Running examples in 'aplore3-Ex.R' failed
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> ### Name: glow500
> ### Title: GLOW500 data
> ### Aliases: glow500
> ### Keywords: datasets
> 
> ### ** Examples
> 
> head(glow500, n = 10)
   sub_id site_id phy_id priorfrac age weight height      bmi premeno momfrac
1       1       1     14        No  62   70.3    158 28.16055      No      No
2       2       4    284        No  65   87.1    160 34.02344      No      No
3       3       6    305       Yes  88   50.8    157 20.60936      No     Yes
4       4       6    309        No  82   62.1    160 24.25781      No      No
5       5       1     37        No  61   68.0    152 29.43213      No      No
6       6       5    299       Yes  67   68.0    161 26.23356      No      No
7       7       5    302        No  84   50.8    150 22.57778      No      No
8       8       1     36       Yes  82   40.8    153 17.42919      No      No
9       9       1      8       Yes  86   62.6    156 25.72321      No      No
10     10       4    282        No  58   63.5    166 23.04398      No      No
   armassist smoke raterisk fracscore fracture
1         No    No     Same         1       No
2         No    No     Same         2       No
3        Yes    No     Less        11       No
4         No    No     Less         5       No
5         No    No     Same         1       No
6         No   Yes     Same         4       No
7         No    No     Less         6       No
8         No    No     Same         7       No
9         No    No     Same         7       No
10        No    No     Less         0       No
> summary(glow500)
     sub_id         site_id          phy_id       priorfrac      age       
 Min.   :  1.0   Min.   :1.000   Min.   :  1.00   No :374   Min.   :55.00  
 1st Qu.:125.8   1st Qu.:2.000   1st Qu.: 57.75   Yes:126   1st Qu.:61.00  
 Median :250.5   Median :3.000   Median :182.50             Median :67.00  
 Mean   :250.5   Mean   :3.436   Mean   :178.55             Mean   :68.56  
 3rd Qu.:375.2   3rd Qu.:5.000   3rd Qu.:298.00             3rd Qu.:76.00  
 Max.   :500.0   Max.   :6.000   Max.   :325.00             Max.   :90.00  
     weight           height           bmi        premeno   momfrac   armassist
 Min.   : 39.90   Min.   :134.0   Min.   :14.88   No :403   No :435   No :312  
 1st Qu.: 59.90   1st Qu.:157.0   1st Qu.:23.27   Yes: 97   Yes: 65   Yes:188  
 Median : 68.00   Median :161.5   Median :26.42                                
 Mean   : 71.82   Mean   :161.4   Mean   :27.55                                
 3rd Qu.: 81.30   3rd Qu.:165.0   3rd Qu.:30.79                                
 Max.   :127.00   Max.   :199.0   Max.   :49.08                                
 smoke        raterisk     fracscore      fracture 
 No :465   Less   :167   Min.   : 0.000   No :375  
 Yes: 35   Same   :186   1st Qu.: 2.000   Yes:125  
           Greater:147   Median : 3.000            
                         Mean   : 3.698            
                         3rd Qu.: 5.000            
                         Max.   :11.000            
> 
> ## Table 2.2 p. 39
> summary(mod2.2 <- glm(fracture ~ age + weight + priorfrac +
+                                  premeno + raterisk,
+                       family = binomial,
+                       data = glow500))

Call:
glm(formula = fracture ~ age + weight + priorfrac + premeno + 
    raterisk, family = binomial, data = glow500)

Deviance Residuals: 
     Min        1Q    Median        3Q       Max  
-1.42250  -0.74873  -0.59711  -0.06046   2.28830  

Coefficients:
                 Estimate Std. Error z value Pr(>|z|)    
(Intercept)     -5.605794   1.220668  -4.592 4.38e-06 ***
age              0.050142   0.013417   3.737 0.000186 ***
weight           0.004080   0.006926   0.589 0.555803    
priorfracYes     0.679457   0.242384   2.803 0.005059 ** 
premenoYes       0.186958   0.276710   0.676 0.499266    
rateriskSame     0.534493   0.275858   1.938 0.052676 .  
rateriskGreater  0.874123   0.289157   3.023 0.002503 ** 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 562.34  on 499  degrees of freedom
Residual deviance: 518.08  on 493  degrees of freedom
AIC: 532.08

Number of Fisher Scoring iterations: 4

> 
> ## Table 2.3 p. 40
> summary(mod2.3 <- update(mod2.2, . ~ . - weight - premeno))

Call:
glm(formula = fracture ~ age + priorfrac + raterisk, family = binomial, 
    data = glow500)

Deviance Residuals: 
     Min        1Q    Median        3Q       Max  
-1.42693  -0.73132  -0.60772  -0.07484   2.23819  

Coefficients:
                Estimate Std. Error z value Pr(>|z|)    
(Intercept)     -4.99060    0.90270  -5.529 3.23e-08 ***
age              0.04591    0.01244   3.690 0.000224 ***
priorfracYes     0.70023    0.24116   2.904 0.003689 ** 
rateriskSame     0.54856    0.27501   1.995 0.046075 *  
rateriskGreater  0.86576    0.28621   3.025 0.002487 ** 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 562.34  on 499  degrees of freedom
Residual deviance: 518.90  on 495  degrees of freedom
AIC: 528.9

Number of Fisher Scoring iterations: 4

> 
> ## Table 2.4 p. 44
> vcov(mod2.3)
                (Intercept)           age  priorfracYes  rateriskSame
(Intercept)      0.81486728 -0.0108886686  0.0445010519 -0.0603876325
age             -0.01088867  0.0001547891 -0.0008344776  0.0002239259
priorfracYes     0.04450105 -0.0008344776  0.0581588491 -0.0031271822
rateriskSame    -0.06038763  0.0002239259 -0.0031271822  0.0756289050
rateriskGreater -0.08055123  0.0005370070 -0.0118441110  0.0462406814
                rateriskGreater
(Intercept)        -0.080551235
age                 0.000537007
priorfracYes       -0.011844111
rateriskSame        0.046240681
rateriskGreater     0.081913370
> 
> ## Table 3.6 p. 58
> contrasts(glow500$raterisk)
        Same Greater
Less       0       0
Same       1       0
Greater    0       1
> 
> ## Contrasts: Table 3.8 and 3.9 p. 60
> contrasts(glow500$raterisk) <- matrix(c(-1,-1,1,0,0,1), byrow= TRUE, ncol = 2)
> summary(mod3.9 <- glm(fracture ~ raterisk, family = binomial,
+                       data = glow500))

Call:
glm(formula = fracture ~ raterisk, family = binomial, data = glow500)

Deviance Residuals: 
    Min       1Q   Median       3Q      Max  
-0.9005  -0.7726  -0.6058  -0.0838   1.8899  

Coefficients:
            Estimate Std. Error z value Pr(>|z|)    
(Intercept)  -1.1172     0.1062 -10.514  < 2e-16 ***
raterisk1     0.0611     0.1437   0.425  0.67067    
raterisk2     0.4240     0.1466   2.892  0.00383 ** 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

(Dispersion parameter for binomial family taken to be 1)

    Null deviance: 562.34  on 499  degrees of freedom
Residual deviance: 550.58  on 497  degrees of freedom
AIC: 556.58

Number of Fisher Scoring iterations: 4

> # cleaning modified dataset ...
> rm(glow500)
> 
> ## Table 5.1 pg 160 - Hosmer-Lemeshow test (with vcdExtra package)
> mod4.16 <- glm(fracture ~ age * priorfrac + height + momfrac * armassist +
+                           I(as.integer(raterisk) == 3) ,
+                family = binomial,
+                data = glow500)
> library(vcdExtra)
Error in library(vcdExtra) : there is no package called 'vcdExtra'
Execution halted