- using R version 2.14.0 (2011-10-31)
- using platform: i386-apple-darwin9.8.0 (32-bit)
- using session charset: ASCII
- 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 if there is a namespace ... NOTE
As from R 2.14.0 all packages need a namespace.
One will be generated on installation, but it is better to handcraft a
NAMESPACE file: R CMD build will produce a suitable starting point.
- checking for executable files ... 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 for sufficient/correct file permissions ... 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
<
<
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
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
1033,1037c1030,1034
< Df Sum of Sq RSS AIC F value Pr(>F)
< <none> 19679 241.49
< id 15 51137 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 *
---
> Df Sum of Sq RSS AIC F value Pr(F)
> <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 51137 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
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
1398c1395
< Df Sum of Sq RSS AIC F value Pr(>F)
---
> Df Sum of Sq RSS AIC F value Pr(F)
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
1696c1693
< Df Deviance AIC LRT Pr(>Chi)
---
> Df Deviance AIC LRT Pr(Chi)
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 *
1710c1707
< Df Deviance AIC LRT Pr(>Chi)
---
> Df Deviance AIC LRT Pr(Chi)
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 *
1723c1720
< Df Deviance AIC LRT Pr(>Chi)
---
> Df Deviance AIC LRT Pr(Chi)
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 ***
1735c1732
< Df Deviance AIC LRT Pr(>Chi)
---
> Df Deviance AIC LRT Pr(Chi)
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
1800c1797
< Df Deviance Resid. Df Resid. Dev Pr(>Chi)
---
> Df Deviance Resid. Df Resid. Dev P(>|Chi|)
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
2087,2091c2065,2069
< Df Deviance AIC LRT Pr(>Chi)
< <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 ***
---
> Df Deviance AIC LRT Pr(Chi)
> <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 180.77122 1.93392 93.474 < 2e-16 ***
---
> alpha 180.77125 1.93392 93.474 < 2e-16 ***
2167c2145
< da 62.03692 11.26004 5.509 4.46e-08 ***
---
> da 62.03692 11.26005 5.509 4.46e-08 ***
2176c2154
< Achieved convergence tolerance: 2.166e-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 0.03655498 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 0.05332676 1.377884
< la -0.72610588 0.684268
---
> ymax 15.15339690 41.0308087
> ec50 0.02711647 1.3766294
> la -0.72603028 0.6842553
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] 170
---
> [1] 138
518c516
< [1] "/Volumes/Tiger/Builds/Rdev-web/QA/Simon/packages/leopard-universal/results/2.14/ISwR.Rcheck/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
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
3231c3231
< Df Deviance Resid. Df Resid. Dev Pr(>Chi)
---
> Df Deviance Resid. Df Resid. Dev P(>|Chi|)
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
3249c3247
< Df Deviance Resid. Df Resid. Dev Pr(>Chi)
---
> Df Deviance Resid. Df Resid. Dev P(>|Chi|)
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
3267c3263
< Df Deviance Resid. Df Resid. Dev Pr(>Chi)
---
> Df Deviance Resid. Df Resid. Dev P(>|Chi|)
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
3278,3281c3272,3275
< Df Deviance AIC LRT Pr(>Chi)
< <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 *
---
> Df Deviance AIC LRT Pr(Chi)
> <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
3440,3443c3436,3439
< Df Deviance AIC LRT Pr(>Chi)
< <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 ***
---
> Df Deviance AIC LRT Pr(Chi)
> <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
3582c3581
< Attaching package: `survival'
---
> Attaching package: 'survival'
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
3798,3801c3790,3793
< Df Deviance AIC LRT Pr(>Chi)
< <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 ***
---
> Df Deviance AIC LRT Pr(Chi)
> <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 ***
3811,3813c3803,3805
< Resid. Df Resid. Dev Df Deviance Pr(>Chi)
< 1 15 23.448
< 2 17 23.700 -2 -0.2526 0.8814
---
> Resid. Df Resid. Dev Df Deviance P(>|Chi|)
> 1 15 23.4475
> 2 17 23.7001 -2 -0.2526 0.8814
3819,3822c3811,3814
< Df Deviance AIC LRT Pr(>Chi)
< <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 ***
---
> Df Deviance AIC LRT Pr(Chi)
> <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
>
4033,4036c4029,4032
< Df Deviance AIC LRT Pr(>Chi)
< <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 ***
---
> Df Deviance AIC LRT Pr(Chi)
> <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
>
4104,4109c4102,4107
< Df Deviance AIC LRT Pr(>Chi)
< <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 ***
---
> Df Deviance AIC LRT Pr(Chi)
> <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: 1.199e-08
---
> Achieved convergence tolerance: 6.025e-09
4208c4206
< Achieved convergence tolerance: 5.27e-06
---
> Achieved convergence tolerance: 5.239e-06
4224c4222
< alpha 255.97694 15.03920 17.021 <2e-16 ***
---
> alpha 255.97696 15.03921 17.021 <2e-16 ***
4233c4231
< Achieved convergence tolerance: 2.948e-06
---
> Achieved convergence tolerance: 2.766e-06
4278c4276
< Achieved convergence tolerance: 5.472e-06
---
> Achieved convergence tolerance: 5.412e-06
4287,4289c4285,4287
< alpha 233.5007561 294.76267631
< 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
4292,4294c4290,4292
< alpha 226.50064553 285.45324094
< beta 1.13125578 1.24772849
< gamma 0.05443818 0.08622691
---
> alpha 226.50065424 285.4532573
> beta 1.13125578 1.2477285
> gamma 0.05443818 0.0862269
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