<center> <h1> linear.tools </h1> </center> <center> <h1> </h1> </center>

This package has two parts:


# source("/Users/yangguodaxia/Dropbox/Tech/R/linear_tools_origin.R")

First Part: Manipulate formulas

different forms of x

Variables in R's linear formula/model can have different forms:

  1. Model variables, the items showed up directly in the formula, separated by the '+' sign.
  2. Raw variables, the underlying variables used.
  3. Coefficient variables, the coefficient names; note that un-evaluated formulas don't have those variables.

model variables: get_x(formula/model,'coeff')

data = ggplot2::diamonds
diamond_lm  =  lm(log(price)~  I(carat^   2) + cut  + carat + table + carat:table, data)

At the first sight, the linear model above contains 5 variables:

In linear.tools we call them model variables and can access them using function get_x(.,'model'):


Note that in the original formula, there are redundant spaces 'I(carat^ 2)'; in get_x(.,'model') we deleted them.

raw variables: get_x(formula/model,'coeff')

Sometimes you want to get the underlying raw variables used in the formula, which are

In linear.tools we call them raw variables and can access them using function get_x(.,'raw'):


get_x(.,'model') will show the linkage between model variables and raw variables: it will return a list with names as model variables and elements as their corresponding raw variables.

get_model_pair(diamond_lm, data, 'raw')

coefficient variables: get_x(model,'coeff')

Sometimes you want the the coefficient names of the model


You may also want to see how 'model' variables are linked with 'coeff' variables: get_x(.,'coeff') will return a list with names as model variables and elements as their corresponding coeff variables.

get_model_pair(diamond_lm, data, 'coeff')

link different forms of x: get_x_all(model)

The get_x_all() function will return a data.frame showing all the model variables and their corresponding raw & coefficient variables.

get_x_all(model = diamond_lm)

get y : get_y(formula/model)


contrast: get_contrast(model)

Contrasts are how categorical variables show up in coefficients.

When R evaluate categorical variables in the linear model, R will transform them into sets of 'contrasts' using certain contrast encoding schedule. See UCLA idre for details.

For example, for categorical variable 'cut' in the above model, we can get its contrasts through function get_contrast

# get_contrast will return a list with each element as the contrasts of a categorical variable in the model

You can also return the contrast method.

get_contrast(diamond_lm, return_method = T)

Second Part: Evaluate Marginal Effect

In formula y ~ a + I(a^2) + b, We define 'Marginal Effect' of a on y as: fixing b, how the change of a will affect value of y. Note that the marginal effect here is not just the coefficients for a and I(a^2), neither the sum.

evaluate marginal effect: effect

We provide a easy tool to show the marginal effect and check its monotonicity. The example below will evaluate how the carat of the diamond will affect its price in a particular model.

# more carats, higher price.
diamond_lm3 = lm(price~  carat + I(carat^2) + I(carat^3) , ggplot2::diamonds) # a GLM

test1 = effect(model = diamond_lm3, focus_var_raw = c('carat'), focus_value =list(carat = seq(0.5,1,0.1))) 

You can see that the model did a good job to model monotonic increasing relations between carat and price when carat ranges from 0.5 to 1 ($Monoton_Increase is True).

PS: A more interesting case is that, if you interact carat with the categorical variable cut, you can examine the marginal effects carat under different categories of cut

test_interaction = effect(model = lm(price~  carat*cut + I(carat^2)*cut, ggplot2::diamonds), 
       focus_var_raw = c('carat','cut'), focus_value =list(carat = seq(0.5,1,0.1))

However, in the model diamond_lm3 when we let the carat ranges from 0.5 to 6, the model failed to get the monotonic increasing relations: in the model below, when carat is larger than 3 approximately, the higher the carat, the lower the price!

test2 = effect(model = diamond_lm3, focus_var_raw = c('carat'), focus_value =list(carat = seq(0.5,6,0.1))) 

delete the marginal effect and re-evaluate

When a model has a wrong marginal effect, we can use function deleting_wrongeffect to delete a model variable that potentially causes the wrong marginal impacts and then re-estimate the model. This function can keep doing this until the correct marginal impacts are found.

The example below will

model_correct_effect = deleting_wrongeffect(model = diamond_lm3,
                                            focus_var_raw = 'carat',
                                            focus_value = list(carat=seq(0.5,6,0.1)),
                                            data = ggplot2::diamonds,
                                            PRINT = T,STOP =F, PLOT = T,
                                            Reverse = F)

stepwise regression with correct marginal effect

Stepwise regression is popular in variable selection, but it failed to consider the correctness of marginal effects. stepwise2 enables checking the marginal effects during each step of iteration in stepwise regression; so in each step we will skip those models with wrong marginal effects, and only only choose models among those that have correct marginal effect.

The example below is to use stepwise regression to find the model with highest BIC and with the correct marginal effect.

scope = list(lower = price ~ 1,
             upper = price ~  carat + I(carat^2) + I(carat^3) + I(carat * depth) + depth)

### specify the correct marginal effect here
test_suit = list(
  carat = list( # the list name must be the raw var
    focus_var_raw = "carat", # must specify the focus_var_raw (see deleting_wrongeffect() ) as the raw var
    focus_value = list(carat=seq(0.5,6,0.1))

model_correct_effect =  stepwise2(model = diamond_lm3, scope = scope, trace = T,
                                  data = ggplot2::diamonds, STOP = F, test_suit = test_suit)
# the returned model

compare with step

The model using stepwise2 got correct marginal effect:

test_model_correct_effect = effect(model = model_correct_effect, focus_var_raw = c('carat'), focus_value =list(carat = seq(0.5,6,0.1))) 

whereas the model using traditional algorithm step got wrong marginal effect:

model_wrong_effect =  step(diamond_lm3, scope = scope, trace = F, data = ggplot2::diamonds)
test_wrong_effect = effect(model_wrong_effect, focus_var_raw = c('carat'), focus_value =list(carat = seq(0.5,6,0.1))) 

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linear.tools documentation built on May 2, 2019, 3:17 a.m.