* using log directory 'd:/Rcompile/CRANpkg/local/2.13/ISwR.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* checking for file 'ISwR/DESCRIPTION' ... OK
* this is package 'ISwR' version '2.0-5'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'ISwR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: MASS
* checking tests ... OK
  Running 'allexercises.R'
  Comparing 'allexercises.Rout' to 'allexercises.Rout.save' ...1,2d0
< 
< 
214c212
< W = 0.9687, p-value = 1.376e-06
---
> W = 0.9687, p-value = 1.377e-06
279,280c277
<        1 
< 1305.394 
---
> [1] 1305.394
322c319
<  0.8158420 0.9124999 
---
>  0.815842 0.912500 
396c393
<  -3.22070952 -0.08811401 
---
>  -3.220710 -0.088114 
724c721
<  60-64:4   Hist.ctr.    :6   Median :104.0   Median : 169261                 
---
>  60-64:4   Hist.ctr.    :6   Median :104.0   Median : 169260                 
806c803
< -0.35074 -0.06741 -0.00792  0.05750  0.36360 
---
> -0.350742 -0.067409 -0.007916  0.057502  0.363595 
827c824
< -0.58560 -0.06609  0.00184  0.07479  0.48435 
---
> -0.585598 -0.066089  0.001837  0.074794  0.484352 
872,875c869,872
< <none>              1.0087 -102.626
< age     1   0.03210 1.0408 -103.623
< sex     1   0.03978 1.0485 -103.388
< height  1   0.66546 1.6742  -88.413
---
> <none>                 1.009 -102.626
> age     1     0.032    1.041 -103.623
> sex     1     0.040    1.049 -103.388
> height  1     0.665    1.674  -88.413
882,884c879,881
< <none>              1.0408 -103.623
< sex     1   0.05132 1.0921 -104.083
< height  1   0.71317 1.7540  -88.923
---
> <none>                 1.041 -103.623
> sex     1     0.051    1.092 -104.083
> height  1     0.713    1.754  -88.923
899c896
< -4.936 -1.184  0.113  1.036  4.021 
---
> -4.9357 -1.1839  0.1130  1.0356  4.0212 
919,922c916,919
< age        1  16.386 16.3861  3.7610 0.06132 .
< weight     1   2.454  2.4536  0.5632 0.45848  
< height     1   0.004  0.0036  0.0008 0.97715  
< Residuals 32 139.419  4.3568                  
---
> age        1  16.386  16.386  3.7610 0.06132 .
> weight     1   2.454   2.454  0.5632 0.45848  
> height     1   0.004   0.004  0.0008 0.97715  
> Residuals 32 139.419   4.357                  
947c944
< F-statistic: 10.58 on 5 and 44 DF,  p-value: 1.03e-06 
---
> F-statistic: 10.58 on 5 and 44 DF,  p-value: 1.030e-06 
956c953
< -1.77312 -0.81196 -0.00683  0.76988  2.52240 
---
> -1.773120 -0.811962 -0.006831  0.769878  2.522399 
1034,1037c1031,1034
< <none>              19679 241.49                  
< id     15     51138 70816 252.47  2.4254 0.05287 .
< period  1      1505 21184 241.85  1.0709 0.31830  
< treat   1     11603 31282 254.32  8.2550 0.01228 *
---
> <none>              19679   241                  
> id     15     51137 70816   252  2.4254 0.05287 .
> period  1      1505 21184   242  1.0709 0.31830  
> treat   1     11603 31282   254  8.2550 0.01228 *
1045,1048c1042,1045
< id        15  51138  3409.2  2.4254 0.05287 .
< period     1   4608  4608.0  3.2783 0.09171 .
< treat      1  11603 11603.3  8.2550 0.01228 *
< Residuals 14  19679  1405.6                  
---
> id        15  51137    3409  2.4254 0.05287 .
> period     1   4608    4608  3.2783 0.09171 .
> treat      1  11603   11603  8.2550 0.01228 *
> Residuals 14  19679    1406                  
1109c1106
< -1.72917 -0.22917 -0.08333  0.23438  2.41667 
---
> -1.72917 -0.22917 -0.08333  0.23437  2.41667 
1327c1324
< -0.21260 -0.09068 -0.00472  0.05675  0.43846 
---
> -0.212600 -0.090681 -0.004724  0.056747  0.438465 
1348c1345
< -0.21455 -0.09020 -0.00741  0.05710  0.42968 
---
> -0.214554 -0.090200 -0.007412  0.057104  0.429685 
1400c1397
< age:group  2    2.4995 30.035 -78.391  3.5402 0.03376 *
---
> age:group  2     2.499  30.035 -78.391  3.5402 0.03376 *
1438c1435
< -6.2532 -1.3766 -0.0526  1.1144  6.1815 
---
> -6.25316 -1.37661 -0.05263  1.11439  6.18149 
1460c1457
< -7.832 -1.586 -0.085  1.337 11.111 
---
> -7.83186 -1.58612 -0.08498  1.33699 11.11087 
1483c1480
< -7.7224 -1.5711 -0.0889  1.3310 11.1234 
---
> -7.72243 -1.57106 -0.08887  1.33098 11.12336 
1504c1501
< - mat.weight  1    0.0793 50.919 10.911
---
> - mat.weight  1     0.079 50.919 10.911
1506,1509c1503,1506
< - sex         1    2.9492 53.789 13.652
< - ml.suppl    1    3.7408 54.580 14.383
< - mat.height  1    6.6318 57.471 16.963
< - weight      1   20.2269 71.067 27.580
---
> - sex         1     2.949 53.789 13.652
> - ml.suppl    1     3.741 54.580 14.383
> - mat.height  1     6.632 57.471 16.963
> - weight      1    20.227 71.067 27.580
1516,1519c1513,1516
< - sex         1    2.9023 53.821 11.682
< - ml.suppl    1    4.2735 55.193 12.940
< - mat.height  1   10.0999 61.019 17.958
< - weight      1   22.6741 73.593 27.326
---
> - sex         1     2.902 53.821 11.682
> - ml.suppl    1     4.274 55.193 12.940
> - mat.height  1    10.100 61.019 17.958
> - weight      1    22.674 73.593 27.326
1527c1524
< -1.77312 -0.81196 -0.00683  0.76988  2.52240 
---
> -1.773120 -0.811962 -0.006831  0.769878  2.522399 
1640c1637
< -2.00075  -0.36457  -0.09559   0.57964   1.68281  
---
> -2.0007  -0.3646  -0.0956   0.5796   1.6828  
1669c1666
< -1.9886  -0.4001  -0.2386   0.5503   1.8189  
---
> -1.9885  -0.4001  -0.2386   0.5503   1.8189  
1698,1702c1695,1699
< rcpage      1   26.291 38.291 0.0382 0.84495  
< donage      1   28.082 40.082 1.8292 0.17622  
< type        2   28.959 38.959 2.7064 0.25841  
< preg        1   28.447 40.447 2.1947 0.13849  
< log(index)  1   32.343 44.343 6.0904 0.01359 *
---
> rcpage      1   26.291 38.291  0.038 0.84495  
> donage      1   28.082 40.082  1.829 0.17622  
> type        2   28.959 38.959  2.706 0.25841  
> preg        1   28.447 40.447  2.195 0.13849  
> log(index)  1   32.343 44.343  6.090 0.01359 *
1712,1715c1709,1712
< donage      1   28.832 38.832 2.5411 0.11092  
< type        2   29.403 37.403 3.1126 0.21092  
< preg        1   28.812 38.812 2.5218 0.11228  
< log(index)  1   32.630 42.630 6.3397 0.01181 *
---
> donage      1   28.832 38.832  2.541 0.11092  
> type        2   29.403 37.403  3.113 0.21092  
> preg        1   28.812 38.812  2.522 0.11228  
> log(index)  1   32.630 42.630  6.340 0.01181 *
1725,1727c1722,1724
< donage      1   33.654 39.654  4.2506 0.0392375 *  
< preg        1   31.068 37.068  1.6653 0.1968922    
< log(index)  1   41.723 47.723 12.3198 0.0004482 ***
---
> donage      1   33.654 39.654  4.251 0.0392375 *  
> preg        1   31.068 37.068  1.665 0.1968922    
> log(index)  1   41.723 47.723 12.320 0.0004482 ***
1769,1771c1766,1768
< (Intercept) -10.38849705 -1.9550010
< donage        0.03262764  0.2946854
< log(index)    0.89146245  4.0706703
---
> (Intercept) -10.38957922 -1.9553765
> donage        0.03262422  0.2946919
> log(index)    0.89230108  4.0712645
1802,1805c1799,1800
< age   2  134.857         3      2.054    <2e-16 ***
< type  1    1.273         2      0.780    0.2591    
< ---
< Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 
---
> age   2  134.857         3      2.054 5.202e-30
> type  1    1.273         2      0.780     0.259
1812c1807,1808
< glm.fit: fitted probabilities numerically 0 or 1 occurred 
---
> In glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart,  :
>   fitted probabilities numerically 0 or 1 occurred
1816c1812,1813
< glm.fit: fitted probabilities numerically 0 or 1 occurred 
---
> In glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart,  :
>   fitted probabilities numerically 0 or 1 occurred
1825c1822
< -2.59247  -0.04329   0.00000   0.00063   2.60152  
---
> -2.592e+00  -4.329e-02   2.107e-08   6.283e-04   2.602e+00  
1840c1837
< AIC: 199.8
---
> AIC: 199.80
1852c1849
< -2.5641  -0.0247   0.0000   0.0000   2.5668  
---
> -2.564e+00  -2.470e-02   2.107e-08   4.325e-07   2.567e+00  
1882c1879,1880
< The following object(s) are masked from 'package:ISwR':
---
> 
> 	The following object(s) are masked from package:ISwR :
1901,1906c1899,1901
<   n= 37, number of events= 18 
< 
<        coef exp(coef) se(coef)     z Pr(>|z|)  
< gvhd 1.2419    3.4620   0.5144 2.414   0.0158 *
< ---
< Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 
---
>   n= 37 
>      coef exp(coef) se(coef)    z     p
> gvhd 1.24      3.46    0.514 2.41 0.016
1909c1904
< gvhd     3.462     0.2888     1.263     9.489
---
> gvhd      3.46      0.289      1.26      9.49
1911d1905
< Concordance= 0.671  (se = 0.061 )
1913,1915c1907,1909
< Likelihood ratio test= 6.19  on 1 df,   p=0.01286
< Wald test            = 5.83  on 1 df,   p=0.01577
< Score (logrank) test = 6.55  on 1 df,   p=0.01046
---
> Likelihood ratio test= 6.19  on 1 df,   p=0.0129
> Wald test            = 5.83  on 1 df,   p=0.0158
> Score (logrank) test = 6.55  on 1 df,   p=0.0105
1923,1932c1917,1923
<   n= 37, number of events= 18 
< 
<                coef exp(coef) se(coef)      z Pr(>|z|)  
< gvhd        1.29074   3.63548  0.69131  1.867   0.0619 .
< log(index) -0.49623   0.60882  0.35579 -1.395   0.1631  
< donage      0.03440   1.03500  0.04000  0.860   0.3899  
< rcpage     -0.01230   0.98778  0.04085 -0.301   0.7634  
< preg        1.13641   3.11555  0.57058  1.992   0.0464 *
< ---
< Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 
---
>   n= 37 
>               coef exp(coef) se(coef)      z     p
> gvhd        1.2907     3.635   0.6913  1.867 0.062
> log(index) -0.4962     0.609   0.3558 -1.395 0.160
> donage      0.0344     1.035   0.0400  0.860 0.390
> rcpage     -0.0123     0.988   0.0408 -0.301 0.760
> preg        1.1364     3.116   0.5706  1.992 0.046
1935,1939c1926,1930
< gvhd          3.6355     0.2751    0.9378    14.093
< log(index)    0.6088     1.6425    0.3031     1.223
< donage        1.0350     0.9662    0.9569     1.119
< rcpage        0.9878     1.0124    0.9118     1.070
< preg          3.1155     0.3210    1.0183     9.533
---
> gvhd           3.635      0.275     0.938     14.09
> log(index)     0.609      1.643     0.303      1.22
> donage         1.035      0.966     0.957      1.12
> rcpage         0.988      1.012     0.912      1.07
> preg           3.116      0.321     1.018      9.53
1941d1931
< Concordance= 0.748  (se = 0.074 )
1943,1945c1933,1935
< Likelihood ratio test= 14.33  on 5 df,   p=0.01367
< Wald test            = 14.86  on 5 df,   p=0.01097
< Score (logrank) test = 17.48  on 5 df,   p=0.003679
---
> Likelihood ratio test= 14.3  on 5 df,   p=0.0137
> Wald test            = 14.9  on 5 df,   p=0.0110
> Score (logrank) test = 17.5  on 5 df,   p=0.00368
1957,1963c1947,1950
<   n= 829, number of events= 485 
< 
<             coef exp(coef) se(coef)      z Pr(>|z|)    
< age     0.049289  1.050524 0.004374 11.268   <2e-16 ***
< sexMale 0.022332  1.022584 0.100717  0.222    0.825    
< ---
< Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 
---
>   n= 829 
>           coef exp(coef) se(coef)      z    p
> age     0.0493      1.05  0.00437 11.268 0.00
> sexMale 0.0223      1.02  0.10072  0.222 0.82
1966,1967c1953,1954
< age         1.051     0.9519    1.0416     1.060
< sexMale     1.023     0.9779    0.8394     1.246
---
> age          1.05      0.952      1.04      1.06
> sexMale      1.02      0.978      0.84      1.25
1969d1955
< Concordance= 0.66  (se = 0.014 )
1971,1973c1957,1959
< Likelihood ratio test= 158.6  on 2 df,   p=0
< Wald test            = 137.7  on 2 df,   p=0
< Score (logrank) test = 136.3  on 2 df,   p=0
---
> Likelihood ratio test= 159  on 2 df,   p=0
> Wald test            = 138  on 2 df,   p=0
> Score (logrank) test = 136  on 2 df,   p=0
1979,1984c1965,1967
<   n= 829, number of events= 485 
< 
<             coef exp(coef) se(coef)      z Pr(>|z|)    
< sexMale -0.36571   0.69371  0.09615 -3.803 0.000143 ***
< ---
< Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 
---
>   n= 829 
>           coef exp(coef) se(coef)    z       p
> sexMale -0.366     0.694   0.0962 -3.8 0.00014
1987c1970
< sexMale    0.6937      1.442    0.5746    0.8376
---
> sexMale     0.694       1.44     0.575     0.838
1989d1971
< Concordance= 0.547  (se = 0.012 )
1991,1993c1973,1975
< Likelihood ratio test= 14.97  on 1 df,   p=0.0001091
< Wald test            = 14.47  on 1 df,   p=0.0001428
< Score (logrank) test = 14.63  on 1 df,   p=0.0001311
---
> Likelihood ratio test= 15.0  on 1 df,   p=0.000109
> Wald test            = 14.5  on 1 df,   p=0.000143
> Score (logrank) test = 14.6  on 1 df,   p=0.000131
2009,2015c1991,1994
<   n= 2441, number of events= 485 
< 
<             coef exp(coef) se(coef)      z Pr(>|z|)    
< age     0.049289  1.050524 0.004374 11.268   <2e-16 ***
< sexMale 0.022332  1.022584 0.100717  0.222    0.825    
< ---
< Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 
---
>   n= 2441 
>           coef exp(coef) se(coef)      z    p
> age     0.0493      1.05  0.00437 11.268 0.00
> sexMale 0.0223      1.02  0.10072  0.222 0.82
2018,2019c1997,1998
< age         1.051     0.9519    1.0416     1.060
< sexMale     1.023     0.9779    0.8394     1.246
---
> age          1.05      0.952      1.04      1.06
> sexMale      1.02      0.978      0.84      1.25
2021d1999
< Concordance= 0.66  (se = 0.014 )
2023,2025c2001,2003
< Likelihood ratio test= 158.6  on 2 df,   p=0
< Wald test            = 137.7  on 2 df,   p=0
< Score (logrank) test = 136.3  on 2 df,   p=0
---
> Likelihood ratio test= 159  on 2 df,   p=0
> Wald test            = 138  on 2 df,   p=0
> Score (logrank) test = 136  on 2 df,   p=0
2078c2056
< AIC: 202.4
---
> AIC: 202.40
2088,2091c2066,2069
< <none>            5.458 202.41                     
< age:period   5   34.792 221.74 29.334 1.994e-05 ***
< age:area     5   17.279 204.23 11.822 0.0373179 *  
< period:area  1   16.775 211.72 11.317 0.0007678 ***
---
> <none>            5.458 202.405                      
> age:period   5   34.792 221.739  29.334 1.994e-05 ***
> age:area     5   17.279 204.226  11.821 0.0373179 *  
> period:area  1   16.775 211.722  11.317 0.0007678 ***
2097c2075
< -0.4663402 -0.1213920 
---
> -0.4663390 -0.1213948 
2164c2142
< alpha 180.77132    1.93393  93.473  < 2e-16 ***
---
> alpha 180.77125    1.93392  93.474  < 2e-16 ***
2167c2145
< da     62.03690   11.26006   5.509 4.46e-08 ***
---
> da     62.03692   11.26005   5.509 4.46e-08 ***
2176c2154
< Achieved convergence tolerance: 1.811e-06 
---
> Achieved convergence tolerance: 1.937e-06 
2186c2164
< 2   1124      47896  3  11580  90.581 < 2.2e-16 ***
---
> 2   1124      47896    3  11579  90.581 < 2.2e-16 ***
2212,2217c2190,2193
< ymax 15.16409523 41.0317406
< ec50  0.03655499  1.3770101
< la   -0.72605274  0.6841776
< > # p <- profile(fit, alphamax=.2)
< > # alphamax semantics got changed in R 2.8
< > p <- profile(fit)
---
> ymax 15.1835221 41.0321436
> ec50         NA  1.3797919
> la   -0.7268405  0.6848855
> > p <- profile(fit, alphamax=.2)
2222,2224c2198,2200
< ymax 15.16043812 41.031201
< ec50  0.05332677  1.377884
< la   -0.72610588  0.684268
---
> ymax 15.15339690 41.0308087
> ec50  0.02711647  1.3766294
> la   -0.72603028  0.6842553
2237c2213
< la   -0.02688    0.42805  -0.063  0.95196   
---
> la   -0.02689    0.42805  -0.063  0.95196   
2257c2233
< la   -0.02689    0.42805  -0.063  0.95196   
---
> la   -0.02689    0.42805  -0.063  0.95195   
  Running 'allscripts.R'
  Comparing 'allscripts.Rout' to 'allscripts.Rout.save' ...1,2d0
< 
< 
486c484
< [1] 158
---
> [1] 138
518c516
< [1] "d:/RCompile/CRANpkg/lib/2.13/ISwR/rawdata/thuesen.txt"
---
> [1] "/home/pd/Rlibrary/ISwR/rawdata/thuesen.txt"
615,621c613,619
<  Min.   : 25.0   Min.   :  1.00   Min.   :  1.000  
<  1st Qu.:202.2   1st Qu.:  1.00   1st Qu.:  1.000  
<  Median :313.5   Median :  2.00   Median :  3.000  
<  Mean   :340.2   Mean   :  2.64   Mean   :  7.896  
<  3rd Qu.:462.8   3rd Qu.:  5.00   3rd Qu.: 15.000  
<  Max.   :915.0   Max.   :  5.00   Max.   : 30.000  
<  NA's   :321.0   NA's   :240.00   NA's   :859.000  
---
>  Min.   : 25.0   Min.   :  1.000   Min.   :  1.000  
>  1st Qu.:202.2   1st Qu.:  1.000   1st Qu.:  1.000  
>  Median :313.5   Median :  2.000   Median :  3.000  
>  Mean   :340.2   Mean   :  2.640   Mean   :  7.896  
>  3rd Qu.:462.8   3rd Qu.:  5.000   3rd Qu.: 15.000  
>  Max.   :915.0   Max.   :  5.000   Max.   : 30.000  
>  NA's   :321.0   NA's   :240.000   NA's   :859.000  
1260c1258,1259
< [1] NA
---
> Error in cor(blood.glucose, short.velocity) : 
>   missing observations in cov/cor
1325,1326c1324,1325
< ventilation  2  15516  7757.9  3.7113 0.04359 *
< Residuals   19  39716  2090.3                  
---
> ventilation  2  15516    7758  3.7113 0.04359 *
> Residuals   19  39716    2090                  
1366c1365
< (Intercept)            316.63      16.16  19.588 4.65e-14 ***
---
> (Intercept)            316.62      16.16  19.588 4.65e-14 ***
1368c1367
< ventilationO2,24h      -38.63      26.06  -1.482   0.1548    
---
> ventilationO2,24h      -38.62      26.06  -1.482   0.1548    
1494,1496c1493,1495
< subj       8 8966.6 1120.82 90.6391 4.863e-16 ***
< time       3  151.0   50.32  4.0696   0.01802 *  
< Residuals 24  296.8   12.37                      
---
> subj       8 8966.6  1120.8 90.6391 4.863e-16 ***
> time       3  151.0    50.3  4.0696   0.01802 *  
> Residuals 24  296.8    12.4                      
1516,1517c1515,1516
< blood.glucose  1 0.20727 0.207269   4.414 0.0479 *
< Residuals     21 0.98610 0.046957                 
---
> blood.glucose  1 0.20727 0.20727   4.414 0.0479 *
> Residuals     21 0.98610 0.04696                 
1732c1731
<               n = 137.604
---
>               n = 137.6040
1821,1822c1820,1821
<   Length    Class     Mode 
<      829 difftime  numeric 
---
>    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NA's 
>     0.0     8.0    28.0   225.7   268.5  1836.0   338.0 
2125c2124,2125
< The following object(s) are masked from 'package:ISwR':
---
> 
> 	The following object(s) are masked from package:ISwR :
2127a2128
> 
2232c2233
< -38.072 -10.067   0.113  13.526  36.990 
---
> -38.0718 -10.0665   0.1132  13.5259  36.9902 
2286c2287
< -43.238  -7.403  -0.081  15.534  36.028 
---
> -43.23832  -7.40344  -0.08133  15.53412  36.02770 
2371c2372
< F-statistic: 7.041 on 3 and 21 DF,  p-value: 0.00187 
---
> F-statistic: 7.041 on 3 and 21 DF,  p-value: 0.001870 
2401c2402
< -44.30 -22.69   2.23  15.91  48.41 
---
> -44.305 -22.691   2.230  15.908  48.408 
2496c2497,2498
< The following object(s) are masked from 'package:ISwR':
---
> 
> 	The following object(s) are masked from package:ISwR :
2498a2501
> 
2612,2613c2615,2616
< x          1  8.945  8.9450  142.87 5.376e-10 ***
< Residuals 18  1.127  0.0626                      
---
> x          1 8.9450  8.9450  142.87 5.376e-10 ***
> Residuals 18 1.1270  0.0626                      
2750,2752d2752
< Warning message:
< In anova.lm(lm(tryp.mean ~ gr + factor(gr), weights = n)) :
<   ANOVA F-tests on an essentially perfect fit are unreliable
2896c2896
< -0.021919 -0.004977  0.000056  0.005597  0.016625 
---
> -2.192e-02 -4.977e-03  5.598e-05  5.597e-03  1.663e-02 
2916c2916
< -0.026722 -0.004888  0.000056  0.003767  0.017608 
---
> -2.672e-02 -4.888e-03  5.598e-05  3.767e-03  1.761e-02 
2938c2938
< -0.025243 -0.005733 -0.000195  0.004894  0.018914 
---
> -0.0252426 -0.0057329 -0.0001950  0.0048943  0.0189136 
3233,3237c3233,3235
< smoking  1   0.0022         6    14.1237  0.962724   
< obesity  1   6.8274         5     7.2963  0.008977 **
< snoring  1   5.6779         4     1.6184  0.017179 * 
< ---
< Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 
---
> smoking  1   0.0022         6    14.1237    0.9627
> obesity  1   6.8274         5     7.2963    0.0090
> snoring  1   5.6779         4     1.6184    0.0172
3251,3255c3249,3251
< snoring  1   6.7887         6     7.3372  0.009174 **
< obesity  1   5.6591         5     1.6781  0.017365 * 
< smoking  1   0.0597         4     1.6184  0.806938   
< ---
< Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 
---
> snoring  1   6.7887         6     7.3372    0.0092
> obesity  1   5.6591         5     1.6781    0.0174
> smoking  1   0.0597         4     1.6184    0.8069
3269,3272c3265,3266
< obesity  1   6.8260         6     7.2999  0.008984 **
< snoring  1   5.6218         5     1.6781  0.017738 * 
< ---
< Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 
---
> obesity  1   6.8260         6     7.2999    0.0090
> snoring  1   5.6218         5     1.6781    0.0177
3279,3281c3273,3275
< <none>       1.6781 32.597                 
< obesity  1   7.3372 36.256 5.6591 0.01737 *
< snoring  1   7.2999 36.219 5.6218 0.01774 *
---
> <none>        1.678 32.597                 
> obesity  1    7.337 36.256  5.659 0.01737 *
> snoring  1    7.300 36.219  5.622 0.01774 *
3298c3292
< -0.18531   0.00877  -0.32760   0.34087   1.04313  -0.66215  
---
> -0.185309   0.008767  -0.327604   0.340866   1.043130  -0.662148  
3357,3359c3351,3353
< (Intercept) -3.2101098 -1.718094
< obesityYes   0.1254244  1.246789
< snoringYes   0.1410076  1.715763
---
> (Intercept) -3.2102369 -1.718143
> obesityYes   0.1254382  1.246788
> snoringYes   0.1410865  1.715860
3371,3373c3365,3367
< (Intercept) 0.09143963 0.04035218 0.1794079
< obesityYes  2.00454846 1.13362951 3.4791517
< snoringYes  2.37609483 1.15143343 5.5609161
---
> (Intercept) 0.09143963 0.04034706 0.1793989
> obesityYes  2.00454846 1.13364514 3.4791490
> snoringYes  2.37609483 1.15152424 5.5614585
3379c3373,3374
< The following object(s) are masked from 'package:MASS':
---
> 
> 	The following object(s) are masked from package:MASS :
3381a3377
> 
3428,3429c3424,3425
<     Null deviance: 604.19  on 435  degrees of freedom
< Residual deviance: 106.60  on 430  degrees of freedom
---
>     Null deviance: 604.2  on 435  degrees of freedom
> Residual deviance: 106.6  on 430  degrees of freedom
3441,3443c3437,3439
< <none>      106.60 118.60                     
< age     1   124.50 134.50 17.901 2.327e-05 ***
< tanner  4   161.88 165.88 55.282 2.835e-11 ***
---
> <none>     106.599 118.599                      
> age     1  124.500 134.500  17.901 2.327e-05 ***
> tanner  4  161.881 165.881  55.282 2.835e-11 ***
3515c3511
< -2.45697  -0.15434   0.00835   0.09505   2.59033  
---
> -2.456972  -0.154339   0.008348   0.095055   2.590335  
3568,3569c3564,3567
< 1: glm.fit: fitted probabilities numerically 0 or 1 occurred 
< 2: glm.fit: fitted probabilities numerically 0 or 1 occurred 
---
> 1: In glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart,  :
>   fitted probabilities numerically 0 or 1 occurred
> 2: In method(x = x[, varseq <= i, drop = FALSE], y = object$y, weights = object$prior.weights,  :
>   fitted probabilities numerically 0 or 1 occurred
3572c3570,3571
< glm.fit: fitted probabilities numerically 0 or 1 occurred 
---
> In glm.fit(x = X, y = Y, weights = weights, start = start, etastart = etastart,  :
>   fitted probabilities numerically 0 or 1 occurred
3584c3583,3584
< The following object(s) are masked from 'package:ISwR':
---
> 
> 	The following object(s) are masked from package:ISwR :
3616,3617c3616,3617
< records   n.max n.start  events  median 0.95LCL 0.95UCL 
<     205     205     205      57      NA      NA      NA 
---
>       n  events  median 0.95LCL 0.95UCL 
>     205      57     Inf     Inf     Inf 
3708,3713c3708,3710
<   n= 205, number of events= 57 
< 
<       coef exp(coef) se(coef)     z Pr(>|z|)  
< sex 0.6622    1.9390   0.2651 2.498   0.0125 *
< ---
< Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 
---
>   n= 205 
>      coef exp(coef) se(coef)   z     p
> sex 0.662      1.94    0.265 2.5 0.013
3716c3713
< sex     1.939     0.5157     1.153      3.26
---
> sex      1.94      0.516      1.15      3.26
3718d3714
< Concordance= 0.59  (se = 0.033 )
3720,3722c3716,3718
< Likelihood ratio test= 6.15  on 1 df,   p=0.01314
< Wald test            = 6.24  on 1 df,   p=0.01251
< Score (logrank) test = 6.47  on 1 df,   p=0.01098
---
> Likelihood ratio test= 6.15  on 1 df,   p=0.0131
> Wald test            = 6.24  on 1 df,   p=0.0125
> Score (logrank) test = 6.47  on 1 df,   p=0.0110
3729,3735c3725,3728
<   n= 205, number of events= 57 
< 
<              coef exp(coef) se(coef)     z Pr(>|z|)   
< sex        0.3600    1.4333   0.2702 1.332   0.1828   
< log(thick) 0.5599    1.7505   0.1784 3.139   0.0017 **
< ---
< Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1 
---
>   n= 205 
>            coef exp(coef) se(coef)    z      p
> sex        0.36      1.43    0.270 1.33 0.1800
> log(thick) 0.56      1.75    0.178 3.14 0.0017
3738,3739c3731,3732
< sex            1.433     0.6977     0.844     2.434
< log(thick)     1.750     0.5713     1.234     2.483
---
> sex             1.43      0.698     0.844      2.43
> log(thick)      1.75      0.571     1.234      2.48
3741d3733
< Concordance= 0.673  (se = 0.058 )
3743,3745c3735,3737
< Likelihood ratio test= 13.3  on 2 df,   p=0.001296
< Wald test            = 12.88  on 2 df,   p=0.001598
< Score (logrank) test = 12.98  on 2 df,   p=0.00152
---
> Likelihood ratio test= 13.3  on 2 df,   p=0.00130
> Wald test            = 12.9  on 2 df,   p=0.00160
> Score (logrank) test = 13.0  on 2 df,   p=0.00152
3799,3801c3791,3793
< <none>      23.447 137.84                    
< city    3   28.307 136.69   4.859  0.1824    
< age     5  126.515 230.90 103.068  <2e-16 ***
---
> <none>      23.447 137.836                    
> city    3   28.307 136.695   4.859  0.1824    
> age     5  126.515 230.903 103.068  <2e-16 ***
3812,3813c3804,3805
< 1        15     23.448                      
< 2        17     23.700 -2  -0.2526    0.8814
---
> 1        15    23.4475                      
> 2        17    23.7001 -2  -0.2526    0.8814
3820,3822c3812,3814
< <none>                    23.700 134.09                    
< city == "Fredericia"  1   28.307 136.69   4.606 0.03185 *  
< age                   5  127.117 227.50 103.417 < 2e-16 ***
---
> <none>                    23.700 134.088                    
> city == "Fredericia"  1   28.307 136.695   4.606 0.03185 *  
> age                   5  127.117 227.505 103.417 < 2e-16 ***
3873,3879c3865,3871
< (Intercept)              0.002582626 0.001776585  0.003617461
< city == "Fredericia"TRUE 1.384992752 1.029364554  1.841214351
< age55-59                 3.008134852 1.843566451  4.902377896
< age60-64                 4.573665854 2.912314202  7.248205161
< age65-69                 5.863391064 3.752718512  9.256967983
< age70-74                 6.418715646 4.053251339 10.234350656
< age75+                   4.142034525 2.527103521  6.771889935
---
> (Intercept)              0.002582626 0.001776461  0.003617228
> city == "Fredericia"TRUE 1.384992752 1.029362341  1.841224091
> age55-59                 3.008134852 1.843578634  4.902339637
> age60-64                 4.573665854 2.912314045  7.248143959
> age65-69                 5.863391064 3.752718226  9.256907108
> age70-74                 6.418715646 4.053262281 10.234338998
> age75+                   4.142034525 2.527117848  6.771833979
3911c3903,3904
< The following object(s) are masked from 'package:ISwR':
---
> 
> 	The following object(s) are masked from package:ISwR :
3913a3907
> 
3984c3978
< -0.6758  -0.3159  -0.1821  -0.0918   4.1972  
---
> -0.67584  -0.31593  -0.18214  -0.09184   4.19724  
4023c4017,4018
< The following object(s) are masked from 'package:ISwR':
---
> 
> 	The following object(s) are masked from package:ISwR :
4025a4021
> 
4034,4036c4030,4032
< <none>      1069.7 1367.7                    
< A       5   1073.8 1361.8  4.082   0.5376    
< Y       6   1118.5 1404.5 48.770 8.29e-09 ***
---
> <none>     1069.73 1367.73                     
> A       5  1073.81 1361.81    4.08   0.5376    
> Y       6  1118.50 1404.50   48.77 8.29e-09 ***
4094c4090,4091
< The following object(s) are masked from 'package:ISwR':
---
> 
> 	The following object(s) are masked from package:ISwR :
4096a4094
> 
4105,4109c4103,4107
< <none>      1052.9 1356.9                     
< TFE     4   1107.3 1403.3 54.425 4.287e-11 ***
< AFE     3   1055.0 1353.0  2.079 0.5560839    
< YFE     3   1058.1 1356.1  5.155 0.1608219    
< EXP     4   1072.0 1368.0 19.072 0.0007606 ***
---
> <none>     1052.91 1356.91                      
> TFE     4  1107.33 1403.33   54.43 4.287e-11 ***
> AFE     3  1054.99 1352.99    2.08 0.5560839    
> YFE     3  1058.06 1356.06    5.15 0.1608219    
> EXP     4  1071.98 1367.98   19.07 0.0007606 ***
4171c4169
< Achieved convergence tolerance: 1.08e-08 
---
> Achieved convergence tolerance: 6.025e-09 
4233c4231
< Achieved convergence tolerance: 2.794e-06 
---
> Achieved convergence tolerance: 2.766e-06 
4278c4276
< Achieved convergence tolerance: 5.417e-06 
---
> Achieved convergence tolerance: 5.412e-06 
4287,4289c4285,4287
< alpha 233.5007561 294.76267646
< beta    1.1442683   1.27411439
< gamma   0.0550577   0.08574974
---
> alpha 233.49714410 294.76621773
> beta    1.14429949   1.27416342
> gamma   0.05505776   0.08574984
4292c4290
< alpha 226.50065194 285.4532596
---
> alpha 226.50065424 285.4532573
* checking PDF version of manual ... OK