Bees: Captive and maltreated bees

In friendly/heplots: Visualizing Hypothesis Tests in Multivariate Linear Models

Captive and maltreated bees

Description

Pabalan, Davey and Packe (2000) studied the effects of captivity and maltreatment on reproductive capabilities of queen and worker bees in a complex factorial design.

Format

A data frame with 246 observations on the following 6 variables.

caste

a factor with levels Queen Worker

treat

a factor with levels "" CAP MAL

time

an ordered factor: time of treatment

Iz

an index of ovarian development

Iy

an index of ovarian reabsorption

trtime

a factor with levels 0 CAP05 CAP07 CAP10 CAP12 CAP15 MAL05 MAL07 MAL10 MAL12 MAL15

Details

Bees were placed in a small tube and either held captive (CAP) or shaken periodically (MAL) for one of 5, 7.5, 10, 12.5 or 15 minutes, after which they were sacrificed and two measures: ovarian development (Iz) and ovarian reabsorption (Iy), were taken. A single control group was measured with no such treatment, i.e., at time 0; there are n=10 per group.

The design is thus nearly a three-way factorial, with factors caste (Queen, Worker), treat (CAP, MAL) and time, except that there are only 11 combinations of Treatment and Time; we call these trtime below.

Models for the three-way factorial design, using the formula cbind(Iz,Iy) ~ caste*treat*time ignore the control condition at time==0, where treat==NA.

To handle the additional control group at time==0, while separating the effects of Treatment and Time, 10 contrasts can be defined for the trtime factor in the model cbind(Iz,Iy) ~ caste*trtime See demo(bees.contrasts) for details.

In the heplot examples below, the default size="evidence" displays are too crowded to interpret, because some effects are so highly significant. The alternative effect-size scaling, size="effect", makes the relations clearer.

Source

Pabalan, N., Davey, K. G. & Packe, L. (2000). Escalation of Aggressive Interactions During Staged Encounters in Halictus ligatus Say (Hymenoptera: Halictidae), with a Comparison of Circle Tube Behaviors with Other Halictine Species Journal of Insect Behavior, 13, 627-650.

References

Friendly, M. (2006). Data Ellipses, HE Plots and Reduced-Rank Displays for Multivariate Linear Models: SAS Software and Examples Journal of Statistical Software, 17, 1-42.

Examples

data(Bees)
require(car)

# 3-way factorial, ignoring 0 group
bees.mod <- lm(cbind(Iz,Iy) ~ caste*treat*time, data=Bees)
car::Anova(bees.mod)

op<-palette(c(palette()[1:4],"brown","magenta", "olivedrab","darkgray"))
heplot(bees.mod, 
    xlab="Iz: Ovarian development", 
    ylab="Iz: Ovarian reabsorption",
		main="Bees: ~caste*treat*time")

heplot(bees.mod, size="effect",
    xlab="Iz: Ovarian development", 
    ylab="Iz: Ovarian reabsorption",
    main="Bees: ~caste*treat*time", 
    )

# two-way design, using trtime
bees.mod1 <- lm(cbind(Iz,Iy) ~ caste*trtime, data=Bees)
Anova(bees.mod1)

# HE plots for this model, with both significance and effect size scaling

heplot(bees.mod1, 
    xlab="Iz: Ovarian development", 
    ylab="Iz: Ovarian reabsorption",
		main="Bees: ~caste*trtime")
heplot(bees.mod1, 
    xlab="Iz: Ovarian development", 
    ylab="Iz: Ovarian reabsorption",
    main="Bees: ~caste*trtime",
    size="effect")
palette(op)

# effect plots for separate responses
if(require(effects)) {
	bees.lm1 <-lm(Iy ~ treat*caste*time, data=Bees)
	bees.lm2 <-lm(Iz ~ treat*caste*time, data=Bees)
	
	bees.eff1 <- allEffects(bees.lm1)
	plot(bees.eff1,multiline=TRUE,ask=FALSE)
	
	bees.eff2 <- allEffects(bees.lm2)
	plot(bees.eff2,multiline=TRUE,ask=FALSE)
}

friendly/heplots documentation built on May 4, 2024, 12:05 a.m.