Interaction Regressions

Alison L. Gould, Vivian Zhang, Lisa Lamberti, Eric W. Jones, Benjamin Obadia, Nikolaos Korasidis, Alex Gavryushkin, Jean M. Carlson, Niko Beerenwinkel, William B. Ludington

We applied a multivariate linear regression model, a common statistical test for interactions between experimental variables (28, 29). Here, our variables are the five bacterial species. We detected evidence of widespread pairwise interactions in the data (SI Appendix, Tables S2–S5).

Survival

SurvivalData.csv
mydata<-read.csv(
SurvivalData.csv
, header=TRUE, sep=",")
attach(mydata)
LP<-as.factor(LP)
LB<-as.factor(LB)
AP<-as.factor(AP)
AT<-as.factor(AT)
AO<-as.factor(AO)
modLp<-lm(time.to.death..days.~LP, data = mydata)
summary(modLp)
modLb<-lm(time.to.death..days.~LB, data = mydata)
summary(modLb)
modAp<-lm(time.to.death..days.~AP, data = mydata)
summary(modAp)
modAt<-lm(time.to.death..days.~AT, data = mydata)
summary(modAt)
modAo<-lm(time.to.death..days.~AO, data = mydata)
summary(modAo)
modLpLb<-lm(time.to.death..days.~LP*LB, data = mydata)
summary(modLpLb)
modLpAp<-lm(time.to.death..days.~LP*AP, data = mydata)
summary(modLpAp)
modLpAt<-lm(time.to.death..days.~LP*AT, data = mydata)
summary(modLpAt)
modLpAo<-lm(time.to.death..days.~LP*AO, data = mydata)
summary(modLpAo)
modLbAp<-lm(time.to.death..days.~LB*AP, data = mydata)
summary(modLbAp)
modLbAt<-lm(time.to.death..days.~LB*AT, data = mydata)
summary(modLbAt)
modLbAo<-lm(time.to.death..days.~LB*AO, data = mydata)
summary(modLbAo)
modApAt<-lm(time.to.death..days.~AP*AT, data = mydata)
summary(modApAt)
modApAo<-lm(time.to.death..days.~AP*AO, data = mydata)
summary(modApAo)
modAtAo<-lm(time.to.death..days.~AT*AO, data = mydata)
summary(modAtAo)
modLpLbAp<-lm(time.to.death..days.~LP*LB*AP, data = mydata)
summary(modLpLbAp)
modLpLbAt<-lm(time.to.death..days.~LP*LB*AT, data = mydata)
summary(modLpLbAt)
modLpLbAo<-lm(time.to.death..days.~LP*LB*AO, data = mydata)
summary(modLpLbAo)
modLpApAt<-lm(time.to.death..days.~LP*AP*AT, data = mydata)
summary(modLpApAt)
modLpApAo<-lm(time.to.death..days.~LP*AP*AO, data = mydata)
summary(modLpApAo)
modLpAtAo<-lm(time.to.death..days.~LP*AT*AO, data = mydata)
summary(modLpAtAo)
modLbApAt<-lm(time.to.death..days.~LB*AP*AT, data = mydata)
summary(modLbApAt)
modLbApAo<-lm(time.to.death..days.~LB*AP*AO, data = mydata)
summary(modLbApAo)
modLbAtAo<-lm(time.to.death..days.~LB*AT*AO, data = mydata)
summary(modLbAtAo)
modApAtAo<-lm(time.to.death..days.~AP*AT*AO, data = mydata)
summary(modApAtAo)
modLpLbApAt<-lm(time.to.death..days.~LP*LB*AP*AT, data = mydata)
summary(modLpLbApAt)
modLpLbApAo<-lm(time.to.death..days.~LP*LB*AP*AO, data = mydata)
summary(modLpLbApAo)
modLpLbAtAo<-lm(time.to.death..days.~LP*LB*AT*AO, data = mydata)
summary(modLpLbAtAo)
modLpApAtAo<-lm(time.to.death..days.~LP*AP*AT*AO, data = mydata)
summary(modLpApAtAo)
modLbApAtAo<-lm(time.to.death..days.~LB*AP*AT*AO, data = mydata)
summary(modLbApAtAo)
modALL<-lm(time.to.death..days.~LP*LB*AP*AT*AO, data = mydata)
summary(modALL)
1.6s
R
R Default

Development

DevelopmentData.csv
mydata<-read.csv(
DevelopmentData.csv
, header=TRUE, sep=",")
attach(mydata)
LP<-as.factor(LP)
LB<-as.factor(LB)
AP<-as.factor(AP)
AT<-as.factor(AT)
AO<-as.factor(AO)
modLp<-lm(development..days.~LP, data = mydata)
summary(modLp)
modLb<-lm(development..days.~LB, data = mydata)
summary(modLb)
modAp<-lm(development..days.~AP, data = mydata)
summary(modAp)
modAt<-lm(development..days.~AT, data = mydata)
summary(modAt)
modAo<-lm(development..days.~AO, data = mydata)
summary(modAo)
modLpLb<-lm(development..days.~LP*LB, data = mydata)
summary(modLpLb)
modLpAp<-lm(development..days.~LP*AP, data = mydata)
summary(modLpAp)
modLpAt<-lm(development..days.~LP*AT, data = mydata)
summary(modLpAt)
modLpAo<-lm(development..days.~LP*AO, data = mydata)
summary(modLpAo)
modLbAp<-lm(development..days.~LB*AP, data = mydata)
summary(modLbAp)
modLbAt<-lm(development..days.~LB*AT, data = mydata)
summary(modLbAt)
modLbAo<-lm(development..days.~LB*AO, data = mydata)
summary(modLbAo)
modApAt<-lm(development..days.~AP*AT, data = mydata)
summary(modApAt)
modApAo<-lm(development..days.~AP*AO, data = mydata)
summary(modApAo)
modAtAo<-lm(development..days.~AT*AO, data = mydata)
summary(modAtAo)
modLpLbAp<-lm(development..days.~LP*LB*AP, data = mydata)
summary(modLpLbAp)
modLpLbAt<-lm(development..days.~LP*LB*AT, data = mydata)
summary(modLpLbAt)
modLpLbAo<-lm(development..days.~LP*LB*AO, data = mydata)
summary(modLpLbAo)
modLpApAt<-lm(development..days.~LP*AP*AT, data = mydata)
summary(modLpApAt)
modLpApAo<-lm(development..days.~LP*AP*AO, data = mydata)
summary(modLpApAo)
modLpAtAo<-lm(development..days.~LP*AT*AO, data = mydata)
summary(modLpAtAo)
modLbApAt<-lm(development..days.~LB*AP*AT, data = mydata)
summary(modLbApAt)
modLbApAo<-lm(development..days.~LB*AP*AO, data = mydata)
summary(modLbApAo)
modLbAtAo<-lm(development..days.~LB*AT*AO, data = mydata)
summary(modLbAtAo)
modApAtAo<-lm(development..days.~AP*AT*AO, data = mydata)
summary(modApAtAo)
modLpLbApAt<-lm(development..days.~LP*LB*AP*AT, data = mydata)
summary(modLpLbApAt)
modLpLbApAo<-lm(development..days.~LP*LB*AP*AO, data = mydata)
summary(modLpLbApAo)
modLpLbAtAo<-lm(development..days.~LP*LB*AT*AO, data = mydata)
summary(modLpLbAtAo)
modLpApAtAo<-lm(development..days.~LP*AP*AT*AO, data = mydata)
summary(modLpApAtAo)
modLbApAtAo<-lm(development..days.~LB*AP*AT*AO, data = mydata)
summary(modLbApAtAo)
modALL<-lm(development..days.~LP*LB*AP*AT*AO, data = mydata)
summary(modALL)
1.3s
R
R Default

Fecundity

DailyFecundityData.csv
mydata<-read.csv(
DailyFecundityData.csv
, header=TRUE, sep=",")
attach(mydata)
LP<-as.factor(LP)
LB<-as.factor(LB)
AP<-as.factor(AP)
AT<-as.factor(AT)
AO<-as.factor(AO)
modLp<-lm(fecundity..eggs.female.~LP, data = mydata)
summary(modLp)
modLb<-lm(fecundity..eggs.female.~LB, data = mydata)
summary(modLb)
modAp<-lm(fecundity..eggs.female.~AP, data = mydata)
summary(modAp)
modAt<-lm(fecundity..eggs.female.~AT, data = mydata)
summary(modAt)
modAo<-lm(fecundity..eggs.female.~AO, data = mydata)
summary(modAo)
modLpLb<-lm(fecundity..eggs.female.~LP*LB, data = mydata)
summary(modLpLb)
modLpAp<-lm(fecundity..eggs.female.~LP*AP, data = mydata)
summary(modLpAp)
modLpAt<-lm(fecundity..eggs.female.~LP*AT, data = mydata)
summary(modLpAt)
modLpAo<-lm(fecundity..eggs.female.~LP*AO, data = mydata)
summary(modLpAo)
modLbAp<-lm(fecundity..eggs.female.~LB*AP, data = mydata)
summary(modLbAp)
modLbAt<-lm(fecundity..eggs.female.~LB*AT, data = mydata)
summary(modLbAt)
modLbAo<-lm(fecundity..eggs.female.~LB*AO, data = mydata)
summary(modLbAo)
modApAt<-lm(fecundity..eggs.female.~AP*AT, data = mydata)
summary(modApAt)
modApAo<-lm(fecundity..eggs.female.~AP*AO, data = mydata)
summary(modApAo)
modAtAo<-lm(fecundity..eggs.female.~AT*AO, data = mydata)
summary(modAtAo)
modLpLbAp<-lm(fecundity..eggs.female.~LP*LB*AP, data = mydata)
summary(modLpLbAp)
modLpLbAt<-lm(fecundity..eggs.female.~LP*LB*AT, data = mydata)
summary(modLpLbAt)
modLpLbAo<-lm(fecundity..eggs.female.~LP*LB*AO, data = mydata)
summary(modLpLbAo)
modLpApAt<-lm(fecundity..eggs.female.~LP*AP*AT, data = mydata)
summary(modLpApAt)
modLpApAo<-lm(fecundity..eggs.female.~LP*AP*AO, data = mydata)
summary(modLpApAo)
modLpAtAo<-lm(fecundity..eggs.female.~LP*AT*AO, data = mydata)
summary(modLpAtAo)
modLbApAt<-lm(fecundity..eggs.female.~LB*AP*AT, data = mydata)
summary(modLbApAt)
modLbApAo<-lm(fecundity..eggs.female.~LB*AP*AO, data = mydata)
summary(modLbApAo)
modLbAtAo<-lm(fecundity..eggs.female.~LB*AT*AO, data = mydata)
summary(modLbAtAo)
modApAtAo<-lm(fecundity..eggs.female.~AP*AT*AO, data = mydata)
summary(modApAtAo)
modLpLbApAt<-lm(fecundity..eggs.female.~LP*LB*AP*AT, data = mydata)
summary(modLpLbApAt)
modLpLbApAo<-lm(fecundity..eggs.female.~LP*LB*AP*AO, data = mydata)
summary(modLpLbApAo)
modLpLbAtAo<-lm(fecundity..eggs.female.~LP*LB*AT*AO, data = mydata)
summary(modLpLbAtAo)
modLpApAtAo<-lm(fecundity..eggs.female.~LP*AP*AT*AO, data = mydata)
summary(modLpApAtAo)
modLbApAtAo<-lm(fecundity..eggs.female.~LB*AP*AT*AO, data = mydata)
summary(modLbApAtAo)
modALL<-lm(fecundity..eggs.female.~LP*LB*AP*AT*AO, data = mydata)
summary(modALL)
1.4s
R
R Default

Bacterial Load

FlygutCFUsData.csv
mydata<-read.csv(
FlygutCFUsData.csv
, header=TRUE, sep=",")
attach(mydata)
LP<-as.factor(LP)
LB<-as.factor(LB)
AP<-as.factor(AP)
AT<-as.factor(AT)
AO<-as.factor(AO)
modLp<-lm(Total.CFU~LP, data = mydata)
summary(modLp)
modLb<-lm(Total.CFU~LB, data = mydata)
summary(modLb)
modAp<-lm(Total.CFU~AP, data = mydata)
summary(modAp)
modAt<-lm(Total.CFU~AT, data = mydata)
summary(modAt)
modAo<-lm(Total.CFU~AO, data = mydata)
summary(modAo)
modLpLb<-lm(Total.CFU~LP*LB, data = mydata)
summary(modLpLb)
modLpAp<-lm(Total.CFU~LP*AP, data = mydata)
summary(modLpAp)
modLpAt<-lm(Total.CFU~LP*AT, data = mydata)
summary(modLpAt)
modLpAo<-lm(Total.CFU~LP*AO, data = mydata)
summary(modLpAo)
modLbAp<-lm(Total.CFU~LB*AP, data = mydata)
summary(modLbAp)
modLbAt<-lm(Total.CFU~LB*AT, data = mydata)
summary(modLbAt)
modLbAo<-lm(Total.CFU~LB*AO, data = mydata)
summary(modLbAo)
modApAt<-lm(Total.CFU~AP*AT, data = mydata)
summary(modApAt)
modApAo<-lm(Total.CFU~AP*AO, data = mydata)
summary(modApAo)
modAtAo<-lm(Total.CFU~AT*AO, data = mydata)
summary(modAtAo)
modLpLbAp<-lm(Total.CFU~LP*LB*AP, data = mydata)
summary(modLpLbAp)
modLpLbAt<-lm(Total.CFU~LP*LB*AT, data = mydata)
summary(modLpLbAt)
modLpLbAo<-lm(Total.CFU~LP*LB*AO, data = mydata)
summary(modLpLbAo)
modLpApAt<-lm(Total.CFU~LP*AP*AT, data = mydata)
summary(modLpApAt)
modLpApAo<-lm(Total.CFU~LP*AP*AO, data = mydata)
summary(modLpApAo)
modLpAtAo<-lm(Total.CFU~LP*AT*AO, data = mydata)
summary(modLpAtAo)
modLbApAt<-lm(Total.CFU~LB*AP*AT, data = mydata)
summary(modLbApAt)
modLbApAo<-lm(Total.CFU~LB*AP*AO, data = mydata)
summary(modLbApAo)
modLbAtAo<-lm(Total.CFU~LB*AT*AO, data = mydata)
summary(modLbAtAo)
modApAtAo<-lm(Total.CFU~AP*AT*AO, data = mydata)
summary(modApAtAo)
modLpLbApAt<-lm(Total.CFU~LP*LB*AP*AT, data = mydata)
summary(modLpLbApAt)
modLpLbApAo<-lm(Total.CFU~LP*LB*AP*AO, data = mydata)
summary(modLpLbApAo)
modLpLbAtAo<-lm(Total.CFU~LP*LB*AT*AO, data = mydata)
summary(modLpLbAtAo)
modLpApAtAo<-lm(Total.CFU~LP*AP*AT*AO, data = mydata)
summary(modLpApAtAo)
modLbApAtAo<-lm(Total.CFU~LB*AP*AT*AO, data = mydata)
summary(modLbApAtAo)
modALL<-lm(Total.CFU~LP*LB*AP*AT*AO, data = mydata)
summary(modALL)
1.3s
R
R Default

References

28. R Core Team (2017) R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna), Version 3.3.3.

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