Beyond the exponential family

Most glm families (Poisson, Gamma, Gaussian, Binomial) are exponential families

$$f(x|\theta) \sim exp(\sum_i \eta_i(\theta)T_i(x) - A(\theta))$$

• Computationally easy
• Has sufficient statistics: easier to estimate parameter variance
• … but it doesn't describe everything
• mgcv has expanded to cover many new families
• Lets you model a much wider range of scenarios with smooths

• “Counts”: Negative binomial and Tweedie distributions
• Modelling proportions with the Beta distribution
• Robust regression with the Student's t distribution
• Ordered and unorderd categorical data
• Multivariate normal data

• Modelling exta zeros with zero-inflated and adjusted families

• NOTE: All the distributions we're covering here have their own quirks. Read the help files carefully before using them!

The binomial model also model's proportions — more specifically it models the number of successes in $m$ trials. If you have data of this form then model the binomial counts as this can yield predicted counts if required.

If you have true percentage or proportion data, say estimated proportional plant cover in a quadrat, then the beta model is appropriate.

Also, if all you have is the percentages, the beta model is unlikely to be terribly bad.

To illustrate the use of the betar() family in mgcv we use a behavioural data set of observations on captive cheetahs. These data are provided and extensively analysed in Zuur et al () and originate from Quirke et al (2012).

• data collected from nine zoos
• at randomised times of day a random number of scans (videos) of captive cheetah behaviour were recorded and analysed over a period of several months
• presence of stereotypical behaviour was recorded
• all individuals in an enclosure were assessed; where more than 1 individual data were aggregated over individuals to achieve 1 data point per enclosure per sampling occasion
• a number of covariates were also recorded
• data technically a binomial counts but we'll ignore count data and model the proportion of scans showing stereotypical behaviour

cheetah <- read.table("../data/beta-regression/ZooData.txt", header = TRUE)
names(cheetah)

 [1] "Number"     "Scans"      "Proportion" "Size"       "Visual"    
 [6] "Raised"     "Visitors"   "Feeding"    "Oc"         "Other"     
[11] "Enrichment" "Group"      "Sex"        "Enclosure"  "Vehicle"   
[16] "Diet"       "Age"        "Zoo"        "Eps"       

cheetah <- transform(cheetah, Raised = factor(Raised),
                     Feeding = factor(Feeding),
                     Oc = factor(Oc),
                     Other = factor(Other),
                     Enrichment = factor(Enrichment),
                     Group = factor(Group),
                     Sex = factor(Sex, labels = c("Male","Female")),
                     Zoo = factor(Zoo))

m <- gam(Proportion ~ s(log(Size)) + s(Visitors) + s(Enclosure) +
           s(Vehicle) + s(Age) + s(Zoo, bs = "re") + 
           Feeding + Oc + Other + Enrichment + Group + Sex,
         data = cheetah, family = betar(), method = "REML")

• Models continuous data w/ longer tails than normal
• Far less sensitive to outliers
• Has one extra parameter: df.
• bigger df: t dist approaches normal

set.seed(4)
n=300
dat = data.frame(x=seq(0,10,length=n))
dat$f = 20*exp(-dat$x)*dat$x
dat$y  = 1*rt(n,df = 3) + dat$f
norm_mod =  gam(y~s(x,k=20), data=dat, family=gaussian(link="identity"))
t_mod = gam(y~s(x,k=20), data=dat, family=scat(link="identity"))

Family: Scaled t(2.976,0.968) 
Link function: identity 

Formula:
y ~ s(x, k = 20)

Parametric coefficients:
            Estimate Std. Error z value Pr(>|z|)    
(Intercept)  2.02664    0.06853   29.57   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Approximate significance of smooth terms:
       edf Ref.df Chi.sq p-value    
s(x) 13.27  15.71   1221  <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

R-sq.(adj) =  0.695   Deviance explained = 63.1%
-REML = 546.75  Scale est. = 1         n = 300

• Assumes data are in discrete categories, and categories fall in order
• e.g.: conservation status: “least concern”, “vulnerable”, “endangered”, “extinct”
• fits a linear latent model using covariates, w/ threshold for each level
• First cut-off always occurs at -1

n= 200
dat = data.frame(x1 = runif(n,-1,1),x2=2*pi*runif(n))
dat$f = dat$x1^2 + sin(dat$x2)
dat$y_latent = dat$f + rnorm(n,dat$f)
dat$y = ifelse(dat$y_latent<0,1, ifelse(dat$y_latent<0.5,2,3))
ocat_model = gam(y~s(x1)+s(x2), family=ocat(R=3),data=dat)
plot(ocat_model,page=1)

summary(ocat_model)

Family: Ordered Categorical(-1,-0.09) 
Link function: identity 

Formula:
y ~ s(x1) + s(x2)

Parametric coefficients:
            Estimate Std. Error z value Pr(>|z|)  
(Intercept)   0.5010     0.2792   1.794   0.0727 .
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Approximate significance of smooth terms:
        edf Ref.df Chi.sq  p-value    
s(x1) 3.452  4.282  18.67  0.00133 ** 
s(x2) 5.195  6.270  84.34 1.09e-15 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Deviance explained = 57.7%
-REML =  97.38  Scale est. = 1         n = 200

• What do you do if categorical data doesn't fall in a nice order?

• Model probability of a category occuring relative to an (arbitrary) reference level
• one linear equation for each category except the reference class
• $p(y=i|\mathbf{x}) = exp(\mu_i(\mathbf{x}))/(1+\sum_j exp(\mu_j(\mathbf{x}))$
• $\mu_i(\mathbf{x}) = s_{1,j}(x_1) + s_{2,j}(x_2)$
• $p(y=0|\mathbf{x})= 1/(1+\sum_j exp(\mu_j(\mathbf{x}))$

multinom_pred_data = as.data.frame(expand.grid(road_dist =seq(0,10,length=50),
                                               tree_cover =c(0,0.33,0.66,1)))
multinom_pred = predict(multinom_model, multinom_pred_data,type = "response")
colnames(multinom_pred) = c("monkey","deer","pig")
multinom_pred_data = cbind(multinom_pred_data,multinom_pred)
multinom_pred_data_long = multinom_pred_data %>%
  gather(species, probability, monkey, deer,pig)%>%
  mutate(tree_cover =paste("tree cover = ", tree_cover,sep=""))
ggplot(aes(road_dist, probability,color=species),data=multinom_pred_data_long)+
  geom_line()+
  facet_grid(.~tree_cover)+
  theme_bw(20)

• Fit a different smooth model for multiple y-variables, but allowing correlation between y's
• Example uses: multi-species distribution models, measuring latent correlations between environmental predictors
• mgcv code: formula=list(y1~s(x1)+s(x2), y2 = s(x1)+s(x3)), family = mvn(d=2)

• Censored data: y measures time until an event occurs, or the study was stopped (censoring)
• Measures relative rates, rather than absolute rates (no intercepts)
• Example uses: time until an individual is infected, time until a subpopulation goes extinct, time until lake is invaded
• mgcv code: formula = y~s(x1)+s(x2), weights= censor.var,family=cox.ph
• censor.var = 0 if censored, 1 if not

• Model both the mean (“location”) and variance (“scale”) as smooth functions of predictors
• Example uses: detecting early warning signs in time series, finding factors driving population variability
• mgcv code: formula = list(y~s(x1)+s(x2), ~s(x2)+s(x3)), family=gaulss

• Models the probability of zeros seperately from mean counts given that you've observed more than zero at a location.
• Example uses: Counts of prey caught when a predator might switch between not hunting at all (zeros) and active hunting
• mgcv code: formula = list(y~s(x1)+s(x2), ~s(x2)+s(x3)), family=ziplss

That's the end of this section! We convene after lunch (1:00 PM). You'll get to work through a few more advanced examples of your choice.