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Chapter 10: Regression models
Douglas Bates
11/07/2014
ioslides_presentation
wide small
true
true
library(knitr)
library(ggplot2)
library(lattice)
library(EngrExpt)
opts_chunkset(cache=TRUE,fig.align='center') options(width=100,show.signif.stars = FALSE)  # 10.1 Inference for a regression line ## Section 10.1: Inference for a regression line • Recall that the simple linear regression model is $$\mathcal{Y}_i=\beta_0+\beta_1 x_i+\epsilon_i,\quad i=1,\dots,n\quad \epsilon_i\sim\mathcal{N}(0,\sigma^2)$$ • The least squares estimates,\widehat{\beta}_0$and$\widehat{\beta}_1$, of the coefficients are functions of the data and hence are random variables. We associate standard errors with these estimates. • The text derives formulas for the variance of the estimators. The formulas can be interesting but do not easily extend to more complex models. It is easier to simply read the standard error from the output. • In the R output each coefficient estimate is accompanied by a Std. Error (standard error), a t value (the ratio of the estimate to its standard error) and a Pr(>|t|), which is the p-value for the two-sided hypothesis test. The confint extractor can be used to determine confidence intervals. ## The timetemp data qplot(temp,time,data=timetemp) + geom_point(aes(color=type)) + geom_smooth(method="lm",aes(color=type)) + xlab("Temperature in freezer (degrees C)") + ylab("Time to reach operating temperature of -10 C (min)")  ## Examples 10.1.1 and 10.1.2 summary(fm1 <- lm(time ~ temp, timetemp, subset = type == "Repaired"))  cat(paste(capture.output(summary(fm1 <- lm(time ~ temp, timetemp, subset = type == "Repaired")))[-(1:8)], collapse = "\n"), "\n")  confint(fm1)  • The confidence interval,$[-2.099,-1.629]$, on$\beta_1$, the slope, is of interest. • The other confidence interval is not of interest because$\beta_0$is not meaningful for these data. ## Example 10.1.3 fm2 <- lm(gloss ~ build, fbuild) print(xyplot(gloss ~ build, fbuild, type = c("g","p","r"), xlab = "Film build", ylab = "gloss", aspect = 1), split = c(1,1,3,1), more = TRUE) print(xyplot(resid(fm2) ~ fitted(fm2), type = c("g", "p", "smooth")), split = c(2,1,3,1), more = TRUE) print(qqmath(~resid(fm2), aspect = 1, ylab = "Residuals", type = c("g", "p"), xlab = "Standard normal quantiles"), split = c(3,1,3,1))  cat(paste(capture.output(summary(fm2))[-(1:9)], collapse = "\n"), "\n")  ## Confidence intervals on the parameters confint(fm2)  ## Inference for coefficients • As seen in the previous slides, we can evaluate confidence intervals on the coefficients,$\beta_0$and$\beta_1$, with the confint extractor function. • The formula for the$(1-\alpha)$confidence interval on$\beta_1$is $$\widehat{\beta}1\pm t(\alpha/2, \nu),s{\beta_1}$$ where$\nu$is the degrees of freedom for residuals ($n-2$for a simple linear regression) and$s_{\beta_1}$is the standard error for the coefficient. • The observed$t$statistic,$\widehat{\beta}1/s{\beta_1}$, is used to perform tests of the hypothesis$H_0:\beta_1=0$. The p-value for the two-sided alternative is given in the coefficient table. The p-value for the one-sided alternative that is indicated by the data will be half this value. By "indicated by the data". I mean the alternative$H_a:\beta_1>0$, if$\widehat{\beta}_1>0$and vice versa. ## More on inference for coefficients • Testing$H_0:\beta_1=0$versus the appropriate alternative is usually of interest. Tests on$\beta_0$are not always of interest as the intercept may not represent a meaningful response. • For a simple linear regression the F test reported in the summary compares the model that was fit to a trivial model in which all the fitted values are equal to$\bar{y}$. You can also obtain this test as anova(fm1)  • This test is equivalent to the t-test of$H_0:\beta_1=0$vs.$H_a:\beta_1\ne0$. ## Extracting the coefficients table only • The analysis of variance table can also be obtained by explicitly comparing the model that was fit to the trivial model. anova(update(fm1, . ~ . - temp), fm1)  • Sometimes it is convenient to extract the table of coefficients, standard errors and test statistics. You can do this by coef(summary(fm1))  ## Inference on the expected response for$x=x_0$• In a regression model we consider the response as having a normal distribution conditional on a particular value of the covariate,$x=x_o$. • This distribution has an expected value, which we write as$\mu_{\mathcal{Y}|x=x_o}$or$\mathrm{E}(\mathcal{Y}|x=x_0)$. Our estimate of this conditional mean is$\widehat{\beta}_0+\widehat{\beta}_1x_0$. • Just as$\widehat{\beta}_0$and$\widehat{\beta}1$are random variables with standard errors, our estimate$\widehat{\mu}{\mathcal{Y}|x=x_o}$has a standard error. • The estimate and its standard error can be evaluated with predict and the optional argument se.fit = TRUE. str(predict(fm2, list(build = 2.6), se.fit = TRUE)) # Ex 10.1.7  ## Confidence intervals on the mean response • Typically we use the standard errors to form a confidence interval on$\mu_{\mathcal{Y}|x=x_0}$, which we can create with the optional argument interval = "conf" to predict. • In example 10.1.7 we wish to form a 90% confidence interval on the mean gloss when the film build is 2.6 mm predict(fm2, list(build = 2.6), int = "conf", level = 0.90)  • We can use the estimate and its standard error to conduct hypothesis tests but generally we are more interested in the confidence intervals. Occasionally we want to test$H_0:\beta_0=0$versus one of the alternatives and this is a test on the mean response when$x=0$. We can obtain the p-value for this test from the table of coefficients. ## Inference for a future value of$\mathcal{Y}$• Note that the confidence interval on$\mu_{\mathcal{Y}|x=x_0}$refers to the mean response at$x=x_0$, not the response that we will observe. • If we want a prediction interval at$x=x_0$then we must formulate it as$\mathcal{Y}0=\mu{\mathcal{Y}|x=x_0}+\epsilon_0$which we estimate as $$\mathrm{E}[\mathcal{Y}0]=\widehat{\beta_0}+\widehat{\beta_1}x_0$$ with a standard error of$\sqrt{s{\hat{\mu}}^2+s^2}$. • A 90% prediction interval on the gloss at a build of 3 mm. is predict(fm2, list(build = 3:4), int = "pred", level = 0.90)  ## Testing for lack of fit • One of the assumptions in a simple linear regression is that the relationship between$\mathcal{Y}$and$x$is reasonably close to a straight line over the range of interest. • If we have replicates in the data then we can check this assumption by evaluating the sum of squares due to replication (the pooled sum of squares of the deviations about the average within replicates) and what is called the mean square for lack of fit. • There are various ways of calculating these quantities, some with unsatisfactory numerical properties. A simple way of doing this test is to compare the linear model to a model with the covariate$x$as a factor. ## Example 10.1.10 fm4 <- lm(phnew ~ phold,phmeas) print(xyplot(phnew ~ phold, phmeas, type = c("g","p","r"), xlab = "pH by old method", ylab = "pH by new method", aspect = 1), split = c(1,1,3,1), more = TRUE) print(xyplot(resid(fm4) ~ fitted(fm4), type = c("g", "p", "smooth")), split = c(2,1,3,1), more = TRUE) print(qqmath(~resid(fm4), aspect = 1, ylab = "Residuals", type = c("g", "p"), xlab = "Standard normal quantiles"), split = c(3,1,3,1))  cat(paste(capture.output(summary(fm4))[-(1:9)], collapse = "\n"), "\n")  To perform the lack of fit test we compare this model fit to one with phold treated as a factor. ## Example 10.1.10 (cont'd) anova(fm4, lm(phnew ~ factor(phold), phmeas))  • Note that this result is different from the result shown in the text. In the text they use only one of the sets of replicates. Here we use both. • The computer is better at picking up repetitions in the covariate than are humans. • In either calculation there is no significant evidence of lack of fit. We prefer the calculation with more denominator degrees of freedom (the one shown above). More denominator degrees of freedom produces a more powerful test. # 10.2 Inference for other regression models ## Section 10.2: Inference for other regression models • As seen in chapter 3, regression models can incorporate many different types of terms (see p. 386). • Inferences on the coefficients in such a model can be performed using the information in the coefficients table. • We must, however, be careful of the interpretation of the tests. For example, if we fit a quadratic (next slide) then we generally are not interested in testing$H_0:\beta_1=0$in the presence of the quadratic term. • The general rule is that the t-test in the coef table is a test of removing only that term and keeping all the other terms in the model. Ask yourself if it would be a sensible model with that term omitted. ex336 <- data.frame(x = c(18,18,20,20,22,22,24,24,26,26), y = c(4.0,4.2,5.6,6.1,6.5,6.8,5.4,5.6,3.3,3.6))  ## Example 10.2.1 fm5 <- lm(y ~ x + I(x^2), ex336) print(xyplot(y ~ x, ex336, type = c("g","p"), xlab = "Vacuum setting", ylab = "Particle size", aspect = 1), split = c(1,1,3,1), more = TRUE) print(xyplot(resid(fm5) ~ fitted(fm5), type = c("g", "p", "smooth")), split = c(2,1,3,1), more = TRUE) print(qqmath(~resid(fm5), aspect = 1, ylab = "Residuals", type = c("g", "p"), xlab = "Standard normal quantiles"), split = c(3,1,3,1))  cat(paste(capture.output(summary(fm5))[-(1:9)], collapse = "\n"), "\n")  ## Confidence intervals on the coefficients of the quadratic confint(fm5)  ## Prediction intervals and confidence intervals • Prediction intervals and confidence intervals on$\mu_{\mathcal{Y}|x=x_0}$are calculated as before. We must specify values for all the covariates in the model but we do not need to specify both$x$and$x^2\$. Higher-order terms are evaluated from the formula.
predict(fm5, list(x = 21), int = "pred")
predict(fm5, list(x = 21), int = "conf")


## Testing lack of fit

• We test lack of fit as before. If we have more than one covariate we must use a cell-means model with all of the covariates as factors.
anova(fm5, lm(y ~ factor(x), ex336))


# Models with continuous and categorical covariates

## Both continuous and categorical (timetemp)

qplot(temp,time,data=timetemp) + geom_point(aes(color=type)) + geom_smooth(method="lm",aes(color=type)) +
xlab("Temperature in freezer (degrees C)") + ylab("Time to reach operating temperature of -10 C (min)")


## Model with main effects for type only

summary(fm6 <- lm(time ~ 1 + type + temp, timetemp))

• the typeOEM coefficient is the change in intercept from Repaired to OEM. The time coefficient is the common slope.

## Model with main effects and interaction

summary(fm7 <- lm(time ~ 1 + type*temp, timetemp))


# Regression plots using ggplot2

## The fortify function

• The ggplot2 package provides a fortify function that, when applied to a fitted model produces a frame like the model frame but with several additional columns. See the docs
str(fm6f <- fortify(fm6))


## Producing a quantile-quantile plot with fortify

• Using stat = "qq" in qplot produces a plot of sample quantiles versus standard normal quantiles.
qplot(sample=.stdresid,data=fm6f,stat="qq") + xlab("Standard normal quantiles") + ylab("Standardized residuals")+coord_equal()


## Plotting fitted values

qplot(temp,time,data=fm6f)+geom_point(aes(color=type)) + geom_line(aes(x=temp,y=.fitted,color=type))+xlab("Temperature in freezer (degrees C)") + ylab("Time to reach operating temperature of -10 C (min)")