I am using NBA shot data and am attempting to create shot prediction models using different regression techniques. However, I am running into the following warning message when trying to use a logistic regression model: Warning message:
glm.fit: algorithm did not converge. Also, it seems that the predictions do not work at all (not changed from the original Y variable (make or miss)). I will provide my code below. I got the data from here: Shot Data.
nba_shots <- read.csv("shot_logs.csv")
library(dplyr)
library(ggplot2)
library(data.table)
library("caTools")
library(glmnet)
library(caret)
nba_shots_clean <- data.frame("game_id" = nba_shots$GAME_ID, "location" =
nba_shots$LOCATION, "shot_number" = nba_shots$SHOT_NUMBER,
"closest_defender" = nba_shots$CLOSEST_DEFENDER,
"defender_distance" = nba_shots$CLOSE_DEF_DIST, "points" = nba_shots$PTS,
"player_name" = nba_shots$player_name, "dribbles" = nba_shots$DRIBBLES,
"shot_clock" = nba_shots$SHOT_CLOCK, "quarter" = nba_shots$PERIOD,
"touch_time" = nba_shots$TOUCH_TIME, "game_result" = nba_shots$W
, "FGM" = nba_shots$FGM)
mean(nba_shots_clean$shot_clock) # NA
# this gave NA return which means that there are NAs in this column that we
# need to clean up
# if the shot clock was NA I assume that this means it was the end of a
# quarter and the shot clock was off.
# For now I'm going to just set all of these NAs equal to zero, so all zeros
# mean it is the end of a quarter
# checking the amount of NAs
last_shots <- nba_shots_clean[is.na(nba_shots_clean$shot_clock),]
nrow(last_shots) # this tells me there is 5567 shots taken when the shot
# clock was turned off at the end of a quarter
# setting these NAs equal to zero
nba_shots_clean[is.na(nba_shots_clean)] <- 0
# checking to see if it worked
nrow(nba_shots_clean[is.na(nba_shots_clean$shot_clock),]) # it worked
# create a test and train set
split = sample.split(nba_shots_clean, SplitRatio=0.75)
nbaTrain = subset(nba_shots_clean, split==TRUE)
nbaTest = subset(nba_shots_clean, split==FALSE)
# logistic regression
nbaLogitModel <- glm(FGM ~ location + shot_number + defender_distance +
points + dribbles + shot_clock + quarter + touch_time, data=nbaTrain,
family="binomial", na.action = na.omit)
nbaPredict = predict(nbaLogitModel, newdata=nbaTest, type="response")
cm = table(nbaTest$FGM, nbaPredict > 0.5)
print(cm)
This gives me the output of the following, which tells me the prediction didn't do anything, as it's the same as before.
FALSE TRUE
0 21428 0
1 0 17977
I would really appreciate any guidance.
The confusion matrix of your model (model prediction vs. nbaTest$FGM) tells you that your model has a 100% accuracy !
This is due to the points variable in your dataset which is perfectly associated to the dependent variable:
table(nba_shots_clean$points, nba_shots_clean$FGM)
0 1
0 87278 0
2 0 58692
3 0 15133
Try to delete points from your model:
# create a test and train set
set.seed(1234)
split = sample.split(nba_shots_clean, SplitRatio=0.75)
nbaTrain = subset(nba_shots_clean, split==TRUE)
nbaTest = subset(nba_shots_clean, split==FALSE)
# logistic regression
nbaLogitModel <- glm(FGM ~ location + shot_number + defender_distance +
dribbles + shot_clock + quarter + touch_time, data=nbaTrain,
family="binomial", na.action = na.omit)
summary(nbaLogitModel)
No warning messages now and the estimated model is:
Call:
glm(formula = FGM ~ location + shot_number + defender_distance +
dribbles + shot_clock + quarter + touch_time, family = "binomial",
data = nbaTrain, na.action = na.omit)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.8995 -1.1072 -0.9743 1.2284 1.6799
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.427688 0.025446 -16.808 < 2e-16 ***
locationH 0.037920 0.012091 3.136 0.00171 **
shot_number 0.007972 0.001722 4.630 0.000003656291 ***
defender_distance -0.006990 0.002242 -3.117 0.00182 **
dribbles 0.010582 0.004859 2.178 0.02941 *
shot_clock 0.032759 0.001083 30.244 < 2e-16 ***
quarter -0.043100 0.007045 -6.118 0.000000000946 ***
touch_time -0.038006 0.005700 -6.668 0.000000000026 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 153850 on 111532 degrees of freedom
Residual deviance: 152529 on 111525 degrees of freedom
AIC: 152545
Number of Fisher Scoring iterations: 4
The confusion matrix is:
nbaPredict = predict(nbaLogitModel, newdata=nbaTest, type="response")
cm = table(nbaTest$FGM, nbaPredict > 0.5)
print(cm)
FALSE TRUE
0 21554 5335
1 16726 5955
Related
For Y = % of population with income below poverty level and X = per capita income of population, I have constructed a box-cox plot and found that the lambda = 0.02020:
bc <- boxcox(lm(Percent_below_poverty_level ~ Per_capita_income, data=tidy.CDI), plotit=T)
bc$x[which.max(bc$y)] # gives lambda
Now I want to fit a simple linear regression using the transformed data, so I've entered this code
transform <- lm((Percent_below_poverty_level**0.02020) ~ (Per_capita_income**0.02020))
transform
But all I get is the error message
'Error in terms.formula(formula, data = data) : invalid power in formula'. What is my mistake?
You could use bcPower() from the car package.
## make sure you do install.packages("car") if you haven't already
library(car)
data(Prestige)
p <- powerTransform(prestige ~ income + education + type ,
data=Prestige,
family="bcPower")
summary(p)
# bcPower Transformation to Normality
# Est Power Rounded Pwr Wald Lwr Bnd Wald Upr Bnd
# Y1 1.3052 1 0.9408 1.6696
#
# Likelihood ratio test that transformation parameter is equal to 0
# (log transformation)
# LRT df pval
# LR test, lambda = (0) 41.67724 1 1.0765e-10
#
# Likelihood ratio test that no transformation is needed
# LRT df pval
# LR test, lambda = (1) 2.623915 1 0.10526
mod <- lm(bcPower(prestige, 1.3052) ~ income + education + type, data=Prestige)
summary(mod)
#
# Call:
# lm(formula = bcPower(prestige, 1.3052) ~ income + education +
# type, data = Prestige)
#
# Residuals:
# Min 1Q Median 3Q Max
# -44.843 -13.102 0.287 15.073 62.889
#
# Coefficients:
# Estimate Std. Error t value Pr(>|t|)
# (Intercept) -3.736e+01 1.639e+01 -2.279 0.0250 *
# income 3.363e-03 6.928e-04 4.854 4.87e-06 ***
# education 1.205e+01 2.009e+00 5.999 3.78e-08 ***
# typeprof 2.027e+01 1.213e+01 1.672 0.0979 .
# typewc -1.078e+01 7.884e+00 -1.368 0.1746
# ---
# Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#
# Residual standard error: 22.25 on 93 degrees of freedom
# (4 observations deleted due to missingness)
# Multiple R-squared: 0.8492, Adjusted R-squared: 0.8427
# F-statistic: 131 on 4 and 93 DF, p-value: < 2.2e-16
Powers (more often represented by ^ than ** in R, FWIW) have a special meaning inside formulas [they represent interactions among variables rather than mathematical operations]. So if you did want to power-transform both sides of your equation you would use the I() or "as-is" operator:
I(Percent_below_poverty_level^0.02020) ~ I(Per_capita_income^0.02020)
However, I think you should do what #DaveArmstrong suggested anyway:
it's only the predictor variable that gets transformed
the Box-Cox transformation is actually (y^lambda-1)/lambda (although the shift and scale might not matter for your results)
I am working with an interaction model similar to this one below:
set.seed(1993)
moderating <- sample(c("Yes", "No"),100, replace = T)
x <- sample(c("Yes", "No"), 100, replace = T)
y <- sample(1:100, 100, replace = T)
df <- data.frame(y, x, moderating)
Results <- lm(y ~ x*moderating)
summary(Results)
Call:
lm(formula = y ~ x * moderating)
Residuals:
Min 1Q Median 3Q Max
-57.857 -29.067 3.043 22.960 59.043
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 52.4000 6.1639 8.501 2.44e-13 ***
xYes 8.4571 9.1227 0.927 0.356
moderatingYes -11.4435 8.9045 -1.285 0.202
xYes:moderatingYes -0.1233 12.4563 -0.010 0.992
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 30.82 on 96 degrees of freedom
Multiple R-squared: 0.04685, Adjusted R-squared: 0.01707
F-statistic: 1.573 on 3 and 96 DF, p-value: 0.2009
I'm learning how to calculate the fitted value of a interaction from a regression table. In the example, the base category (or omitted category) is x= No and moderating = No.
Thus far, I know the following fitted values:
#Calulate Fitted Value From a Regression Interaction by hand
#Omitted Variable = X_no.M_no
X_no.M_no <- 52.4000
X_yes.M_no <- 52.4000 + 8.4571
X_no.M_yes <- 52.4000 + -11.4435
X_yes.M_yes #<- ?
I do not understand how the final category, X_yes.M_yes, is calculated. My initial thoughts were X_yes.M_yes <- 52.4000 + -0.1233, (the intercept plus the interaction term) but that is incorrect. I know its incorrect because, using the predict function, the fitted value of X_yes.M_yes = 49.29032, not 52.4000 + -0.1233 = 52.2767.
How do I calculate, by hand, the predicted value of the X_yes.M_yes category?
Here are the predicted values as generated from the predict function in R
#Validated Here Using the Predict Function:
newdat <- NULL
for(m in na.omit(unique(df$moderating))){
for(i in na.omit(unique(df$x))){
moderating <- m
x <- i
newdat<- rbind(newdat, data.frame(x, moderating))
}
}
Prediction.1 <- cbind(newdat, predict(Results, newdat, se.fit = TRUE))
Prediction.1
Your regression looks like this in math:
hat_y = a + b x + c m + d m x
Where x = 1 when "yes" and 0 when "no" and m is similarly defined by moderating.
Then X_yes.M_yes implies x = 1 and m = 1, so your prediction is a + b + c + d.
or in your notation X_yes.M_yes = 52.4000 + 8.4571 - 11.4435 - 0.1233
I have run a logistic regression in R using glm to predict the likelihood that an individual in 1993 will have arthritis in 2004 (Arth2004) based on gender (Gen), smoking status (Smoke1993), hypertension (HT1993), high cholesterol (HC1993), and BMI (BMI1993) status in 1993. My sample size is n=7896. All variables are binary with 0 and 1 for false and true except BMI, which is continuous numeric. For gender, male=1 and female=0.
When I run the regression in R, I get good p-values, but when I actually use the regression for prediction, I get values greater than one quite often for very standard individuals. I apologize for the large code block, but I thought more information may be helpful.
library(ResourceSelection)
library(MASS)
data=read.csv(file.choose())
data$Arth2004 = as.factor(data$Arth2004)
data$Gen = as.factor(data$Gen)
data$Smoke1993 = as.factor(data$Smoke1993)
data$HT1993 = as.factor(data$HT1993)
data$HC1993 = as.factor(data$HC1993)
data$BMI1993 = as.numeric(data$BMI1993)
logistic <- glm(Arth2004 ~ Gen + Smoke1993 + BMI1993 + HC1993 + HT1993, data=data, family="binomial")
summary(logistic)
hoslem.test(logistic$y, fitted(logistic))
confint(logistic)
min(data$BMI1993)
median(data$BMI1993)
max(data$BMI1993)
e=2.71828
The output is as follows:
Call:
glm(formula = Arth2004 ~ Gen + Smoke1993 + BMI1993 + HC1993 +
HT1993, family = "binomial", data = data)
Deviance Residuals:
Min 1Q Median 3Q Max
-2.0362 -1.0513 -0.7831 1.1844 1.8807
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -2.346104 0.158043 -14.845 < 2e-16 ***
Gen1 -0.748286 0.048398 -15.461 < 2e-16 ***
Smoke19931 -0.059342 0.064606 -0.919 0.358
BMI1993 0.084056 0.006005 13.997 < 2e-16 ***
HC19931 0.388217 0.047820 8.118 4.72e-16 ***
HT19931 0.341375 0.058423 5.843 5.12e-09 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 10890 on 7895 degrees of freedom
Residual deviance: 10309 on 7890 degrees of freedom
AIC: 10321
Number of Fisher Scoring iterations: 4
Hosmer and Lemeshow goodness of fit (GOF) test
data: logistic$y, fitted(logistic)
X-squared = 18.293, df = 8, p-value = 0.01913
Waiting for profiling to be done...
2.5 % 97.5 %
(Intercept) -2.65715966 -2.03756775
Gen1 -0.84336906 -0.65364134
Smoke19931 -0.18619647 0.06709748
BMI1993 0.07233866 0.09588198
HC19931 0.29454661 0.48200673
HT19931 0.22690608 0.45595006
[1] 18
[1] 26
[1] 43
A non-smoking female w/ median BMI (26), hypertension, and high cholesterol yields the following:
e^(26*0.084056+1*0.388217+1*0.341375-0*0.748286-0*0.059342-2.346104)
[1] 1.7664
I think the issue is related somehow to BMI considering that is the only variable that is numeric. Does anyone know why this regression produces probabilities greater than 1?
By default, family = "binomial" uses the logit link function (see ?family). So the probability you're looking for is 1.7664 / (1+1.7664).
I have run the Hosmer Lemeshow statistic in R, but I have obtained an p-value of 1. This seems strange to me. I know that a high p-valvalue means that we do not reject the null hypothesis that observed and expected are the same, but is it possible i have an error somewhere?
How do i interpret such p-value?
Below is the code i have used to run the test. I also attach how my model looks like. Response variable is a count variable, while all regressors are continous. I have run a negative binomial model, due to detected overdispersion in my initial poisson model.
> hosmerlem <- function(y, yhat, g=10)
+ {cutyhat <- cut(yhat, breaks = quantile(yhat, probs=seq(0,1, 1/g)), include.lowest=TRUE)
+ obs <- xtabs(cbind(1 - y, y) ~ cutyhat)
+ expect <- xtabs(cbind(1 - yhat, yhat) ~ cutyhat)
+ chisq <- sum((obs - expect)^2/expect)
+ P <- 1 - pchisq(chisq, g - 2)
+ return(list(chisq=chisq,p.value=P))}
> hosmerlem(y=TOT.N, yhat=fitted(final.model))
$chisq
[1] -2.529054
$p.value
[1] 1
> final.model <-glm.nb(TOT.N ~ D.PARK + OPEN.L + L.WAT.C + sqrt(L.P.ROAD))
> summary(final.model)
Call:
glm.nb(formula = TOT.N ~ D.PARK + OPEN.L + L.WAT.C + sqrt(L.P.ROAD),
init.theta = 4.979895131, link = log)
Deviance Residuals:
Min 1Q Median 3Q Max
-3.08218 -0.70494 -0.09268 0.55575 1.67860
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 4.032e+00 3.363e-01 11.989 < 2e-16 ***
D.PARK -1.154e-04 1.061e-05 -10.878 < 2e-16 ***
OPEN.L -1.085e-02 3.122e-03 -3.475 0.00051 ***
L.WAT.C 1.597e-01 7.852e-02 2.034 0.04195 *
sqrt(L.P.ROAD) 4.924e-01 3.101e-01 1.588 0.11231
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
(Dispersion parameter for Negative Binomial(4.9799) family taken to be 1)
Null deviance: 197.574 on 51 degrees of freedom
Residual deviance: 51.329 on 47 degrees of freedom
AIC: 383.54
Number of Fisher Scoring iterations: 1
Theta: 4.98
Std. Err.: 1.22
2 x log-likelihood: -371.542
As correctly pointed out by #BenBolker, Hosmer-Lemeshow is a test for logistic regression, not for a negative binomial generalized linear model.
If we consider to apply the test to a logistic regression,
the inputs of the function hosmerlem (a copy of the hoslem.test function in the package ResourceSelection) should be:
- y = a numeric vector of observations, binary (0/1)
- yhat = expected values (probabilities)
Here is an illustrative example that shows how to get the correct inputs:
set.seed(123)
n <- 500
x <- rnorm(n)
y <- rbinom(n, 1, plogis(0.1 + 0.5*x))
logmod <- glm(y ~ x, family=binomial)
# Important: use the type="response" option
yhat <- predict(logmod, type="response")
hosmerlem(y, yhat)
########
$chisq
[1] 4.522719
$p.value
[1] 0.8071559
The same result is given by the function hoslem.test:
library(ResourceSelection)
hoslem.test(y, yhat)
########
Hosmer and Lemeshow goodness of fit (GOF) test
data: y, yhat
X-squared = 4.5227, df = 8, p-value = 0.8072
As already mentioned, HL-test is not appropriate for the specified model. It is also important to know that a large p-value doesn't necessarily mean a good fit. It could also be that there isn't enough evidence to prove it's a poor fit.
Meanwhile, the gofcat package implementation of the HL-test provides for passing model objects directly to the function without necessarily supplying the observed and predicted values. For the simulated data one has:
library(gofcat)
set.seed(123)
n <- 500
x <- rnorm(n)
y <- rbinom(n, 1, plogis(0.1 + 0.5*x))
logmod <- glm(y ~ x, family=binomial)
hosmerlem(logmod, group = 10)
Hosmer-Lemeshow Test:
Chi-sq df pr(>chi)
binary(Hosmerlem) 4.5227 8 0.8072
H0: No lack of fit dictated
rho: 100%
I could be missing something about prediction -- but my multiple linear regression is seemingly working as expected:
> bigmodel <- lm(score ~ lean + gender + age, data = mydata)
> summary(bigmodel)
Call:
lm(formula = score ~ lean + gender + age, data = mydata)
Residuals:
Min 1Q Median 3Q Max
-25.891 -4.354 0.892 6.240 18.537
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 70.96455 3.85275 18.419 <2e-16 ***
lean 0.62463 0.05938 10.518 <2e-16 ***
genderM -2.24025 1.40362 -1.596 0.1121
age 0.10783 0.06052 1.782 0.0764 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Residual standard error: 9 on 195 degrees of freedom
Multiple R-squared: 0.4188, Adjusted R-squared: 0.4098
F-statistic: 46.83 on 3 and 195 DF, p-value: < 2.2e-16
> head(predict(bigmodel),20)
1 2 3 4 5 6 7 8 9 10
75.36711 74.43743 77.02533 78.76903 79.95515 79.09251 80.38647 81.65807 80.14846 78.96234
11 12 13 14 15 16 17 18 19 20
82.39052 82.04468 81.05187 81.26753 84.50240 81.80667 80.92169 82.40895 81.76197 82.94809
But I can't wrap my head around the prediction after reading ?predict.lm. This output looks good to me for my original dataset -- but what if I want to run the prediction against a different dataset than the one I used to create bigmodel?
For example, if I import a .csv file into R called newmodel with 200 people complete with leans, gender, and age -- how can I use the regression formula from bigmodel to produce predictions for newmodel?
Thanks!
If you read the documentation for predict.lm, you will see the following. So, use the newdata argument to pass the newmodel data you imported to get predictions.
predict(object, newdata, se.fit = FALSE, scale = NULL, df = Inf,
interval = c("none", "confidence", "prediction"),
level = 0.95, type = c("response", "terms"),
terms = NULL, na.action = na.pass,
pred.var = res.var/weights, weights = 1, ...)
Arguments
object
Object of class inheriting from "lm"
newdata
An optional data frame in which to look for variables with which to predict.
If omitted, the fitted values are used.
UPDATE. On the question of exporting data with predictions, here is how you can do it.
predictions = cbind(newmodel, pred = predict(bigmodel, newdata = newmodel))
write.csv(predictions, 'predictions.csv', row.names = F)
UPDATE 2. A full minimally reproducible solution
bigmodel <- lm(mpg ~ wt, data = mtcars)
newdata = data.frame(wt = runif(20, min = 1.5, max = 6))
cbind(
newdata,
mpg = predict(bigmodel, newdata = newdata)
)