Check results for 'survival'

using R version 2.13.0 Under development (unstable) (2011-03-13 r54781)
using platform: i386-apple-darwin9.8.0 (32-bit)
using session charset: ASCII
checking for file 'survival/DESCRIPTION' ... OK
this is package 'survival' version '2.36-5'
checking package name space information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking for executable files ... OK
checking whether package 'survival' 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
loading checks for arch 'i386'
** 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 whether the name space can be loaded with stated dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
loading checks for arch 'ppc'
** 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 whether the name space can be loaded with stated dependencies ... OK
** checking whether the name space can be unloaded cleanly ... OK
loading checks for arch 'x86_64'
** 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 whether the name space can be loaded with stated dependencies ... OK
** checking whether the name space 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 ... NOTE
anova.survreglist: no visible global function definition for 'as.anova'
predict.survreg: no visible global function definition for 'labels.lm'
predict.survreg: no visible global function definition for
'Build.terms'
pyears: no visible global function definition for 'month.day.year'
pyears: no visible global function definition for 'as.date'
pyears: no visible global function definition for 'date.mdy'
pyears: no visible global function definition for 'mdy.date'
ratetableDate.chron: no visible global function definition for 'chron'
ratetableDate.timeDate: no visible global function definition for
'timeDate'
survexp.fit: no visible global function definition for 'month.day.year'
survexp.fit: no visible global function definition for 'as.date'
survexp.fit: no visible global function definition for 'date.mdy'
survexp.fit: no visible global function definition for 'mdy.date'
survpenal.fit: no visible global function definition for 'new.frame'
survpenal.fit: possible error in get("coxlist1", frame = rho): unused
argument(s) (frame = rho)
survpenal.fit: possible error in get("coxlist2", frame = rho): unused
argument(s) (frame = rho)
survreg.fit: no visible global function definition for 'new.frame'
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 line endings in C/C++/Fortran sources/headers ... OK
checking line endings in Makefiles ... OK
checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'ppc' ... OK
** running examples for arch 'x86_64' ... OK
checking for unstated dependencies in tests ... NOTE
'library' or 'require' call not declared from: cmprsk
checking tests ...
** running tests for arch 'i386' OK
Running 'aareg.R'
Comparing 'aareg.Rout' to 'aareg.Rout.save' ...259,260c259,260
< [1,] 7738.6204 -125.5077
< [2,] -125.5077 2.0768
---
> [1,] 7738.6204 -125.507657
> [2,] -125.5077 2.076800
264c264
< [1,] 4.22624
---
> [1,] 4.226240
321,325c321,325
< Intercept 0.00137589
< age 0.19055946
< sex 0.00112454
< ph.karno 0.24100515
< pat.karno 0.08316385
---
> Intercept 0.001375890
> age 0.190559455
> sex 0.001124540
> ph.karno 0.241005145
> pat.karno 0.083163853
344,348c344,348
< [1,] 22525.42254 -109.0376340 -1294.620657 -135.7477106 -24.1718358
< [2,] -109.03763 1.6505060 2.562655 0.1774270 -0.1206339
< [3,] -1294.62066 2.5626546 566.194480 7.4865489 -4.7691882
< [4,] -135.74771 0.1774270 7.486549 2.2974694 -0.9877341
< [5,] -24.17184 -0.1206339 -4.769188 -0.9877341 1.4499155
---
> [1,] 22525.42254 -109.0376340 -1294.620657 -135.747711 -24.1718358
> [2,] -109.03763 1.6505060 2.562655 0.177427 -0.1206339
> [3,] -1294.62066 2.5626546 566.194480 7.486549 -4.7691882
> [4,] -135.74771 0.1774270 7.486549 2.297469 -0.9877341
> [5,] -24.17184 -0.1206339 -4.769188 -0.987734 1.4499155
Running 'anova.R'
Comparing 'anova.Rout' to 'anova.Rout.save' ... OK
Running 'bladder.R'
Comparing 'bladder.Rout' to 'bladder.Rout.save' ...19,30c19,30
< rx -0.5176 0.596 0.3158 0.3075 -1.683 0.0920
< size 0.0679 1.070 0.1012 0.0853 0.796 0.4300
< number 0.2360 1.266 0.0761 0.0721 3.274 0.0011
< rx:strata(enum)enum=2 -0.1018 0.903 0.5043 0.3265 -0.312 0.7600
< rx:strata(enum)enum=3 -0.1823 0.833 0.5579 0.3916 -0.465 0.6400
< rx:strata(enum)enum=4 -0.1332 0.875 0.6581 0.4968 -0.268 0.7900
< size:strata(enum)enum=2 -0.1440 0.866 0.1680 0.1119 -1.287 0.2000
< size:strata(enum)enum=3 -0.2792 0.756 0.2086 0.1511 -1.847 0.0650
< size:strata(enum)enum=4 -0.2711 0.763 0.2515 0.1856 -1.460 0.1400
< number:strata(enum)enum=2 -0.0984 0.906 0.1193 0.1144 -0.861 0.3900
< number:strata(enum)enum=3 -0.0662 0.936 0.1298 0.1167 -0.567 0.5700
< number:strata(enum)enum=4 0.0928 1.097 0.1466 0.1175 0.790 0.4300
---
> rx -0.5176 0.596 0.316 0.3075 -1.683 0.0920
> size 0.0679 1.070 0.101 0.0853 0.796 0.4300
> number 0.2360 1.266 0.076 0.0721 3.274 0.0011
> rx:strata(enum)enum=2 -0.1018 0.903 0.504 0.3265 -0.312 0.7600
> rx:strata(enum)enum=3 -0.1823 0.833 0.558 0.3916 -0.465 0.6400
> rx:strata(enum)enum=4 -0.1332 0.875 0.658 0.4968 -0.268 0.7900
> size:strata(enum)enum=2 -0.1440 0.866 0.168 0.1119 -1.287 0.2000
> size:strata(enum)enum=3 -0.2792 0.756 0.209 0.1511 -1.847 0.0650
> size:strata(enum)enum=4 -0.2711 0.763 0.251 0.1856 -1.460 0.1400
> number:strata(enum)enum=2 -0.0984 0.906 0.119 0.1144 -0.861 0.3900
> number:strata(enum)enum=3 -0.0662 0.936 0.130 0.1167 -0.567 0.5700
> number:strata(enum)enum=4 0.0928 1.097 0.147 0.1175 0.790 0.4300
42,45c42,45
< [1,] 0.09455501 0.06017669 0.05677331 0.0437777
< [2,] 0.06017669 0.13242834 0.13011557 0.1160420
< [3,] 0.05677331 0.13011557 0.17235879 0.1590865
< [4,] 0.04377770 0.11604200 0.15908650 0.2398112
---
> [1,] 0.09455501 0.06017669 0.0567733 0.0437777
> [2,] 0.06017669 0.13242834 0.1301156 0.1160420
> [3,] 0.05677331 0.13011557 0.1723588 0.1590865
> [4,] 0.04377770 0.11604200 0.1590865 0.2398112
94,96c94,96
< rx -0.5176 0.596 0.3158 -1.639 0.1000
< size 0.0679 1.070 0.1012 0.671 0.5000
< number 0.2360 1.266 0.0761 3.102 0.0019
---
> rx -0.5176 0.596 0.316 -1.64 0.1000
> size 0.0679 1.070 0.101 0.67 0.5000
> number 0.2360 1.266 0.076 3.10 0.0019
118,120c118,120
< rx -0.25911 0.772 0.4051 -0.6396 0.52
< size -0.11636 0.890 0.1192 -0.9759 0.33
< number -0.00571 0.994 0.0967 -0.0591 0.95
---
> rx -0.25911 0.772 0.4051 -0.640 0.52
> size -0.11636 0.890 0.1192 -0.976 0.33
> number -0.00571 0.994 0.0967 -0.059 0.95
Running 'book1.R'
Comparing 'book1.Rout' to 'book1.Rout.save' ... OK
Running 'book2.R'
Comparing 'book2.Rout' to 'book2.Rout.save' ...117c117
< 0.157512 0.421244 -0.578756 0.000000
---
> 0.1575120 0.4212440 -0.5787560 0.0000000
Running 'book3.R'
Comparing 'book3.Rout' to 'book3.Rout.save' ...112,115c112,115
< 1 2 3 4 5 6
< 0.52111895 0.65741078 0.78977654 0.24738772 -0.60629349 0.36902492
< 7 8 9 10
< -0.06876579 -1.06876579 -0.42044692 -0.42044692
---
> 1 2 3 4 5 6 7
> 0.5211189 0.6574108 0.7897765 0.2473877 -0.6062935 0.3690249 -0.0687658
> 8 9 10
> -1.0687658 -0.4204469 -0.4204469
Running 'book4.R'
Comparing 'book4.Rout' to 'book4.Rout.save' ...114,115c114,115
< [1] -0.0105526 0.0105526 0.0105526 -0.0105526 0.0105526 -0.0105526
< [7] -0.0105526 -0.0105526 0.0105526 0.0105526
---
> [1] -0.01055260 0.01055260 0.01055260 -0.01055260 0.01055260 -0.01055260
> [7] -0.01055260 -0.01055260 0.01055260 0.01055260
126,135c126,135
< 1 -0.0105526
< 2 0.0105526
< 3 0.0105526
< 4 -0.0105526
< 5 0.0105526
< 6 -0.0105526
< 7 -0.0105526
< 8 -0.0105526
< 9 0.0105526
< 10 0.0105526
---
> 1 -0.01055260
> 2 0.01055260
> 3 0.01055260
> 4 -0.01055260
> 5 0.01055260
> 6 -0.01055260
> 7 -0.01055260
> 8 -0.01055260
> 9 0.01055260
> 10 0.01055260
137c137
< [1] -0.0105526
---
> [1] -0.01055260
140,143c140,143
< 1 2 3 4 5 6 7
< -0.0105526 0.0105526 0.0105526 -0.0105526 0.0105526 -0.0105526 -0.0105526
< 8 9 10
< -0.0105526 0.0105526 0.0105526
---
> 1 2 3 4 5 6
> -0.01055260 0.01055260 0.01055260 -0.01055260 0.01055260 -0.01055260
> 7 8 9 10
> -0.01055260 -0.01055260 0.01055260 0.01055260
178,187c178,187
< 1 -0.0105526
< 2 0.0105526
< 3 0.0105526
< 4 -0.0105526
< 5 0.0105526
< 6 -0.0105526
< 7 -0.0105526
< 8 -0.0105526
< 9 0.0105526
< 10 0.0105526
---
> 1 -0.01055260
> 2 0.01055260
> 3 0.01055260
> 4 -0.01055260
> 5 0.01055260
> 6 -0.01055260
> 7 -0.01055260
> 8 -0.01055260
> 9 0.01055260
> 10 0.01055260
189c189
< [1] -0.0105526
---
> [1] -0.01055260
Running 'book5.R'
Comparing 'book5.Rout' to 'book5.Rout.save' ... OK
Running 'book6.R'
Comparing 'book6.Rout' to 'book6.Rout.save' ... OK
Running 'cancer.R'
Comparing 'cancer.Rout' to 'cancer.Rout.save' ...49,61c49,61
< 30 46 5 0.9000 0.0424 0.82057 0.987
< 60 43 2 0.8600 0.0491 0.76900 0.962
< 90 40 3 0.8000 0.0566 0.69647 0.919
< 120 34 4 0.7174 0.0641 0.60216 0.855
< 150 31 3 0.6541 0.0680 0.53342 0.802
< 180 26 6 0.5275 0.0719 0.40385 0.689
< 210 21 4 0.4431 0.0717 0.32266 0.608
< 240 17 3 0.3766 0.0705 0.26100 0.543
< 270 17 0 0.3766 0.0705 0.26100 0.543
< 300 13 3 0.3102 0.0677 0.20223 0.476
< 330 11 2 0.2624 0.0651 0.16135 0.427
< 365 9 2 0.2147 0.0614 0.12258 0.376
< 730 1 6 0.0371 0.0345 0.00601 0.229
---
> 30 46 5 0.9000 0.0424 0.821 0.987
> 60 43 2 0.8600 0.0491 0.769 0.962
> 90 40 3 0.8000 0.0566 0.696 0.919
> 120 34 4 0.7174 0.0641 0.602 0.855
> 150 31 3 0.6541 0.0680 0.533 0.802
> 180 26 6 0.5275 0.0719 0.404 0.689
> 210 21 4 0.4431 0.0717 0.323 0.608
> 240 17 3 0.3766 0.0705 0.261 0.543
> 270 17 0 0.3766 0.0705 0.261 0.543
> 300 13 3 0.3102 0.0677 0.202 0.476
> 330 11 2 0.2624 0.0651 0.161 0.427
> 365 9 2 0.2147 0.0614 0.123 0.376
> 730 1 6 0.0371 0.0345 0.006 0.229
156,163c156,163
< ph.ecog 0.0276 0.1078 0.7427
< ph.karno 0.1331 2.0018 0.1571
< pat.karno 0.0250 0.0841 0.7718
< wt.loss -0.0386 0.2122 0.6451
< sex 0.0399 0.1800 0.6713
< age 0.0639 0.5600 0.4543
< meal.cal 0.1611 3.6945 0.0546
< GLOBAL NA 9.0115 0.2518
---
> ph.ecog 0.0276 0.108 0.7427
> ph.karno 0.1331 2.002 0.1571
> pat.karno 0.0250 0.084 0.7718
> wt.loss -0.0386 0.212 0.6451
> sex 0.0399 0.180 0.6713
> age 0.0639 0.560 0.4543
> meal.cal 0.1611 3.695 0.0546
> GLOBAL NA 9.012 0.2518
Running 'concordance.R'
Comparing 'concordance.Rout' to 'concordance.Rout.save' ... OK
Running 'counting.R'
Comparing 'counting.Rout' to 'counting.Rout.save' ... OK
Running 'coxsurv.R'
Comparing 'coxsurv.Rout' to 'coxsurv.Rout.save' ... OK
Running 'coxsurv2.R'
Comparing 'coxsurv2.Rout' to 'coxsurv2.Rout.save' ... OK
Running 'coxsurv3.R'
Comparing 'coxsurv3.Rout' to 'coxsurv3.Rout.save' ... OK
Running 'coxsurv4.R'
Comparing 'coxsurv4.Rout' to 'coxsurv4.Rout.save' ... OK
Running 'detail.R'
Comparing 'detail.Rout' to 'detail.Rout.save' ... OK
Running 'difftest.R'
Comparing 'difftest.Rout' to 'difftest.Rout.save' ...34,35c34,35
< x=Maintained 11 7 10.69 1.27 3.4
< x=Nonmaintained 12 11 7.31 1.86 3.4
---
> x=Maintained 11 7 10.69 1.27 3.40
> x=Nonmaintained 12 11 7.31 1.86 3.40
44,45c44,45
< x=Maintained 11 7 10.69 1.27 3.4
< x=Nonmaintained 12 11 7.31 1.86 3.4
---
> x=Maintained 11 7 10.69 1.27 3.40
> x=Nonmaintained 12 11 7.31 1.86 3.40
Running 'doaml.R'
Comparing 'doaml.Rout' to 'doaml.Rout.save' ...83,84c83,84
< aml$x=Maintained 11 7 10.69 1.27 3.4
< aml$x=Nonmaintained 12 11 7.31 1.86 3.4
---
> aml$x=Maintained 11 7 10.69 1.27 3.40
> aml$x=Nonmaintained 12 11 7.31 1.86 3.40
Running 'doweight.R'
Comparing 'doweight.Rout' to 'doweight.Rout.save' ... OK
Running 'expected.R'
Comparing 'expected.Rout' to 'expected.Rout.save' ... OK
Running 'expected2.R'
Comparing 'expected2.Rout' to 'expected2.Rout.save' ... OK
Running 'factor.R'
Comparing 'factor.Rout' to 'factor.Rout.save' ... OK
Running 'factor2.R'
Comparing 'factor2.Rout' to 'factor2.Rout.save' ... OK
Running 'fr_cancer.R'
Comparing 'fr_cancer.Rout' to 'fr_cancer.Rout.save' ...64c64
< Theta= 0.691
---
> Theta= 0.69
97c97
< Theta= 0.779
---
> Theta= 0.78
Running 'fr_colon.R'
Comparing 'fr_colon.Rout' to 'fr_colon.Rout.save' ...19,22c19,22
< rxLev -0.0362 0.964 0.0768 0.1056 -0.343 7.3e-01
< rxLev+5FU -0.4488 0.638 0.0840 0.1168 -3.842 1.2e-04
< extent 0.5155 1.674 0.0796 0.1097 4.701 2.6e-06
< node4 0.8799 2.411 0.0681 0.0961 9.160 0.0e+00
---
> rxLev -0.0362 0.964 0.0768 0.106 -0.343 7.3e-01
> rxLev+5FU -0.4488 0.638 0.0840 0.117 -3.842 1.2e-04
> extent 0.5155 1.674 0.0796 0.110 4.701 2.6e-06
> node4 0.8799 2.411 0.0681 0.096 9.160 0.0e+00
Running 'fr_kidney.R'
Comparing 'fr_kidney.Rout' to 'fr_kidney.Rout.save' ...106c106
< Likelihood ratio test=63.8 on 21 df, p=3.27e-06 n= 76
---
> Likelihood ratio test=63.8 on 21.0 df, p=3.27e-06 n= 76
121,125c121,125
< age 0.00489 0.015 0.0106 0.11 1.0 0.74000
< sex -1.69728 0.461 0.3617 13.55 1.0 0.00023
< diseaseGN 0.17986 0.545 0.3927 0.11 1.0 0.74000
< diseaseAN 0.39294 0.545 0.3982 0.52 1.0 0.47000
< diseasePKD -1.13631 0.825 0.6173 1.90 1.0 0.17000
---
> age 0.00489 0.0150 0.0106 0.11 1.0 0.74000
> sex -1.69728 0.4610 0.3617 13.55 1.0 0.00023
> diseaseGN 0.17986 0.5449 0.3927 0.11 1.0 0.74000
> diseaseAN 0.39294 0.5448 0.3982 0.52 1.0 0.47000
> diseasePKD -1.13631 0.8252 0.6173 1.90 1.0 0.17000
209,210c209,210
< age 0.00364 0.0105 0.00891 0.12 1.00 0.73000
< sex -1.31953 0.3956 0.32497 11.13 1.00 0.00085
---
> age 0.00364 0.0105 0.0089 0.12 1.00 0.73000
> sex -1.31953 0.3956 0.3250 11.13 1.00 0.00085
224,225c224,225
< age 0.00561 0.012 0.00872 0.22 1.0 0.64000
< sex -1.65487 0.483 0.38527 11.74 1.0 0.00061
---
> age 0.00561 0.0120 0.00872 0.22 1.0 0.64000
> sex -1.65487 0.4829 0.38527 11.74 1.0 0.00061
257,258c257,258
< age 0.00785 0.015 0.00823 0.27 1.0 0.60000
< sex -1.88990 0.561 0.39941 11.34 1.0 0.00076
---
> age 0.00785 0.0150 0.00823 0.27 1.0 0.60000
> sex -1.88990 0.5611 0.39941 11.34 1.0 0.00076
275,276c275,276
< age 0.00561 0.012 0.00872 0.22 1.0 0.64000
< sex -1.65487 0.483 0.38527 11.74 1.0 0.00061
---
> age 0.00561 0.0120 0.00872 0.22 1.0 0.64000
> sex -1.65487 0.4829 0.38527 11.74 1.0 0.00061
Running 'fr_lung.R'
Comparing 'fr_lung.Rout' to 'fr_lung.Rout.save' ... OK
Running 'fr_ovarian.R'
Comparing 'fr_ovarian.Rout' to 'fr_ovarian.Rout.save' ...47,48c47,48
< rx -0.373 0.761 0.749 0.24 1.00 0.6200
< pspline(age, df = 4), lin 0.139 0.044 0.044 9.98 1.00 0.0016
---
> rx -0.373 0.761 0.7485 0.24 1.00 0.6200
> pspline(age, df = 4), lin 0.139 0.044 0.0440 9.98 1.00 0.0016
Running 'fr_rat1.R'
Comparing 'fr_rat1.Rout' to 'fr_rat1.Rout.save' ...77c77
< Likelihood ratio test=50.7 on 23.7 df, p=0.001 n= 150
---
> Likelihood ratio test=50.7 on 23.7 df, p=0.00100 n= 150
85c85
< frailty(litter) 18 14.6 0.24
---
> frailty(litter) 18.0 14.6 0.24
Running 'fr_rat2.R'
Comparing 'fr_rat2.Rout' to 'fr_rat2.Rout.save' ...49c49
< Likelihood ratio test=32.9 on 1 df, p=9.89e-09 n= 253, number of events= 212
---
> Likelihood ratio test=32.9 on 1 df, p=9.9e-09 n= 253, number of events= 212
69c69
< rx -0.79 0.22 0.154 12.9 1.0 3.2e-04
---
> rx -0.79 0.220 0.154 12.9 1.0 3.2e-04
75c75
< Likelihood ratio test=118 on 25.4 df, p=6.99e-14 n= 253
---
> Likelihood ratio test=118 on 25.4 df, p=7e-14 n= 253
106c106
< rx -0.838 0.23 0.151 13.3 1.0 0.00026
---
> rx -0.838 0.230 0.151 13.3 1.0 0.00026
Running 'fr_resid.R'
Comparing 'fr_resid.Rout' to 'fr_resid.Rout.save' ...78,153c78,153
< 1 -0.073981042 1.039553 0.59814468
< 2 -0.073981042 1.039553 0.59814468
< 3 0.020278123 -0.371269 0.38512389
< 4 0.020278123 -0.371269 0.38512389
< 5 -0.055129209 1.039553 0.20210998
< 6 -0.055129209 1.039553 0.20210998
< 7 -0.059842167 -0.371269 -0.55932015
< 8 -0.055129209 -0.371269 -0.55932015
< 9 -0.158814289 1.039553 0.28558387
< 10 -0.158814289 1.039553 0.28558387
< 11 -0.130536540 -0.371269 0.06628942
< 12 -0.125823582 -0.371269 0.06628942
< 13 0.034416998 1.039553 0.80505119
< 14 0.034416998 1.039553 0.80505119
< 15 0.053268830 -0.371269 -0.43834241
< 16 0.057981789 -0.371269 -0.43834241
< 17 0.119250245 -0.371269 -0.05631649
< 18 0.119250245 -0.371269 -0.05631649
< 19 0.034416998 1.039553 -0.49980572
< 20 0.039129956 1.039553 -0.49980572
< 21 0.001426290 -0.371269 -0.13028264
< 22 0.001426290 -0.371269 -0.13028264
< 23 -0.045703292 -0.371269 0.06377401
< 24 -0.045703292 -0.371269 0.06377401
< 25 -0.040990334 -0.371269 0.38815296
< 26 -0.040990334 -0.371269 0.38815296
< 27 -0.007999626 -0.371269 -0.47650510
< 28 -0.007999626 -0.371269 -0.47650510
< 29 -0.125823582 -0.371269 -0.66986830
< 30 -0.125823582 -0.371269 -0.66986830
< 31 0.076833621 1.039553 0.19359678
< 32 0.076833621 1.039553 0.19359678
< 33 0.076833621 -0.371269 -0.16483200
< 34 0.076833621 -0.371269 -0.16483200
< 35 -0.003286668 -0.371269 -0.15794998
< 36 0.001426290 -0.371269 -0.15794998
< 37 0.043842914 -0.371269 -0.46236014
< 38 0.043842914 -0.371269 -0.46236014
< 39 0.001426290 -0.371269 0.12603308
< 40 0.001426290 -0.371269 0.12603308
< 41 0.010852206 1.039553 -1.74303142
< 42 0.015565165 1.039553 -1.74303142
< 43 -0.064555125 -0.371269 -0.45211210
< 44 -0.064555125 -0.371269 -0.45211210
< 45 0.086259538 -0.371269 0.51574106
< 46 0.090972496 -0.371269 0.51574106
< 47 -0.007999626 -0.371269 0.09475123
< 48 -0.003286668 -0.371269 0.09475123
< 49 -0.003286668 1.039553 0.05790354
< 50 -0.003286668 1.039553 0.05790354
< 51 0.062694747 -0.371269 -0.37933234
< 52 0.067407705 -0.371269 -0.37933234
< 53 -0.158814289 -0.371269 0.11248891
< 54 -0.158814289 -0.371269 0.11248891
< 55 0.039129956 -0.371269 0.54791210
< 56 0.039129956 -0.371269 0.54791210
< 57 0.043842914 1.039553 0.45873482
< 58 0.043842914 1.039553 0.45873482
< 59 0.048555872 -0.371269 0.35639797
< 60 0.048555872 -0.371269 0.35639797
< 61 0.057981789 -0.371269 0.48803342
< 62 0.057981789 -0.371269 0.48803342
< 63 0.029704039 -0.371269 0.25597325
< 64 0.034416998 -0.371269 0.25597325
< 65 0.062694747 -0.371269 0.23054948
< 66 0.062694747 -0.371269 0.23054948
< 67 0.001426290 -0.371269 -0.13680005
< 68 0.006139248 -0.371269 -0.13680005
< 69 -0.102258791 -0.371269 0.51977995
< 70 -0.102258791 -0.371269 0.51977995
< 71 -0.007999626 -0.371269 -0.23878154
< 72 -0.007999626 -0.371269 -0.23878154
< 73 0.039129956 -0.371269 0.17174306
< 74 0.039129956 -0.371269 0.17174306
< 75 0.076833621 1.039553 -0.35822829
< 76 0.076833621 1.039553 -0.35822829
---
> 1 -0.073981042 1.0395533 0.59814468
> 2 -0.073981042 1.0395533 0.59814468
> 3 0.020278123 -0.3712690 0.38512389
> 4 0.020278123 -0.3712690 0.38512389
> 5 -0.055129209 1.0395533 0.20210998
> 6 -0.055129209 1.0395533 0.20210998
> 7 -0.059842167 -0.3712690 -0.55932015
> 8 -0.055129209 -0.3712690 -0.55932015
> 9 -0.158814289 1.0395533 0.28558387
> 10 -0.158814289 1.0395533 0.28558387
> 11 -0.130536540 -0.3712690 0.06628942
> 12 -0.125823582 -0.3712690 0.06628942
> 13 0.034416998 1.0395533 0.80505119
> 14 0.034416998 1.0395533 0.80505119
> 15 0.053268830 -0.3712690 -0.43834241
> 16 0.057981789 -0.3712690 -0.43834241
> 17 0.119250245 -0.3712690 -0.05631649
> 18 0.119250245 -0.3712690 -0.05631649
> 19 0.034416998 1.0395533 -0.49980572
> 20 0.039129956 1.0395533 -0.49980572
> 21 0.001426290 -0.3712690 -0.13028264
> 22 0.001426290 -0.3712690 -0.13028264
> 23 -0.045703292 -0.3712690 0.06377401
> 24 -0.045703292 -0.3712690 0.06377401
> 25 -0.040990334 -0.3712690 0.38815296
> 26 -0.040990334 -0.3712690 0.38815296
> 27 -0.007999626 -0.3712690 -0.47650510
> 28 -0.007999626 -0.3712690 -0.47650510
> 29 -0.125823582 -0.3712690 -0.66986830
> 30 -0.125823582 -0.3712690 -0.66986830
> 31 0.076833621 1.0395533 0.19359678
> 32 0.076833621 1.0395533 0.19359678
> 33 0.076833621 -0.3712690 -0.16483200
> 34 0.076833621 -0.3712690 -0.16483200
> 35 -0.003286668 -0.3712690 -0.15794998
> 36 0.001426290 -0.3712690 -0.15794998
> 37 0.043842914 -0.3712690 -0.46236014
> 38 0.043842914 -0.3712690 -0.46236014
> 39 0.001426290 -0.3712690 0.12603308
> 40 0.001426290 -0.3712690 0.12603308
> 41 0.010852206 1.0395533 -1.74303142
> 42 0.015565165 1.0395533 -1.74303142
> 43 -0.064555125 -0.3712690 -0.45211210
> 44 -0.064555125 -0.3712690 -0.45211210
> 45 0.086259538 -0.3712690 0.51574106
> 46 0.090972496 -0.3712690 0.51574106
> 47 -0.007999626 -0.3712690 0.09475123
> 48 -0.003286668 -0.3712690 0.09475123
> 49 -0.003286668 1.0395533 0.05790354
> 50 -0.003286668 1.0395533 0.05790354
> 51 0.062694747 -0.3712690 -0.37933234
> 52 0.067407705 -0.3712690 -0.37933234
> 53 -0.158814289 -0.3712690 0.11248891
> 54 -0.158814289 -0.3712690 0.11248891
> 55 0.039129956 -0.3712690 0.54791210
> 56 0.039129956 -0.3712690 0.54791210
> 57 0.043842914 1.0395533 0.45873482
> 58 0.043842914 1.0395533 0.45873482
> 59 0.048555872 -0.3712690 0.35639797
> 60 0.048555872 -0.3712690 0.35639797
> 61 0.057981789 -0.3712690 0.48803342
> 62 0.057981789 -0.3712690 0.48803342
> 63 0.029704039 -0.3712690 0.25597325
> 64 0.034416998 -0.3712690 0.25597325
> 65 0.062694747 -0.3712690 0.23054948
> 66 0.062694747 -0.3712690 0.23054948
> 67 0.001426290 -0.3712690 -0.13680005
> 68 0.006139248 -0.3712690 -0.13680005
> 69 -0.102258791 -0.3712690 0.51977995
> 70 -0.102258791 -0.3712690 0.51977995
> 71 -0.007999626 -0.3712690 -0.23878154
> 72 -0.007999626 -0.3712690 -0.23878154
> 73 0.039129956 -0.3712690 0.17174306
> 74 0.039129956 -0.3712690 0.17174306
> 75 0.076833621 1.0395533 -0.35822829
> 76 0.076833621 1.0395533 -0.35822829
297,312c297,309
< [1] 0.696003729 0.696003729 0.244575316 0.244575316 0.494175549
< [6] 0.494175549 -0.659248798 -0.659248798 0.521423106 0.521423106
< [11] -0.114492938 -0.114492938 0.800127481 0.800127481 -0.488101282
< [16] -0.488101282 -0.120396647 -0.120396647 0.131121515 0.131121515
< [21] -0.214987009 -0.214987009 -0.054872789 -0.054872789 0.184657295
< [26] 0.184657295 -0.510007747 -0.510007747 -0.790746805 -0.790746805
< [31] 0.324674289 0.324674289 -0.239374060 -0.239374060 -0.264428564
< [36] -0.264428564 -0.472698773 -0.472698773 0.006304049 0.006304049
< [41] -0.873434085 -0.873434085 -0.530880840 -0.530880840 0.351411783
< [46] 0.351411783 -0.037212138 -0.037212138 0.442049266 0.442049266
< [51] -0.419206550 -0.419206550 -0.108012854 -0.108012854 0.346332076
< [56] 0.346332076 0.659300205 0.659300205 0.197278585 0.197278585
< [61] 0.304868889 0.304868889 0.139712997 0.139712997 0.093574024
< [66] 0.093574024 -0.209690355 -0.209690355 0.302070834 0.302070834
< [71] -0.278962288 -0.278962288 0.068599919 0.068599919 0.078493616
< [76] 0.078493616
---
> [1] 0.69600373 0.69600373 0.24457532 0.24457532 0.49417555 0.49417555
> [7] -0.65924880 -0.65924880 0.52142311 0.52142311 -0.11449294 -0.11449294
> [13] 0.80012748 0.80012748 -0.48810128 -0.48810128 -0.12039665 -0.12039665
> [19] 0.13112152 0.13112152 -0.21498701 -0.21498701 -0.05487279 -0.05487279
> [25] 0.18465729 0.18465729 -0.51000775 -0.51000775 -0.79074681 -0.79074681
> [31] 0.32467429 0.32467429 -0.23937406 -0.23937406 -0.26442856 -0.26442856
> [37] -0.47269877 -0.47269877 0.00630405 0.00630405 -0.87343409 -0.87343409
> [43] -0.53088084 -0.53088084 0.35141178 0.35141178 -0.03721214 -0.03721214
> [49] 0.44204927 0.44204927 -0.41920655 -0.41920655 -0.10801285 -0.10801285
> [55] 0.34633208 0.34633208 0.65930021 0.65930021 0.19727858 0.19727858
> [61] 0.30486889 0.30486889 0.13971300 0.13971300 0.09357402 0.09357402
> [67] -0.20969035 -0.20969035 0.30207083 0.30207083 -0.27896229 -0.27896229
> [73] 0.06859992 0.06859992 0.07849362 0.07849362
333c330
< frailty(id, dist = "gauss 23 13.8 0.057
---
> frailty(id, dist = "gauss 23.0 13.8 0.057
Running 'fr_simple.R'
Comparing 'fr_simple.Rout' to 'fr_simple.Rout.save' ... OK
Running 'frailty.R'
Comparing 'frailty.Rout' to 'frailty.Rout.save' ... OK
Running 'frank.R'
Comparing 'frank.Rout' to 'frank.Rout.save' ... OK
Running 'infcox.R'
Comparing 'infcox.Rout' to 'infcox.Rout.save' ... OK
Running 'jasa.R'
Comparing 'jasa.Rout' to 'jasa.Rout.save' ... OK
Running 'model.matrix.R'
Comparing 'model.matrix.Rout' to 'model.matrix.Rout.save' ... OK
Running 'mrtest.R'
Comparing 'mrtest.Rout' to 'mrtest.Rout.save' ... OK
Running 'ovarian.R'
Comparing 'ovarian.Rout' to 'ovarian.Rout.save' ...78c78
< ecog.ps 0.398 1.49 0.586 0.679 0.5
---
> ecog.ps 0.398 1.49 0.586 0.68 0.5
92c92
< Likelihood ratio test=6.03 on 3 df, p=0.11 n= 26, number of events= 12
---
> Likelihood ratio test=6.03 on 3 df, p=0.110 n= 26, number of events= 12
Running 'prednew.R'
Comparing 'prednew.Rout' to 'prednew.Rout.save' ... OK
Running 'pyear.R'
Comparing 'pyear.Rout' to 'pyear.Rout.save' ... OK
Running 'r_capacitor.R'
Comparing 'r_capacitor.Rout' to 'r_capacitor.Rout.save' ... OK
Running 'r_donnell.R'
Comparing 'r_donnell.Rout' to 'r_donnell.Rout.save' ... OK
Running 'r_lung.R'
Comparing 'r_lung.Rout' to 'r_lung.Rout.save' ...85c85
< 6.273435252 0.401090541 -0.007475439 -0.339638098
---
> 6.27343525 0.40109054 -0.00747544 -0.33963810
Running 'r_peterson.R'
Comparing 'r_peterson.Rout' to 'r_peterson.Rout.save' ...82c82
< Variance of random effect= 0.17 I-likelihood = -10.1
---
> Variance of random effect= 0.170 I-likelihood = -10.1
Running 'r_resid.R'
Comparing 'r_resid.Rout' to 'r_resid.Rout.save' ... OK
Running 'r_sas.R'
Comparing 'r_sas.Rout' to 'r_sas.Rout.save' ... OK
Running 'r_scale.R'
Comparing 'r_scale.Rout' to 'r_scale.Rout.save' ... OK
Running 'r_stanford.R'
Comparing 'r_stanford.Rout' to 'r_stanford.Rout.save' ... OK
Running 'r_strata.R'
Comparing 'r_strata.Rout' to 'r_strata.Rout.save' ... OK
Running 'r_tdist.R'
Comparing 'r_tdist.Rout' to 'r_tdist.Rout.save' ... OK
Running 'r_user.R'
Comparing 'r_user.Rout' to 'r_user.Rout.save' ... OK
Running 'ratetable.R'
Comparing 'ratetable.Rout' to 'ratetable.Rout.save' ... OK
Running 'rounding.R'
Comparing 'rounding.Rout' to 'rounding.Rout.save' ... OK
Running 'singtest.R'
Comparing 'singtest.Rout' to 'singtest.Rout.save' ... OK
Running 'strata2.R'
Comparing 'strata2.Rout' to 'strata2.Rout.save' ... OK
Running 'stratatest.R'
Comparing 'stratatest.Rout' to 'stratatest.Rout.save' ... OK
Running 'summary_survfit.R'
Comparing 'summary_survfit.Rout' to 'summary_survfit.Rout.save' ... OK
Running 'surv.R'
Comparing 'surv.Rout' to 'surv.Rout.save' ... OK
Running 'survfit2.R'
Comparing 'survfit2.Rout' to 'survfit2.Rout.save' ... OK
Running 'survreg2.R'
Comparing 'survreg2.Rout' to 'survreg2.Rout.save' ... OK
Running 'survtest.R'
Comparing 'survtest.Rout' to 'survtest.Rout.save' ... OK
Running 'testci.R'
Comparing 'testci.Rout' to 'testci.Rout.save' ... OK
Running 'testci2.R'
Comparing 'testci2.Rout' to 'testci2.Rout.save' ... OK
Running 'testnull.R'
Comparing 'testnull.Rout' to 'testnull.Rout.save' ... OK
Running 'testreg.R'
Comparing 'testreg.Rout' to 'testreg.Rout.save' ...193,196c193,196
< (Intercept) 11.5268 1.528 7.542 4.62e-14
< age -0.0888 0.024 -3.703 2.13e-04
< ecog.ps 0.0818 0.364 0.225 8.22e-01
< Log(scale) -0.8023 0.271 -2.965 3.03e-03
---
> (Intercept) 11.5268 1.5283 7.542 4.62e-14
> age -0.0888 0.0240 -3.703 2.13e-04
> ecog.ps 0.0818 0.3642 0.225 8.22e-01
> Log(scale) -0.8023 0.2706 -2.965 3.03e-03
Running 'turnbull.R'
Comparing 'turnbull.Rout' to 'turnbull.Rout.save' ... OK
** running tests for arch 'x86_64' OK
Running 'aareg.R'
Comparing 'aareg.Rout' to 'aareg.Rout.save' ...259,260c259,260
< [1,] 7738.6204 -125.5077
< [2,] -125.5077 2.0768
---
> [1,] 7738.6204 -125.507657
> [2,] -125.5077 2.076800
264c264
< [1,] 4.22624
---
> [1,] 4.226240
321,325c321,325
< Intercept 0.00137589
< age 0.19055946
< sex 0.00112454
< ph.karno 0.24100515
< pat.karno 0.08316385
---
> Intercept 0.001375890
> age 0.190559455
> sex 0.001124540
> ph.karno 0.241005145
> pat.karno 0.083163853
344,348c344,348
< [1,] 22525.42254 -109.0376340 -1294.620657 -135.7477106 -24.1718358
< [2,] -109.03763 1.6505060 2.562655 0.1774270 -0.1206339
< [3,] -1294.62066 2.5626546 566.194480 7.4865489 -4.7691882
< [4,] -135.74771 0.1774270 7.486549 2.2974694 -0.9877341
< [5,] -24.17184 -0.1206339 -4.769188 -0.9877341 1.4499155
---
> [1,] 22525.42254 -109.0376340 -1294.620657 -135.747711 -24.1718358
> [2,] -109.03763 1.6505060 2.562655 0.177427 -0.1206339
> [3,] -1294.62066 2.5626546 566.194480 7.486549 -4.7691882
> [4,] -135.74771 0.1774270 7.486549 2.297469 -0.9877341
> [5,] -24.17184 -0.1206339 -4.769188 -0.987734 1.4499155
Running 'anova.R'
Comparing 'anova.Rout' to 'anova.Rout.save' ... OK
Running 'bladder.R'
Comparing 'bladder.Rout' to 'bladder.Rout.save' ...19,30c19,30
< rx -0.5176 0.596 0.3158 0.3075 -1.683 0.0920
< size 0.0679 1.070 0.1012 0.0853 0.796 0.4300
< number 0.2360 1.266 0.0761 0.0721 3.274 0.0011
< rx:strata(enum)enum=2 -0.1018 0.903 0.5043 0.3265 -0.312 0.7600
< rx:strata(enum)enum=3 -0.1823 0.833 0.5579 0.3916 -0.465 0.6400
< rx:strata(enum)enum=4 -0.1332 0.875 0.6581 0.4968 -0.268 0.7900
< size:strata(enum)enum=2 -0.1440 0.866 0.1680 0.1119 -1.287 0.2000
< size:strata(enum)enum=3 -0.2792 0.756 0.2086 0.1511 -1.847 0.0650
< size:strata(enum)enum=4 -0.2711 0.763 0.2515 0.1856 -1.460 0.1400
< number:strata(enum)enum=2 -0.0984 0.906 0.1193 0.1144 -0.861 0.3900
< number:strata(enum)enum=3 -0.0662 0.936 0.1298 0.1167 -0.567 0.5700
< number:strata(enum)enum=4 0.0928 1.097 0.1466 0.1175 0.790 0.4300
---
> rx -0.5176 0.596 0.316 0.3075 -1.683 0.0920
> size 0.0679 1.070 0.101 0.0853 0.796 0.4300
> number 0.2360 1.266 0.076 0.0721 3.274 0.0011
> rx:strata(enum)enum=2 -0.1018 0.903 0.504 0.3265 -0.312 0.7600
> rx:strata(enum)enum=3 -0.1823 0.833 0.558 0.3916 -0.465 0.6400
> rx:strata(enum)enum=4 -0.1332 0.875 0.658 0.4968 -0.268 0.7900
> size:strata(enum)enum=2 -0.1440 0.866 0.168 0.1119 -1.287 0.2000
> size:strata(enum)enum=3 -0.2792 0.756 0.209 0.1511 -1.847 0.0650
> size:strata(enum)enum=4 -0.2711 0.763 0.251 0.1856 -1.460 0.1400
> number:strata(enum)enum=2 -0.0984 0.906 0.119 0.1144 -0.861 0.3900
> number:strata(enum)enum=3 -0.0662 0.936 0.130 0.1167 -0.567 0.5700
> number:strata(enum)enum=4 0.0928 1.097 0.147 0.1175 0.790 0.4300
42,45c42,45
< [1,] 0.09455501 0.06017669 0.05677331 0.0437777
< [2,] 0.06017669 0.13242834 0.13011557 0.1160420
< [3,] 0.05677331 0.13011557 0.17235879 0.1590865
< [4,] 0.04377770 0.11604200 0.15908650 0.2398112
---
> [1,] 0.09455501 0.06017669 0.0567733 0.0437777
> [2,] 0.06017669 0.13242834 0.1301156 0.1160420
> [3,] 0.05677331 0.13011557 0.1723588 0.1590865
> [4,] 0.04377770 0.11604200 0.1590865 0.2398112
94,96c94,96
< rx -0.5176 0.596 0.3158 -1.639 0.1000
< size 0.0679 1.070 0.1012 0.671 0.5000
< number 0.2360 1.266 0.0761 3.102 0.0019
---
> rx -0.5176 0.596 0.316 -1.64 0.1000
> size 0.0679 1.070 0.101 0.67 0.5000
> number 0.2360 1.266 0.076 3.10 0.0019
118,120c118,120
< rx -0.25911 0.772 0.4051 -0.6396 0.52
< size -0.11636 0.890 0.1192 -0.9759 0.33
< number -0.00571 0.994 0.0967 -0.0591 0.95
---
> rx -0.25911 0.772 0.4051 -0.640 0.52
> size -0.11636 0.890 0.1192 -0.976 0.33
> number -0.00571 0.994 0.0967 -0.059 0.95
Running 'book1.R'
Comparing 'book1.Rout' to 'book1.Rout.save' ... OK
Running 'book2.R'
Comparing 'book2.Rout' to 'book2.Rout.save' ...117c117
< 0.157512 0.421244 -0.578756 0.000000
---
> 0.1575120 0.4212440 -0.5787560 0.0000000
Running 'book3.R'
Comparing 'book3.Rout' to 'book3.Rout.save' ...112,115c112,115
< 1 2 3 4 5 6
< 0.52111895 0.65741078 0.78977654 0.24738772 -0.60629349 0.36902492
< 7 8 9 10
< -0.06876579 -1.06876579 -0.42044692 -0.42044692
---
> 1 2 3 4 5 6 7
> 0.5211189 0.6574108 0.7897765 0.2473877 -0.6062935 0.3690249 -0.0687658
> 8 9 10
> -1.0687658 -0.4204469 -0.4204469
Running 'book4.R'
Comparing 'book4.Rout' to 'book4.Rout.save' ...114,115c114,115
< [1] -0.0105526 0.0105526 0.0105526 -0.0105526 0.0105526 -0.0105526
< [7] -0.0105526 -0.0105526 0.0105526 0.0105526
---
> [1] -0.01055260 0.01055260 0.01055260 -0.01055260 0.01055260 -0.01055260
> [7] -0.01055260 -0.01055260 0.01055260 0.01055260
126,135c126,135
< 1 -0.0105526
< 2 0.0105526
< 3 0.0105526
< 4 -0.0105526
< 5 0.0105526
< 6 -0.0105526
< 7 -0.0105526
< 8 -0.0105526
< 9 0.0105526
< 10 0.0105526
---
> 1 -0.01055260
> 2 0.01055260
> 3 0.01055260
> 4 -0.01055260
> 5 0.01055260
> 6 -0.01055260
> 7 -0.01055260
> 8 -0.01055260
> 9 0.01055260
> 10 0.01055260
137c137
< [1] -0.0105526
---
> [1] -0.01055260
140,143c140,143
< 1 2 3 4 5 6 7
< -0.0105526 0.0105526 0.0105526 -0.0105526 0.0105526 -0.0105526 -0.0105526
< 8 9 10
< -0.0105526 0.0105526 0.0105526
---
> 1 2 3 4 5 6
> -0.01055260 0.01055260 0.01055260 -0.01055260 0.01055260 -0.01055260
> 7 8 9 10
> -0.01055260 -0.01055260 0.01055260 0.01055260
178,187c178,187
< 1 -0.0105526
< 2 0.0105526
< 3 0.0105526
< 4 -0.0105526
< 5 0.0105526
< 6 -0.0105526
< 7 -0.0105526
< 8 -0.0105526
< 9 0.0105526
< 10 0.0105526
---
> 1 -0.01055260
> 2 0.01055260
> 3 0.01055260
> 4 -0.01055260
> 5 0.01055260
> 6 -0.01055260
> 7 -0.01055260
> 8 -0.01055260
> 9 0.01055260
> 10 0.01055260
189c189
< [1] -0.0105526
---
> [1] -0.01055260
Running 'book5.R'
Comparing 'book5.Rout' to 'book5.Rout.save' ... OK
Running 'book6.R'
Comparing 'book6.Rout' to 'book6.Rout.save' ... OK
Running 'cancer.R'
Comparing 'cancer.Rout' to 'cancer.Rout.save' ...49,61c49,61
< 30 46 5 0.9000 0.0424 0.82057 0.987
< 60 43 2 0.8600 0.0491 0.76900 0.962
< 90 40 3 0.8000 0.0566 0.69647 0.919
< 120 34 4 0.7174 0.0641 0.60216 0.855
< 150 31 3 0.6541 0.0680 0.53342 0.802
< 180 26 6 0.5275 0.0719 0.40385 0.689
< 210 21 4 0.4431 0.0717 0.32266 0.608
< 240 17 3 0.3766 0.0705 0.26100 0.543
< 270 17 0 0.3766 0.0705 0.26100 0.543
< 300 13 3 0.3102 0.0677 0.20223 0.476
< 330 11 2 0.2624 0.0651 0.16135 0.427
< 365 9 2 0.2147 0.0614 0.12258 0.376
< 730 1 6 0.0371 0.0345 0.00601 0.229
---
> 30 46 5 0.9000 0.0424 0.821 0.987
> 60 43 2 0.8600 0.0491 0.769 0.962
> 90 40 3 0.8000 0.0566 0.696 0.919
> 120 34 4 0.7174 0.0641 0.602 0.855
> 150 31 3 0.6541 0.0680 0.533 0.802
> 180 26 6 0.5275 0.0719 0.404 0.689
> 210 21 4 0.4431 0.0717 0.323 0.608
> 240 17 3 0.3766 0.0705 0.261 0.543
> 270 17 0 0.3766 0.0705 0.261 0.543
> 300 13 3 0.3102 0.0677 0.202 0.476
> 330 11 2 0.2624 0.0651 0.161 0.427
> 365 9 2 0.2147 0.0614 0.123 0.376
> 730 1 6 0.0371 0.0345 0.006 0.229
156,163c156,163
< ph.ecog 0.0276 0.1078 0.7427
< ph.karno 0.1331 2.0018 0.1571
< pat.karno 0.0250 0.0841 0.7718
< wt.loss -0.0386 0.2122 0.6451
< sex 0.0399 0.1800 0.6713
< age 0.0639 0.5600 0.4543
< meal.cal 0.1611 3.6945 0.0546
< GLOBAL NA 9.0115 0.2518
---
> ph.ecog 0.0276 0.108 0.7427
> ph.karno 0.1331 2.002 0.1571
> pat.karno 0.0250 0.084 0.7718
> wt.loss -0.0386 0.212 0.6451
> sex 0.0399 0.180 0.6713
> age 0.0639 0.560 0.4543
> meal.cal 0.1611 3.695 0.0546
> GLOBAL NA 9.012 0.2518
Running 'concordance.R'
Comparing 'concordance.Rout' to 'concordance.Rout.save' ... OK
Running 'counting.R'
Comparing 'counting.Rout' to 'counting.Rout.save' ... OK
Running 'coxsurv.R'
Comparing 'coxsurv.Rout' to 'coxsurv.Rout.save' ... OK
Running 'coxsurv2.R'
Comparing 'coxsurv2.Rout' to 'coxsurv2.Rout.save' ... OK
Running 'coxsurv3.R'
Comparing 'coxsurv3.Rout' to 'coxsurv3.Rout.save' ... OK
Running 'coxsurv4.R'
Comparing 'coxsurv4.Rout' to 'coxsurv4.Rout.save' ... OK
Running 'detail.R'
Comparing 'detail.Rout' to 'detail.Rout.save' ... OK
Running 'difftest.R'
Comparing 'difftest.Rout' to 'difftest.Rout.save' ...34,35c34,35
< x=Maintained 11 7 10.69 1.27 3.4
< x=Nonmaintained 12 11 7.31 1.86 3.4
---
> x=Maintained 11 7 10.69 1.27 3.40
> x=Nonmaintained 12 11 7.31 1.86 3.40
44,45c44,45
< x=Maintained 11 7 10.69 1.27 3.4
< x=Nonmaintained 12 11 7.31 1.86 3.4
---
> x=Maintained 11 7 10.69 1.27 3.40
> x=Nonmaintained 12 11 7.31 1.86 3.40
Running 'doaml.R'
Comparing 'doaml.Rout' to 'doaml.Rout.save' ...83,84c83,84
< aml$x=Maintained 11 7 10.69 1.27 3.4
< aml$x=Nonmaintained 12 11 7.31 1.86 3.4
---
> aml$x=Maintained 11 7 10.69 1.27 3.40
> aml$x=Nonmaintained 12 11 7.31 1.86 3.40
Running 'doweight.R'
Comparing 'doweight.Rout' to 'doweight.Rout.save' ... OK
Running 'expected.R'
Comparing 'expected.Rout' to 'expected.Rout.save' ... OK
Running 'expected2.R'
Comparing 'expected2.Rout' to 'expected2.Rout.save' ... OK
Running 'factor.R'
Comparing 'factor.Rout' to 'factor.Rout.save' ... OK
Running 'factor2.R'
Comparing 'factor2.Rout' to 'factor2.Rout.save' ... OK
Running 'fr_cancer.R'
Comparing 'fr_cancer.Rout' to 'fr_cancer.Rout.save' ...64c64
< Theta= 0.691
---
> Theta= 0.69
97c97
< Theta= 0.779
---
> Theta= 0.78
Running 'fr_colon.R'
Comparing 'fr_colon.Rout' to 'fr_colon.Rout.save' ...19,22c19,22
< rxLev -0.0362 0.964 0.0768 0.1056 -0.343 7.3e-01
< rxLev+5FU -0.4488 0.638 0.0840 0.1168 -3.842 1.2e-04
< extent 0.5155 1.674 0.0796 0.1097 4.701 2.6e-06
< node4 0.8799 2.411 0.0681 0.0961 9.160 0.0e+00
---
> rxLev -0.0362 0.964 0.0768 0.106 -0.343 7.3e-01
> rxLev+5FU -0.4488 0.638 0.0840 0.117 -3.842 1.2e-04
> extent 0.5155 1.674 0.0796 0.110 4.701 2.6e-06
> node4 0.8799 2.411 0.0681 0.096 9.160 0.0e+00
Running 'fr_kidney.R'
Comparing 'fr_kidney.Rout' to 'fr_kidney.Rout.save' ...106c106
< Likelihood ratio test=63.8 on 21 df, p=3.27e-06 n= 76
---
> Likelihood ratio test=63.8 on 21.0 df, p=3.27e-06 n= 76
121,125c121,125
< age 0.00489 0.015 0.0106 0.11 1.0 0.74000
< sex -1.69728 0.461 0.3617 13.55 1.0 0.00023
< diseaseGN 0.17986 0.545 0.3927 0.11 1.0 0.74000
< diseaseAN 0.39294 0.545 0.3982 0.52 1.0 0.47000
< diseasePKD -1.13631 0.825 0.6173 1.90 1.0 0.17000
---
> age 0.00489 0.0150 0.0106 0.11 1.0 0.74000
> sex -1.69728 0.4610 0.3617 13.55 1.0 0.00023
> diseaseGN 0.17986 0.5449 0.3927 0.11 1.0 0.74000
> diseaseAN 0.39294 0.5448 0.3982 0.52 1.0 0.47000
> diseasePKD -1.13631 0.8252 0.6173 1.90 1.0 0.17000
209,210c209,210
< age 0.00364 0.0105 0.00891 0.12 1.00 0.73000
< sex -1.31953 0.3956 0.32497 11.13 1.00 0.00085
---
> age 0.00364 0.0105 0.0089 0.12 1.00 0.73000
> sex -1.31953 0.3956 0.3250 11.13 1.00 0.00085
224,225c224,225
< age 0.00561 0.012 0.00872 0.22 1.0 0.64000
< sex -1.65487 0.483 0.38527 11.74 1.0 0.00061
---
> age 0.00561 0.0120 0.00872 0.22 1.0 0.64000
> sex -1.65487 0.4829 0.38527 11.74 1.0 0.00061
257,258c257,258
< age 0.00785 0.015 0.00823 0.27 1.0 0.60000
< sex -1.88990 0.561 0.39941 11.34 1.0 0.00076
---
> age 0.00785 0.0150 0.00823 0.27 1.0 0.60000
> sex -1.88990 0.5611 0.39941 11.34 1.0 0.00076
275,276c275,276
< age 0.00561 0.012 0.00872 0.22 1.0 0.64000
< sex -1.65487 0.483 0.38527 11.74 1.0 0.00061
---
> age 0.00561 0.0120 0.00872 0.22 1.0 0.64000
> sex -1.65487 0.4829 0.38527 11.74 1.0 0.00061
Running 'fr_lung.R'
Comparing 'fr_lung.Rout' to 'fr_lung.Rout.save' ... OK
Running 'fr_ovarian.R'
Comparing 'fr_ovarian.Rout' to 'fr_ovarian.Rout.save' ...47,48c47,48
< rx -0.373 0.761 0.749 0.24 1.00 0.6200
< pspline(age, df = 4), lin 0.139 0.044 0.044 9.98 1.00 0.0016
---
> rx -0.373 0.761 0.7485 0.24 1.00 0.6200
> pspline(age, df = 4), lin 0.139 0.044 0.0440 9.98 1.00 0.0016
Running 'fr_rat1.R'
Comparing 'fr_rat1.Rout' to 'fr_rat1.Rout.save' ...77c77
< Likelihood ratio test=50.7 on 23.7 df, p=0.001 n= 150
---
> Likelihood ratio test=50.7 on 23.7 df, p=0.00100 n= 150
85c85
< frailty(litter) 18 14.6 0.24
---
> frailty(litter) 18.0 14.6 0.24
Running 'fr_rat2.R'
Comparing 'fr_rat2.Rout' to 'fr_rat2.Rout.save' ...49c49
< Likelihood ratio test=32.9 on 1 df, p=9.89e-09 n= 253, number of events= 212
---
> Likelihood ratio test=32.9 on 1 df, p=9.9e-09 n= 253, number of events= 212
69c69
< rx -0.79 0.22 0.154 12.9 1.0 3.2e-04
---
> rx -0.79 0.220 0.154 12.9 1.0 3.2e-04
75c75
< Likelihood ratio test=118 on 25.4 df, p=6.99e-14 n= 253
---
> Likelihood ratio test=118 on 25.4 df, p=7e-14 n= 253
106c106
< rx -0.838 0.23 0.151 13.3 1.0 0.00026
---
> rx -0.838 0.230 0.151 13.3 1.0 0.00026
Running 'fr_resid.R'
Comparing 'fr_resid.Rout' to 'fr_resid.Rout.save' ...78,153c78,153
< 1 -0.073981042 1.039553 0.59814468
< 2 -0.073981042 1.039553 0.59814468
< 3 0.020278123 -0.371269 0.38512389
< 4 0.020278123 -0.371269 0.38512389
< 5 -0.055129209 1.039553 0.20210998
< 6 -0.055129209 1.039553 0.20210998
< 7 -0.059842167 -0.371269 -0.55932015
< 8 -0.055129209 -0.371269 -0.55932015
< 9 -0.158814289 1.039553 0.28558387
< 10 -0.158814289 1.039553 0.28558387
< 11 -0.130536540 -0.371269 0.06628942
< 12 -0.125823582 -0.371269 0.06628942
< 13 0.034416998 1.039553 0.80505119
< 14 0.034416998 1.039553 0.80505119
< 15 0.053268830 -0.371269 -0.43834241
< 16 0.057981789 -0.371269 -0.43834241
< 17 0.119250245 -0.371269 -0.05631649
< 18 0.119250245 -0.371269 -0.05631649
< 19 0.034416998 1.039553 -0.49980572
< 20 0.039129956 1.039553 -0.49980572
< 21 0.001426290 -0.371269 -0.13028264
< 22 0.001426290 -0.371269 -0.13028264
< 23 -0.045703292 -0.371269 0.06377401
< 24 -0.045703292 -0.371269 0.06377401
< 25 -0.040990334 -0.371269 0.38815296
< 26 -0.040990334 -0.371269 0.38815296
< 27 -0.007999626 -0.371269 -0.47650510
< 28 -0.007999626 -0.371269 -0.47650510
< 29 -0.125823582 -0.371269 -0.66986830
< 30 -0.125823582 -0.371269 -0.66986830
< 31 0.076833621 1.039553 0.19359678
< 32 0.076833621 1.039553 0.19359678
< 33 0.076833621 -0.371269 -0.16483200
< 34 0.076833621 -0.371269 -0.16483200
< 35 -0.003286668 -0.371269 -0.15794998
< 36 0.001426290 -0.371269 -0.15794998
< 37 0.043842914 -0.371269 -0.46236014
< 38 0.043842914 -0.371269 -0.46236014
< 39 0.001426290 -0.371269 0.12603308
< 40 0.001426290 -0.371269 0.12603308
< 41 0.010852206 1.039553 -1.74303142
< 42 0.015565165 1.039553 -1.74303142
< 43 -0.064555125 -0.371269 -0.45211210
< 44 -0.064555125 -0.371269 -0.45211210
< 45 0.086259538 -0.371269 0.51574106
< 46 0.090972496 -0.371269 0.51574106
< 47 -0.007999626 -0.371269 0.09475123
< 48 -0.003286668 -0.371269 0.09475123
< 49 -0.003286668 1.039553 0.05790354
< 50 -0.003286668 1.039553 0.05790354
< 51 0.062694747 -0.371269 -0.37933234
< 52 0.067407705 -0.371269 -0.37933234
< 53 -0.158814289 -0.371269 0.11248891
< 54 -0.158814289 -0.371269 0.11248891
< 55 0.039129956 -0.371269 0.54791210
< 56 0.039129956 -0.371269 0.54791210
< 57 0.043842914 1.039553 0.45873482
< 58 0.043842914 1.039553 0.45873482
< 59 0.048555872 -0.371269 0.35639797
< 60 0.048555872 -0.371269 0.35639797
< 61 0.057981789 -0.371269 0.48803342
< 62 0.057981789 -0.371269 0.48803342
< 63 0.029704039 -0.371269 0.25597325
< 64 0.034416998 -0.371269 0.25597325
< 65 0.062694747 -0.371269 0.23054948
< 66 0.062694747 -0.371269 0.23054948
< 67 0.001426290 -0.371269 -0.13680005
< 68 0.006139248 -0.371269 -0.13680005
< 69 -0.102258791 -0.371269 0.51977995
< 70 -0.102258791 -0.371269 0.51977995
< 71 -0.007999626 -0.371269 -0.23878154
< 72 -0.007999626 -0.371269 -0.23878154
< 73 0.039129956 -0.371269 0.17174306
< 74 0.039129956 -0.371269 0.17174306
< 75 0.076833621 1.039553 -0.35822829
< 76 0.076833621 1.039553 -0.35822829
---
> 1 -0.073981042 1.0395533 0.59814468
> 2 -0.073981042 1.0395533 0.59814468
> 3 0.020278123 -0.3712690 0.38512389
> 4 0.020278123 -0.3712690 0.38512389
> 5 -0.055129209 1.0395533 0.20210998
> 6 -0.055129209 1.0395533 0.20210998
> 7 -0.059842167 -0.3712690 -0.55932015
> 8 -0.055129209 -0.3712690 -0.55932015
> 9 -0.158814289 1.0395533 0.28558387
> 10 -0.158814289 1.0395533 0.28558387
> 11 -0.130536540 -0.3712690 0.06628942
> 12 -0.125823582 -0.3712690 0.06628942
> 13 0.034416998 1.0395533 0.80505119
> 14 0.034416998 1.0395533 0.80505119
> 15 0.053268830 -0.3712690 -0.43834241
> 16 0.057981789 -0.3712690 -0.43834241
> 17 0.119250245 -0.3712690 -0.05631649
> 18 0.119250245 -0.3712690 -0.05631649
> 19 0.034416998 1.0395533 -0.49980572
> 20 0.039129956 1.0395533 -0.49980572
> 21 0.001426290 -0.3712690 -0.13028264
> 22 0.001426290 -0.3712690 -0.13028264
> 23 -0.045703292 -0.3712690 0.06377401
> 24 -0.045703292 -0.3712690 0.06377401
> 25 -0.040990334 -0.3712690 0.38815296
> 26 -0.040990334 -0.3712690 0.38815296
> 27 -0.007999626 -0.3712690 -0.47650510
> 28 -0.007999626 -0.3712690 -0.47650510
> 29 -0.125823582 -0.3712690 -0.66986830
> 30 -0.125823582 -0.3712690 -0.66986830
> 31 0.076833621 1.0395533 0.19359678
> 32 0.076833621 1.0395533 0.19359678
> 33 0.076833621 -0.3712690 -0.16483200
> 34 0.076833621 -0.3712690 -0.16483200
> 35 -0.003286668 -0.3712690 -0.15794998
> 36 0.001426290 -0.3712690 -0.15794998
> 37 0.043842914 -0.3712690 -0.46236014
> 38 0.043842914 -0.3712690 -0.46236014
> 39 0.001426290 -0.3712690 0.12603308
> 40 0.001426290 -0.3712690 0.12603308
> 41 0.010852206 1.0395533 -1.74303142
> 42 0.015565165 1.0395533 -1.74303142
> 43 -0.064555125 -0.3712690 -0.45211210
> 44 -0.064555125 -0.3712690 -0.45211210
> 45 0.086259538 -0.3712690 0.51574106
> 46 0.090972496 -0.3712690 0.51574106
> 47 -0.007999626 -0.3712690 0.09475123
> 48 -0.003286668 -0.3712690 0.09475123
> 49 -0.003286668 1.0395533 0.05790354
> 50 -0.003286668 1.0395533 0.05790354
> 51 0.062694747 -0.3712690 -0.37933234
> 52 0.067407705 -0.3712690 -0.37933234
> 53 -0.158814289 -0.3712690 0.11248891
> 54 -0.158814289 -0.3712690 0.11248891
> 55 0.039129956 -0.3712690 0.54791210
> 56 0.039129956 -0.3712690 0.54791210
> 57 0.043842914 1.0395533 0.45873482
> 58 0.043842914 1.0395533 0.45873482
> 59 0.048555872 -0.3712690 0.35639797
> 60 0.048555872 -0.3712690 0.35639797
> 61 0.057981789 -0.3712690 0.48803342
> 62 0.057981789 -0.3712690 0.48803342
> 63 0.029704039 -0.3712690 0.25597325
> 64 0.034416998 -0.3712690 0.25597325
> 65 0.062694747 -0.3712690 0.23054948
> 66 0.062694747 -0.3712690 0.23054948
> 67 0.001426290 -0.3712690 -0.13680005
> 68 0.006139248 -0.3712690 -0.13680005
> 69 -0.102258791 -0.3712690 0.51977995
> 70 -0.102258791 -0.3712690 0.51977995
> 71 -0.007999626 -0.3712690 -0.23878154
> 72 -0.007999626 -0.3712690 -0.23878154
> 73 0.039129956 -0.3712690 0.17174306
> 74 0.039129956 -0.3712690 0.17174306
> 75 0.076833621 1.0395533 -0.35822829
> 76 0.076833621 1.0395533 -0.35822829
297,312c297,309
< [1] 0.696003729 0.696003729 0.244575316 0.244575316 0.494175549
< [6] 0.494175549 -0.659248798 -0.659248798 0.521423106 0.521423106
< [11] -0.114492938 -0.114492938 0.800127481 0.800127481 -0.488101282
< [16] -0.488101282 -0.120396647 -0.120396647 0.131121515 0.131121515
< [21] -0.214987009 -0.214987009 -0.054872789 -0.054872789 0.184657295
< [26] 0.184657295 -0.510007747 -0.510007747 -0.790746805 -0.790746805
< [31] 0.324674289 0.324674289 -0.239374060 -0.239374060 -0.264428564
< [36] -0.264428564 -0.472698773 -0.472698773 0.006304049 0.006304049
< [41] -0.873434085 -0.873434085 -0.530880840 -0.530880840 0.351411783
< [46] 0.351411783 -0.037212138 -0.037212138 0.442049266 0.442049266
< [51] -0.419206550 -0.419206550 -0.108012854 -0.108012854 0.346332076
< [56] 0.346332076 0.659300205 0.659300205 0.197278585 0.197278585
< [61] 0.304868889 0.304868889 0.139712997 0.139712997 0.093574024
< [66] 0.093574024 -0.209690355 -0.209690355 0.302070834 0.302070834
< [71] -0.278962288 -0.278962288 0.068599919 0.068599919 0.078493616
< [76] 0.078493616
---
> [1] 0.69600373 0.69600373 0.24457532 0.24457532 0.49417555 0.49417555
> [7] -0.65924880 -0.65924880 0.52142311 0.52142311 -0.11449294 -0.11449294
> [13] 0.80012748 0.80012748 -0.48810128 -0.48810128 -0.12039665 -0.12039665
> [19] 0.13112152 0.13112152 -0.21498701 -0.21498701 -0.05487279 -0.05487279
> [25] 0.18465729 0.18465729 -0.51000775 -0.51000775 -0.79074681 -0.79074681
> [31] 0.32467429 0.32467429 -0.23937406 -0.23937406 -0.26442856 -0.26442856
> [37] -0.47269877 -0.47269877 0.00630405 0.00630405 -0.87343409 -0.87343409
> [43] -0.53088084 -0.53088084 0.35141178 0.35141178 -0.03721214 -0.03721214
> [49] 0.44204927 0.44204927 -0.41920655 -0.41920655 -0.10801285 -0.10801285
> [55] 0.34633208 0.34633208 0.65930021 0.65930021 0.19727858 0.19727858
> [61] 0.30486889 0.30486889 0.13971300 0.13971300 0.09357402 0.09357402
> [67] -0.20969035 -0.20969035 0.30207083 0.30207083 -0.27896229 -0.27896229
> [73] 0.06859992 0.06859992 0.07849362 0.07849362
333c330
< frailty(id, dist = "gauss 23 13.8 0.057
---
> frailty(id, dist = "gauss 23.0 13.8 0.057
Running 'fr_simple.R'
Comparing 'fr_simple.Rout' to 'fr_simple.Rout.save' ... OK
Running 'frailty.R'
Comparing 'frailty.Rout' to 'frailty.Rout.save' ... OK
Running 'frank.R'
Comparing 'frank.Rout' to 'frank.Rout.save' ... OK
Running 'infcox.R'
Comparing 'infcox.Rout' to 'infcox.Rout.save' ... OK
Running 'jasa.R'
Comparing 'jasa.Rout' to 'jasa.Rout.save' ... OK
Running 'model.matrix.R'
Comparing 'model.matrix.Rout' to 'model.matrix.Rout.save' ... OK
Running 'mrtest.R'
Comparing 'mrtest.Rout' to 'mrtest.Rout.save' ... OK
Running 'ovarian.R'
Comparing 'ovarian.Rout' to 'ovarian.Rout.save' ...78c78
< ecog.ps 0.398 1.49 0.586 0.679 0.5
---
> ecog.ps 0.398 1.49 0.586 0.68 0.5
92c92
< Likelihood ratio test=6.03 on 3 df, p=0.11 n= 26, number of events= 12
---
> Likelihood ratio test=6.03 on 3 df, p=0.110 n= 26, number of events= 12
Running 'prednew.R'
Comparing 'prednew.Rout' to 'prednew.Rout.save' ... OK
Running 'pyear.R'
Comparing 'pyear.Rout' to 'pyear.Rout.save' ... OK
Running 'r_capacitor.R'
Comparing 'r_capacitor.Rout' to 'r_capacitor.Rout.save' ... OK
Running 'r_donnell.R'
Comparing 'r_donnell.Rout' to 'r_donnell.Rout.save' ... OK
Running 'r_lung.R'
Comparing 'r_lung.Rout' to 'r_lung.Rout.save' ...85c85
< 6.273435252 0.401090541 -0.007475439 -0.339638098
---
> 6.27343525 0.40109054 -0.00747544 -0.33963810
Running 'r_peterson.R'
Comparing 'r_peterson.Rout' to 'r_peterson.Rout.save' ...82c82
< Variance of random effect= 0.17 I-likelihood = -10.1
---
> Variance of random effect= 0.170 I-likelihood = -10.1
Running 'r_resid.R'
Comparing 'r_resid.Rout' to 'r_resid.Rout.save' ... OK
Running 'r_sas.R'
Comparing 'r_sas.Rout' to 'r_sas.Rout.save' ... OK
Running 'r_scale.R'
Comparing 'r_scale.Rout' to 'r_scale.Rout.save' ... OK
Running 'r_stanford.R'
Comparing 'r_stanford.Rout' to 'r_stanford.Rout.save' ... OK
Running 'r_strata.R'
Comparing 'r_strata.Rout' to 'r_strata.Rout.save' ... OK
Running 'r_tdist.R'
Comparing 'r_tdist.Rout' to 'r_tdist.Rout.save' ... OK
Running 'r_user.R'
Comparing 'r_user.Rout' to 'r_user.Rout.save' ... OK
Running 'ratetable.R'
Comparing 'ratetable.Rout' to 'ratetable.Rout.save' ... OK
Running 'rounding.R'
Comparing 'rounding.Rout' to 'rounding.Rout.save' ... OK
Running 'singtest.R'
Comparing 'singtest.Rout' to 'singtest.Rout.save' ... OK
Running 'strata2.R'
Comparing 'strata2.Rout' to 'strata2.Rout.save' ... OK
Running 'stratatest.R'
Comparing 'stratatest.Rout' to 'stratatest.Rout.save' ... OK
Running 'summary_survfit.R'
Comparing 'summary_survfit.Rout' to 'summary_survfit.Rout.save' ... OK
Running 'surv.R'
Comparing 'surv.Rout' to 'surv.Rout.save' ... OK
Running 'survfit2.R'
Comparing 'survfit2.Rout' to 'survfit2.Rout.save' ... OK
Running 'survreg2.R'
Comparing 'survreg2.Rout' to 'survreg2.Rout.save' ... OK
Running 'survtest.R'
Comparing 'survtest.Rout' to 'survtest.Rout.save' ... OK
Running 'testci.R'
Comparing 'testci.Rout' to 'testci.Rout.save' ... OK
Running 'testci2.R'
Comparing 'testci2.Rout' to 'testci2.Rout.save' ... OK
Running 'testnull.R'
Comparing 'testnull.Rout' to 'testnull.Rout.save' ... OK
Running 'testreg.R'
Comparing 'testreg.Rout' to 'testreg.Rout.save' ...193,196c193,196
< (Intercept) 11.5268 1.528 7.542 4.62e-14
< age -0.0888 0.024 -3.703 2.13e-04
< ecog.ps 0.0818 0.364 0.225 8.22e-01
< Log(scale) -0.8023 0.271 -2.965 3.03e-03
---
> (Intercept) 11.5268 1.5283 7.542 4.62e-14
> age -0.0888 0.0240 -3.703 2.13e-04
> ecog.ps 0.0818 0.3642 0.225 8.22e-01
> Log(scale) -0.8023 0.2706 -2.965 3.03e-03
Running 'turnbull.R'
Comparing 'turnbull.Rout' to 'turnbull.Rout.save' ... OK
checking PDF version of manual ... OK
elapsed time (check, wall clock): 5:22