# Tag Archives: Renglish

Winter started a bit more than one month ago… but we have already experienced many snow storms… there is still a lot snow in gardens and in the streets,

I was wondering if it was that unusual, but apparently not. Compared with last year, it is (for the first months of winter, until the end of Januray), it +50%, but it is comparable with previous years

Yes, we a simple loop, we can easily extract data from official wesite https://climat.meteo.gc.ca/ (but not too far away, even 2015 contains a lot of missing observations). For this month, we use

url = "https://climat.meteo.gc.ca/climate_data/daily_data_f.html?StationID=51157&timeframe=2&StartYear=1840&EndYear=2023&Day=30&Year=2023&Month=1#"
library(XML)
library(stringr)
k = which(tables[[1]]$JOUR =="Somme") neige = tables[[1]]$Neige tot. Definitioncm [k]
x = as.numeric(sub(",", ".", strsplit(neige, "LegendCarer")[[1]][1], fixed = TRUE))


and then we loop, and store the number we look for in a data frame (yes, we have to convert “50,8LegendCarer^” into the appropriate numerical value (that would be here $50.8$

D = data.frame(annee = c(2023,rep(2022:2015,each=12),c(12,11,10)), mois= c(1,rep(12:1,8),12,11,10), lab = neige, snow = x)
for(i in 2:nrow(D)){
y = D$annee[i] m = D$mois[i]
url = paste("https://climat.meteo.gc.ca/climate_data/daily_data_f.html?StationID=51157&timeframe=2&StartYear=1840&EndYear=2023&Day=30&Year=",y,"&Month=",m,"#",sep="")
k = which(tables[[1]]$JOUR =="Somme") neige = tables[[1]]$Neige tot. Definitioncm [k]
x = as.numeric(sub(",", ".", strsplit(neige, "LegendCarer")[[1]][1], fixed = TRUE))
D[i,3] = neige
D[i,4] = x
}


Here are the most recent months

> head(D)
annee mois              lab snpw
1  2023    1 50,8LegendCarer^ 50.8
2  2022   12             63,0 63.0
3  2022   11             14,6 14.6
4  2022   10              0,0  0.0
5  2022    9              0,0  0.0
6  2022    8              0,0  0.0


Of course, we need some codes to plot, we here, I mainly wanted to keep tracks of the code used to extract meteorological data…

# Could there be incentives to cycle through a red light?

This is of course a rhetorical question! Because cyclists must stop when the light is red! … But … there is always that moment, on a bicycle, when you stop, and  then you say to yourself

the worst part is that the lights are badly regulated, and I know that the next one will also be red once I will reach it … whereas if I had passed, I would have had the next one, and who knows, maybe a green wave afterwards?

Not having wanted to try the experiment with my bike, I wanted to try using simulations, on my computer.

Let us assume that in my city, there are red lights every 250 m, and they go from red to green in 1 minute, and similarly from green to red. Then, I can use a simple loop, where I compute the time from home, each time I pass a light: either the light is green, I go through, and I do not wait; or the light is red, then I wait, until the end of the minute. Here is the code. First, I define the constant parameter, with lights every 250 m, light turning either red or green every 1 minute, and I assume a constant speed here, of 15/60 km per min (or 15km per hour).

v = 15/60 d = .250 t = 1

Suppose that the office is at 10 km from home. The code to compute the time is simply (I do add a random noise on the time it takes to reach the next light, I will get back to that later on)

Dist = seq(0,10,by=.25) Time1=rep(NA,length(D)) Time1[1]==0 for(k in 2:length(Dist)){ noise=rnorm(1,sd=.05) Time1[k]=Time1[k-1]+d/v+noise if((floor(Time1[k])%%2==0)&amp;(k&lt;length(Dist))) Time1[k]=ceiling(Time1[k]) }

I can now visualize myself on my bike

T=seq(0,60,by=1/60) colr = c("red","green") plot(T,T*v,col="white") for(k in 1:40){ points(T,rep(d*k,length(T)),cex=.3,pch=15,col=colr[rep(1:2,each=t*60)]) } points(Time1,Dist,pch=19,cex=.5)

Here, it took me about 51 min to reach the office. And each time I have a red light, I stop and wait. Here is the distribution of the time it will take, as a function of my speed

simul = function(v=.250,sd=.05){ Dist = seq(0,10,by=.25) Time1=Time2=rep(NA,length(D)) Time1[1]=Time2[1]=0 for(k in 2:length(Dist)){ noise=rnorm(1,sd=sd) Time1[k]=Time1[k-1]+d/v+noise if((floor(Time1[k])%%2==0)&amp;(k&lt;length(Dist))) Time1[k]=ceiling(Time1[k]) } max(Time1) } S=function(v=.250,sd=.05,n=1000){ Vectorize(function(x) simul(v=x,sd=sd))(rep(v,n)) } vit = seq(.2,.3,length=101) MS = Vectorize(function(x) S(v=x,sd=.05))(vit) qMSsup = apply(MS,2,function(x) quantile(x,.95)) qMSinf = apply(MS,2,function(x) quantile(x,.05)) MSmed = apply(MS,2,function(x) quantile(x,.5)) MSmean = apply(MS,2,mean) par(mfrow = c(1,1)) plot(vit,MSmed,type="l") polygon(c(vit,rev(vit)),c(qMSinf,rev(qMSsup)),col="light blue",border=NA) lines(vit,MSmed,lwd=2)

Obviously, on average, the faster I cycle, the shorter the ride will be. Of course, 40 min is not a (real) lower bound : if I go much faster, it can be a rather quick ride

Now, consider a simple rhetorical alternative. What if I decide to go through a red light (after checking that there is no danger), say, with 1 chance of out 20 ?

simul_random = function(v=.250,sd=.05){ Dist = seq(0,10,by=.25) Time1=rep(NA,length(D)) Time1[1]=0 for(k in 2:length(Dist)){ noise=rnorm(1,sd=sd) Time1[k]=Time1[k-1]+d/v+noise red = sample(c(0,1),size=1,prob = c(.95,.05)) if((floor(Time1[k])%%2==0)&amp;(k&lt;length(Dist))&amp;(red == 0)) Time1[k]=ceiling(Time1[k]) } max(Time1) }

Here, 1 chance out of 20 could mean that on a 10 km ride, I wil always stop : first, I need a red light, and then 95% of the time, I stop. Here is the average distribution, with confidence bands

S_random=function(v=.250,sd=.05,n=1000){ Vectorize(function(x) simul_random(v=x,sd=sd))(rep(v,n)) } MS3 = Vectorize(function(x) S_random(v=x,sd=.05))(vit) qMSsup3 = apply(MS3,2,function(x) quantile(x,.95)) qMSinf3 = apply(MS3,2,function(x) quantile(x,.05)) MSmed3 = apply(MS3,2,function(x) quantile(x,.5))

It is possible to compare the two actually (on average times)

plot(MSmed,MSmed3,type="l") abline(a=0,b=1,col="red",lty=2) plot(MSmed,(MSmed-MSmed3)/MSmed*100,type="l")

which means that, somehow I can save some time, maybe from 3% to 5% if I do not cycle to fast, otherwise probably less than 2%. I would not claim, here, that it is worth it.

Consider another rhetorical alternative. What if I decide to go through the red light only if it is during the very first second ?

simul_1sec = function(v=.250,sd=.05){ Dist = seq(0,10,by=.25) Time1=rep(NA,length(D)) Time1[1]=0 for(k in 2:length(Dist)){ noise=rnorm(1,sd=sd) Time1[k]=Time1[k-1]+d/v+noise if((floor(Time1[k])%%2==0)&amp;(k&lt;length(Dist))&amp;(Time1[k]-floor(Time1[k])&gt;1/60)) Time1[k]=ceiling(Time1[k]) } max(Time1) }

Here is the time it takes to go to the office

and here is the potential gain

We can now clearly see the impact of those nonlinearities : with my average 15 km per hour speed, I can save 8% of the time if I go through red during the very first second. Of course, I will never do such a think, but mathematically speaking, it is stricking. Here is the gain for the first 2 seconds (out of a full minute)

so the gain can be about 12%. And now, what if we remove the noise – or more precisely, what if the standard deviation become 0.001 instead of 0.05. Here is the first distribution of the time (when I stop at each red light, and wait)

If I do not go fast enough, I will stop at almost each light, and wait until the end of the minute: going at 20 km per hour or 24 km per hour is exactly the same. But if I can go slightly faster than 25km per hour, that is awesome, and I have my green wave. Now, her is the graph I get when I cycle through the red light only in the very first second

This is now the gain

I can save up to 40% of the time, and more realistically, my 55 min ride could now be a 40 min ride. Which is substantial.

But on that one, observe that another strategy is also possible : what if I do not cycle through red light, but I simply cycle +1% faster ?

simul_faster = function(v=.250,sd=.05){ Dist = seq(0,10,by=.25) Time1=rep(NA,length(D)) Time1[1]=0 for(k in 2:length(Dist)){ noise=rnorm(1,sd=sd) Time1[k]=Time1[k-1]+d/(v*1.01)+noise if((floor(Time1[k])%%2==0)&amp;(k&lt;length(Dist))&amp;(Time1[k]-floor(Time1[k])&gt;1/60)) Time1[k]=ceiling(Time1[k]) } max(Time1) }

We have a similar result here, since riding 1% faster can actually help me save up to 50% of my time ! and (more realistically) if I ride 1% faster with a large random noise in the time between two light, I get almost the same as previously (when passing through the red light)

Again, my point here is not that we should cycle through a red light, of course not. But there may be accumulation of (small) nonlinear effects that might have a major impact at the end. And I believe that the best way to avoid this is to offer a green wave to cyclists, assuming that they ride at a reasonnable speed…

# From multinomial regression to binary classification on some Siamese data

There are two kinds of people in the world: people who think there are two kinds of people in the world and people who don’t

(borrowed from Menand (2018)). Because things are always simpler when we face only binary choice, aren’t they? But consider here the case were multiple options are possible, and let us see if we cannot get back to simpler binary choices. Consider a collection of observations $(y_i,\boldsymbol{x}_i)$ where $y_i$ is some categorical variable, $y_i\in\mathcal{A}$ where $\mathcal{A}=\lbrace A_1,\cdots,A_\kappa \rbrace$, with $\kappa$ possible categories. Let $\mathcal{I}_k=\lbrace i:y_i\in A_k \rbrace$.

In a classical multinomial logistic regression, suppose that $A_1$ is the reference, then $$\mathbb{P}[Y=A_j|\boldsymbol{X}=\boldsymbol{x}]=\frac{\exp[\boldsymbol{x}^\top\boldsymbol{\beta}_j]}{1+\exp[\boldsymbol{x}^\top\boldsymbol{\beta}_2]+\cdots+\exp[\boldsymbol{x}^\top\boldsymbol{\beta}_k]}$$With a lot a categories, and a small number of observations, inference can be complicated, and non-robust.

• the Siamese dataset

The name Siamese I use, here, comes from Siamese Networks. Or sort of… As we say in French, it is an « histoire de l’homme qui a vu l’homme qui a vu l’ours » (story of the man who saw the man who saw the bear). A few years ago, a student tried to explain to me the idea of Siamese Networks and this is what I understood. I might be completely wrong, but the idea I got from it did make sense, in my mind at least. That is the story of that blog post…

The idea of the siamese algorithm will be to consider all pairs of observations, $(y_i,\boldsymbol{x}_i)$ and $(y_j,\boldsymbol{x}_j)$ :

1. $\tilde y_{i,j}=\boldsymbol{1}(y_i=y_j)$ indicating if individuals $i$ and $j$ are in the same category
2. $\tilde{\boldsymbol{x}}_{i,j}$ is a collection of $p-1$ variables,
• $\tilde {x}_{k:i,j}={x}_{k:i}-{x}_{k:j}$ if $x_k$ is continuous, or $\tilde {x}_{k:i,j}=|{x}_{k:i}-{x}_{k:j}|$ (we can use another metric, e.g. $\tilde {x}_{k:i,j}=|{x}_{k:i}-{x}_{k:j}|^2$, and this is why I decided to use some GAM model in the logistic regression on the Siamese dataset)
• $\tilde {x}_{k:i,j}=({x}_{k:i},{x}_{k:j})\in\mathcal{X}_k\times\mathcal{X}_k$ if $x_k$ is a categorical variables (taking values in the set $\mathcal{X}_k$), or $\tilde {x}_{k:i,j}=\boldsymbol{1}({x}_{k:i}\neq{x}_{k:j})\in\{0,1\}$

The original dataset was a $n\times p$ matrix, and (if there are no categorical variable), it becomes a $n(n-1)/2\times p$ matrix. The key point is that if the original variable $y_i$ was multinomial, $y_{i,j}$ is now binomial. For instance, if our initial dataset was the following, with two covariates, one continuous and one categorical

its siamese counterpart is the following

• Classification step

On the dataset $(\tilde y_{i,j},\tilde {x}_{k:i,j})_{i,j}$, fit a logistic regression, $$\mathbb{P}[\tilde Y|\tilde{\boldsymbol{X}}=\tilde{\boldsymbol{x}}]=\frac{\exp[\tilde{\boldsymbol{x}}^\top\boldsymbol{\beta}]}{1+\exp[\tilde{\boldsymbol{x}}^\top\boldsymbol{\beta}]}$$(or any classification model – CART, random forest, etc). But that is the easy part (unless $n$ is large, because the siamese dataset has (roughly) $n^2/2$ rows). The difficult task is the prediction

• Prediction step

Consider a new input variable $\boldsymbol{x}_{\cdot}$, and define its siamese version, $\tilde{\boldsymbol{x}}_{\cdot}=(\tilde{\boldsymbol{x}}_{\cdot,j})_j$, i.e. a database with $n$ rows. Then compute
$$p_{\cdot,j}=\mathbb{P}[\tilde Y|\tilde{\boldsymbol{X}}=\tilde{\boldsymbol{x}}_{\cdot,j}]=\frac{\exp[\tilde{\boldsymbol{x}}_{\cdot,j}^\top\boldsymbol{\beta}]}{1+\exp[\tilde{\boldsymbol{x}}_{\cdot,j}^\top\boldsymbol{\beta}]}$$ where $p_{\cdot,j}$ is the probability that $(y_j,\boldsymbol{x}_{j})$ and $(y_{\cdot},\boldsymbol{x}_{\cdot})$ are in the same category, as well as $$p_{i,j}=\mathbb{P}[\tilde Y|\tilde{\boldsymbol{X}}=\tilde{\boldsymbol{x}}_{i,j}]=\frac{\exp[\tilde{\boldsymbol{x}}_{i,j}^\top\boldsymbol{\beta}]}{1+\exp[\tilde{\boldsymbol{x}}_{i,j}^\top\boldsymbol{\beta}]}$$
Let $\boldsymbol{p}_{\cdot}=(p_{\cdot,j})$, and similarly $\boldsymbol{p}_{i}=(p_{i,j})$. Then several techniques can be used to predict $y_{\cdot}$.

1. $\widehat{y}_{\cdot}=y_{j^\star}$ where ${j^\star}=\underset{j=1,\cdots,n}{\text{argmax}}\{p_{\cdot,j}\}$: the predicted class is the one of the observation the most likely to be other same class
2. $\widehat{y}_{\cdot}=y_{j^\star}$ where ${j^\star}=\underset{\ell=1,\cdots,k}{\text{argmax}}\{\overline{p}_{\ell}\}$, where$$\overline{p}_{\ell} = \frac{1}{n_{\ell}}\sum_{j\in\mathcal{I}_s} \boldsymbol{1}(y_j =y_{\ell}),\text{ where }\mathcal{I}_s=\lbrace i:p_{\cdot,i}>s\rbrace$$consider only probabilities sufficiently high to be considered, and predict the most important class (majority rule)
3. $\widehat{y}_{\cdot}=y_{j^\star}$ where $${j^\star}=\underset{i=1,\cdots,n}{\text{argmax}}\{\theta_i\}$$ where $$\theta_i=\cos(\boldsymbol{p}_{\cdot},\boldsymbol{p}_{i})=\displaystyle{\frac{\boldsymbol{p}_{\cdot}\cdot\boldsymbol{p}_{i}}{\|\boldsymbol{p}_{\cdot}\|\|\boldsymbol{p}_{i}\|}}$$
4. $\widehat{y}_{\cdot}=y_{j^\star}$ where $${j^\star}=\underset{i=1,\cdots,n}{\text{argmax}}\{KL_{\cdot|i}\}$$ and $KL_{\cdot|i}=\displaystyle{\sum_{j=1}^n p_{\cdot,j}\log\frac{p_{\cdot,j}}{p_{i,j}}}$ (but one can select another metric)
5. $\widehat{y}_{\cdot}=y_{j^\star}$ where ${j^\star}=\underset{j\in\mathcal{J}}{\text{argmax}}\{p_{\cdot,j}\}$ and $\mathcal{J}$ is a sample of $k$ observations, chosen randomly, one in each group (one-shot procedure): the predicted class is the one of the observation the most likely to be other same class

Heuristically, it can be related to some $k$ nearest neighbors strategy: we give the attribute that most neighbors have. The total distance is a weighted sum of the componentwise distances (for the logistic regression).

• Simulation study

In order to test that technique, let us generate some multinomial model where $y$ has 10 possible labels, with 6 (independent) covariates $x_1,\cdots,x_6$, and $\mathbb{P}[Y=A_k|\boldsymbol{X}=\boldsymbol{x}]\propto \exp[\boldsymbol{x}^\top\boldsymbol{\beta}_k]$ (where coefficients $\boldsymbol{\beta}_k$ where generated randomly) for $k\in\{1,2,\cdots,10\}$ (there were 10 categories) and with $n=700$ observations.

n=700 X1=rnorm(n) X2=rnorm(n) X3=rnorm(n) X4=rnorm(n) X5=rnorm(n) X6=rnorm(n) X=cbind(1,X1,X2,X3,sqrt(abs(X4)),X5*X1,X6) k = 10 PARAM = matrix(rnorm(k*6),k,6) PARAM[,1]=PARAM[,1]-1 PARAM=cbind(PARAM,0) P=matrix(NA,n,k-1) for(j in 1:(k-1)) P[,j] = X %*% (PARAM[j,])+rnorm(n) P=cbind(P,0) S=apply(exp(P),1,sum) Pb = exp(P)/S tirage = function(i){ sample(1:10,size=1,prob = Pb[i,]) } Y = LETTERS[Vectorize(tirage)(1:n)] dbase = data.frame(Y=as.factor(Y),X1,X2,X3,X4,X5)

In the paragraph previously, I suggested to take the most likely one. Being wrong means that it was not the first choice. But perhaps being the second or the third choice is not that bad, actually. So in my simulations, I look at the proportion of predictions were our prediction is the good one (top 1), if the true one is either the most likely or the second most likely (top 2), or in the top 3. That will be on my $x$-axis. I draw some line, but we simply have three points (top 1, top 2 and top 3). I compute the proportion of good prediction, using cross-validation techniques (10-fold). The black lines are one of the methods described above. The red one is the standard multinomial model (with a logistic link function). For the Siamese model, I tried several models. I tried a logistic regression, and some smooth version (GAM) on top

and a classification tree, on the left, as well as some random forest on the right, below.

It looks like the multinomial approach performs always better than any Siamese one… and to be honest, I am disappointed.

Here is the code I did use when I considered a logistic regression on the Siamese dataset,

set.seed(1) kfold = sample(rep(1:10,n/10))   KFOLDglm = function(i){ i_test=which(kfold==i) i_calibration=which(kfold!=i) y=credit[i_calibration,"Y"] tirage = function(){ v=c(sample(i_calibration[y==levels(y)[1]],size=1), sample(i_calibration[y==levels(y)[2]],size=1), sample(i_calibration[y==levels(y)[3]],size=1), sample(i_calibration[y==levels(y)[4]],size=1), sample(i_calibration[y==levels(y)[5]],size=1), sample(i_calibration[y==levels(y)[6]],size=1), sample(i_calibration[y==levels(y)[7]],size=1), sample(i_calibration[y==levels(y)[8]],size=1), sample(i_calibration[y==levels(y)[9]],size=1), sample(i_calibration[y==levels(y)[10]],size=1)) names(v)=levels(y) return(v) }   LogisticModel &lt;- multinom(Y ~ ., data = credit[i_calibration,], trace=FALSE)   comparaisonx = function(base,x=base[1,]){ mix_base = base for(j in 1:ncol(base)){ xj = as.numeric(x[j])-base[,j] mix_base[,j] = (xj) } mix_base } comparaisony = function(base,y=base[1]){ as.factor(base == y) } creditx = credit[,-which(names(credit) == "Y")] nc=length(i_calibration) B=comparaisonx(base = creditx[i_calibration[2:nc],],x=creditx[i_calibration[1],]) B$Y=comparaisony(base = credit[i_calibration[2:nc],"Y"],y=credit[i_calibration[1],"Y"]) for(i in 2:(nc-1)){ B0=comparaisonx(base = creditx[i_calibration[(i+1):nc],],x=creditx[i_calibration[i],]) B0$Y=comparaisony(base = credit[i_calibration[(i+1):nc],"Y"],y=credit[i_calibration[i],"Y"]) B=rbind(B,B0) } credit_mix = B   OneShotLogisticModel &lt;- glm(Y ~ ., data = credit_mix, family=binomial) A_ref = table(credit[i_calibration,"Y"])/length(i_calibration)   vect_oneshot = function(i){ B2=comparaisonx(base = creditx[i_calibration,],x=creditx[i,]) predict(OneShotLogisticModel,type="response",newdata=B2) }   prediction_oneshot = function(i,type=1){ B2=comparaisonx(base = creditx[i_calibration,],x=creditx[i,]) p=predict(OneShotLogisticModel,type="response",newdata=B2) y=credit[i_calibration,"Y"] base = data.frame(p,y) base = base[rev(order(base$p)),] if(type==1){T = table(base$y[1:11]) return(names(which.max(T)))} if(type==2){return(base$y[1])} if(type==3){A=table(base$y[1:10])/10 T=A/A_ref return(names(which.max(T)))} if(type==4){ costheta = rep(NA,length(i_calibration)) for(j in 1:length(i_calibration)){ vecteur_proba = vect_oneshot(i_calibration[j]) costheta[j] = sum(vecteur_proba*p)/(sqrt(sum(vecteur_proba^2))*sqrt(sum(p^2))) } return(y[which.max(costheta)])} if(type==5){ kl = rep(NA,length(i_calibration)) for(j in 1:length(i_calibration)){ vecteur_proba = vect_oneshot(i_calibration[j]) kl[j] = sum(p*log(vecteur_proba/p)) } return(y[which.max(as.vector(kl))])} if(type==6){ ## one shot : tirer au hasard un de chaque, et dire lequel est plus credible !   y=credit[i_calibration,"Y"] tirage = function(){ v=c(sample(i_calibration[y==levels(y)[1]],size=1), sample(i_calibration[y==levels(y)[2]],size=1), sample(i_calibration[y==levels(y)[3]],size=1), sample(i_calibration[y==levels(y)[4]],size=1), sample(i_calibration[y==levels(y)[5]],size=1), sample(i_calibration[y==levels(y)[6]],size=1), sample(i_calibration[y==levels(y)[7]],size=1), sample(i_calibration[y==levels(y)[8]],size=1), sample(i_calibration[y==levels(y)[9]],size=1), sample(i_calibration[y==levels(y)[10]],size=1)) names(v)=levels(y) return(v) } pd=rep(NA,101) for(ix in 1:101){ ids = tirage() B2=comparaisonx(base = creditx[ids,],x=creditx[i,]) p=predict(OneShotLogisticModel,type="response",newdata=B2) pd[ix]=levels(y)[which.max(p)] } levels(y)[which.max(table(pd))] } } PRED0=as.character(credit[i_test,"Y"]) PRED1=as.character(predict(LogisticModel,type = "class", newdata=credit[i_test,])) PRED21=as.character(Vectorize(function(i) prediction_oneshot(i,type=1)) (i_test)) PRED22=as.character(Vectorize(function(i) prediction_oneshot(i,type=2))(i_test)) PRED23=as.character(Vectorize(function(i) prediction_oneshot(i,type=3))(i_test)) PRED24=as.character(Vectorize(function(i) prediction_oneshot(i,type=4))(i_test)) PRED25=as.character(Vectorize(function(i) prediction_oneshot(i,type=5))(i_test)) PRED26=as.character(Vectorize(function(i) prediction_oneshot(i,type=6))(i_test)) B=data.frame(PRED0,PRED1,PRED21,PRED22,PRED23,PRED24,PRED25,PRED26) B }   s=1/100;setTxtProgressBar(pb, s*2) for(i in 2:10){ PREDICTION = rbind(PREDICTION,KFOLDglm(i)) s=s+1/100;setTxtProgressBar(pb, s*2)} for(j in 1:5) PREDICTION[,j]=as.character(PREDICTION[,j]) L=list() v=mean(PREDICTION[,1]!=PREDICTION[,2]) names(v)="logistic" L[["logistic"]]=v v=c(mean(PREDICTION[,1]!=PREDICTION[,3]), mean(PREDICTION[,1]!=PREDICTION[,4]), mean(PREDICTION[,1]!=PREDICTION[,5]), mean(PREDICTION[,1]!=PREDICTION[,6]), mean(PREDICTION[,1]!=PREDICTION[,7]), mean(PREDICTION[,1]!=PREDICTION[,8])) names(v)=c("top10","max","10norm","cos","KL","OS") L[["glm"]]=v

# Some general thoughts on Partial Dependence Plots with correlated covariates

The partial dependence plot is a nice tool to analyse the impact of some explanatory variables when using nonlinear models, such as a random forest, or some gradient boosting.The idea (in dimension 2), given a model $m(x_1,x_2)$ for $\mathbb{E}[Y|X_1=x_1,X_2=x_2]$. The partial dependence plot for variable $x_1$ is model $m$ is function $p_1$ defined as $x_1\mapsto\mathbb{E}_{\mathbb{P}_{X_2}}[m(x_1,X_2)]$. This can be approximated, using some dataset using $$\widehat{p}_1(x_1)=\frac{1}{n}\sum_{i=1}^n m(x_1,x_{2,i})$$My concern here what the interpretation of that plot when there are some (strongly) correlated covariates. Let us generate some dataset to start with

n=1000 library(mnormt) r=.7 set.seed(1234) X = rmnorm(n,mean = c(0,0),varcov = matrix(c(1,r,r,1),2,2)) Y = 1+X[,1]-2*X[,2]+rnorm(n)/2 df = data.frame(Y=Y,X1=X[,1],X2=X[,2])

As we can see, the true model is here is $y_i=\beta_0+\beta_1 x_{1,i}+\beta_2x_{2,i}+\varepsilon_i$ where $\beta_1 =1$ but the two variables are positively correlated, and the second one has a strong negative impact. Note that here

reg = lm(Y~.,data=df) summary(reg)   Coefficients: Estimate Std. Error t value Pr(&gt;|t|) (Intercept) 1.01414 0.01601 63.35 &lt;2e-16 *** X1 1.02268 0.02305 44.37 &lt;2e-16 *** X2 -2.03248 0.02342 -86.80 &lt;2e-16 ***

If we estimate a wrongly specified model $y_i=b_0+b_1 x_{1,i}+\eta_i$, we would get

reg1 = lm(Y~X1,data=df) summary(reg1)   Coefficients: Estimate Std. Error t value Pr(&gt;|t|) (Intercept) 1.03522 0.04680 22.121 &lt;2e-16 *** X1 -0.44148 0.04591 -9.616 &lt;2e-16 ***

Thus, on the proper model, $\widehat{\beta}_1\sim+1.02$ while $\widehat{b}_1\sim-0.44$  on the mispecified model.

Now, let us look at the parial dependence plot of the good model, using standard R dedicated packages,

library(pdp) pdp::partial(reg, pred.var = "X1", plot = TRUE, plot.engine = "ggplot2")

which is the linear line $y=1+x$, that corresponds to $y=\beta_0+\beta_1x$.

library(DALEX) plot(DALEX::single_variable(DALEX::explain(reg, data=df),variable = "X1",type = "pdp"))

which corresponds to the previous graph. Here, it is also possible to creaste our own function to compute that partial dependence plot,

pdp1 = function(x1){ nd = data.frame(X1=x1,X2=df$X2) mean(predict(reg,newdata=nd)) } that will be the straight line below (the dotted line is the theoretical one $y=1+x$, vx=seq(-3.5,3.5,length=101) vpdp1 = Vectorize(pdp1)(vx) plot(vx,vpdp1,type="l") abline(a=1,b=1,lty=2) which is very different from the univariate regression on $x_1$ abline(reg1,col="red") Actually, the later is very consistent with a local regression, only on $x_1$ library(locfit) lines(locfit(Y~X1,data=df),col="blue") Now, to get back to the definition of the partial dependence plot, $x_1\mapsto\mathbb{E}_{\mathbb{P}_{X_2}}[m(x_1,X_2)]$, in the context of correlated variable, I was wondering if it would not make more sense to consider some local version actually, something like $x_1\mapsto\mathbb{E}_{\mathbb{P}_{X_2|X_1}}[m(x_1,X_2)]$. My intuition was that, somehow, it did not make any sense to consider any $X_2$ while $X_1$ was fixed (and equal to $x_1$). But it would make more sense actually to look at more valid $X_2$‘s given the value of $X_1$. And a natural estimate could be some $k$ neareast-neighbors, i.e. $$\tilde{p}_1(x_1)=\frac{1}{k}\sum_{i\in\mathcal{V}_k(x)}^n m(x_1,x_{2,i})$$ where $\mathcal{V}_k(x)$ is the set of indices of the $k$ $x_i$‘s that are the closest to $x$, i.e. lpdp1 = function(x1){ nd = data.frame(X1=x1,X2=df$X2) idx = rank(abs(df$X1-x1)) mean(predict(reg,newdata=nd[idx&lt;50,])) } vlpdp1 = Vectorize(lpdp1)(vx) lines(vx,vlpdp1,col="darkgreen",lwd=2) Surprisingly (?), this local partial dependence plot gives a curve that corresponds to the simple regression… # Lilliefors, Kolmogorov-Smirnov and cross-validation In statistics, Kolmogorov–Smirnov test is a popular procedure to test, from a sample $\{x_1,\cdots,x_n\}$ is drawn from a distribution $F$, or usually $F_{\theta_0}$, where $F_{\theta}$ is some parametric distribution. For instance, we can test $H_0:X_i\sim\mathcal{N(0,1)}$ (where $\theta_0=(\mu_0,\sigma_0^2)=(0,1)$) using that test. More specifically, I wanted to discuss today $p$-values. Given $n$ let us draw $\mathcal{N}(0,1)$ samples of size $n$, and compute the $p$-values of Kolmogorov–Smirnov tests n=300 p = rep(NA,1e5) for(s in 1:1e5){ X = rnorm(n,0,1) p[s] = ks.test(X,"pnorm",0,1)$p.value }

We can visualise the distribution of the $p$-values below (I added some Beta distribution fit here)

library(fitdistrplus) fit.dist = fitdist(p,"beta") hist(p,probability = TRUE,main="",xlab="",ylab="") vu = seq(0,1,by=.01) vv = dbeta(vu,shape1 = fit.dist$estimate[1], shape2 = fit.dist$estimate[2]) lines(vu,vv,col="dark red", lwd=2)

It looks like it is quite uniform (theoretically, the $p$-value is uniform). More specifically, the $p$-value was lower than 5% in 5% of the samples

[note: here I compute ‘mean(p<=.05)’ but I have some trouble with the ‘<‘ and ‘>’ symbols, as always]

mean(p&lt;=.05) [1] 0.0479

i.e. we wrongly reject $H_0:X_i\sim\mathcal{N(0,1)}$ is 5% of the samples.

As discussed previously on the blog, in many cases, we do care about the distribution, and not really the parameters, so we wish to test something like $H_0:X_i\sim\mathcal{N(\mu,\sigma^2)}$, for some $\mu$ and $\sigma^2$. Therefore, a natural idea can be to test $H_0:X_i\sim\mathcal{N(\hat\mu,\hat\sigma^2)}$, for some estimates of $\mu$ and $\sigma^2$. That’s the idea of Lilliefors test. More specifically, Lilliefors test suggests to use , Kolmogorov–Smirnov statistics, but corrects the $p$-value. Indeed, if we draw many samples, and use Kolmogorov–Smirnov statistics and its classical $p$-value to test for $H_0:X_i\sim\mathcal{N(\hat\mu,\hat\sigma^2)}$,

n=300 p = rep(NA,1e5) for(s in 1:1e5){ X = rnorm(n,0,1) p[s] = ks.test(X,"pnorm",mean(X),sd(X))$p.value } we see clearly that the distribution of $p$-values is no longer uniform fit.dist = fitdist(p,"beta") hist(p,probability = TRUE,main="",xlab="",ylab="") vu = seq(0,1,by=.01) vv = dbeta(vu,shape1 = fit.dist$estimate[1], shape2 = fit.dist$estimate[2]) lines(vu,vv,col="dark red", lwd=2) More specifically, if $x_i$‘s are actually drawn from some Gaussian distribution, there are no chance to reject $H_0$, the $p$-value being almost never below 5% mean(p&lt;=.05) [1] 0.00012 Usually, to interpret that result, the heuristics is that $\hat\mu$ and $\hat\sigma^2$ are both based on the sample, while previously $0$ and $1$ where based on some prior knowledge. Somehow, it reminded me on the classical problem when mention when we introduce cross-validation, which is Goodhart’s law When a measure becomes a target, it ceases to be a good measure i.e. we cannot assess goodness of fit using the same data as the ones used to estimate parameters. So here, why not use some hold-out (or cross-validation) procedure : split the dataset in two parts, $\{x_1,\cdots,x_k\}$ (with $k) to estimate parameters $\mu$ and $\sigma^2$ and then use $\{x_{k+1},\cdots,x_n\}$ and Kolmogorov–Smirnov statistics on it to test if $x_i$‘s are drawn from some Gaussian distribution. More precisely, will the $p$-value computed using the standard Kolmogorov–Smirnov procedure be ok here. Here, I tried two scenarios, $k/n$ being either $1/3$ or $2/3$, p = matrix(NA,1e5,4) for(s in 1:1e5){ X = rnorm(n,0,1) p[s,1] = ks.test(X,"pnorm",0,1)$p.value p[s,2] = ks.test(X,"pnorm",mean(X),sd(X))$p.value p[s,3] = ks.test(X[1:200],"pnorm",mean(X[201:300]),sd(X[201:300]))$p.value p[s,4] = ks.test(X[201:300],"pnorm",mean(X[1:200]),sd(X[1:200]))$p.value } Again, we can visualize the distributions of $p$-values, in the case where $1/3$ of the data is used to estimate $\mu$ and $\sigma^2$, and $2/3$ of the data is used to test fit.dist = fitdist(p[,3],"beta") hist(p[,3],probability = TRUE,main="",xlab="",ylab="") vu=seq(0,1,by=.01) vv=dbeta(vu,shape1 = fit.dist$estimate[1], shape2 = fit.dist$estimate[2]) lines(vu,vv,col="dark red", lwd=2) and in the case where $2/3$ of the data is used to estimate $\mu$ and $\sigma^2$, and $1/3$ of the data is used to test fit.dist = fitdist(p[,4],"beta") hist(p[,4],probability = TRUE,main="",xlab="",ylab="") vu=seq(0,1,by=.01) vv=dbeta(vu,shape1 = fit.dist$estimate[1], shape2 = fit.dist$estimate[2]) lines(vu,vv,col="dark red", lwd=2) Observe here that we (wrongly) reject too frequently $H_0$, since the $p$-values are below 5% in 25% of the scenarios, in the first case (less data used to estimate), and 9% of the scenarios, in the second case (less data used to test) mean(p[,3]&lt;=.05) [1] 0.24168 mean(p[,4]&lt;=.05) [1] 0.09334 We can actually compute that probability as a function of $k/n$ n=300 p = matrix(NA,1e4,99) for(s in 1:1e4){ X = rnorm(n,0,1) KS = function(p) ks.test(X[1:(p*n)],"pnorm",mean(X[(p*n+1):n]),sd(X[(p*n+1):n]))$p.value p[s,] = Vectorize(KS)((1:99)/100) }

The evolution of the probability is the following

prob5pc = apply(p,2,function(x) mean(x&lt;=.05)) plot((1:99)/100,prob5pc)

so, it looks like we can use some sort of hold-out procedure to test for $H_0:X_i\sim\mathcal{N(\mu,\sigma^2)}$, for some $\mu$ and $\sigma^2$, using Kolmogorov–Smirnov test with $\mu=\hat\mu$ and $\sigma^2=\hat\sigma^2$ but the proportion of data used to estimate those quantities should be (much) larger that the one used to compute the statistics. Otherwise, we clearly reject too frequently $H_0$.

# Insurance Pricing Game

Would you like to put your data science skills to the test?

Imperial College London, Universite du Quebec à Montreal (UQAM), and actuarial institutes in Singapore, the UK, including the IFoA, and Australia, ASTIN, the Casualty Actuarial Society are co-organising a global data science competition.

Would you like to accurately predict the cost of insurance by putting your data science skills to the test? We are hosting two competitions with separate datasets, a loss prediction competition on Kaggle with synthetic workers’ compensation data, and a pricing competition in a simulated market hosted on AI Crowd with real-world motor insurance contracts. Codes can be either in R or python. The competition is being sponsored by a number of different organisations, with a total of US$12,000 in cash prizes to be won. For more information about how to take part please visit www.pricing-game.com # Trees and forests For my ACT6100 weekly quiz, I usually generate some datasets, and then ask students to compare various predictive algorithms. Last week, it was about classification trees and random forests. And students were surprised to have such differences (they had to estimate the probability to have a specific label, for the barycenter of the covariates). Usually, I use the following to generate some (here 12) covariates that could be correlated library(FactoMineR) n=279 library(clusterGeneration) library(mnormt) k=12 S=genPositiveDefMat("unifcorrmat",dim=k) X=round(rmnorm(n,varcov=S$Sigma)+8,2) rownames(X)=1:n colnames(X)=LETTERS[1:k]

Then I need to generate some data, based on some covariates (5 out of 12), with various strengths

idx = sample(1:k,size=5) u = sample(c(-(4:1),1:4),5) beta = rep(0,k) beta[idx] = u U = X%*%beta U = U-min(U) U = U/max(U)*6-3 p = exp(( U))/(1+exp((U ))) Y = rbinom(n,size=1,prob=p) df = data.frame(Y=as.factor(Y),X) levels(df$Y)=levels=c("blue","red") We can run a classification tree library(rpart) arbre = rpart(Y~., data=df) and a random forest, library(randomForest) set.seed(1) arbres = randomForest(Y~., data=df) Here are the partial plots for 4 of the explanatory variables that actually have an impact partialPlot(arbres,pred.data = df, x.var = "A") Predictions for the “average” point of the dataset is here (parbre = predict(arbre,newdata=data.frame(t(apply(df[,-1],2,mean))),type = "prob")) blue red 1 0.8064516 0.1935484 (parbres = predict(arbres,newdata=data.frame(t(apply(df[,-1],2,mean))),type = "prob")) blue red 1 0.422 0.578 attr(,"class") [1] "matrix" "votes" and there is a substantial difference, with a probability of 19% with a single tree, 58% with 500 trees (the default value of the function). To understand why we can have such a difference, we should not only focus on the bagging stratgy, but look at the variability of the predictions, obtained with trees, B=1e4 parbres = rep(NA,B) m=data.frame(t(apply(df[,-1],2,mean))) for(b in 1:B){ idx = sample(1:nrow(df),size=nrow(df),replace=TRUE) arbre = rpart(Y~., data=df[idx,]) parbres[b] = predict(arbre,newdata=m,type = "prob")[2] } hist(parbres) Surprisingly, we have here a bimodal function for $\hat{y}$ which is either very small for some trees, of very large for others. On average, we have a value close to 55%… I think I will use more that generative algorithm for future quiz… # R0 and the exponential growth of a pandemic, an update A few days ago, I wrote a blog post – R0 and the exponential growth of a pandemic – where I was trying to generate some visualization of some exponential growth, in the context of a pandemic. After giving some thoughts, the previous graph might not be the best one to see an exponential based contagion. Having graphs evolving, from the left to the right, gives us the (false) idea of some temporal evolution. Which is no necessarily correct. It simply means that contaminated people will contaminate other people, and we look at the number of iterations here. So maybe some concentric dots would look better. And from a technical perspective, what I did was fun, but probably too complicated. In my previous post, I wanted to pack optimally $k$ identical disks intro a unit circle. On http://hydra.nat.uni-magdeburg.de/packing, it was possible to get the “best known packings of equal circles in a circle”, with the coordinates. But as we will see, we can use something much more simple here. My idea is now to create some picture like one below, with concentric colored dot. In the center, we have the first people that were contaminated, and then, we can see the transmission, somehow From a technical perspective, here, I use a different strategy. I decided to draw random points, uniformly. The problem with randomness is the natural high discrepancy, with monte carlo methods: it is very likely that some disks will overlap. It is not a major issue, but it might distort the message. So I decided to use some low-discrepancy sequences, such as Halton‘s sequence. library(randtoolbox) S = halton(n=5000, dim = 2)*2-1 Here, I have disk coordinates in $[-1,+1]^2$. Then, to get disks in a circle, I simply compute the distance to the origin $(0,0)$, D0 = S[,1]^2+S[,2]^2 and take the ranks. If I want to visualize $k=200$ people, I consider the 200 smaller ranks. To get concentric circles, each part having $k_i$ individuals, I use as thresholds $R_0^{\bar k_{i-1}},R_0^{\bar k_{i}},R_0^{\bar k_{i+1}}$, etc, where $\bar k_i=\bar k_{i-1}+k_i$, R0 = rank(D0,ties.method = "random") C0 = as.numeric(cut(R0,c(0,cumsum(k)+.5)),100000) where R0=1.8 k=round(R0^(seq(1,9,by=2))) Then we can plot the dots, with appropriate colors, points(S,pch=19,col=colrpal[C0],cex=.75) And of course, we can try that with different values, for $R_0$ R0=2.2 k=round(R0^(seq(1,9,by=2))) kmax=max(k) S = halton(n=5000, dim = 2)*2-1 plot(S,col="light yellow",axes=FALSE,xlab="",ylab="",xlim=c(-1.3,1),ylim=c(-1,1),cex=.75,pch=19) D0 = S[,1]^2+S[,2]^2 R0 = rank(D0,ties.method = "random") C0 = as.numeric(cut(R0,c(0,cumsum(k)+.5)),100000) points(S,pch=19,col=colrpal[C0],cex=.75) # R0 and the exponential growth of a pandemic For some dissemination work, I want to create a nice graph to explain the exponential growth in pandemics, related to the value of $R_0$. Recall that $R_0$ corresponds to the average number of people that a contagious person can infect. Hence, with $R_0=1.5$, 4 people will contaminate 6 people, and those 6 will contaminate 9, etc. After $n$ iteration, the number of contaminated people is simply $R_0{}^n$. As explained by Daniel Kahneman people, certainly including myself, don’t seem to be able to think straight about exponential growth. What we see today are infections that occurred 2 or 3 weeks ago and the deaths today are people who got infected 4 or 5 weeks ago. All of this is I think beyond intuitive human comprehension For different values of $R_0$ (on each row), I wanted to visualise the number of contaminated people after 3, 5 or 7 iterations, since graphs are usually the most simple way to give some intuition. The graph I had in mind was the following (to be honest, I am quite sure I had seen it somewhere, but I cannot find where). The main challenge here is pack optimally $k$ identical circles intro a unit circle: we need here the location of the points (center of the disks) and the radius. It seems to be a rather complicated mathematical problem. Nicely, on http://hydra.nat.uni-magdeburg.de/packing, it is possible to get the “best known packings of equal circles in a circle” (up to 5000, but many $k$‘s are missing). For instance, for $k=37$, we have And interestingly, on the same website, we can get the coordinates of the centers, for example with 37 disks, so it is possible to recreate the R graph. k = 37 base = read.table(paste("http://hydra.nat.uni-magdeburg.de/packing/cci/txt/cci",k,".txt",sep=""), header=FALSE) The problem, as discussed earlier, is that some cases are not solved, yes, for instance $k=2^{12}=4096$: the next feasable case is 4105. To avoid that issue, one can use T = "Error" while(T == "Error"){ T = substr(try(base = read.table(paste("http://hydra.nat.uni-magdeburg.de/packing/cci/txt/cci",k,".txt",sep=""), header=FALSE),silent = TRUE),1,5) k=k+1 } k=k-1 Now we can almost plot it. The problem is that the radius of the circles is missing, here. But we can compute it D=as.matrix(dist(x = base[,2:3])) diag(D)=1e5 i=which(D == min(D), arr.ind = TRUE) r = D[i[1,1],i[1,2]] Here the radius is r [1] 0.2959118 To plot it, use plot(base$V2,base$V3,xlim=c(-1,1),ylim=c(-1,1)) n=100 theta=seq(0,pi,length=n+1) circ= function(x,y,r,h=1){ vu=x+r*cos(theta) vv=r*sin(theta) cbind(c(vu,rev(vu))*h,c(y+vv,y-rev(vv))*h) } for(i in 1:k) polygon(circ(base[i,2],base[i,3],r/2*.95),col=colr,border=NA) We can now use that code to create the graph above, with $k=R_0{}^n$ for various values of $n$ And we can also use it to visualize more subtile differences, like $R_0=1.1$, $R_0=1.3$, $R_0=1.5$ and $R_0=1.7$ # Hidding values in the output of the summary function for a (linear) regression Since our Fall 2020 session will be 100% online (and off-site), I have to work hard this summer to prepare online quizz and exams. I started intensively to play with Achim’s awesome r-exams package. But there are still a few things that I wanted to add, so I will post a series of posts on my blogs to keep tracks of updated functions I will write. Most of them a modification of R internal functions, so the code is hard to read. Here is the file, and I will update it frequently url = "http://freakonometrics.free.fr/onlineExams.R" source(url) I have updated the summary function (more precisely the summary.lm function). To see how it works, consider a simple regression library(car) reg = lm(prestige ~ women, data=Prestige) my_summary(reg) Call: lm(formula = prestige ~ women, data = Prestige) Residuals: Min 1Q Median 3Q Max -33.444 -12.391 -4.126 13.034 39.185 Coefficients: Estimate Std. Error t value Pr(&gt;|t|) (Intercept) 48.69300 2.30760 21.101 2e-16 *** women -0.06417 0.05385 -1.192 0.236 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 17.17 on 100 degrees of freedom Multiple R-squared: 0.014, Adjusted R-squared: 0.004143 F-statistic: 1.42 on 1 and 100 DF, p-value: 0.2362 A classical question I ask in my quizz is to hide the $p$-value of the F-test, and ask what it is (to make sure that students understand the equivalence between the F and the t test, in a simple regression). To hide the $p$-value, use my_summary(reg, Fisher=TRUE) Call: lm(formula = prestige ~ women, data = Prestige) Residuals: Min 1Q Median 3Q Max -33.444 -12.391 -4.126 13.034 39.185 Coefficients: Estimate Std. Error t value Pr(&gt;|t|) (Intercept) 48.69300 2.30760 21.101 2e-16 *** women -0.06417 0.05385 -1.192 0.236 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 17.17 on 100 degrees of freedom Multiple R-squared: 0.014, Adjusted R-squared: 0.004143 F-statistic: 1.42 on 1 and 100 DF, p-value: ■■■■■ (and then, in a multiple choice exam, I ask if it is 1%, 5%, 12%, 23%, 47%, for example). That one was easy, since all those lines are based on the cat function, so I just modify it, if necessary if(Fisher) cat("\nF-statistic:", formatC(x$fstatistic[1L], digits = digits), "on", x$fstatistic[2L], "and", x$fstatistic[3L], "DF, p-value:", "■■■■■") if(!Fisher) cat("\nF-statistic:", formatC(x$fstatistic[1L], digits = digits), "on", x$fstatistic[2L], "and", x$fstatistic[3L], "DF, p-value:", format.pval(pf(x$fstatistic[1L], x$fstatistic[2L], x$fstatistic[3L], lower.tail = FALSE), digits = digits))

(here I use the unicode ‘black square‘ symbol to hide numbers). Of course, I can hide the value of $\sigma$, or the (adjusted or not) $R ^2$, etc.

Now, a little bit more tricky: what if we want to change the regression table, with the coefficients, their standard deviation, etc.  It is tricky since those values are numeric, with an appropriate format (not too many digits), but it can be done easily since that formating is done through the printCoefmat function.  So in my code, I have my internal function, where I ask to put some ‘black square‘ (and the good number to keep a readable format) at some specific locations. Consider a more complex regression

reg = lm(prestige ~ ., data=Prestige)

and assume that we want to hide the value of the intercet, $\widehat{\beta}_0$ (i.e. located at $(1,1)$ in the matrix) and the $p$-value of the t-test for the fourth one (i.e. located at $(4,4)$ in the matrix – since the first colum is $\widehat{\beta}_3$, the second one its standard deviation, the thirst one the $t$ value, and then, the fourth one, the $p$-value of the test). I use the following two vectors

vligne = c(1,4), vcolonne = c(1,4)

with rows and columns in the matrix (of course, the two should have the same length). Then, the good thing is that the printCoefmat function convert numerical values into characters (to have things that look like columns actually). So we simply have to remove numerical digits, and use squares instead

Cf2=Cf if(length(vligne)&gt;0){ for(i in 1:length(vligne)){ long = nchar(Cf[vligne[i],vcolonne[i]]) Cf2[vligne[i],vcolonne[i]] = paste(rep("■",long),collapse = "") }}

Then, we print the updated version of the table

print.default(Cf2, quote = quote, right = right, na.print = na.print,...)

For example, here, it would be

my_summary(reg, vligne=c(1,4), vcolonne=c(1,4))   Call: lm(formula = prestige ~ ., data = Prestige)   Residuals: Min 1Q Median 3Q Max -12.9863 -4.9813 0.6983 4.8690 19.2402   Coefficients: Estimate Std. Error t value Pr(&gt;|t|) (Intercept) ■■■■■■■■■■ 8.018e+00 -1.513 0.13380 education 3.933e+00 6.535e-01 6.019 3.64e-08 *** income 9.946e-04 2.601e-04 3.824 0.00024 *** women 1.310e-02 3.019e-02 0.434 ■■■■■■■ census 1.156e-03 6.183e-04 1.870 0.06471 . typeprof 1.077e+01 4.676e+00 2.303 0.02354 * typewc 2.877e-01 3.139e+00 0.092 0.92718 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1   Residual standard error: 7.037 on 91 degrees of freedom (4 observations deleted due to missingness) Multiple R-squared: 0.841, Adjusted R-squared: 0.8306 F-statistic: 80.25 on 6 and 91 DF, p-value: &lt; 2.2e-16

Of course, it is hand made, I do not check for typos (like you should not ask to put squares in the seventh column), but that works well enough to generate random regressions in a quizz (or identical regressions on subsamples of a large dataset), and to hide values, in a quizz.

# Sharing pictures from holidays in the Canadian Rockies (with R)

My kids have a very popular blog (at least among their grandmothers) where they frequently post pictures from everyday’s life (since they live 5000km from them), as well as pictures taken from holidays. This afternoon, I tried to used the popupImage function from the leaflet package to post pictures, on a map (to explain where we spent our holiday this summer). This post is just to keep tracks of that code.

First, we need to load the appropriate R packages

library(leaflet) library(mapview)

Then, we take a picture, and we locate it, for instance Mirror Lake (on the trail to Lake Agnes). Since leaflet uses openstreetmap, I recommend to use it also for location (and not google maps… coordinates can be slightly different)

df=data.frame(lat =51.41603, long=-116.23946, nom = "Miror Lake",photo="http://freakonometrics.free.fr/jaspeR/_DSC5967.jpg")

I guess you can also use the metadata if you take pictures with a cell phone, and you add the location… but I am (very) old fashioned, and still use a camera to take pictures. Then you can add a dozen pictures

df=rbind(df, data.frame(lat =51.4164, long=-116.2442, nom = "Lake Agnes",photo="http://freakonometrics.free.fr/jaspeR/_DSC6003.jpg")) df=rbind(df, data.frame(lat =51.3215642,long=-116.193718, nom="Moraine Lake",photo="http://freakonometrics.free.fr/jaspeR/_DSC5957.jpg"))

From that dataframe, we need two kinds of information: the location, and the url of the picture,

data_df=df[,c("lat","long")] images = as.character(df$photo) Then we can create the leaflet map (sorry for typos, but wordpress converts the > symbol into some “&gt;” characters… which makes R pipe operator hard to read) m = leaflet(data_df) %&gt;% addTiles() %&gt;% addCircleMarkers( fillOpacity = 0.8, radius = 5, lng = ~long, lat =~lat, popup = popupImage(images) ) and export it (in a nice html file) library(htmlwidgets) saveWidget(m, file="jaspR.html") # Regression discontinuity model for TV series In September, we are usually happy to see our favorite TV series back on air… Or not? Because, admit it, if we are happy to see those characters back, most of the time, we are disappointed, too. So why not look at the data, to confirm this feeling? Nazareno Andrade shared some nice codes to get IMDB ratings in a nice csv file (you can either use the large csv file, or run your own codes) download.file("https://github.com/nazareno/imdb-series/raw/master/data/series_from_imdb.csv", destfile="series_from_imdb.csv") base = read.csv("series_from_imdb.csv") It is a large dataset, with more than 64,000 episodes of almost 890 TV series, str(base) 'data.frame': 64018 obs. of 18 variables:$ series_name: Factor w/ 889 levels "'Allo 'Allo!",..: 137 137 137 137 137 137 137 137 137 137 ... $episode : Factor w/ 54090 levels "-30-","¡Viva los muertos!",..: 32314 7446 16 7176 17748 9562 1379 36218 17845 5553 ...$ series_ep : int 1 2 3 4 5 6 7 8 9 10 ... $season : int 1 1 1 1 1 1 1 2 2 2 ...$ season_ep : int 1 2 3 4 5 6 7 1 2 3 ... $user_rating: num 8.9 8.7 8.7 8.2 8.3 9.2 8.8 8.7 9.2 8.3 ... Just pick a TV series, for instance Dan Harmon’s Community, sbase = base[base$series_name=="Community",]

We can plot the evolution of the rating over the 110 episodes.

sbase=sbase[!duplicated(sbase[,c(1,2,4,5)]),] sbase$series_ep=1:nrow(sbase) ()since there could be some problem with the data (such as duplicates, let us clean it quickly) plot(sbase$series_ep,sbase$UserRating,xlab=sbase$series_name[1]) idx=c(0,which(diff(sbase$season)!=0),nrow(sbase)) abline(v=idx+.5,lty=2,col=colr[2]) a = unique(sbase$season) for(u in a){ ssbase = sbase[sbase$season==u,] reg = lm(UserRating~series_ep,data=ssbase) lines(ssbase$series_ep,predict(reg),col=colr[3],lwd=2) }

The vertical lines are here to visualize the seasons. On issue is that the lenght can vary with time. Consider Linwood Boomer’s Malcom in The Middle,

sbase = base[base$series_name=="Malcolm in the Middle",] or Craig Thomas and Carter Bays’s How I Met Your Mother, sbase = base[base$series_name=="How I Met Your Mother",]

On those two, the evolution is rather stable. Look at AMC’s The Walking Dead,

sbase = base[base$series_name=="The Walking Dead",] Now, look at Howard Gordon and Alex Gansa’s Homeland, sbase = base[base$series_name=="Homeland",]

There is an issue here with the last episode of season4, “Long Time Coming“, that has a very poor rating. If we remove that point, we get the thin line. Note that the regression line is always increasing. For Michael Hirst’s Vickings, we have

sbase = base[base$series_name=="Vicking",] If we look more carefully on the previous graph, for five seasons (out of six), we have a positive slope. Well, to be honest, it is not significantly positive most of the time, but still. Out of 80 shows, and a total of 583 seasons, the slope is postive 75% of the time (433) and negative 25% of the time (150). BASE = NULL L80 = unique(base$series_name) for(j in 1:length(L)){ sbase=base[base$series_name==L[j],] sbase=sbase[!duplicated(sbase[,c(1,2,4,5)]),] sbase=sbase[sbase$season&gt;0,] sbase$series_ep=1:nrow(sbase) a=unique(sbase$season) a=a[!is.na(a)] for(u in a){ ssbase=sbase[sbase$season==u,] reg=lm(UserRating~series_ep,data=ssbase) pente = NA if((!is.na(coefficients(reg)[2]))&amp;(!is.na((summary(reg)$coefficients[2,4])))){ if((summary(reg)$coefficients[2,4]&lt;.05)&amp;(coefficients(reg)[2]&gt;0)) pente="positive" if((summary(reg)$coefficients[2,4]&lt;.05)&amp;(coefficients(reg)[2]&lt;0)) pente="negative" sdf=data.frame(nom=sbase$series_name[1],season=u,slope=coefficients(reg)[2],inf=confint(reg)[2,1],sup=confint(reg)[2,2],signe=pente) BASE=rbind(BASE,sdf)} }} str(BASE) 'data.frame': 583 obs. of 6 variables:$ nom : Factor w/ 80 levels "Friends","Game of Thrones",..: 1 1 1 1 1 1 1 1 1 1 ...   mean(BASE$slope&gt;0) [1] 0.7427101 table(BASE$signe) negative positive 15 144

Most of the time, the slope is not significant. To be more specific, 72% of the time, the slope is not significant. But when it is, 90% of the time, it is positive (144 seasons). Let us look at other TV series, for instance Joel Surnow and Robert Cochran’s 24,

sbase = base[base$series_name=="24",] Álex Pina’s La Casa de Papel, sbase = base[base$series_name=="La Casa de Papel",]

Steven Knight’s Peaky Blinders,

sbase = base[base$series_name=="Peaky Blinders",] or David Simon’s The Wire, sbase = base[base$series_name=="The Wire",]

The slope is increasing over almost all seasons. But a major drawback is that when we get back to our show, for a new season, we usually get disapointed. More specifically, we can quantify the difference in red below

that can be estimated using

sbase12 = sbase[sbase$season%in%c(a[ij],a[ij+1]),] seuil = sbase12$series_ep[which(diff(sbase12$season)!=0)]+.5 s = function(x) (x-seuil)*(x&gt;seuil) reg = lm(UserRating~series_ep+s(series_ep)+I(series_ep&gt;seuil),data=sbase12) Here we have summary(reg) Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 8.45000 0.16338 51.719 2e-16 *** series_ep 0.10000 0.03235 3.091 0.008598 ** s(series_ep) 0.02000 0.04218 0.474 0.643291 I(series_ep)TRUE. -1.01778 0.20486 -4.968 0.000257 *** so the drop of 1 point (out of 10) cannot be claimed as being significant. That is the idea of regression discontinuity. If we loop again over all our series, we have 485 pairs of consecutive seasons. As expected, in 75% of the casse, from season $t-1$ to season $t$, we observe a negative rupture. As previously, in 70% of the cases, it is not significat (with linear models before and after), and when it is significant, it is negative in 96% of the cases ! But an alternative can be to use nonparametric models, on both sides. To illustrate, consider David Benioff and D. B. Weiss’s Game of Thrones, sbase = base[base$series_name=="Game of Thrones",]

but let us remove the last season (no spoiler here, but clearly not worst watching)

Consider for instance the drop between season 1 and season 2,

library(rdd) sbase12=sbase[sbase$season%in%c(1,2),] lmr=RDestimate(UserRating~series_ep,data=sbase12,cutpoint=mean(range(sbase12$series_ep))) plot(lmr)

This is very consistent with what we observed with our linear regressions actually,

seuil=10.5 s = function(x) (x-seuil)*(x&gt;seuil) reg = lm(UserRating~series_ep+s(series_ep)+I(series_ep&gt;seuil),data=sbase12) summary(reg)   Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 8.70000 0.15458 56.281 2e-16 *** series_ep 0.07273 0.02491 2.919 0.01003 * s(series_ep) 0.01455 0.03523 0.413 0.68520 I(series_ep)TRUE -0.94000 0.20316 -4.627 0.00028 ***

Here, the drop of one point is significant…

So, your favorite show had an outstanding finale ? and you can’t wait to watch the new season… Well, statistically, it’s very likely that you will be disapointed by the first episode of the forthcoming season…

# Testing for Covid-19 in the U.S.

For almost a month, on a daily basis, we are working with colleagues (Romuald, Chi and Mathieu) on modeling the dynamics of the recent pandemic. I learn of lot of things discussing with them, but we keep struggling with the tests. Paul, in Montréal, helped me a little bit, but I think we will still have to more to get a better understand. To but honest, we stuggle with two very simple questions

• how many people are tested on a daily basis ?

Recently, I discovered Modelling COVID-19 exit strategies for policy makers in the United Kingdom, which is very close to what we try to do… and in the document two interesting scenarios are discussed, with, for the first one, “1 million ‘reliable’ daily tests are deployed” (in the U.K.) and “5 million ‘useless’ daily tests are deployed”. There are about 65 millions unhabitants in the U.K. so we talk here about 1.5% people tested, on a daily basis, or 7.69% people ! It could make sense, but our question was, at some point, is that realistic ? where are we today with testing ? In the U.S. https://covidtracking.com/ collects interesting data, on a daily basis, per state.

url = "https://raw.githubusercontent.com/COVID19Tracking/covid-tracking-data/master/data/states_daily_4pm_et.csv" download.file(url,destfile="covid.csv") base = read.csv("covid.csv")

Unfortunately, there is no information about the population. That we can find on wikipedia. But in that table, the state is given by its full name (and the symbol in the previous dataset). So we new also to match the two datasets properly,

url="https://en.wikipedia.org/wiki/List_of_states_and_territories_of_the_United_States_by_population" download.file(url,destfile = "popUS.html") #pas contaminé 2/3 R=3 library(XML) tables=readHTMLTable("popUS.html") T=tables[[1]][3:54,c("V3","V4")] names(T)=c("state","pop") url="https://en.wikipedia.org/wiki/List_of_U.S._state_abbreviations" download.file(url,destfile = "nameUS.html") tables=readHTMLTable("nameUS.html") T2=tables[[1]][13:63,c(1,4)] names(T2)=c("state","symbol") T=merge(T,T2) T$population = as.numeric(gsub(",", "", T$pop, fixed = TRUE)) names(base)[2]="symbol" base = merge(base,T[,c("symbol","population")])

Now our dataset is fine… and we can get a function to plot the number of people tested in the U.S. (cumulated). Here, we distinguish between the positive and the negative,

drawing = function(st ="NY"){ sbase=base[base$symbol==st,c("date","positive","negative","population")] sbase$DATE = as.Date(as.character(sbase$date),"%Y%m%d") sbase=sbase[order(sbase$DATE),] par(mfrow=c(1,2)) plot(sbase$DATE,(sbase$positive+sbase$negative)/sbase$population,ylab="Proportion Test (/population of state)",type="l",xlab="",col="blue",lwd=3) lines(sbase$DATE,sbase$positive/sbase$population,col="red",lwd=2) legend("topleft",c("negative","positive"),lwd=2,col=c("blue","red"),bty="n") title(st) plot(sbase$DATE,sbase$positive/(sbase$positive+sbase$negative),ylab="Ratio of positive tests",ylim=c(0,1),type="l",xlab="",col="black",lwd=3) title(st)} Let us start with New York drawing("NY") As at now, 4% of the entiere population got tested… over 6 weeks…. The graph on the right is the proportion of people who tested positive… I won’t get back on that one here today, I keep it for our work. In New Jersey, we got about 2.5% of the entiere population tested, overall, drawing("NJ") Let us try a last one, Florida drawing("FL") As at today, it is 1.5% of the population, over 6 weeks. Overall, in the U.S. less than 0.1% people are tested, on a daily basis. Which is far from the 1.5% in the U.K. scenarios. Now, here come the second question, • what are we actually testing for ? On that one, my experience in biology is… very limited, and Paul helped me. He mentioned this morning a nice report, from a lab in UC Berkeley One of my question was for instance, if you get tested positive, and you do it again, can you test negative ? Or, in the context of our data, do we test different people ? are some people tested on a regular basis (perhaps every week) ? For instance, with antigen tests (Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) – also called molecular or PCR – Polymerase Chain Reaction – test) we test if someone is infectious, while with antibody test (using serological immunoassays that detect viral-specific antibodies — Immunoglobin M (IgM) and G (IgG) — also called serology test), we test for immunity. Which is rather different… I have no idea what we have in our database, to be honest… and for the past six weeks, I have seen a lot of databases, and most of the time, I don’t know how to interpret, I don’t know what is measured… and it is scary. So, so far, we try to do some maths, to test dynamics by tuning parameters “the best we can” (and not estimate them). But if anyone has good references on testing, in the context of Covid-19 (for instance on specificity, sensitivity of all those tests) I would love to hear about it ! # Function basis and regression In the first part of the course on linear models, we’ve seen how to construct a linear model when the vector of covariates $\boldsymbol{x}$ is given, so that $\mathbb{E}(Y|\boldsymbol{X}=\boldsymbol{x})$ is either simply $\boldsymbol{x}^\top\boldsymbol{\beta}$ (for standard linear models) or a functional of $\boldsymbol{x}^\top\boldsymbol{\beta}$ (in GLMs). But more generally, we can consider transformations of the covariates, so that a linear model can be used. In a very general setting, consider $$\sum_{j=1}^m\beta_j h_j(\boldsymbol{x})$$with $h_j:\mathbb{R}^p\rightarrow\mathbb{R}$. The standard linear model is obtained when $m=p$ and $h_j(\boldsymbol{x})=x_j$ , but of course, much more general models can be obtained, for instance with $h_k(\boldsymbol{x})=x_j^2$ or $h_k(\boldsymbol{x})=x_{j}x_{j'}$, that could be used to achieve high-order Taylor expansions. In that case, we will obtain the polynomial regression, that we will discuss first. We might also think of piecewise constant functions, $h_k(\boldsymbol{x})=\boldsymbol{1}(x_j\in [a,b])$ , that could be related to regression trees (but that is not in the scope in the STT5100 course). And if we go on step futher, we might think of piecewise linear or piecewise polynomial function, possibly with additional continuity constraints, that will lead us to spline basis. • Polynomial regression For pedagogical purpose, when I talk about polynomial regression, I always have in mind (in the univariate case) $$y=\beta_0+\beta_1x+\beta_2x^2+\cdots+\beta_kx^k+\varepsilon$$but if we use lm(y~poly(x,k)) in R, the output is not the $\beta_j$‘s. As discussed in Kennedy & Gentle (1980) Statistical Computing, Recall that orthogonal polynomials are defined with respect to the classical inner-product (on the finite interval $(a,b)$)$${\displaystyle \langle f,g\rangle =\int _{a}^{b}f(x)g(x)~\mathrm {d} x}$$ And a sequence of orthogonal polynomials is $(P_n)$ where $P_n$ is a polynomial of degree $n$, for all $n$, and such that $P_m\perp P_n$ for all $m\neq n$. Note that those polyomials are orthogonal with respect to the inner product defined above, i.e. given some finite interval $(a,b)$. But if $(a,b)$ changes, the polynomials will be different. A popular family of orthogonal polynomial, on finite interval $(-1,+1)$ is the family of Legendre polynomials, satisfying$${\displaystyle \int _{-1}^{1}P_{m}(x)P_{n}(x)~\mathrm {d} x=0}$$as soon as $m\neq n$. Those polynomials satisfy Bonnet’s recursion formula$${\displaystyle (n+1)P_{n+1}(x)=(2n+1)xP_{n}(x)-nP_{n-1}(x)}$$ or Rodrigues’ formula $${\displaystyle P_{n}(x)={\frac {1}{2^{n}n!}}{\frac {d^{n}}{dx^{n}}}(x^{2}-1)^{n}}$$The first values are here$${\displaystyle P_{0}(x)=1}$$$${\displaystyle P_{1}(x)=x}$$$${\displaystyle P_{2}(x)={\frac {3x^{2}-1}{2}}}$$$${\displaystyle P_{3}(x)={\frac {5x^{3}-3x}{2}}}$$$${\displaystyle P_{4}(x)={\frac {35x^{4}-30x^{2}+3}{8}}}$$ Interestingly, we can get those polynomial functions using library(orthopolynom) (leg4coef = legendre.polynomials(n=4)) [[1]] 1 [[2]] x [[3]] -0.5 + 1.5*x^2 [[4]] -1.5*x + 2.5*x^3 [[5]] 0.375 - 3.75*x^2 + 4.375*x^4 Of course, there are many families of orthogonal polynomials (Jacobi polynomials, Laguerre polynomials, Hermite polynomials, etc). Now, in R, there is the standard poly function, that we use in polynomial regression. x = seq(-1,1,length=101) y = poly(x,4) y 1 2 3 4 [1,] -1.706475e-01 0.215984813 -2.480753e-01 0.270362873 [2,] -1.672345e-01 0.203025724 -2.183063e-01 0.216290298 ... [100,] 1.672345e-01 0.203025724 2.183063e-01 0.216290298 [101,] 1.706475e-01 0.215984813 2.480753e-01 0.270362873 attr(,"coefs") attr(,"coefs")$alpha [1] 3.157229e-17 2.655145e-16 9.799244e-17 5.368224e-16   attr(,"coefs")$norm2 [1] 1.0000000 101.0000000 34.3400000 9.3377328 2.4472330 0.6330176 attr(,"degree") [1] 1 2 3 4 attr(,"class") [1] "poly" "matrix" But these are not Legendre polynomials… As explained in 李哲源‘s post on stackoverflow, the idea is to start with $P_{-1}(x)=0$, $P_{0}(x)=1$ and $P_{1}(x)=x$, and then define $\ell_n=\langle P_n,P_n\rangle$ as well as $\alpha_n=\langle P_nP_1,P_1\rangle/\ell_n=\langle P_n^2,P_1\rangle/\ell_i=$ and $\beta_n=\ell_n/\ell_{n-1}$. Finally, define recursively$${\displaystyle P_{n}(x)=(x-\alpha_{n-1})P_{n-1}(x)-\beta_{i-1}P_{i-2}(x)}$$and its normalized version, $\tilde{P}_{n}=P_n/\sqrt{\ell_n}$. That is what poly computes. So, for pedagogical purpose, I said that I like to use $y=\boldsymbol{x}^\top\boldsymbol{\beta}+\varepsilon$ where$$\boldsymbol{x}=(1,x,x^2,\cdots,xˆ{k-1},x^k)$$And actually, when using poly, we use the QR decomposition of that matrix. As discussed in in 李哲源‘s post, we can almost reproduce the poly function using my_poly - function (x, degree = 1) { xbar = mean(x) x = x - xbar QR = qr(outer(x, 0:degree, "^")) X = qr.qy(QR, diag(diag(QR$qr), length(x), degree + 1))[, -1, drop = FALSE] X2 = X * X norm2 = colSums(X * X) alpha = drop(crossprod(X2, x)) / norm2 beta = norm2 / (c(length(x), norm2[-degree])) colnames(X) = 1:degree scale = sqrt(norm2) X = X * rep(1 / scale, each = length(x)) X}

Nevertheless, the two models are equivalent. More precisely,

plot(cars) reg1 = lm(dist~speed+I(speed^2)+I(speed^3),data=cars) reg2 = lm(dist~poly(speed,3),data=cars) u = seq(3,26,by=.1) v1 = predict(reg1,newdata=data.frame(speed=u)) v2 = predict(reg2,newdata=data.frame(speed=u)) lines(u,v1,col="blue") lines(u,v2,col="red",lty=2)

We have exactly the same prediction here

v1[u==15] 121 38.43919 v2[u==15] 121 38.43919

And probably also quite interesting : the coefficients do not have the same interpretation (since we do not have the same basis), but the $p$-value for the highest degree is exactly the same here ! Here the two models reject, with the same confidence, the polynomial of degree three,

summary(reg1)   Coefficients: Estimate Std. Error t value Pr(&gt;|t|) (Intercept) -19.50505 28.40530 -0.687 0.496 speed 6.80111 6.80113 1.000 0.323 I(speed^2) -0.34966 0.49988 -0.699 0.488 I(speed^3) 0.01025 0.01130 0.907 0.369   Residual standard error: 15.2 on 46 degrees of freedom Multiple R-squared: 0.6732, Adjusted R-squared: 0.6519 F-statistic: 31.58 on 3 and 46 DF, p-value: 3.074e-11   summary(reg2)   Coefficients: Estimate Std. Error t value Pr(&gt;|t|) (Intercept) 42.98 2.15 19.988 &lt; 2e-16 *** poly(speed, 3)1 145.55 15.21 9.573 1.6e-12 *** poly(speed, 3)2 23.00 15.21 1.512 0.137 poly(speed, 3)3 13.80 15.21 0.907 0.369 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1   Residual standard error: 15.2 on 46 degrees of freedom Multiple R-squared: 0.6732, Adjusted R-squared: 0.6519 F-statistic: 31.58 on 3 and 46 DF, p-value: 3.074e-11
• B-splines regression (and GAMs)

Splines are also important in regression models, especially when we start talking about Generalized Additive Models. See Perperoglou, Sauerbrei, Abrahamowicz & Schmid (2019) for a review. In the univariate case, I introduce (linear) splines through positive parts, in the sense that$$y=\beta_0+\beta_1x+\beta_2(x-s_1)_++\cdots+\beta_k(x-s_{k-1})_++\varepsilon$$where $(x-s)_+$ equals $0$ if $x and $x-s$ if $x>s$. Those functions are nice since they are continuous, so the model is continuous (the weighted sum of continuous functions is continuous). And we can go one step further, with $$y=\beta_0+\beta_1x+\beta_2x^2+\beta_3(x-s_1)^2_++\cdots+\beta_k(x-s_{k-2})^2_++\varepsilon$$with quadratic splines, or $$y=\beta_0+\beta_1x+\beta_2x^2+\beta_3x^3+\beta_4(x-s_1)^3_++\cdots+\beta_k(x-s_{k-3})^3_++\varepsilon$$for cubic splines. Interestingly, quadratic splines are not only continuous, but their first derivative is also continuous (and the second one for cubic splines). So the knot discontinuity is $s_1,s_2,\cdots$ is now invisible…

I like those models since they are easy to interprete. For example, the simple model $$\beta_1 x+\beta_2(x-s)_+$$ is the following piecewise linear function, continuous, with a “rupture” at knot $s$.

Observe also the following interpretation: for small values of $x$, there is a linear increase, with slope $\beta_1$, and for lager values of $x$, there is a linear decrease, with slope $\beta_1+\beta_2$. Hence, $\beta_2$ is interpreted as a change of the slope.

Unfortunately, it is now what R is using when using the bs function in R, which are the standard B-splines. Just to visualize (I will skip the maths here), with R, we have

library(splines) clr6 = c("#1b9e77","#d95f02","#7570b3","#e7298a","#66a61e","#e6ab02") x = seq(5,25,by=.25) B = bs(x,knots=c(10,20),Boundary.knots=c(5,55),degre=1) matplot(x,B,type="l",lty=1,lwd=2,col=clr6) B=bs(x,knots=c(10,20),Boundary.knots=c(5,55),degre=2) matplot(x,B,type="l",col=clr6,lty=1,lwd=2)

while the functions I mentioned were (more or less) the following

pos = function(x,s) (x-s)*(x&gt;s) par(mfrow=c(1,2)) clr6 = c("#1b9e77","#d95f02","#7570b3","#e7298a","#66a61e","#e6ab02") x = seq(5,25,by=.25) B = cbind(pos(x,5),pos(x,10),pos(x,20)) matplot(x,B,type="l",lty=1,lwd=2,col=clr6) pos2 = function(x,s) (x-s)^2*(x&gt;s) B = cbind(pos(x,5)*20,pos2(x,5),pos2(x,10),pos2(x,20)) matplot(x,B,type="l",col=clr6,lty=1,lwd=2)

And as for the polynomial regression, the two models are equivalent. For example

plot(cars) reg1 = lm(dist~speed+pos(speed,10)+pos(speed,20),data=cars) reg2 = lm(dist~bs(speed,degree=1,knots=c(10,20)),data=cars) v1 = predict(reg1,newdata=data.frame(speed=u)) v2 = predict(reg2,newdata=data.frame(speed=u)) lines(u,v1,col="blue") lines(u,v2,col="red",lty=2)

or more specifically

v1[u==15] 121 39.35747 v2[u==15] 121 39.35747

So one more time, the two models are equivalent, but I still find the approach with the positive part more intuitive, and easy to understand. As well as the interpretation of coefficients,

summary(reg1)   Coefficients: Estimate Std. Error t value Pr(&gt;|t|) (Intercept) -7.6305 16.2941 -0.468 0.6418 speed 3.0630 1.8238 1.679 0.0998 . pos(speed, 10) 0.2087 2.2453 0.093 0.9263 pos(speed, 20) 4.2812 2.2843 1.874 0.0673 . --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1   Residual standard error: 15 on 46 degrees of freedom Multiple R-squared: 0.6821, Adjusted R-squared: 0.6613 F-statistic: 32.89 on 3 and 46 DF, p-value: 1.643e-11   summary(reg2)   Coefficients: Estimate Std. Error t value Pr(&gt;|t|) (Intercept) 4.621 9.344 0.495 0.6233 bs(speed, degree = 1, knots = c(10, 20))1 18.378 10.943 1.679 0.0998 . bs(speed, degree = 1, knots = c(10, 20))2 51.094 10.040 5.089 6.51e-06 *** bs(speed, degree = 1, knots = c(10, 20))3 88.859 12.047 7.376 2.49e-09 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1   Residual standard error: 15 on 46 degrees of freedom Multiple R-squared: 0.6821, Adjusted R-squared: 0.6613 F-statistic: 32.89 on 3 and 46 DF, p-value: 1.643e-11

Here we can see directly that the first knot was not interesting (the slope did not change significantly) while the second one was…

# Testing for a causal effect (with 2 time series)

A few days ago, I came back on a sentence I found (in a French newspaper), where someone was claiming that

“… an old variable explains 85% of the change in a new variable. So we can talk about causality”

and I tried to explain that it was just stupid : if we consider the regression of the temperature on day $t+1$ against the number of cyclist on day $t$, the $R^2$ exceeds 80%… but it is hard to claim that the number of cyclists on specific day will actually cause the temperature on the next day…

Nevertheless, that was frustrating, and I was wondering if there was a clever way to test for causality in that case. A popular one is Granger causality (I can mention a paper we published a few years ago where we use such a test, Tents, Tweets, and Events: The Interplay Between Ongoing Protests and Social Media). To explain that test, consider a bivariate time series (just like the one we have here), $\boldsymbol{z}_t=(x_t,y_t)$, and consider some bivariate autoregressive model
$${\displaystyle {\begin{bmatrix}x_{t}\\y_{t}\end{bmatrix}}={\begin{bmatrix}c_{1}\\c_{2}\end{bmatrix}}+{\begin{bmatrix}a_{1,1}&\textcolor{red}{a_{1,2}}\\\textcolor{blue}{a_{2,1}}&a_{2,2}\end{bmatrix}}{\begin{bmatrix}x_{t-1}\\y_{t-1}\end{bmatrix}}+{\begin{bmatrix}u_{t}\\v_{t}\end{bmatrix}}}$$where $\boldsymbol{\varepsilon}_t=(u_t,v_t)$ is some bivariate white noise, in the sense that (i) ${\displaystyle \mathbb{E} (\boldsymbol{\varepsilon}_{t})=\boldsymbol{0}}$ (the noise is centered) (ii) ${\displaystyle \mathbb{E} (\boldsymbol{\varepsilon}_{t}\boldsymbol{\varepsilon}_{t}^\top)=\Omega }$, so the variance matrix is constant, but possibly non-diagonal (iii) ${\displaystyle \mathbb{E} (\boldsymbol{\varepsilon}_{t}\boldsymbol{\varepsilon}_{t-h}^\top)=\boldsymbol{0} }$ for all $h\neq 0$. Note that we can use the simplified expression$${\displaystyle {\boldsymbol{z}_t=\boldsymbol{c}+\boldsymbol{A}\boldsymbol{z}_{t-1}+\boldsymbol{\varepsilon}_t}}$$Now, Granger test is based on several quantities. With off-diagonal terms of matrix $\Omega$, we have a so-called instantaneous causality, and since $\Omega$ is symmetry, we will write $x\leftrightarrow y$. With off-diagonal terms of matrix $\boldsymbol{A}$, we have a so-called lagged causality, with either $\textcolor{blue}{x\rightarrow y}$ or $\textcolor{red}{x\leftarrow y}$ (and possibly both, if both terms are significant).

So I wanted to try on my two-variable problem.

df = read.csv("cyclistsTempHKI.csv") dfts = cbind(C=ts(df$cyclists,start = c(2014, 1,2), frequency = 365), T=ts(df$meanTemp,start = c(2014, 1,2), frequency = 365)) library(vars)

I now have “time series” objects, and we can fit a VAR model,

var2 = VAR(dfts, p = 1, type = "const") coefficients(var2) $C Estimate Std. Error t value Pr(&gt;|t|) C.l1 0.8684009 0.02889424 30.054460 8.080226e-107 T.l1 70.3042012 20.07247411 3.502518 5.102094e-04 const 807.6394001 187.75472482 4.301566 2.110412e-05$T Estimate Std. Error t value Pr(&gt;|t|) C.l1 0.0003865391 6.257596e-05 6.177118 1.540467e-09 T.l1 0.6611135594 4.347074e-02 15.208241 6.086394e-42 const -1.6413074565 4.066184e-01 -4.036481 6.446018e-05

For instant, we can run a causality, to test if the number of cyclists can cause the temperature (on the next day)

causality(var2, cause = "C") $Granger Granger causality H0: C do not Granger-cause T data: VAR object var2 F-Test = 38.157, df1 = 1, df2 = 842, p-value = 1.015e-09 Here, we should clearly reject $H_0$, which is that there is no causal effect. Which is the way statisticians say that there should be some causal effect between the number of cyclist and the temperature… So clearly, something is wrong here. Either it is some sort of superpower that cyclists are not aware of. Or this test that was used for forty years (Clive Granger even got a Nobel price for it) is not working. Or we missed something. Actually… I think we missed something here. Possibly because the series are not stationary. We can almost see it with Phi = matrix(c(coefficients(var2)$C[1:2,1],coefficients(var2)$T[1:2,1]),2,2) eigen(Phi) eigen() decomposition$values [1] 0.9594810 0.5700335

where the highest eigenvalue is very close to one. But actually, we look here at the temperature…

plot(dfts)

so, at least, we should expect some seasonal unit root here. So let us use two techniques. The first one is a classical one-year difference, $\Delta_{365}\boldsymbol{z}_t=\boldsymbol{z}_t-\boldsymbol{z}_{t-365}$

var2 = VAR(diff(dfts,365), p = 1, type = "const") coefficients(var2) $C Estimate Std. Error t value Pr(&gt;|t|) C.l1 0.8376424 0.07259969 11.537823 1.993355e-16 T.l1 42.2638410 28.58783276 1.478386 1.449076e-01 const -507.5514795 219.40240747 -2.313336 2.440042e-02$T Estimate Std. Error t value Pr(&gt;|t|) C.l1 0.000518209 0.0003277295 1.5812096 1.194623e-01 T.l1 0.598425288 0.1290511945 4.6371154 2.162476e-05 const 0.547828079 0.9904263469 0.5531235 5.823804e-01

The test on the fited VAR model yields

causality(var2, cause = "C") $Granger Granger causality H0: C do not Granger-cause T data: VAR object var2 F-Test = 2.5002, df1 = 1, df2 = 112, p-value = 0.1167 i.e., with a 11% $p$-value, we should reject the assumption that the number of cyclists cause the temperature (on the next day), and actually, we should also reject the other way causality(var2, cause = "T")$Granger   Granger causality H0: T do not Granger-cause C   data: VAR object var2 F-Test = 2.1856, df1 = 1, df2 = 112, p-value = 0.1421

Nevertheless, if we look at the instantaneous causality, this one makes more sense

$Instant H0: No instantaneous causality between: T and C data: VAR object var2 Chi-squared = 13.081, df = 1, p-value = 0.0002982 The second idea would be to use a one day difference, $\Delta_{1}\boldsymbol{z}_t=\boldsymbol{z}_t-\boldsymbol{z}_{t-1}$ and to fit a VAR model on that one VARselect(diff(dfts,1), lag.max = 4, type="const")$selection AIC(n) HQ(n) SC(n) FPE(n) 3 3 2 3

but on that one, a VAR(1) model – with only one lag – might not be sufficient. It might be better to consider a VAR(3)

var2 = VAR(diff(dfts,1), p = 3, type = "const")

and on that one, one more time, we should reject the causal effect of the number of cyclists on the temperature (on the next day)

causality(var2, cause = "C") $Granger Granger causality H0: C do not Granger-cause T data: VAR object var2 F-Test = 0.67644, df1 = 3, df2 = 828, p-value = 0.5666 and this time, there could be a (lagged) causal effect of the temperature on the number of cyclists causality(var2, cause = "T")$Granger   Granger causality H0: T do not Granger-cause C   data: VAR object var2 F-Test = 7.7981, df1 = 3, df2 = 828, p-value = 3.879e-05   \$Instant   H0: No instantaneous causality between: T and C   data: VAR object var2 Chi-squared = 55.83, df = 1, p-value = 7.905e-14

but nothing instantaneously… So it looks like Granger causality performs well on that one !