1$Predation) # LWS2AripoOpsinTime2 <- lm(AripoOpsinTime2$LWS2~ AripoOpsinTime2$Predation) # LWS2AripoOpsinTime3 <- lm(AripoOpsinTime3$LWS2~ AripoOpsinTime3$Predation) LWS2AripoOpsinTime4 <- lm(AripoOpsinTime4$LWS2~ AripoOpsinTime4$Predation) # summary.aov(LWS2AripoOpsinTime1) # summary.aov(LWS2AripoOpsinTime2) # summary.aov(LWS2AripoOpsinTime3) summary.aov(LWS2AripoOpsinTime4) ## LWS3 ## # LWS3AripoOpsinTime1 <- lm(AripoOpsinTime1$LWS3~ AripoOpsinTime1$Predation) LWS3AripoOpsinTime2 <- lm(AripoOpsinTime2$LWS3~ AripoOpsinTime2$Predation) LWS3AripoOpsinTime3 <- lm(AripoOpsinTime3$LWS3~ AripoOpsinTime3$Predation) LWS3AripoOpsinTime4 <- lm(AripoOpsinTime4$LWS3~ AripoOpsinTime4$Predation) # summary.aov(LWS3AripoOpsinTime1) summary.aov(LWS3AripoOpsinTime2) summary.aov(LWS3AripoOpsinTime3) summary.aov(LWS3AripoOpsinTime4) ## LWSR ## LWSRAripoOpsinTime1 <- lm(AripoOpsinTime1$LWSR~ AripoOpsinTime1$Predation) LWSRAripoOpsinTime2 <- lm(AripoOpsinTime2$LWSR~ AripoOpsinTime2$Predation) # LWSRAripoOpsinTime3 <- lm(AripoOpsinTime3$LWSR~ AripoOpsinTime3$Predation) # LWSRAripoOpsinTime4 <- lm(AripoOpsinTime4$LWSR~ AripoOpsinTime4$Predation) summary.aov(LWSRAripoOpsinTime1) summary.aov(LWSRAripoOpsinTime2) # summary.aov(LWSRAripoOpsinTime3) # summary.aov(LWSRAripoOpsinTime4) ## RH21 ## # RH21AripoOpsinTime1 <- lm(AripoOpsinTime1$RH21~ AripoOpsinTime1$Predation) # RH21AripoOpsinTime2 <- lm(AripoOpsinTime2$RH21~ AripoOpsinTime2$Predation) RH21AripoOpsinTime3 <- lm(AripoOpsinTime3$RH21~ AripoOpsinTime3$Predation) # RH21AripoOpsinTime4 <- lm(AripoOpsinTime4$RH21~ AripoOpsinTime4$Predation) # summary.aov(RH21AripoOpsinTime1) # summary.aov(RH21AripoOpsinTime2) summary.aov(RH21AripoOpsinTime3) # summary.aov(RH21AripoOpsinTime4) ## RH22 ## RH22AripoOpsinTime1 <- lm(AripoOpsinTime1$RH22~ AripoOpsinTime1$Predation) RH22AripoOpsinTime2 <- lm(AripoOpsinTime2$RH22~ AripoOpsinTime2$Predation) RH22AripoOpsinTime3 <- lm(AripoOpsinTime3$RH22~ AripoOpsinTime3$Predation) RH22AripoOpsinTime4 <- lm(AripoOpsinTime4$RH22~ AripoOpsinTime4$Predation) summary.aov(RH22AripoOpsinTime1) summary.aov(RH22AripoOpsinTime2) summary.aov(RH22AripoOpsinTime3) summary.aov(RH22AripoOpsinTime4) ## SWS1 ## SWS1AripoOpsinTime1 <- lm(AripoOpsinTime1$SWS1~ AripoOpsinTime1$Predation) # SWS1AripoOpsinTime2 <- lm(AripoOpsinTime2$SWS1~ AripoOpsinTime2$Predation) SWS1AripoOpsinTime3 <- lm(AripoOpsinTime3$SWS1~ AripoOpsinTime3$Predation) # SWS1AripoOpsinTime4 <- lm(AripoOpsinTime4$SWS1~ AripoOpsinTime4$Predation) summary.aov(SWS1AripoOpsinTime1) # summary.aov(SWS1AripoOpsinTime2) summary.aov(SWS1AripoOpsinTime3) # summary.aov(SWS1AripoOpsinTime4) ## SWS2A ## SWS2AAripoOpsinTime1 <- lm(AripoOpsinTime1$SWS2A~ AripoOpsinTime1$Predation) # SWS2AAripoOpsinTime2 <- lm(AripoOpsinTime2$SWS2A~ AripoOpsinTime2$Predation) # SWS2AAripoOpsinTime3 <- lm(AripoOpsinTime3$SWS2A~ AripoOpsinTime3$Predation) SWS2AAripoOpsinTime4 <- lm(AripoOpsinTime4$SWS2A~ AripoOpsinTime4$Predation) summary.aov(SWS2AAripoOpsinTime1) # summary.aov(SWS2AAripoOpsinTime2) # summary.aov(SWS2AAripoOpsinTime3) summary.aov(SWS2AAripoOpsinTime4) ## SWS2B ## # SWS2BAripoOpsinTime1 <- lm(AripoOpsinTime1$SWS2B~ AripoOpsinTime1$Predation) SWS2BAripoOpsinTime2 <- lm(AripoOpsinTime2$SWS2B~ AripoOpsinTime2$Predation) SWS2BAripoOpsinTime3 <- lm(AripoOpsinTime3$SWS2B~ AripoOpsinTime3$Predation) SWS2BAripoOpsinTime4 <- lm(AripoOpsinTime4$SWS2B~ AripoOpsinTime4$Predation) # summary.aov(SWS2BAripoOpsinTime1) summary.aov(SWS2BAripoOpsinTime2) summary.aov(SWS2BAripoOpsinTime3) summary.aov(SWS2BAripoOpsinTime4) ### Marianne Proportional Opsin by time running by Predation ## ## LWS1 ## LWS1MarianneOpsinTime1 <- lm(MarianneOpsinTime1$LWS1~ MarianneOpsinTime1$Predation) LWS1MarianneOpsinTime2 <- lm(MarianneOpsinTime2$LWS1~ MarianneOpsinTime2$Predation) LWS1MarianneOpsinTime3 <- lm(MarianneOpsinTime3$LWS1~ MarianneOpsinTime3$Predation) LWS1MarianneOpsinTime4 <- lm(MarianneOpsinTime4$LWS1~ MarianneOpsinTime4$Predation) summary.aov(LWS1MarianneOpsinTime1) summary.aov(LWS1MarianneOpsinTime2) summary.aov(LWS1MarianneOpsinTime3) summary.aov(LWS1MarianneOpsinTime4) ## LWS2 ## # LWS2MarianneOpsinTime1 <- lm(MarianneOpsinTime1$LWS2~ MarianneOpsinTime1$Predation) # LWS2MarianneOpsinTime2 <- lm(MarianneOpsinTime2$LWS2~ MarianneOpsinTime2$Predation) # LWS2MarianneOpsinTime3 <- lm(MarianneOpsinTime3$LWS2~ MarianneOpsinTime3$Predation) LWS2MarianneOpsinTime4 <- lm(MarianneOpsinTime4$LWS2~ MarianneOpsinTime4$Predation) # summary.aov(LWS2MarianneOpsinTime1) # summary.aov(LWS2MarianneOpsinTime2) # summary.aov(LWS2MarianneOpsinTime3) summary.aov(LWS2MarianneOpsinTime4) ## LWS3 ## # LWS3MarianneOpsinTime1 <- lm(MarianneOpsinTime1$LWS3~ MarianneOpsinTime1$Predation) LWS3MarianneOpsinTime2 <- lm(MarianneOpsinTime2$LWS3~ MarianneOpsinTime2$Predation) LWS3MarianneOpsinTime3 <- lm(MarianneOpsinTime3$LWS3~ MarianneOpsinTime3$Predation) LWS3MarianneOpsinTime4 <- lm(MarianneOpsinTime4$LWS3~ MarianneOpsinTime4$Predation) # summary.aov(LWS3MarianneOpsinTime1) summary.aov(LWS3MarianneOpsinTime2) summary.aov(LWS3MarianneOpsinTime3) summary.aov(LWS3MarianneOpsinTime4) ## LWSR ## LWSRMarianneOpsinTime1 <- lm(MarianneOpsinTime1$LWSR~ MarianneOpsinTime1$Predation) LWSRMarianneOpsinTime2 <- lm(MarianneOpsinTime2$LWSR~ MarianneOpsinTime2$Predation) # LWSRMarianneOpsinTime3 <- lm(MarianneOpsinTime3$LWSR~ MarianneOpsinTime3$Predation) # LWSRMarianneOpsinTime4 <- lm(MarianneOpsinTime4$LWSR~ MarianneOpsinTime4$Predation) summary.aov(LWSRMarianneOpsinTime1) summary.aov(LWSRMarianneOpsinTime2) # summary.aov(LWSRMarianneOpsinTime3) # summary.aov(LWSRMarianneOpsinTime4) ## RH21 ## # RH21MarianneOpsinTime1 <- lm(MarianneOpsinTime1$RH21~ MarianneOpsinTime1$Predation) # RH21MarianneOpsinTime2 <- lm(MarianneOpsinTime2$RH21~ MarianneOpsinTime2$Predation) RH21MarianneOpsinTime3 <- lm(MarianneOpsinTime3$RH21~ MarianneOpsinTime3$Predation) # RH21MarianneOpsinTime4 <- lm(MarianneOpsinTime4$RH21~ MarianneOpsinTime4$Predation) # summary.aov(RH21MarianneOpsinTime1) # summary.aov(RH21MarianneOpsinTime2) summary.aov(RH21MarianneOpsinTime3) # summary.aov(RH21MarianneOpsinTime4) ## RH22 ## RH22MarianneOpsinTime1 <- lm(MarianneOpsinTime1$RH22~ MarianneOpsinTime1$Predation) RH22MarianneOpsinTime2 <- lm(MarianneOpsinTime2$RH22~ MarianneOpsinTime2$Predation) RH22MarianneOpsinTime3 <- lm(MarianneOpsinTime3$RH22~ MarianneOpsinTime3$Predation) RH22MarianneOpsinTime4 <- lm(MarianneOpsinTime4$RH22~ MarianneOpsinTime4$Predation) summary.aov(RH22MarianneOpsinTime1) summary.aov(RH22MarianneOpsinTime2) summary.aov(RH22MarianneOpsinTime3) summary.aov(RH22MarianneOpsinTime4) ## SWS1 ## SWS1MarianneOpsinTime1 <- lm(MarianneOpsinTime1$SWS1~ MarianneOpsinTime1$Predation) # SWS1MarianneOpsinTime2 <- lm(MarianneOpsinTime2$SWS1~ MarianneOpsinTime2$Predation) SWS1MarianneOpsinTime3 <- lm(MarianneOpsinTime3$SWS1~ MarianneOpsinTime3$Predation) # SWS1MarianneOpsinTime4 <- lm(MarianneOpsinTime4$SWS1~ MarianneOpsinTime4$Predation) summary.aov(SWS1MarianneOpsinTime1) # summary.aov(SWS1MarianneOpsinTime2) summary.aov(SWS1MarianneOpsinTime3) # summary.aov(SWS1MarianneOpsinTime4) ## SWS2A ## SWS2AMarianneOpsinTime1 <- lm(MarianneOpsinTime1$SWS2A~ MarianneOpsinTime1$Predation) # SWS2AMarianneOpsinTime2 <- lm(MarianneOpsinTime2$SWS2A~ MarianneOpsinTime2$Predation) # SWS2AMarianneOpsinTime3 <- lm(MarianneOpsinTime3$SWS2A~ MarianneOpsinTime3$Predation) SWS2AMarianneOpsinTime4 <- lm(MarianneOpsinTime4$SWS2A~ MarianneOpsinTime4$Predation) summary.aov(SWS2AMarianneOpsinTime1) # summary.aov(SWS2AMarianneOpsinTime2) # summary.aov(SWS2AMarianneOpsinTime3) summary.aov(SWS2AMarianneOpsinTime4) ## SWS2B ## # SWS2BMarianneOpsinTime1 <- lm(MarianneOpsinTime1$SWS2B~ MarianneOpsinTime1$Predation) SWS2BMarianneOpsinTime2 <- lm(MarianneOpsinTime2$SWS2B~ MarianneOpsinTime2$Predation) SWS2BMarianneOpsinTime3 <- lm(MarianneOpsinTime3$SWS2B~ MarianneOpsinTime3$Predation) SWS2BMarianneOpsinTime4 <- lm(MarianneOpsinTime4$SWS2B~ MarianneOpsinTime4$Predation) # summary.aov(SWS2BMarianneOpsinTime1) summary.aov(SWS2BMarianneOpsinTime2) summary.aov(SWS2BMarianneOpsinTime3) summary.aov(SWS2BMarianneOpsinTime4) ############################################################################################################### ############################################################################################################### ############################################################################################################### ############################################################################################################### ############################################################################################################### ############################################################################################################### ############################################################################################################### ############################################################################################################### ############################################################################################################### ############################################################################################################### ############################################################################################################### ####################################################### #/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\## ####################################################### ########________RELATIVE HOUSE ANALYSES________######## ####################################################### #/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\## ####################################################### RelHouseAll <- read.table("/.../RelHouseFinal.txt", header=T) summary(RelHouseAll) ########________MANOVAs________######## ## Running MANOVA with all factors of interest ** NOTE: Predation is nested within Watershed ** (For non-nested code see 'unused code' section at bottom. ## BoundHouse <- cbind (RelHouseAll$LWS1, RelHouseAll$LWS2, RelHouseAll$LWS3, RelHouseAll$LWSR, RelHouseAll$RH21, RelHouseAll$RH22, RelHouseAll$SWS1, RelHouseAll$SWS2A, RelHouseAll$SWS2B) ## __ Binding all factors for MANOVA run __ ## HouseAllMANOVAnested <- manova (log(BoundHouse) ~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Sex * RelHouseAll$Time, as.factor(RelHouseAll$Time)) ## __ Log tranformed the data to meet assumptions of test and running MANOVA with factors: Predation(nested in watershed0), Sex, Watershed, and Time __ ## ## NOTE: Time is being run as a factor rather than a continous variable. ## summary(HouseAllMANOVAnested) ## __ Shows sex is never significant (p=0.6568) or involved in any interactions that are significant __ ## ### __ Removing 'Sex' from the MANOVA and rerunning __ ### HouseNoSexMANOVAnested <- manova (log(BoundHouse) ~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Time, as.factor(RelHouseAll$Time)) ## __ Log tranformed the data and running MANOVA with factors: Predation(nested in watershed), Watershed, and Time __ ## summary(HouseNoSexMANOVAnested) ## __ Shows all factors (Watershed (p= 2.528e-09), Time (p<2.2e-16)), Watershed*Predation(p<2.2e-16) and all interactions are highly signficant (Watershed*Time: p<2.2e-16) (Watershed*Predation*Time: p=<2.2e-16) __ ## ### __ Simple Main Effects: Subsetting the data by watershed __ ### HouseAripo <- subset(RelHouseAll, Watershed == "Aripo") HouseMarianne <- subset(RelHouseAll, Watershed == "Marianne") ## __ Binding the opsins within Watershed __ ## HouseBoundAripo <- cbind(HouseAripo$LWS1, HouseAripo$LWS2, HouseAripo$LWS3, HouseAripo$LWSR, HouseAripo$RH21, HouseAripo$RH22, HouseAripo$SWS1, HouseAripo$SWS2A, HouseAripo$SWS2B) HouseBoundMarianne <- cbind(HouseMarianne$LWS1, HouseMarianne$LWS2, HouseMarianne$LWS3, HouseMarianne$LWSR, HouseMarianne$RH21, HouseMarianne$RH22, HouseMarianne$SWS1, HouseMarianne$SWS2A, HouseMarianne$SWS2B) ### __ Running MANOVA on Aripo with factors Predation and Time __ ### AripoHouseMANOVA <- manova(log(HouseBoundAripo) ~ HouseAripo$Predation * HouseAripo$Time, as.factor(HouseAripo$Time)) summary(AripoHouseMANOVA) ## __ Shows highly significant effect of Predation (p=7.038e-09), Time (p<2.2e-16) and Predation*Time (p=1.176e-11) __ ## ### __ Running MANOVA on Marianne with factors Predation and Time __ ### MarianneHouseMANOVA <- manova(log(HouseBoundMarianne) ~ HouseMarianne$Predation * HouseMarianne$Time, as.factor(HouseMarianne$Time)) summary(MarianneHouseMANOVA) ## __ Shows highly significant effect of Predation (p<2.2e-16), Time (p<2.2e-16) and Predation*Time (p=4.813e-15) __ ## ### Subsetting by timepoint AripoHouseTime1 <- subset(HouseAripo, Time == "1") AripoHouseTime2 <- subset(HouseAripo, Time == "2") AripoHouseTime3 <- subset(HouseAripo, Time == "3") AripoHouseTime4 <- subset(HouseAripo, Time == "4") MarianneHouseTime1 <- subset(HouseMarianne, Time == "1") MarianneHouseTime2 <- subset(HouseMarianne, Time == "2") MarianneHouseTime3 <- subset(HouseMarianne, Time == "3") MarianneHouseTime4 <- subset(HouseMarianne, Time == "4") ## __ Binding the opsins within Watershed & Timepoint __ ## HouseBoundAripoTime1 <- cbind(AripoHouseTime1$LWS1, AripoHouseTime1$LWS2, AripoHouseTime1$LWS3, AripoHouseTime1$LWSR, AripoHouseTime1$RH21, AripoHouseTime1$RH22, AripoHouseTime1$SWS1, AripoHouseTime1$SWS2A, AripoHouseTime1$SWS2B) HouseBoundAripoTime2 <- cbind(AripoHouseTime2$LWS1, AripoHouseTime2$LWS2, AripoHouseTime2$LWS3, AripoHouseTime2$LWSR, AripoHouseTime2$RH21, AripoHouseTime2$RH22, AripoHouseTime2$SWS1, AripoHouseTime2$SWS2A, AripoHouseTime2$SWS2B) HouseBoundAripoTime3 <- cbind(AripoHouseTime3$LWS1, AripoHouseTime3$LWS2, AripoHouseTime3$LWS3, AripoHouseTime3$LWSR, AripoHouseTime3$RH21, AripoHouseTime3$RH22, AripoHouseTime3$SWS1, AripoHouseTime3$SWS2A, AripoHouseTime3$SWS2B) HouseBoundAripoTime4 <- cbind(AripoHouseTime4$LWS1, AripoHouseTime4$LWS2, AripoHouseTime4$LWS3, AripoHouseTime4$LWSR, AripoHouseTime4$RH21, AripoHouseTime4$RH22, AripoHouseTime4$SWS1, AripoHouseTime4$SWS2A, AripoHouseTime4$SWS2B) HouseBoundMarianneTime1 <- cbind(MarianneHouseTime1$LWS1, MarianneHouseTime1$LWS2, MarianneHouseTime1$LWS3, MarianneHouseTime1$LWSR, MarianneHouseTime1$RH21, MarianneHouseTime1$RH22, MarianneHouseTime1$SWS1, MarianneHouseTime1$SWS2A, MarianneHouseTime1$SWS2B) HouseBoundMarianneTime2 <- cbind(MarianneHouseTime2$LWS1, MarianneHouseTime2$LWS2, MarianneHouseTime2$LWS3, MarianneHouseTime2$LWSR, MarianneHouseTime2$RH21, MarianneHouseTime2$RH22, MarianneHouseTime2$SWS1, MarianneHouseTime2$SWS2A, MarianneHouseTime2$SWS2B) HouseBoundMarianneTime3 <- cbind(MarianneHouseTime3$LWS1, MarianneHouseTime3$LWS2, MarianneHouseTime3$LWS3, MarianneHouseTime3$LWSR, MarianneHouseTime3$RH21, MarianneHouseTime3$RH22, MarianneHouseTime3$SWS1, MarianneHouseTime3$SWS2A, MarianneHouseTime3$SWS2B) HouseBoundMarianneTime4 <- cbind(MarianneHouseTime4$LWS1, MarianneHouseTime4$LWS2, MarianneHouseTime4$LWS3, MarianneHouseTime4$LWSR, MarianneHouseTime4$RH21, MarianneHouseTime4$RH22, MarianneHouseTime4$SWS1, MarianneHouseTime4$SWS2A, MarianneHouseTime4$SWS2B) ### __ Running MANOVA on Aripo by Timepoint with factor Predation __ ### AripoHouseMANOVATime1 <- manova(log(HouseBoundAripoTime1) ~ AripoHouseTime1$Predation) summary(AripoHouseMANOVATime1) ## __ Shows highly significant effect of Predation (p=2.13e-08) ## AripoHouseMANOVATime2 <- manova(log(HouseBoundAripoTime2) ~ AripoHouseTime2$Predation) summary(AripoHouseMANOVATime2) ## __ Shows highly significant effect of Predation (p=2.429e-09) ## AripoHouseMANOVATime3 <- manova(log(HouseBoundAripoTime3) ~ AripoHouseTime3$Predation) summary(AripoHouseMANOVATime3) ## __ Shows highly significant effect of Predation (p=6.011e-07) ## AripoHouseMANOVATime4 <- manova(log(HouseBoundAripoTime4) ~ AripoHouseTime4$Predation) summary(AripoHouseMANOVATime4) ## __ Shows highly significant effect of Predation (p=1.283e-09) ## ### __ Running MANOVA on Marianne by Timepoint with factor Predation __ ### MarianneHouseMANOVATime1 <- manova(log(HouseBoundMarianneTime1) ~ MarianneHouseTime1$Predation) summary(MarianneHouseMANOVATime1) ## __ Shows highly significant effect of Predation (p=7.92e-14) ## MarianneHouseMANOVATime2 <- manova(log(HouseBoundMarianneTime2) ~ MarianneHouseTime2$Predation) summary(MarianneHouseMANOVATime2) ## __ Shows highly significant effect of Predation (p=6.005e-16) ## MarianneHouseMANOVATime3 <- manova(log(HouseBoundMarianneTime3) ~ MarianneHouseTime3$Predation) summary(MarianneHouseMANOVATime3) ## __ Shows highly significant effect of Predation (p=< 2.2e-16) ## MarianneHouseMANOVATime4 <- manova(log(HouseBoundMarianneTime4) ~ MarianneHouseTime4$Predation) summary(MarianneHouseMANOVATime4) ## __ Shows highly significant effect of Predation (p=< 2.2e-16) ## #/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\## ## _ CONCLUSIONS TO THIS POINT: Just like with relative opsin expression: Relative House expression profiles differ by watershed, time, predation and interactions but not by sex. Time of day is expected as it's seen in many other studies. Watershed could be interesting but focus will stay on predation as that difference is likely more interesting in light of previous work and can comment on behavioral differences more easily. No sex differences is both not suprising (as it lines up with nearly all other studies of opsin expression in fish) and interesting since it goes against Laver and Taylor 2011. Since we see the same story coming from both Relative Opsin expression and Relative House expression it's a good sign that we are seeing biologically relevant differences (rather than methodological or statistical artifacts) _ ## #/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\## ########________ANOVAs on each gene followed by removal of non-significant terms (including RH1)________######## ## LWS1 ## LWS1HouseAll <- lm(RelHouseAll$LWS1~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Sex * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(LWS1HouseAll) ## Significant terms: Watershed, Predation*Watershed. Non-significant terms for removal: Sex, Time. ## # Removing non-significant terms # LWS1HouseSigFactor <- lm(RelHouseAll$LWS1~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Watershed) summary.aov(LWS1HouseSigFactor) ## Significant terms: Watershed, Predation*Watershed. ## ## Leaving in Time to make a more complete ANOVA table ## LWS1HouseNoSex <- lm(RelHouseAll$LWS1~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(LWS1HouseNoSex) ## LWS2 ## LWS2HouseAll <- lm(RelHouseAll$LWS2~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Sex * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(LWS2HouseAll) ## Significant terms: Watershed, Time, Watershed*Time. Non-significant terms for removal: Sex, Predation. ## # Removing non-significant terms # LWS2HouseSigFactor <- lm(RelHouseAll$LWS2~ RelHouseAll$Watershed * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(LWS2HouseSigFactor) ## Significant terms: Watershed, Time, Watershed*Time. ## ## Leaving in Predation to make a nicer ANOVA table ## LWS2HouseNoSex <- lm(RelHouseAll$LWS2~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(LWS2HouseNoSex) ## LWS3 ## LWS3HouseAll <- lm(RelHouseAll$LWS3~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Sex * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(LWS3HouseAll) ## Significant terms: Predation*Watershed*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # LWS3HouseSigFactor <- lm(RelHouseAll$LWS3~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(LWS3HouseSigFactor) ## Significant terms: Predation*Watershed*Time. ## ## LWSR ## LWSRHouseAll <- lm(RelHouseAll$LWSR~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Sex * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(LWSRHouseAll) ## Significant terms: Predation, Watershed, Predation*Watershed, Predation*Time, Watershed*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # LWSRHouseSigFactor <- lm(RelHouseAll$LWSR~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(LWSRHouseSigFactor) ## Significant terms: Predation, Watershed, Time, Predation*Watershed, Predation*Time, Watershed*Time. ## ## RH21 ## RH21HouseAll <- lm(RelHouseAll$RH21~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Sex * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(RH21HouseAll) ## Significant terms: Predation*Watershed, Predation*Watershed*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # RH21HouseSigFactor <- lm(RelHouseAll$RH21~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(RH21HouseSigFactor) ## Significant terms: Predation*Watershed, Predation*Watershed*Time. ## ## RH22 ## RH22HouseAll <- lm(RelHouseAll$RH22~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Sex * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(RH22HouseAll) ## Significant terms: Predation, Watershed, Time, Predation*Time, Predation*Watershed*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # RH22HouseSigFactor <- lm(RelHouseAll$RH22~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(RH22HouseSigFactor) ## Significant terms: Predation, Watershed, Time, Predation*Time, Predation*Watershed*Time. ## ## SWS1 ## SWS1HouseAll <- lm(RelHouseAll$SWS1~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Sex * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(SWS1HouseAll) ## Significant terms: Predation, Predation*Watershed, Predation*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # SWS1HouseSigFactor <- lm(RelHouseAll$SWS1~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(SWS1HouseSigFactor) ## Significant terms: Predation, Predation*Watershed, Predation*Time, Watershed*Time. ## ## SWS2A ## SWS2AHouseAll <- lm(RelHouseAll$SWS2A~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Sex * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(SWS2AHouseAll) ## Significant terms: Time. Non-significant terms for removal: Sex, , Predation*Watershed, watershed. ## # Removing non-significant terms (leaving all but sex in to fit ANOVA table) # SWS2AHouseSigFactor <- lm(RelHouseAll$SWS2A~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(SWS2AHouseSigFactor) ## Significant terms: Time, Predation*Sex*Time. ## ## SWS2B ## SWS2BHouseAll <- lm(RelHouseAll$SWS2B~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Sex * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(SWS2BHouseAll) ## Significant terms: Time, Predation*Watershed*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # SWS2BHouseSigFactor <- lm(RelHouseAll$SWS2B~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(SWS2BHouseSigFactor) ## Significant terms: Time, Predation*Watershed*Time. ## ## RH1 ## RH1HouseAll <- lm(RelHouseAll$RH1~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Sex * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(RH1HouseAll) ## Significant terms: Predation, Watershed, Time, Predation*Watershed, Predation*Time, Watershed*Time, Predation*Watershed*Time. Non-significant terms for removal: Sex. ## # Removing non-significant terms # RH1HouseSigFactor <- lm(RelHouseAll$RH1~ RelHouseAll$Watershed/RelHouseAll$Predation * RelHouseAll$Time, as.factor(RelHouseAll$Time)) summary.aov(RH1HouseSigFactor) ## Significant terms: Predation, Watershed, Time, Predation*Watershed, Predation*Time, Watershed*Time, Predation*Watershed*Time. ## #/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\## ## _ CONCLUSIONS TO THIS POINT: Sex did not show up...ever. _ ## ## Running ANOVA's of Predation * Watershed for each Timepoint (pooled across days) Relative to Housekeeping ## ### Subsetting by timepoint HouseTime1 <- subset(RelHouseAll, Time == "1") HouseTime2 <- subset(RelHouseAll, Time == "2") HouseTime3 <- subset(RelHouseAll, Time == "3") HouseTime4 <- subset(RelHouseAll, Time == "4") ## LWS1 ## LWS1HouseTime1 <- lm(HouseTime1$LWS1~ HouseTime1$Watershed/HouseTime1$Predation) LWS1HouseTime2 <- lm(HouseTime2$LWS1~ HouseTime2$Watershed/HouseTime2$Predation) LWS1HouseTime3 <- lm(HouseTime3$LWS1~ HouseTime3$Watershed/HouseTime3$Predation) LWS1HouseTime4 <- lm(HouseTime4$LWS1~ HouseTime4$Watershed/HouseTime4$Predation) summary.aov(LWS1HouseTime1) summary.aov(LWS1HouseTime2) summary.aov(LWS1HouseTime3) summary.aov(LWS1HouseTime4) ## LWS2 ## LWS2HouseTime1 <- lm(HouseTime1$LWS2~ HouseTime1$Watershed/HouseTime1$Predation) LWS2HouseTime2 <- lm(HouseTime2$LWS2~ HouseTime2$Watershed/HouseTime2$Predation) LWS2HouseTime3 <- lm(HouseTime3$LWS2~ HouseTime3$Watershed/HouseTime3$Predation) LWS2HouseTime4 <- lm(HouseTime4$LWS2~ HouseTime4$Watershed/HouseTime4$Predation) summary.aov(LWS2HouseTime1) summary.aov(LWS2HouseTime2) summary.aov(LWS2HouseTime3) summary.aov(LWS2HouseTime4) ## LWS3 ## LWS3HouseTime1 <- lm(HouseTime1$LWS3~ HouseTime1$Watershed/HouseTime1$Predation) LWS3HouseTime2 <- lm(HouseTime2$LWS3~ HouseTime2$Watershed/HouseTime2$Predation) LWS3HouseTime3 <- lm(HouseTime3$LWS3~ HouseTime3$Watershed/HouseTime3$Predation) LWS3HouseTime4 <- lm(HouseTime4$LWS3~ HouseTime4$Watershed/HouseTime4$Predation) summary.aov(LWS3HouseTime1) summary.aov(LWS3HouseTime2) summary.aov(LWS3HouseTime3) summary.aov(LWS3HouseTime4) ## LWSR ## LWSRHouseTime1 <- lm(HouseTime1$LWSR~ HouseTime1$Watershed/HouseTime1$Predation) LWSRHouseTime2 <- lm(HouseTime2$LWSR~ HouseTime2$Watershed/HouseTime2$Predation) LWSRHouseTime3 <- lm(HouseTime3$LWSR~ HouseTime3$Watershed/HouseTime3$Predation) LWSRHouseTime4 <- lm(HouseTime4$LWSR~ HouseTime4$Watershed/HouseTime4$Predation) summary.aov(LWSRHouseTime1) summary.aov(LWSRHouseTime2) summary.aov(LWSRHouseTime3) summary.aov(LWSRHouseTime4) ## RH1 ## RH1HouseTime1 <- lm(HouseTime1$RH1~ HouseTime1$Watershed/HouseTime1$Predation) RH1HouseTime2 <- lm(HouseTime2$RH1~ HouseTime2$Watershed/HouseTime2$Predation) RH1HouseTime3 <- lm(HouseTime3$RH1~ HouseTime3$Watershed/HouseTime3$Predation) RH1HouseTime4 <- lm(HouseTime4$RH1~ HouseTime4$Watershed/HouseTime4$Predation) summary.aov(RH1HouseTime1) summary.aov(RH1HouseTime2) summary.aov(RH1HouseTime3) summary.aov(RH1HouseTime4) ## RH21 ## RH21HouseTime1 <- lm(HouseTime1$RH21~ HouseTime1$Watershed/HouseTime1$Predation) RH21HouseTime2 <- lm(HouseTime2$RH21~ HouseTime2$Watershed/HouseTime2$Predation) RH21HouseTime3 <- lm(HouseTime3$RH21~ HouseTime3$Watershed/HouseTime3$Predation) RH21HouseTime4 <- lm(HouseTime4$RH21~ HouseTime4$Watershed/HouseTime4$Predation) summary.aov(RH21HouseTime1) summary.aov(RH21HouseTime2) summary.aov(RH21HouseTime3) summary.aov(RH21HouseTime4) ## RH22 ## RH22HouseTime1 <- lm(HouseTime1$RH22~ HouseTime1$Watershed/HouseTime1$Predation) RH22HouseTime2 <- lm(HouseTime2$RH22~ HouseTime2$Watershed/HouseTime2$Predation) RH22HouseTime3 <- lm(HouseTime3$RH22~ HouseTime3$Watershed/HouseTime3$Predation) RH22HouseTime4 <- lm(HouseTime4$RH22~ HouseTime4$Watershed/HouseTime4$Predation) summary.aov(RH22HouseTime1) summary.aov(RH22HouseTime2) summary.aov(RH22HouseTime3) summary.aov(RH22HouseTime4) ## SWS1 ## SWS1HouseTime1 <- lm(HouseTime1$SWS1~ HouseTime1$Watershed/HouseTime1$Predation) SWS1HouseTime2 <- lm(HouseTime2$SWS1~ HouseTime2$Watershed/HouseTime2$Predation) SWS1HouseTime3 <- lm(HouseTime3$SWS1~ HouseTime3$Watershed/HouseTime3$Predation) SWS1HouseTime4 <- lm(HouseTime4$SWS1~ HouseTime4$Watershed/HouseTime4$Predation) summary.aov(SWS1HouseTime1) summary.aov(SWS1HouseTime2) summary.aov(SWS1HouseTime3) summary.aov(SWS1HouseTime4) ## SWS2A ## SWS2AHouseTime1 <- lm(HouseTime1$SWS2A~ HouseTime1$Watershed/HouseTime1$Predation) SWS2AHouseTime2 <- lm(HouseTime2$SWS2A~ HouseTime2$Watershed/HouseTime2$Predation) SWS2AHouseTime3 <- lm(HouseTime3$SWS2A~ HouseTime3$Watershed/HouseTime3$Predation) SWS2AHouseTime4 <- lm(HouseTime4$SWS2A~ HouseTime4$Watershed/HouseTime4$Predation) summary.aov(SWS2AHouseTime1) summary.aov(SWS2AHouseTime2) summary.aov(SWS2AHouseTime3) summary.aov(SWS2AHouseTime4) ## SWS2B ## SWS2BHouseTime1 <- lm(HouseTime1$SWS2B~ HouseTime1$Watershed/HouseTime1$Predation) SWS2BHouseTime2 <- lm(HouseTime2$SWS2B~ HouseTime2$Watershed/HouseTime2$Predation) SWS2BHouseTime3 <- lm(HouseTime3$SWS2B~ HouseTime3$Watershed/HouseTime3$Predation) SWS2BHouseTime4 <- lm(HouseTime4$SWS2B~ HouseTime4$Watershed/HouseTime4$Predation) summary.aov(SWS2BHouseTime1) summary.aov(SWS2BHouseTime2) summary.aov(SWS2BHouseTime3) summary.aov(SWS2BHouseTime4) ## Running ANOVA's of Predation within each Watershed for each Timepoint (pooled across days) Relative to Housekeeping ## ### Subsetting timepoint by Watershed AripoHouseTime1 <- subset(HouseTime1, Watershed == "Aripo") AripoHouseTime2 <- subset(HouseTime2, Watershed == "Aripo") AripoHouseTime3 <- subset(HouseTime3, Watershed == "Aripo") AripoHouseTime4 <- subset(HouseTime4, Watershed == "Aripo") MarianneHouseTime1 <- subset(HouseTime1, Watershed == "Marianne") MarianneHouseTime2 <- subset(HouseTime2, Watershed == "Marianne") MarianneHouseTime3 <- subset(HouseTime3, Watershed == "Marianne") MarianneHouseTime4 <- subset(HouseTime4, Watershed == "Marianne") ### Aripo Housekeeping by time running by Predation ## ## ** Commented out are the Timepoints that did not show a Watershed*Predation interaction above ** ## ## LWS1 ## LWS1AripoHouseTime1 <- lm(AripoHouseTime1$LWS1~ AripoHouseTime1$Predation) # LWS1AripoHouseTime2 <- lm(AripoHouseTime2$LWS1~ AripoHouseTime2$Predation) LWS1AripoHouseTime3 <- lm(AripoHouseTime3$LWS1~ AripoHouseTime3$Predation) # LWS1AripoHouseTime4 <- lm(AripoHouseTime4$LWS1~ AripoHouseTime4$Predation) summary.aov(LWS1AripoHouseTime1) # summary.aov(LWS1AripoHouseTime2) summary.aov(LWS1AripoHouseTime3) # summary.aov(LWS1AripoHouseTime4) ## LWS2 ## LWS2AripoHouseTime1 <- lm(AripoHouseTime1$LWS2~ AripoHouseTime1$Predation) # LWS2AripoHouseTime2 <- lm(AripoHouseTime2$LWS2~ AripoHouseTime2$Predation) # LWS2AripoHouseTime3 <- lm(AripoHouseTime3$LWS2~ AripoHouseTime3$Predation) # LWS2AripoHouseTime4 <- lm(AripoHouseTime4$LWS2~ AripoHouseTime4$Predation) summary.aov(LWS2AripoHouseTime1) # summary.aov(LWS2AripoHouseTime2) # summary.aov(LWS2AripoHouseTime3) # summary.aov(LWS2AripoHouseTime4) ## LWS3 ## # LWS3AripoHouseTime1 <- lm(AripoHouseTime1$LWS3~ AripoHouseTime1$Predation) LWS3AripoHouseTime2 <- lm(AripoHouseTime2$LWS3~ AripoHouseTime2$Predation) LWS3AripoHouseTime3 <- lm(AripoHouseTime3$LWS3~ AripoHouseTime3$Predation) # LWS3AripoHouseTime4 <- lm(AripoHouseTime4$LWS3~ AripoHouseTime4$Predation) # summary.aov(LWS3AripoHouseTime1) summary.aov(LWS3AripoHouseTime2) summary.aov(LWS3AripoHouseTime3) # summary.aov(LWS3AripoHouseTime4) ## LWSR ## LWSRAripoHouseTime1 <- lm(AripoHouseTime1$LWSR~ AripoHouseTime1$Predation) # LWSRAripoHouseTime2 <- lm(AripoHouseTime2$LWSR~ AripoHouseTime2$Predation) LWSRAripoHouseTime3 <- lm(AripoHouseTime3$LWSR~ AripoHouseTime3$Predation) # LWSRAripoHouseTime4 <- lm(AripoHouseTime4$LWSR~ AripoHouseTime4$Predation) summary.aov(LWSRAripoHouseTime1) # summary.aov(LWSRAripoHouseTime2) summary.aov(LWSRAripoHouseTime3) # summary.aov(LWSRAripoHouseTime4) ## RH1 ## RH1AripoHouseTime1 <- lm(AripoHouseTime1$RH1~ AripoHouseTime1$Predation) RH1AripoHouseTime2 <- lm(AripoHouseTime2$RH1~ AripoHouseTime2$Predation) RH1AripoHouseTime3 <- lm(AripoHouseTime3$RH1~ AripoHouseTime3$Predation) # RH1AripoHouseTime4 <- lm(AripoHouseTime4$RH1~ AripoHouseTime4$Predation) summary.aov(RH1AripoHouseTime1) summary.aov(RH1AripoHouseTime2) summary.aov(RH1AripoHouseTime3) # summary.aov(RH1AripoHouseTime4) ## RH21 ## RH21AripoHouseTime1 <- lm(AripoHouseTime1$RH21~ AripoHouseTime1$Predation) # RH21AripoHouseTime2 <- lm(AripoHouseTime2$RH21~ AripoHouseTime2$Predation) RH21AripoHouseTime3 <- lm(AripoHouseTime3$RH21~ AripoHouseTime3$Predation) # RH21AripoHouseTime4 <- lm(AripoHouseTime4$RH21~ AripoHouseTime4$Predation) summary.aov(RH21AripoHouseTime1) # summary.aov(RH21AripoHouseTime2) summary.aov(RH21AripoHouseTime3) # summary.aov(RH21AripoHouseTime4) ## RH22 ## RH22AripoHouseTime1 <- lm(AripoHouseTime1$RH22~ AripoHouseTime1$Predation) RH22AripoHouseTime2 <- lm(AripoHouseTime2$RH22~ AripoHouseTime2$Predation) RH22AripoHouseTime3 <- lm(AripoHouseTime3$RH22~ AripoHouseTime3$Predation) RH22AripoHouseTime4 <- lm(AripoHouseTime4$RH22~ AripoHouseTime4$Predation) summary.aov(RH22AripoHouseTime1) summary.aov(RH22AripoHouseTime2) summary.aov(RH22AripoHouseTime3) summary.aov(RH22AripoHouseTime4) ## SWS1 ## SWS1AripoHouseTime1 <- lm(AripoHouseTime1$SWS1~ AripoHouseTime1$Predation) SWS1AripoHouseTime2 <- lm(AripoHouseTime2$SWS1~ AripoHouseTime2$Predation) SWS1AripoHouseTime3 <- lm(AripoHouseTime3$SWS1~ AripoHouseTime3$Predation) # SWS1AripoHouseTime4 <- lm(AripoHouseTime4$SWS1~ AripoHouseTime4$Predation) summary.aov(SWS1AripoHouseTime1) summary.aov(SWS1AripoHouseTime2) summary.aov(SWS1AripoHouseTime3) # summary.aov(SWS1AripoHouseTime4) ## SWS2A ## # SWS2AAripoHouseTime1 <- lm(AripoHouseTime1$SWS2A~ AripoHouseTime1$Predation) # SWS2AAripoHouseTime2 <- lm(AripoHouseTime2$SWS2A~ AripoHouseTime2$Predation) SWS2AAripoHouseTime3 <- lm(AripoHouseTime3$SWS2A~ AripoHouseTime3$Predation) # SWS2AAripoHouseTime4 <- lm(AripoHouseTime4$SWS2A~ AripoHouseTime4$Predation) # summary.aov(SWS2AAripoHouseTime1) # summary.aov(SWS2AAripoHouseTime2) summary.aov(SWS2AAripoHouseTime3) # summary.aov(SWS2AAripoHouseTime4) ## SWS2B ## SWS2BAripoHouseTime1 <- lm(AripoHouseTime1$SWS2B~ AripoHouseTime1$Predation) SWS2BAripoHouseTime2 <- lm(AripoHouseTime2$SWS2B~ AripoHouseTime2$Predation) SWS2BAripoHouseTime3 <- lm(AripoHouseTime3$SWS2B~ AripoHouseTime3$Predation) # SWS2BAripoHouseTime4 <- lm(AripoHouseTime4$SWS2B~ AripoHouseTime4$Predation) summary.aov(SWS2BAripoHouseTime1) summary.aov(SWS2BAripoHouseTime2) summary.aov(SWS2BAripoHouseTime3) # summary.aov(SWS2BAripoHouseTime4) ### Marianne Housekeeping by time running by Predation ## ## LWS1 ## LWS1MarianneHouseTime1 <- lm(MarianneHouseTime1$LWS1~ MarianneHouseTime1$Predation) # LWS1MarianneHouseTime2 <- lm(MarianneHouseTime2$LWS1~ MarianneHouseTime2$Predation) LWS1MarianneHouseTime3 <- lm(MarianneHouseTime3$LWS1~ MarianneHouseTime3$Predation) # LWS1MarianneHouseTime4 <- lm(MarianneHouseTime4$LWS1~ MarianneHouseTime4$Predation) summary.aov(LWS1MarianneHouseTime1) # summary.aov(LWS1MarianneHouseTime2) summary.aov(LWS1MarianneHouseTime3) # summary.aov(LWS1MarianneHouseTime4) ## LWS2 ## LWS2MarianneHouseTime1 <- lm(MarianneHouseTime1$LWS2~ MarianneHouseTime1$Predation) # LWS2MarianneHouseTime2 <- lm(MarianneHouseTime2$LWS2~ MarianneHouseTime2$Predation) # LWS2MarianneHouseTime3 <- lm(MarianneHouseTime3$LWS2~ MarianneHouseTime3$Predation) # LWS2MarianneHouseTime4 <- lm(MarianneHouseTime4$LWS2~ MarianneHouseTime4$Predation) summary.aov(LWS2MarianneHouseTime1) # summary.aov(LWS2MarianneHouseTime2) # summary.aov(LWS2MarianneHouseTime3) # summary.aov(LWS2MarianneHouseTime4) ## LWS3 ## # LWS3MarianneHouseTime1 <- lm(MarianneHouseTime1$LWS3~ MarianneHouseTime1$Predation) LWS3MarianneHouseTime2 <- lm(MarianneHouseTime2$LWS3~ MarianneHouseTime2$Predation) LWS3MarianneHouseTime3 <- lm(MarianneHouseTime3$LWS3~ MarianneHouseTime3$Predation) # LWS3MarianneHouseTime4 <- lm(MarianneHouseTime4$LWS3~ MarianneHouseTime4$Predation) # summary.aov(LWS3MarianneHouseTime1) summary.aov(LWS3MarianneHouseTime2) summary.aov(LWS3MarianneHouseTime3) # summary.aov(LWS3MarianneHouseTime4) ## LWSR ## LWSRMarianneHouseTime1 <- lm(MarianneHouseTime1$LWSR~ MarianneHouseTime1$Predation) # LWSRMarianneHouseTime2 <- lm(MarianneHouseTime2$LWSR~ MarianneHouseTime2$Predation) LWSRMarianneHouseTime3 <- lm(MarianneHouseTime3$LWSR~ MarianneHouseTime3$Predation) # LWSRMarianneHouseTime4 <- lm(MarianneHouseTime4$LWSR~ MarianneHouseTime4$Predation) summary.aov(LWSRMarianneHouseTime1) # summary.aov(LWSRMarianneHouseTime2) summary.aov(LWSRMarianneHouseTime3) # summary.aov(LWSRMarianneHouseTime4) ## RH1 ## RH1MarianneHouseTime1 <- lm(MarianneHouseTime1$RH1~ MarianneHouseTime1$Predation) RH1MarianneHouseTime2 <- lm(MarianneHouseTime2$RH1~ MarianneHouseTime2$Predation) RH1MarianneHouseTime3 <- lm(MarianneHouseTime3$RH1~ MarianneHouseTime3$Predation) # RH1MarianneHouseTime4 <- lm(MarianneHouseTime4$RH1~ MarianneHouseTime4$Predation) summary.aov(RH1MarianneHouseTime1) summary.aov(RH1MarianneHouseTime2) summary.aov(RH1MarianneHouseTime3) # summary.aov(RH1MarianneHouseTime4) ## RH21 ## RH21MarianneHouseTime1 <- lm(MarianneHouseTime1$RH21~ MarianneHouseTime1$Predation) # RH21MarianneHouseTime2 <- lm(MarianneHouseTime2$RH21~ MarianneHouseTime2$Predation) RH21MarianneHouseTime3 <- lm(MarianneHouseTime3$RH21~ MarianneHouseTime3$Predation) # RH21MarianneHouseTime4 <- lm(MarianneHouseTime4$RH21~ MarianneHouseTime4$Predation) summary.aov(RH21MarianneHouseTime1) # summary.aov(RH21MarianneHouseTime2) summary.aov(RH21MarianneHouseTime3) # summary.aov(RH21MarianneHouseTime4) ## RH22 ## RH22MarianneHouseTime1 <- lm(MarianneHouseTime1$RH22~ MarianneHouseTime1$Predation) RH22MarianneHouseTime2 <- lm(MarianneHouseTime2$RH22~ MarianneHouseTime2$Predation) RH22MarianneHouseTime3 <- lm(MarianneHouseTime3$RH22~ MarianneHouseTime3$Predation) RH22MarianneHouseTime4 <- lm(MarianneHouseTime4$RH22~ MarianneHouseTime4$Predation) summary.aov(RH22MarianneHouseTime1) summary.aov(RH22MarianneHouseTime2) summary.aov(RH22MarianneHouseTime3) summary.aov(RH22MarianneHouseTime4) ## SWS1 ## SWS1MarianneHouseTime1 <- lm(MarianneHouseTime1$SWS1~ MarianneHouseTime1$Predation) SWS1MarianneHouseTime2 <- lm(MarianneHouseTime2$SWS1~ MarianneHouseTime2$Predation) SWS1MarianneHouseTime3 <- lm(MarianneHouseTime3$SWS1~ MarianneHouseTime3$Predation) # SWS1MarianneHouseTime4 <- lm(MarianneHouseTime4$SWS1~ MarianneHouseTime4$Predation) summary.aov(SWS1MarianneHouseTime1) summary.aov(SWS1MarianneHouseTime2) summary.aov(SWS1MarianneHouseTime3) # summary.aov(SWS1MarianneHouseTime4) ## SWS2A ## # SWS2AMarianneHouseTime1 <- lm(MarianneHouseTime1$SWS2A~ MarianneHouseTime1$Predation) # SWS2AMarianneHouseTime2 <- lm(MarianneHouseTime2$SWS2A~ MarianneHouseTime2$Predation) SWS2AMarianneHouseTime3 <- lm(MarianneHouseTime3$SWS2A~ MarianneHouseTime3$Predation) # SWS2AMarianneHouseTime4 <- lm(MarianneHouseTime4$SWS2A~ MarianneHouseTime4$Predation) # summary.aov(SWS2AMarianneHouseTime1) # summary.aov(SWS2AMarianneHouseTime2) summary.aov(SWS2AMarianneHouseTime3) # summary.aov(SWS2AMarianneHouseTime4) ## SWS2B ## SWS2BMarianneHouseTime1 <- lm(MarianneHouseTime1$SWS2B~ MarianneHouseTime1$Predation) SWS2BMarianneHouseTime2 <- lm(MarianneHouseTime2$SWS2B~ MarianneHouseTime2$Predation) SWS2BMarianneHouseTime3 <- lm(MarianneHouseTime3$SWS2B~ MarianneHouseTime3$Predation) # SWS2BMarianneHouseTime4 <- lm(MarianneHouseTime4$SWS2B~ MarianneHouseTime4$Predation) summary.aov(SWS2BMarianneHouseTime1) summary.aov(SWS2BMarianneHouseTime2) summary.aov(SWS2BMarianneHouseTime3) # summary.aov(SWS2BMarianneHouseTime4) ############################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################# #/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\## ####################################################### ########________Checking for Covariance between LWS________######## ####################################################### #/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\## ####################################################### cov(HouseAripo$LWS1, HouseAripo$LWS3) cov(HouseMarianne$LWS1, HouseMarianne$LWS3) cov(HouseAripo$LWS1, HouseAripo$LWS2) cov(HouseMarianne$LWS1, HouseMarianne$LWS2) cov(HouseAripo$LWS1, HouseAripo$LWSR) cov(HouseMarianne$LWS1, HouseMarianne$LWSR) cov(RelHouseAll$LWS1, RelHouseAll$LWS2) cov(RelHouseAll$LWS1, RelHouseAll$LWS3) cov(RelHouseAll$LWS1, RelHouseAll$LWSR) cov(RelHouseAll$LWS2, RelHouseAll$LWS3) cov(RelHouseAll$LWS2, RelHouseAll$LWSR) cov(RelHouseAll$LWS3, RelHouseAll$LWSR) ############################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################################# #/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\## ####################################################### ########________Comparing Environmental Parameters Between High and Low Predation Popualtions Within Watersheds________######## ####################################################### #/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\/\## ####################################################### ################### lambda p50 measures of lighting environment ################## lambdaP50 <- read.csv("/.../lambdaP50.csv", header=T) summary(lambdaP50) Aripo <- subset(lambdaP50, Watershed == "Aripo") summary(Aripo) Marianne <- subset(lambdaP50, Watershed == "Marianne") summary(Marianne) AripoAnova15UP <- lm(Aripo$lambda15UP~ Aripo$Predation) summary.aov(AripoAnova15UP) MarianneAnova15UP <- lm(Marianne$lambda15UP~ Marianne$Predation) summary.aov(MarianneAnova15UP) AripoHigh <- subset(Aripo, Predation=="High") summary(AripoHigh) AripoLow <- subset(Aripo, Predation=="Low") summary(AripoLow) t.test(AripoHigh$lambda15UP, AripoLow$lambda15UP) MarianneHigh <- subset(Marianne, Predation=="High") summary(MarianneHigh) MarianneLow <- subset(Marianne, Predation=="Low") summary(MarianneLow) t.test(MarianneHigh$lambda15UP, MarianneLow$lambda15UP) ################### Environmental Parameters ################## Environ <- read.csv("/.../Trinidad Environment.csv", header=T) summary(Environ) Marianne <- subset(Environ, Watershed=="Marianne") Aripo <- subset(Environ, Watershed=="Aripo") summary(Marianne) summary(Aripo) MarianneLow <- subset(Marianne, Predation=="Low") MarianneHigh <- subset(Marianne, Predation=="High") AripoLow <- subset(Aripo, Predation=="Low") AripoHigh <- subset(Aripo, Predation=="High") t.test(MarianneLow$DO, MarianneHigh$DO) t.test(AripoLow$DO, AripoHigh$DO) t.test(MarianneLow$Domg, MarianneHigh$Domg) t.test(AripoLow$Domg, AripoHigh$Domg) t.test(MarianneLow$Temp, MarianneHigh$Temp) t.test(AripoLow$Temp, AripoHigh$Temp) t.test(MarianneLow$Conduct, MarianneHigh$Conduct) t.test(AripoLow$Conduct, AripoHigh$Conduct) t.test(MarianneLow$pH, MarianneHigh$pH) t.test(AripoLow$pH, AripoHigh$pH) t.test(MarianneLow$TDS, MarianneHigh$TDS) t.test(AripoLow$TDS, AripoHigh$TDS) t.test(MarianneLow$Salinity, MarianneHigh$Salinity) t.test(AripoLow$Salinity, AripoHigh$Salinity) t.test(MarianneLow$Resistivity, MarianneHigh$Resistivity) t.test(AripoLow$Resistivity, AripoHigh$Resistivity)