Check results for 'ISwR'

using R version 2.14.1 Patched (2012-02-07 r58290)
using platform: x86_64-unknown-linux-gnu (64-bit)
using session charset: UTF-8
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: 1.65e-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
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] "/home/hornik/tmp/R.check/r-patched/Work/build/Packages/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: 7.238e-09
---
> Achieved convergence tolerance: 6.025e-09
4208c4206
< Achieved convergence tolerance: 5.297e-06
---
> Achieved convergence tolerance: 5.239e-06
4224c4222
< alpha 255.97695 15.03921 17.021 <2e-16 ***
---
> alpha 255.97696 15.03921 17.021 <2e-16 ***
4233c4231
< Achieved convergence tolerance: 2.73e-06
---
> Achieved convergence tolerance: 2.766e-06
4278c4276
< Achieved convergence tolerance: 5.485e-06
---
> Achieved convergence tolerance: 5.412e-06
4287,4289c4285,4287
< alpha 233.5007561 294.76267643
< 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 226.50065212 285.4532555
---
> alpha 226.50065424 285.4532573
checking PDF version of manual ... OK