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R code: logistic regression

What is "logistic" about logistic regression?


# Logit: logarithm of odds,
# where the odds of a probability p is p/(1-p)
#
# The logit is
# f(p) = log( p / (1-p) )
logit = function(p) { log(p/(1-p)) }

# Note the sigmoid shape of the plot
xvals = seq(0.001,.999,.001)
plot(xvals,logit(xvals), type="l")

# The inverse logit function (aka logistic function, aka sigmoid
# function) maps any value into a value between 0 and 1.
# Note: exp(x) is e (the Euler number) to the power of x
#
# The logistic function is
# f(x) = exp(x) / (exp(x) + 1) = 1 / (1 + exp(-x))
invlogit = function(x) { 1/(1+exp(-x)) }

# logit and invlogit are inverse functions:
logit(0.8)
invlogit(1.386294)


# again, note the sigmoid shape of the plot
xvals = -6:6
plot(xvals,invlogit(xvals),type="l")

Why we need something different than linear regression when the dependent variable (the variable we want to predict) is categorial


# Now remember linear regression: We model a dependent variable Y as
# linearly dependent on a predictor X:
#
# Y = Beta_0 + Beta_1 X
#
# Beta_0 is the intercept, and Beta_1 is the slope.
#
# When we do logistic regression, we predict Y to be
# Y = invlogit(Beta_0 + Beta_1 X)
#
# where invlogit is the logistic function.
# So Y will be a value between 0 and 1.

## An example using a languageR dataset.
# regularity: languageR dataset containing information on
# regular and irregular Dutch verbs.
# regularity$Regularity is a factor with values "regular", "irregular".
# We map it to a number, either 0 (for "irregular") or 1 (for "regular").
library(languageR)
reg = regularity
reg$Regularity = as.numeric(regularity$Regularity=="regular")

# Relation between regularity and written frequency of a verb:
# irregular verbs tend to be more frequent
plot(Regularity~WrittenFrequency,data=reg)

# Regularity has two values, 0 or 1. First, we try to fit a linear model:
reg.lm = lm(Regularity~WrittenFrequency,data=reg)
summary(reg.lm)


# We plot regularity and written frequency again, and
# add the fitted model as a line.
# Because this is linear regression,
# we predict regularity values below 0 and above 1
# (which makes no sense)
plot(Regularity~WrittenFrequency,data=reg)
abline(reg.lm)

# Now we use logistic regression.
# NEW: using library rms instead of the outdated library Design
# used in the Baayen book
library(rms)
reg.dd = datadist(reg)
options(datadist="reg.dd")

reg.lrm = lrm(Regularity~WrittenFrequency,data=reg)

# inspect by just typing reg.lrm
# We see that the coefficient for WrittenFrequency is negative,
# which means that the higher WrittenFrequency, the more likely Regularity is going to be
# near zero (that is, the more likely Regularity is going to be "irregular")

# We use this model to get predictions for Regularity
# for the WrittenFrequency values in the dataset
reg.predicted = predict(reg.lrm)

# When we inspect the results, we see that what we get is
# Beta_0 + Beta_1 X, rather than invlogit(Beta_0 + Beta_1 X)
range(reg.predicted)

# Compare:
# > reg.predicted[1]
#       1
# 4.278845
# > coef(reg.lrm)[1] + coef(reg.lrm)[2] * reg[1,]$WrittenFrequency
# Intercept
#  4.278845
# > range(invlogit(reg.predicted))
# [1] 0.1029522 0.9944239


# Now let's plot the invlogit() of these points
points(reg$WrittenFrequency, invlogit(predict(reg.lrm)), col="orange")


Another logistic regression example: The Dative Alternation



library(languageR)

head(verb)

# we would like to predict the realization of the receiver:
# NP: "John gave Mary the book"
# PP: "John gave the book to Mary"
# How does the length of the Theme ("book" versus "the book that I read last week")
# affect the realization
of the Recipient?
# As we would expect, longer Themes tend to come at the end:


aggregate(verbs$LengthOfTheme, list(verbs$RealizationOfRec), mean)


# Now we do logistic regression to predict Realization of Recipient from Length of Theme.
# As above, we first have to "register" the dataset with the rms package

v.dd = datadist(verbs)
options(datadist="v.dd")

# Read the output of lrm: What does the coefficient for LengthOfTheme say about the influence of this predictor?


lrm(RealizationOfRec ~ LengthOfTheme, data = verbs)

# Another possible predictor is the animacy of the Recipient:
# "send the book to Mary" versus "send the book to the office"


# Note that this is a categorial predictor! What would you expect this predictor to do?
# We first check by hand what we can expect to see


xtabs(~RealizationOfRec + AnimacyOfRec, data = verbs)


# Then we do the regression.

lrm(RealizationOfRec ~ AnimacyOfRec, data = verbs)

# Putting multiple predictors together

lrm(RealizationOfRec ~ LengthOfTheme + AnimacyOfRec + AnimacyOfTheme, data = verbs)


# The 'dative' dataset contains the data in 'verbs', plus additional information
head(dative)

# We use it to predict the realization of the Recipient from the semantic class of the verb:
# abstract, communication, future transfer of possession, prevention of possession,
# transfer of possession

d.dd = datadist(dative)
options(datadist = "d.dd")
lrm(RealizationOfRecipient ~ SemanticClass, data = dative)

# We can now build a wide variety of models:
m1 = lrm(RealizationOfRecipient ~ AnimacyOfRec, data = dative)
m2 = lrm(RealizationOfRecipient ~ DefinOfRec, data = dative)
m3 = lrm(RealizationOfRecipient ~ AnimacyOfRec + DefinOfRec, data = dative)
m4 = lrm(RealizationOfRecipient ~ SemanticClass, data = dative)
m5 = lrm(RealizationOfRecipient ~ SemanticClass + AnimacyOfRec + DefinOfRec, data = dative)
m6 = lrm(RealizationOfRecipient ~ LengthOfTheme, data = dative)

# Which one should we choose?


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