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primary composite outcome

R Software Module: rwasp_logisticregression.wasp (opens new window with default values)
Title produced by software: Bias-Reduced Logistic Regression
Date of computation: Fri, 10 Oct 2008 03:14:33 -0600
 
Cite this page as follows:
Statistical Computations at FreeStatistics.org, Office for Research Development and Education, URL http://www.freestatistics.org/blog/date/2008/Oct/10/t1223630382q08n7j4h2tlnswy.htm/, Retrieved Fri, 10 Oct 2008 09:19:42 +0000
 
BibTeX entries for LaTeX users:
@Manual{KEY,
    author = {{YOUR NAME}},
    publisher = {Office for Research Development and Education},
    title = {Statistical Computations at FreeStatistics.org, URL http://www.freestatistics.org/blog/date/2008/Oct/10/t1223630382q08n7j4h2tlnswy.htm/},
    year = {2008},
}
@Manual{R,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Development Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2008},
    note = {{ISBN} 3-900051-07-0},
    url = {http://www.R-project.org},
}
 
Family? (F = Feedback message, R = changed R code, M = changed R Module, P = changed Parameters, D = changed Data)
 
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Original text written by user:
These are the results for your model with missing data treated properly. Every missing value obtains the label NA.
 
IsPrivate?
This computation is private
 
User-defined keywords:
 
Dataseries X:
» Textbox « » Textfile « » CSV «
0 0 0 1 1 0 1 1 1 1 0 1 1 1 1 1 1 0 0 1 0 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 1 1 0 1 0 1 1 0 1 1 1 0 0 0 1 0 0 0 1 1 1 0 1 1 1 1 0 0 0 1 1 0 0 1 1 1 0 0 1 1 NA 1 0 1 1 1 0 0 1 1 1 0 0 1 1 1 1 0 1 1 1 1 0 1 1 0 1 0 1 1 NA 1 0 1 0 1 1 0 1 0 1 1 0 1 0 1 1 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 1 1 0 1 1 1 NA 0 0 1 0 1 1 0 0 1 1 0 0 1 0 1 0 0 1 0 NA 0 0 0 1 NA 1 0 0 1 0 0 0 1 0 NA 1 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 1 0 NA 0 0 0 1 NA 0 0 1 1 NA 1 0 1 0 0 0 0 1 0 1 0 0 0 1 NA 0 0 1 1 NA 0 0 0 0 NA 1 0 0 0 NA 1 0 1 0 1 1 0 0 0 NA 0 0 1 0 1 1 1 1 0 NA 1 0 1 1 0 1 0 1 1 1 1 0 1 1 0 1 0 1 1 1 1 0 1 1 1 0 0 1 0 1 1 0 1 1 1 1 0 1 1 1 0 0 1 1 1 1 0 0 0 0 0 0 0 1 1 0 1 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 1 1 0 1 0 1 1 1 1 0 1 1 1 1 0 1 0 1 1 0 1 0 0 1 0 0 1 1 1 0 0 1 0 1 0 1 1 1 1 0 1 1 1 1 0 0 1 0 0 0 0 1 1 0 0 1 1 0 1 0 0 0 1 1 0 0 1 1 1 0 1 1 1 1 0 1 1 1 1 1 1 1 0 1 0 1 0 1 1 0 1 1 1 1 0 0 1 1 0 0 0 1 1 0 0 1 1 1 1 0 1 1 1 1 0 1 1 1 1 0 0 1 1 1 0 1 0 1 1 1 1 1 NA NA 0 0 0 0 1 0 1 0 1 1 0 1 1 1 1 0 0 1 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1 1 0 1 0 0 1 1 1 NA 1 1 1 1 0 0 0 1 0 0 0 1 1 1 1 0 1 0 0 NA 0 1 0 0 1 0 1 1 1 0 0 0 0 0 1 0 1 0 1 0 0 1 1 1 0 0 1 0 0 0 0 1 0 1 0 0 1 0 0 1 0 1 1 0 0 0 0 0 NA 0 0 0 1 0 1 0 1 1 1 1 0 0 1 0 1 0 1 1 0 1 0 0 0 1 0 0 0 1 1 0 1 1 1 1 1 0 0 0 1 1 0 1 1 0 0 0 1 1 1 0 0 1 1 1 0 0 0 0 0 1 0 1 1 1 0 0 0 1 NA 0 1 1 1 1 NA 0 0 1 1 1 0 1 0 0 0 0 0 0 1 0 0 1 1 NA 0 0 1 1 NA 0 0 1 0 NA 0 0 0 1 NA 0 0 1 1 1 1 0 1 1 1 0 0 0 0 1 1 0 1 1 1 1 0 1 0 1 1 0 1 0 1 1 0 1 1 1 1 0 1 1 0 0 0 1 1 1 1 0 1 1 0 0 0 1 1 0 1
 
Output produced by software:

Enter (or paste) a matrix (table) containing all data (time) series. Every column represents a different variable and must be delimited by a space or Tab. Every row represents a period in time (or category) and must be delimited by hard returns. The easiest way to enter data is to copy and paste a block of spreadsheet cells. Please, do not use commas or spaces to seperate groups of digits!


Summary of computational transaction
Raw Inputview raw input (R code)
Raw Outputview raw output of R engine
Computing time5 seconds
R Server'Herman Ole Andreas Wold' @ 193.190.124.10:1001


Coefficients of Bias-Reduced Logistic Regression
VariableParameterS.E.t-stat2-sided p-value
(Intercept)-4.03953311170451.41585758558950-2.853064568653370.00506916242873401
IM2.329369827238841.392257493190481.673088375269490.0968108013675668
UC0.3463070567860850.744780232945570.4649788507630730.642755580144504
DIA-0.759026519431170.706295301011985-1.074658883251290.284597508132181
TEN-0.1804839059554980.692816011645475-0.2605077003443360.794900832245201


Summary of Bias-Reduced Logistic Regression
Deviance53.8962223457521
Penalized deviance50.3047894402064
Residual Degrees of Freedom125
ROC Area0.758196721311475
Hosmer–Lemeshow test
Chi-squareNA
Degrees of FreedomNA
P(>Chi)NA


Fit of Logistic Regression
IndexActualFittedError
100.00683362080067247-0.00683362080067247
200.0908445198161321-0.0908445198161321
300.0908445198161321-0.0908445198161321
410.1311706948110210.86882930518898
500.066009123056486-0.066009123056486
600.153142538219492-0.153142538219492
700.0173010927062556-0.0173010927062556
800.0173010927062556-0.0173010927062556
900.0908445198161321-0.0908445198161321
1000.00683362080067247-0.00683362080067247
1100.066009123056486-0.066009123056486
1200.106892552575036-0.106892552575036
1300.0242870285101468-0.0242870285101468
1400.106892552575036-0.106892552575036
1510.1068925525750360.893107447424964
1600.0115180777575777-0.0115180777575777
1700.106892552575036-0.106892552575036
1800.106892552575036-0.106892552575036
1900.106892552575036-0.106892552575036
2000.0908445198161321-0.0908445198161321
2100.0908445198161321-0.0908445198161321
2200.175905232564779-0.175905232564779
2300.066009123056486-0.066009123056486
2400.066009123056486-0.066009123056486
2500.066009123056486-0.066009123056486
2600.00817424056313886-0.00817424056313886
2700.0144854810572694-0.0144854810572694
2800.0173010927062556-0.0173010927062556
2900.00817424056313886-0.00817424056313886
3000.0780465130700821-0.0780465130700821
3100.0115180777575777-0.0115180777575777
3200.066009123056486-0.066009123056486
3300.0115180777575777-0.0115180777575777
3410.07804651307008210.921953486929918
3500.0242870285101468-0.0242870285101468
3600.106892552575036-0.106892552575036
3700.0144854810572694-0.0144854810572694
3800.0173010927062556-0.0173010927062556
3900.153142538219492-0.153142538219492
4000.0780465130700821-0.0780465130700821
4100.066009123056486-0.066009123056486
4200.066009123056486-0.066009123056486
4300.175905232564779-0.175905232564779
4400.0908445198161321-0.0908445198161321
4500.175905232564779-0.175905232564779
4600.0908445198161321-0.0908445198161321
4700.106892552575036-0.106892552575036
4800.066009123056486-0.066009123056486
4900.0908445198161321-0.0908445198161321
5000.106892552575036-0.106892552575036
5100.0908445198161321-0.0908445198161321
5200.0173010927062556-0.0173010927062556
5300.0115180777575777-0.0115180777575777
5400.0908445198161321-0.0908445198161321
5500.175905232564779-0.175905232564779
5600.0908445198161321-0.0908445198161321
5710.1759052325647790.824094767435221
5800.0908445198161321-0.0908445198161321
5900.0908445198161321-0.0908445198161321
6000.066009123056486-0.066009123056486
6100.131170694811021-0.131170694811021
6200.0096343776786181-0.0096343776786181
6300.0203580654727409-0.0203580654727409
6400.0908445198161321-0.0908445198161321
6500.0908445198161321-0.0908445198161321
6600.0242870285101468-0.0242870285101468
6700.0115180777575777-0.0115180777575777
6800.175905232564779-0.175905232564779
6910.006833620800672470.993166379199327
7010.00963437767861810.990365622321382
7100.0908445198161321-0.0908445198161321
7200.0908445198161321-0.0908445198161321
7300.175905232564779-0.175905232564779
7400.066009123056486-0.066009123056486
7500.0908445198161321-0.0908445198161321
7600.0115180777575777-0.0115180777575777
7700.0115180777575777-0.0115180777575777
7800.0908445198161321-0.0908445198161321
7900.0908445198161321-0.0908445198161321
8000.0908445198161321-0.0908445198161321
8100.0096343776786181-0.0096343776786181
8200.066009123056486-0.066009123056486
8300.0144854810572694-0.0144854810572694
8400.066009123056486-0.066009123056486
8500.0908445198161321-0.0908445198161321
8600.0242870285101468-0.0242870285101468
8700.0144854810572694-0.0144854810572694
8810.01448548105726940.98551451894273
8900.0173010927062556-0.0173010927062556
9000.0908445198161321-0.0908445198161321
9100.0780465130700821-0.0780465130700821
9200.106892552575036-0.106892552575036
9300.0242870285101468-0.0242870285101468
9400.0908445198161321-0.0908445198161321
9500.131170694811021-0.131170694811021
9600.106892552575036-0.106892552575036
9700.0144854810572694-0.0144854810572694
9810.07804651307008210.921953486929918
9900.106892552575036-0.106892552575036
10000.153142538219492-0.153142538219492
10100.0780465130700821-0.0780465130700821
10200.131170694811021-0.131170694811021
10300.203614279014127-0.203614279014127
10400.0203580654727409-0.0203580654727409
10500.0908445198161321-0.0908445198161321
10600.0203580654727409-0.0203580654727409
10710.1759052325647790.824094767435221
10800.00817424056313886-0.00817424056313886
10910.01151807775757770.988481922242422
11000.0908445198161321-0.0908445198161321
11100.00683362080067247-0.00683362080067247
11200.203614279014127-0.203614279014127
11300.106892552575036-0.106892552575036
11400.106892552575036-0.106892552575036
11500.0144854810572694-0.0144854810572694
11600.106892552575036-0.106892552575036
11700.0096343776786181-0.0096343776786181
11800.153142538219492-0.153142538219492
11900.00817424056313886-0.00817424056313886
12000.0908445198161321-0.0908445198161321
12100.106892552575036-0.106892552575036
12200.00683362080067247-0.00683362080067247
12300.0908445198161321-0.0908445198161321
12400.066009123056486-0.066009123056486
12500.066009123056486-0.066009123056486
12600.0908445198161321-0.0908445198161321
12700.203614279014127-0.203614279014127
12800.0908445198161321-0.0908445198161321
12910.2036142790141270.796385720985873
13000.175905232564779-0.175905232564779


Type I & II errors for various threshold values
ThresholdType IType II
0.010.1818181818181820.907563025210084
0.020.3636363636363640.747899159663866
0.030.3636363636363640.680672268907563
0.040.3636363636363640.680672268907563
0.050.3636363636363640.680672268907563
0.060.3636363636363640.680672268907563
0.070.3636363636363640.554621848739496
0.080.5454545454545450.521008403361345
0.090.5454545454545450.521008403361345
0.10.5454545454545450.26890756302521
0.110.6363636363636360.142857142857143
0.120.6363636363636360.142857142857143
0.130.6363636363636360.142857142857143
0.140.7272727272727270.117647058823529
0.150.7272727272727270.117647058823529
0.160.7272727272727270.0840336134453782
0.170.7272727272727270.0840336134453782
0.180.9090909090909090.0252100840336134
0.190.9090909090909090.0252100840336134
0.20.9090909090909090.0252100840336134
0.2110
0.2210
0.2310
0.2410
0.2510
0.2610
0.2710
0.2810
0.2910
0.310
0.3110
0.3210
0.3310
0.3410
0.3510
0.3610
0.3710
0.3810
0.3910
0.410
0.4110
0.4210
0.4310
0.4410
0.4510
0.4610
0.4710
0.4810
0.4910
0.510
0.5110
0.5210
0.5310
0.5410
0.5510
0.5610
0.5710
0.5810
0.5910
0.610
0.6110
0.6210
0.6310
0.6410
0.6510
0.6610
0.6710
0.6810
0.6910
0.710
0.7110
0.7210
0.7310
0.7410
0.7510
0.7610
0.7710
0.7810
0.7910
0.810
0.8110
0.8210
0.8310
0.8410
0.8510
0.8610
0.8710
0.8810
0.8910
0.910
0.9110
0.9210
0.9310
0.9410
0.9510
0.9610
0.9710
0.9810
0.9910
 
Charts produced by software:
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Oct/10/t1223630382q08n7j4h2tlnswy/17y811223630062.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Oct/10/t1223630382q08n7j4h2tlnswy/17y811223630062.ps (open in new window)


http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Oct/10/t1223630382q08n7j4h2tlnswy/225sr1223630062.png (open in new window)
http://127.0.0.1/wessadotnet/public_html/freestatisticsdotorg/blog/date/2008/Oct/10/t1223630382q08n7j4h2tlnswy/225sr1223630062.ps (open in new window)


 
Parameters (Session):
 
Parameters (R input):
 
R code (references can be found in the software module):
library(brglm)
roc.plot <- function (sd, sdc, newplot = TRUE, ...)
{
sall <- sort(c(sd, sdc))
sens <- 0
specc <- 0
for (i in length(sall):1) {
sens <- c(sens, mean(sd >= sall[i], na.rm = T))
specc <- c(specc, mean(sdc >= sall[i], na.rm = T))
}
if (newplot) {
plot(specc, sens, xlim = c(0, 1), ylim = c(0, 1), type = 'l',
xlab = '1-specificity', ylab = 'sensitivity', main = 'ROC plot', ...)
abline(0, 1)
}
else lines(specc, sens, ...)
npoints <- length(sens)
area <- sum(0.5 * (sens[-1] + sens[-npoints]) * (specc[-1] -
specc[-npoints]))
lift <- (sens - specc)[-1]
cutoff <- sall[lift == max(lift)][1]
sensopt <- sens[-1][lift == max(lift)][1]
specopt <- 1 - specc[-1][lift == max(lift)][1]
list(area = area, cutoff = cutoff, sensopt = sensopt, specopt = specopt)
}
roc.analysis <- function (object, newdata = NULL, newplot = TRUE, ...)
{
if (is.null(newdata)) {
sd <- object$fitted[object$y == 1]
sdc <- object$fitted[object$y == 0]
}
else {
sd <- predict(object, newdata, type = 'response')[newdata$y ==
1]
sdc <- predict(object, newdata, type = 'response')[newdata$y ==
0]
}
roc.plot(sd, sdc, newplot, ...)
}
hosmerlem <- function (y, yhat, g = 10)
{
cutyhat <- cut(yhat, breaks = quantile(yhat, probs = seq(0,
1, 1/g)), include.lowest = T)
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)
c('X^2' = chisq, Df = g - 2, 'P(>Chi)' = P)
}
x <- as.data.frame(t(y))
r <- brglm(x)
summary(r)
rc <- summary(r)$coeff
try(hm <- hosmerlem(y[1,],r$fitted.values),silent=T)
try(hm,silent=T)
bitmap(file='test0.png')
ra <- roc.analysis(r)
dev.off()
te <- array(0,dim=c(2,99))
for (i in 1:99) {
threshold <- i / 100
numcorr1 <- 0
numfaul1 <- 0
numcorr0 <- 0
numfaul0 <- 0
for (j in 1:length(r$fitted.values)) {
if (y[1,j] > 0.99) {
if (r$fitted.values[j] >= threshold) numcorr1 = numcorr1 + 1 else numfaul1 = numfaul1 + 1
} else {
if (r$fitted.values[j] < threshold) numcorr0 = numcorr0 + 1 else numfaul0 = numfaul0 + 1
}
}
te[1,i] <- numfaul1 / (numfaul1 + numcorr1)
te[2,i] <- numfaul0 / (numfaul0 + numcorr0)
}
bitmap(file='test1.png')
op <- par(mfrow=c(2,2))
plot((1:99)/100,te[1,],xlab='Threshold',ylab='Type I error', main='1 - Specificity')
plot((1:99)/100,te[2,],xlab='Threshold',ylab='Type II error', main='1 - Sensitivity')
plot(te[1,],te[2,],xlab='Type I error',ylab='Type II error', main='(1-Sens.) vs (1-Spec.)')
plot((1:99)/100,te[1,]+te[2,],xlab='Threshold',ylab='Sum of Type I & II error', main='(1-Sens.) + (1-Spec.)')
par(op)
dev.off()
load(file='createtable')
a<-table.start()
a<-table.row.start(a)
a<-table.element(a,'Coefficients of Bias-Reduced Logistic Regression',5,TRUE)
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'Variable',header=TRUE)
a<-table.element(a,'Parameter',header=TRUE)
a<-table.element(a,'S.E.',header=TRUE)
a<-table.element(a,'t-stat',header=TRUE)
a<-table.element(a,'2-sided p-value',header=TRUE)
a<-table.row.end(a)
for (i in 1:length(rc[,1])) {
a<-table.row.start(a)
a<-table.element(a,labels(rc)[[1]][i],header=TRUE)
a<-table.element(a,rc[i,1])
a<-table.element(a,rc[i,2])
a<-table.element(a,rc[i,3])
a<-table.element(a,2*(1-pt(abs(rc[i,3]),r$df.residual)))
a<-table.row.end(a)
}
a<-table.end(a)
table.save(a,file='mytable.tab')
a<-table.start()
a<-table.row.start(a)
a<-table.element(a,'Summary of Bias-Reduced Logistic Regression',2,TRUE)
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'Deviance',1,TRUE)
a<-table.element(a,r$deviance)
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'Penalized deviance',1,TRUE)
a<-table.element(a,r$penalized.deviance)
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'Residual Degrees of Freedom',1,TRUE)
a<-table.element(a,r$df.residual)
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'ROC Area',1,TRUE)
a<-table.element(a,ra$area)
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'Hosmer–Lemeshow test',2,TRUE)
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'Chi-square',1,TRUE)
phm <- array('NA',dim=3)
for (i in 1:3) { try(phm[i] <- hm[i],silent=T) }
a<-table.element(a,phm[1])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'Degrees of Freedom',1,TRUE)
a<-table.element(a,phm[2])
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'P(>Chi)',1,TRUE)
a<-table.element(a,phm[3])
a<-table.row.end(a)
a<-table.end(a)
table.save(a,file='mytable1.tab')
a<-table.start()
a<-table.row.start(a)
a<-table.element(a,'Fit of Logistic Regression',4,TRUE)
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'Index',1,TRUE)
a<-table.element(a,'Actual',1,TRUE)
a<-table.element(a,'Fitted',1,TRUE)
a<-table.element(a,'Error',1,TRUE)
a<-table.row.end(a)
for (i in 1:length(r$fitted.values)) {
a<-table.row.start(a)
a<-table.element(a,i,1,TRUE)
a<-table.element(a,y[1,i])
a<-table.element(a,r$fitted.values[i])
a<-table.element(a,y[1,i]-r$fitted.values[i])
a<-table.row.end(a)
}
a<-table.end(a)
table.save(a,file='mytable2.tab')
a<-table.start()
a<-table.row.start(a)
a<-table.element(a,'Type I & II errors for various threshold values',3,TRUE)
a<-table.row.end(a)
a<-table.row.start(a)
a<-table.element(a,'Threshold',1,TRUE)
a<-table.element(a,'Type I',1,TRUE)
a<-table.element(a,'Type II',1,TRUE)
a<-table.row.end(a)
for (i in 1:99) {
a<-table.row.start(a)
a<-table.element(a,i/100,1,TRUE)
a<-table.element(a,te[1,i])
a<-table.element(a,te[2,i])
a<-table.row.end(a)
}
a<-table.end(a)
table.save(a,file='mytable3.tab')
 





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