Regression

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Linear Regression

Comic https://xkcd.com/1725/

Coefficient of determination R2

[math]\displaystyle{ \begin{align} R^2 &= 1 - \frac{SSE}{SST} \\ &= 1 - \frac{MSE}{Var(y)} \end{align} }[/math]

Pearson correlation and linear regression slope

[math]\displaystyle{ \begin{align} b_1 &= r \frac{S_y}{S_x} \end{align} }[/math]

where [math]\displaystyle{ S_x=\sqrt{\sum(x-\bar{x})^2} }[/math]. 

set.seed(1)
x <- rnorm(10); y <-rnorm(10)
coef(lm(y~x))
# (Intercept)           x
#   0.3170798  -0.5161377

cor(x, y)*sd(y)/sd(x)
# [1] -0.5161377

Different models (in R)

http://www.quantide.com/raccoon-ch-1-introduction-to-linear-models-with-r/

dummy.coef.lm() in R

Extracts coefficients in terms of the original levels of the coefficients rather than the coded variables.

model.matrix, design matrix

Contrasts in linear regression

  • Page 147 of Modern Applied Statistics with S (4th ed)
  • https://biologyforfun.wordpress.com/2015/01/13/using-and-interpreting-different-contrasts-in-linear-models-in-r/ This explains the meanings of 'treatment', 'helmert' and 'sum' contrasts.
  • A (sort of) Complete Guide to Contrasts in R by Rose Maier 
    mat

##      constant NLvMH  NvL  MvH
## [1,]        1  -0.5  0.5  0.0
## [2,]        1  -0.5 -0.5  0.0
## [3,]        1   0.5  0.0  0.5
## [4,]        1   0.5  0.0 -0.5
mat <- mat[ , -1]

model7 <- lm(y ~ dose, data=data, contrasts=list(dose=mat) )
summary(model7)

## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)    
## (Intercept)  118.578      1.076 110.187  < 2e-16 ***
## doseNLvMH      3.179      2.152   1.477  0.14215    
## doseNvL       -8.723      3.044  -2.866  0.00489 ** 
## doseMvH       13.232      3.044   4.347 2.84e-05 ***

# double check your contrasts
attributes(model7$qr$qr)$contrasts
## $dose
##      NLvMH  NvL  MvH
## None  -0.5  0.5  0.0
## Low   -0.5 -0.5  0.0
## Med    0.5  0.0  0.5
## High   0.5  0.0 -0.5

library(dplyr)
dose.means <- summarize(group_by(data, dose), y.mean=mean(y))
dose.means
## Source: local data frame [4 x 2]
## 
##   dose   y.mean
## 1 None 112.6267
## 2  Low 121.3500
## 3  Med 126.7839
## 4 High 113.5517

# The coefficient estimate for the first contrast (3.18) equals the average of 
# the last two groups (126.78 + 113.55 /2 = 120.17) minus the average of 
# the first two groups (112.63 + 121.35 /2 = 116.99).

Multicollinearity

> op <- options(contrasts = c("contr.helmert", "contr.poly"))
> npk.aov <- aov(yield ~ block + N*P*K, npk)
> alias(npk.aov)
Model :
yield ~ block + N * P * K

Complete :
         (Intercept) block1 block2 block3 block4 block5 N1    P1    K1    N1:P1 N1:K1 P1:K1
N1:P1:K1     0           1    1/3    1/6  -3/10   -1/5      0     0     0     0     0     0

> options(op)

Exposure

https://en.mimi.hu/mathematics/exposure_variable.html

Independent variable = predictor = explanatory = exposure variable

Confounders, confounding

Causal inference

  • The intuition behind inverse probability weighting in causal inference*, Confounding in causal inference: what is it, and what to do about it?
    Outcome [math]\displaystyle{ \begin{align} Y = T*Y(1) + (1-T)*Y(0) \end{align} }[/math]
    Causal effect (unobserved) [math]\displaystyle{ \begin{align} \tau = E(Y(1) -Y(0)) \end{align} }[/math]
    where [math]\displaystyle{ E[Y(1)] }[/math] referred to the expected outcome in the hypothetical situation that everyone in the population was assigned to treatment, [math]\displaystyle{ E[Y|T=1] }[/math] refers to the expected outcome for all individuals in the population who are actually assigned to treatment... The key is that the value of [math]\displaystyle{ E[Y|T=1]−E[Y|T=0] }[/math] is only equal to the causal effect, [math]\displaystyle{ E[Y(1)−Y(0)] }[/math] if there are no confounders present.
    Inverse-probability weighting removes confounding by creating a “pseudo-population” in which the treatment is independent of the measured confounders... Add a larger weight to the individuals who are underrepresented in the sample and a lower weight to those who are over-represented... propensity score P(T=1|X), logistic regression, stabilized weights.
  • A Crash Course in Causality: Inferring Causal Effects from Observational Data (Coursera) which includes Inverse Probability of Treatment Weighting (IPTW). R packages used: tableone, ipw, sandwich, survey.

Confidence interval vs prediction interval

Confidence intervals tell you about how well you have determined the mean E(Y). Prediction intervals tell you where you can expect to see the next data point sampled. That is, CI is computed using Var(E(Y|X)) and PI is computed using Var(E(Y|X) + e).

Homoscedasticity, Heteroskedasticity, Check model for (non-)constant error variance

Linear regression with Map Reduce

https://freakonometrics.hypotheses.org/53269

Relationship between multiple variables

Visualizing the relationship between multiple variables

Model fitting evaluation, Q-Q plot

Generalized least squares

Reduced rank regression

Singular value decomposition

  • Moore-Penrose matrix inverse in R 
    > a = matrix(c(2, 3), nr=1)
> MASS::ginv(a) * 8 
         [,1]
[1,] 1.230769
[2,] 1.846154  
# Same solution as matlab lsqminnorm(A,b)

> a %*% MASS::ginv(a)
     [,1]
[1,]    1
> a %*% MASS::ginv(a) %*% a
     [,1] [,2]
[1,]    2    3
> MASS::ginv   # view the source code

Mahalanobis distance and outliers detection

Mahalanobis distance

  • The Mahalanobis distance is a measure of the distance between a point P and a distribution D
  • It is a multi-dimensional generalization of the idea of measuring how many standard deviations away P is from the mean of D.
  • The Mahalanobis distance is thus unitless and scale-invariant, and takes into account the correlations of the data set.
  • Distance is not always what it seems

performance::check_outliers() Outliers detection (check for influential observations)

How to Calculate Mahalanobis Distance in R 

set.seed(1234)
x <- matrix(rnorm(200), nc=10)
x0 <- rnorm(10)
mu <- colMeans(x)
mahalanobis(x0, colMeans(x), var(x)) # 17.76527
t(x0-mu) %*% MASS::ginv(var(x)) %*% (x0-mu) # 17.76527

# Variance is not full rank
x <- matrix(rnorm(200), nc=20)
x0 <- rnorm(20)
mu <- colMeans(x)
t(x0-mu) %*% MASS::ginv(var(x)) %*% (x0-mu)
mahalanobis(x0, colMeans(x), var(x))
# Error in solve.default(cov, ...) : 
#   system is computationally singular: reciprocal condition number = 1.93998e-19

Type 1 error

Linear Regression And Type I Error

More Data Can Hurt for Linear Regression

Sometimes more data can hurt!

Estimating Coefficients for Variables in R

Trying to Trick Linear Regression - Estimating Coefficients for Variables in R

Intercept only model and cross-validation

n <- 20
set.seed(1)
x <- rnorm(n)
y <- 2*x + .5*rnorm(n)
plot(x, y)
df <- data.frame(x=x, y=y)
pred <- double(n)
for(i in 1:n) {
  fit <- lm(y ~ 1, data = df[-i, ])
  pred[i] <- predict(fit, df[i, ])
}
plot(y, pred)
cor(y, pred) # -1

How about 1000 simulated data? 

foo <- function(n=3, debug=F) {
  x <- rnorm(n)
  y <- 2*x + .5*rnorm(n)
  df <- data.frame(x=x, y=y)
  pred <- double(n)
  for(i in 1:n) {
    fit <- lm(y ~ 1, data = df[-i, ])
    pred[i] <- predict(fit, df[i, ])
  }
  if (debug) {
    cat("num=", n*sum(y*pred)-sum(pred)*sum(y), "\n")
    cat("denom=", sqrt(n*sum(y**2) - sum(y)^2)*sqrt(n*sum(pred**2)-sum(pred)^2), "\n")
    invisible(list(y=y, pred=pred, cor=cor(y, pred)))
  } else {
    cor(y, pred)
  }
}

o <- replicate(1000, foo(n=10))
range(o) # [1] -1 -1
all.equal(o, rep(-1, 1000)) # TRUE

Note the property will not happen in k-fold CV (not LOOCV) 

n <- 20; nfold <- 5
set.seed(1)
x <- rnorm(n)
y <- 2*x + .5*rnorm(n)
#plot(x, y)
df <- data.frame(x=x, y=y)
set.seed(1)
folds <- split(sample(1:n), rep(1:nfold, length = n))
pred <- double(n)
for(i in 1:nfold) {
  fit <- lm(y ~ 1, data = df[-folds[[i]], ])
  pred[folds[[i]]] <- predict(fit, df[folds[[i]], ])
}
plot(y, pred)
cor(y, pred) # -0.6696743

See also

lm.fit and multiple responses/genes

Logistic regression

  • Logistic regression or T test?.
    • The t-test is not significant but the logistic regression is
    • The t-test is significant but the logistic regression is not, as in the question

Quantile regression

Isotonic regression

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