# (Advanced) R Crash Course, for Actuaries

The fourth year of the Data Science for Actuaries program started this morning. I will be there for the introduction to R. The slides are available online (created with slidify, the .Rmd file is also available)

A (standard) markdown is also available (as well as the .Rmd file). I have to thank Ewen for his help on slidify (especially for the online quizz, and the integration of leaflet maps or the rgl animated graph….)

# Visualizing effects of a categorical explanatory variable in a regression

Recently, I’ve been working on two problems that might be related to semiotic issues in predictive modeling (i.e. instead of a standard regression table, how can we plot coefficient values in a regression model). To be more specific, I have a variable of interest $Y$ that is observed for several individuals $i$, with explanatory variables $\mathbf{x}_i$, year $t$, in a specific region $z_i\in\{A,B,C,D,E\}$. Suppose that we have a simple (standard) linear model (forget about time here) $$y_i=\beta_0+\beta_1x_{1,i}+\cdots+\beta_kx_{k,i}+\sum_j \alpha_j \mathbf{1}(z_i\in j)+\varepsilon_i$$

Let us forget the temporal effect to focus on the spatial effect today. And consider some simulated dataset. There will be only one (continuous) explanatory variable. And I will generate correlated covariates, just to be more realistic.

n=1000 library(mnormt) r=.5 Sigma &lt;- matrix(c(1,r,r,1), 2, 2) set.seed(1) X=rmnorm(n,c(0,0),Sigma) X1=cut(X[,1],c(-100,quantile(X[,1],c(.1,.4,.7,.85)), 100),labels=LETTERS[1:5]) X2=X[,2] Y=5+X[,1]-X[,2]+rnorm(n)/2 db=data.frame(Y,X1,X2)

Here we have $$y_i=\beta_0+\beta_1x_{1,i}+\sum_{j\in\{A,B,C,D,E\}} \alpha_j \mathbf{1}(z_i\in j)+\varepsilon_i$$ The goal here is to get to graph to visualize the vector $\hat\alpha=(\hat\alpha_A,\cdots,\hat\alpha_E)$. Let us run the linear regression

reg1=lm(Y~X1+X2,data=db) idx=which(substr(names(reg1$coefficients), 1,2)=="X1") v1=reg1$coefficients[idx] names(v1)=LETTERS[2:5] barplot(v1,col=rgb(0,0,1,.4))

Note that it is possible to add some sort of “confidence interval” to discuss significance (or to avoid to spend hours discussing differences in bar heights that are not significantly different)

library(Hmisc) sv1=summary(reg1)$coefficients[idx,2] (bp1=barplot(v1,ylim=range(c(0,v1+2*sv1)))) errbar(bp1[,1],v1,v1-2*sv1,v1+2*sv1,add=TRUE) My main concern here is the “reference” that is considered. Should $A$ be the reference? Why not $B$ db$X1=relevel(db$X1,"B") reg1=lm(Y~X1+X2,data=db) idx=which(substr(names(reg1$coefficients),1,2)=="X1") v1=reg1$coefficients[idx] names(v1)=LETTERS[c(1,3:5)] library(Hmisc) sv1=summary(reg1)$coefficients[idx,2] (bp1=barplot(v1) errbar(bp1[,1],v1,v1-2*sv1,v1+2*sv1,add=TRUE)

Why not the smallest one? Why not the largest one?… What if there is no simple way to choose. Furthermore, let us get back to the original point, which is that there might be some temporal aspects. More precisely, we can have $\hat\alpha^{(t)}=(\hat\alpha_A^{(t)},\cdots,\hat\alpha_E^{(t)})$. If we have also $\hat\alpha^{(t+1)}$ and we get another plot, how do we interpret it. If for $E$ the bar is taller, it means that relative to $A$, the difference has increased. I have the feeling that the interpretation is more complicated because we do not see, on that graph, changes in $\hat\alpha^{(t)}_A$.

Let us try something else. First, let us get back to the original setting

db$X1=relevel(db$X1,"A")

Consider here the regression without the intercept, so that all values remain

reg1=lm(Y~0+X1+X2,data=db) idx=which(substr(names(reg1$coefficients),1,2)=="X1") v1=reg2$coefficients[idx] names(v1)=LETTERS[1:5] barplot(v1)

It can be hard to read, especially if $Y$ takes (very) large values, and you think that barplots should start at 0. But still, having those 5 values is nice. Why not rescale that graph?

A natural idea my be to consider the case where no spatial component is considered, and to look at the difference with that reference.

 reg1=lm(Y~1+X2,data=db) reg2=lm(Y~0+X1+X2,data=db) idx=which(substr(names(reg2$coefficients),1,2)=="X1") v1=reg2$coefficients[idx] v2=v1-reg1$coefficients["(Intercept)"] barplot(v2,col=rgb(0,0,1,.4)) sv2=summary(reg2)$coefficients[idx,2] (bp2=barplot(v2,ylim=range(c(v2-2*sv2,v2+2*sv2)))) errbar(bp2[,1],v2,v2-2*sv2,v2+2*sv2,add=TRUE)

I like that graph, I should admit it. Now, I still have some remaining questions. For instance, can we insure that when only the intercept is considered, the value of $\hat\beta_0$ is somewhere between $\hat\beta_A,\cdots,\hat\beta_E$? Is it possible that $\hat\beta_A-\hat\beta_0,\cdots,\hat\beta_E-\hat\beta_0$ are all positive? In that case, I would find that hard to interpret.

Actually, if I really want values that can be seen as compared to some average, why not consider a (weighted) average of $\hat\beta_A,\cdots,\hat\beta_E$? (weights being here proportion in each class, in each region)

 w=table(db$X1) v3=v1-sum(w*v1)/sum(w) (bp3=barplot(v3,ylim=range(c(v3-2*sv3,v3+2*sv3)))) errbar(bp3[,1],v3,v3-2*sv3,v3+2*sv3,add=TRUE) I like that one. But what if, instead of normalizing at the end, we normalize the original dependent variable. By “normalize”, I mean “rescale”, to have a centered variable. db$Y0=db$Y-mean(db$Y) reg3=lm(Y0~0+X1+X2,data=db) sv3=summary(reg3)$coefficients[idx,2] (bp3=barplot(v3,ylim=range(c(v3-2*sv3,v3+2*sv3)))) errbar(bp3[,1],v3,v3-2*sv3,v3+2*sv3,add=TRUE) This one is nice, because it is extremely simple to explain. But what if instead of a linear regression, we add a logistic one (with $Y\in\{0,1\}$)? or a Poisson regression… So maybe it cannot be the best solution here. Let us try something else… In insurance ratemaking, people like to use “zonier“. It is a two-stage regression. The idea is to run a regression without any spatial components, first. Then, consider the regression of residuals on spatial variables. Here, it would be something like reg1=lm(Y~1+X2,data=db) reg2=lm(Y~0+X1+X2,data=db) Since we focus on residuals, those are centered, and we have an easy interpretation of respective values  sv4=summary(reg4)$coefficients[idx,2] v4=reg4$coefficients (bp4=barplot(v4,names.arg=LETTERS[1:5]))) errbar(bp4[,1],v4,v4-2*sv4,v4+2*sv4,add=TRUE) I guess that it can also be use in generalized linear models, with Pearson (or deviance) residuals. Another possible idea can be the following. Again, the goal is not to have the true values, but to visualize on a graph how regions can be different. Here, all of them are significantly different. And in region $A$, $Y$ is smaller, ceteris paribus (other things equal in the sense that we have taken into account $x_1$). And in region $E$ it is larger. Here, the graph helps to “see” those differences. Why not consider a completely different graph. What if we plot vector $a$ instead of $\alpha$, where $a_A$ can be interpreted as the value of the coefficient if we consider region $A$ against “not region $A$“. What if we consider 5 regressions where dichotomous versions of $Z$ are considered : $Z_j=\mathbf{1}_{Z=j}$. v5=sv5=rep(NA,5) names(v5)=LETTERS[1:5] for(k in 1:5){ reg=lm(Y~I(X1==LETTERS[k])+X2,data=db) v5[k]=reg$coefficients[2] sv5[k]=summary(reg)$coefficients[2,2]} We can plot that sequence of values, including some confidence intervals (that would be related to significance with respect to all other regions) (bp5=barplot(v5,ylim=range(c(v5-2*sv5,v5+2*sv5)))) errbar(bp5[,1],v5,v5-2*sv5,v5+2*sv5,add=TRUE) Looking at values does not give intuitive results, but I have the feeling that it is easy to explain what we plot (we compare each region to “the rest of the world”), and the ordering of $a$ seems to be consistent with $\alpha$ (but I could not prove it). Here are some ideas I got. I should be able to provide other graphs, but I would love to discuss with anyone on that topics, to find a proper and nice way to visualize effects of a categorical explanatory variable in a regression model (that can be a logistic one). Comments are open… # Holt-Winters with a Quantile Loss Function Exponential Smoothing is an old technique, but it can perform extremely well on real time series, as discussed in Hyndman, Koehler, Ord & Snyder (2008)), when Gardner (2005) appeared, many believed that exponential smoothing should be disregarded because it was either a special case of ARIMA modeling or an ad hoc procedure with no statistical rationale. As McKenzie (1985) observed, this opinion was expressed in numerous references to my paper. Since 1985, the special case argument has been turned on its head, and today we know that exponential smoothing methods are optimal for a very general class of state-space models that is in fact broader than the ARIMA class. Furthermore, I like it because I think it has nice pedagogical features. Consider simple exponential smoothing, $$L_{t}=\alpha Y_{t}+(1-\alpha)L_{t-1}$$ where $\alpha\in(0,1)$ is the smoothing weight. It is locally constant, in the sense that ${}_{t}\hat Y_{t+h} = L_{t}$  library(datasets) X=as.numeric(Nile) SimpleSmooth = function(a){ T=length(X) L=rep(NA,T) L[1]=X[1] for(t in 2:T){L[t]=a*X[t]+(1-a)*L[t-1]} return(L) } plot(X,type="b",cex=.6) lines(SimpleSmooth(.2),col="red") When using the standard R function, we get hw=HoltWinters(X,beta=FALSE,gamma=FALSE, l.start=X[1]) hw$alpha [1] 0.2465579

Of course, one can replicate that optimal value

V=function(a){ T=length(X) L=erreur=rep(NA,T) erreur[1]=0 L[1]=X[1] for(t in 2:T){ L[t]=a*X[t]+(1-a)*L[t-1] erreur[t]=X[t]-L[t-1] } return(sum(erreur^2)) } optim(.5,V)$par [1] 0.2464844 Here, the optimal value for $\alpha$ is the one that minimizes the one-step prediction, for the $\ell_2$ loss function, i.e. $$\sum_{t=2}^n(Y_t-{}_{t-1}\hat Y_t)^2$$ where here ${}_{t-1}\hat Y_t = L_{t-1}$. But one can consider another loss function, for instance the quantile loss function, $$\ell_{\tau}(\varepsilon)=\varepsilon(\tau-\mathbb{I}_{\varepsilon\leq 0})$$. The optimal coefficient is then obtained using HWtau=function(tau){ loss=function(e) e*(tau-(e&lt;=0)*1) V=function(a){ T=length(X) L=erreur=rep(NA,T) erreur[1]=0 L[1]=X[1] for(t in 2:T){ L[t]=a*X[t]+(1-a)*L[t-1] erreur[t]=X[t]-L[t-1] } return(sum(loss(erreur))) } optim(.5,V)$par }

Here is the evolution of $\alpha^\star_\tau$ as a function of $\tau$ (the level of the quantile considered).

T=(1:49)/50 HW=Vectorize(HWtau)(T) plot(T,HW,type="l") abline(h= hw$alpha,lty=2,col="red") Note that the optimal $\alpha$ is decreasing with $\tau$. I wonder how general this result can be… Of course, one can consider more general exponential smoothing, for instance the double one, with $$L_t=\alpha Y_t+(1-\alpha)[L_{t-1}+B_{t-1}]$$and$$B_t=\beta[L_t-L_{t-1}]+(1-\beta)B_{t-1}$$so that the prediction is now ${}_{t}\hat Y_{t+h} = L_{t}+hB_t$ (it is now locally linear – and no longer constant). hw=HoltWinters(X,gamma=FALSE,l.start=X[1]) hw$alpha alpha 0.4200241 hw$beta beta 0.05973389 The code to compute the smoothed series is the following DoubleSmooth = function(a,b){ T=length(X) L=B=rep(NA,T) L[1]=X[1]; B[1]=0 for(t in 2:T){ L[t]=a*X[t]+(1-a)*(L[t-1]+B[t-1]) B[t]=b*(L[t]-L[t-1])+(1-b)*B[t-1] } return(L+B) } Here also it is possible to replicate R using the $\ell_2$ loss function V=function(A){ a=A[1] b=A[2] T=length(X) L=B=erreur=rep(NA,T) erreur[1]=0 L[1]=X[1]; B[1]=X[2]-X[1] for(t in 2:T){ L[t]=a*X[t]+(1-a)*(L[t-1]+B[t-1]) B[t]=b*(L[t]-L[t-1])+(1-b)*B[t-1] erreur[t]=X[t]-(L[t-1]+B[t-1]) } return(sum(erreur^2)) } optim(c(.5,.05),V)$par [1] 0.41904510 0.05988304

(up to numerical optimization approximation, I guess). But here also, a quantile loss function can be considered

HWtau=function(tau){ loss=function(e) e*(tau-(e&lt;=0)*1) V=function(A){ a=A[1] b=A[2] T=length(X) L=B=erreur=rep(NA,T) erreur[1]=0 L[1]=X[1]; B[1]=X[2]-X[1] for(t in 2:T){ L[t]=a*X[t]+(1-a)*(L[t-1]+B[t-1]) B[t]=b*(L[t]-L[t-1])+(1-b)*B[t-1] erreur[t]=X[t]-(L[t-1]+B[t-1]) } return(sum(loss(erreur))) } optim(c(.5,.05),V)$par } and we can plot those values on a graph T=(1:49)/50 HW=Vectorize(HWtau)(T) plot(HW[1,],HW[2,],type="l") abline(v= hw$alpha,lwd=.4,lty=2,col="red") abline(h= hw$beta,lwd=.4,lty=2,col="red") points(hw$alpha,hw\$beta,pch=19,col="red")

(with $\alpha$ on the $x$-axis, and $\beta$ on the $y$-axis). So here, it is extremely simple to change the loss function, but so far, it should be done manually. Of course, one do it also for the seasonal exponential smoothing model.