Last updated on 2020-08-01 07:48:07 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.2 | 15.49 | 158.59 | 174.08 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.3.2 | 13.45 | 113.14 | 126.59 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.3.2 | 202.41 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.3.2 | 204.84 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 0.3.2 | 48.00 | 155.00 | 203.00 | ERROR | |
| r-patched-linux-x86_64 | 0.3.2 | 13.65 | 146.04 | 159.69 | ERROR | |
| r-patched-solaris-x86 | 0.3.2 | 290.00 | ERROR | |||
| r-release-linux-x86_64 | 0.3.2 | 12.18 | 147.91 | 160.09 | ERROR | |
| r-release-macos-x86_64 | 0.3.2 | OK | ||||
| r-release-windows-ix86+x86_64 | 0.3.2 | 62.00 | 168.00 | 230.00 | ERROR | |
| r-oldrel-macos-x86_64 | 0.3.2 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 0.3.2 | 39.00 | 151.00 | 190.00 | ERROR |
Version: 0.3.2
Check: examples
Result: ERROR
Running examples in 'coxed-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.coxedExpdur
> ### Title: The mean or median expected duration
> ### Aliases: summary.coxedExpdur
>
> ### ** Examples
>
> require(survival)
> mv.surv <- Surv(martinvanberg$formdur, event = rep(1, nrow(martinvanberg)))
> mv.cox <- coxph(mv.surv ~ postel + prevdef + cont + ident + rgovm + pgovno + tpgovno +
+ minority, method = "breslow", data = martinvanberg)
> summary(mv.cox)
Call:
coxph(formula = mv.surv ~ postel + prevdef + cont + ident + rgovm +
pgovno + tpgovno + minority, data = martinvanberg, method = "breslow")
n= 203, number of events= 203
coef exp(coef) se(coef) z Pr(>|z|)
postel -0.57665 0.56177 0.16862 -3.420 0.000627 ***
prevdef -0.10000 0.90484 0.22987 -0.435 0.663543
cont 1.10047 3.00556 0.23970 4.591 4.41e-06 ***
ident 0.14579 1.15695 0.11859 1.229 0.218938
rgovm -0.21312 0.80806 0.12036 -1.771 0.076625 .
pgovno 1.19057 3.28894 0.12405 9.598 < 2e-16 ***
tpgovno -0.43189 0.64928 0.03476 -12.425 < 2e-16 ***
minority -0.42759 0.65208 0.20793 -2.056 0.039740 *
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
exp(coef) exp(-coef) lower .95 upper .95
postel 0.5618 1.7801 0.4037 0.7818
prevdef 0.9048 1.1052 0.5766 1.4198
cont 3.0056 0.3327 1.8789 4.8079
ident 1.1570 0.8643 0.9170 1.4597
rgovm 0.8081 1.2375 0.6382 1.0231
pgovno 3.2889 0.3040 2.5791 4.1942
tpgovno 0.6493 1.5402 0.6065 0.6951
minority 0.6521 1.5336 0.4338 0.9801
Concordance= 0.903 (se = 0.007 )
Likelihood ratio test= 277.2 on 8 df, p=<2e-16
Wald test = 218.1 on 8 df, p=<2e-16
Score (logrank) test = 279.3 on 8 df, p=<2e-16
>
> # NPSF method
> ed1 <- coxed(mv.cox, method="npsf")
> ed1$baseline.functions
time cbh survivor
1 1 0.01631230 9.838200e-01
2 2 0.03587341 9.647624e-01
3 3 0.04746259 9.536462e-01
4 4 0.07651484 9.263392e-01
5 5 0.09169880 9.123799e-01
6 6 0.12573075 8.818522e-01
7 7 0.16500990 8.478853e-01
8 8 0.18849681 8.282031e-01
9 9 0.20530921 8.143955e-01
10 10 0.24089191 7.859266e-01
11 11 0.29960997 7.411072e-01
12 12 0.33587336 7.147136e-01
13 13 0.34926287 7.052077e-01
14 14 0.44435177 6.412398e-01
15 15 0.47494715 6.219179e-01
16 16 0.52282119 5.928457e-01
17 17 0.55688241 5.729926e-01
18 18 0.64587601 5.242031e-01
19 19 0.78113579 4.578857e-01
20 20 0.85884119 4.236527e-01
21 21 0.94180170 3.899247e-01
22 22 1.00021359 3.678009e-01
23 23 1.09362425 3.350002e-01
24 24 1.22638118 2.933522e-01
25 26 1.33308790 2.636618e-01
26 27 1.44872000 2.348707e-01
27 30 1.81954923 1.620988e-01
28 31 1.92420399 1.459919e-01
29 33 2.14527897 1.170354e-01
30 34 2.26179451 1.041634e-01
31 35 2.44667759 8.658077e-02
32 36 2.80857821 6.029065e-02
33 37 3.14057906 4.325774e-02
34 38 3.24639408 3.891428e-02
35 39 3.80762820 2.220077e-02
36 40 4.19431539 1.508106e-02
37 41 4.34335299 1.299289e-02
38 43 4.49999388 1.110906e-02
39 45 5.02209242 6.590722e-03
40 46 6.18711444 2.055750e-03
41 47 6.69153421 1.241377e-03
42 48 6.95267245 9.560767e-04
43 50 7.23110969 7.237173e-04
44 51 7.51952425 5.423905e-04
45 54 7.84412949 3.920467e-04
46 56 8.19637535 2.756509e-04
47 57 8.62252803 1.800046e-04
48 58 9.08135198 1.137677e-04
49 59 9.60651686 6.728879e-05
50 62 10.19614217 3.731399e-05
51 63 10.91531958 1.817762e-05
52 65 13.20281335 1.845402e-06
53 66 14.19298696 6.855894e-07
54 68 15.37610331 2.100116e-07
55 69 16.63672681 5.953349e-08
56 71 17.97187127 1.566446e-08
57 75 19.77397017 2.583889e-09
58 79 21.86806564 3.182876e-10
59 83 24.35851132 2.637746e-11
60 100 27.07612214 1.741765e-12
61 107 29.88395991 1.050899e-13
62 108 32.74677576 6.001447e-15
63 122 36.04174427 2.224689e-16
64 129 39.49973708 7.006194e-18
65 148 45.31343822 2.092299e-20
66 163 51.28404525 5.340995e-23
67 166 57.37242611 1.211914e-25
68 205 73.48754160 1.215531e-32
> ed1$exp.dur
exp.dur
1 3.462066e+01
2 3.163998e+01
3 3.950909e+01
4 1.471754e+01
5 2.473799e+00
6 4.734767e+01
7 2.232690e+01
8 2.190967e+01
9 2.779519e+01
10 1.485610e+01
11 1.912067e+01
12 1.242269e+01
13 3.007997e+01
14 3.659978e+01
15 3.773806e+01
16 1.357897e+01
17 8.751686e+00
18 1.053473e+01
19 1.988052e+01
20 2.559284e+01
21 4.019031e+00
22 2.829087e+01
23 4.055814e+01
24 2.373287e+01
25 5.878934e+01
26 5.823483e+01
27 5.395568e+01
28 6.511424e+01
29 1.764696e-06
30 8.357956e+01
31 1.650684e+02
32 8.599634e+00
33 8.315060e+01
34 2.249185e+01
35 7.087216e+00
36 4.747175e+01
37 5.046366e+01
38 1.767727e+02
39 1.009101e+01
40 1.779990e+00
41 1.015981e+01
42 9.100677e+00
43 2.514407e+00
44 1.117863e+01
45 2.756237e-01
46 4.211441e+00
47 5.151383e-01
48 7.904575e+00
49 8.942254e+00
50 7.001254e+00
51 1.376298e+01
52 3.955364e+00
53 1.275698e+01
54 1.584214e+01
55 1.141698e+01
56 8.059208e-01
57 8.023809e+00
58 1.408503e+01
59 4.794977e+00
60 2.833782e-03
61 2.192574e+01
62 6.931307e+00
63 5.025603e+00
64 6.672316e+00
65 4.422389e+01
66 5.637958e-01
67 4.790266e+00
68 1.316113e+01
69 3.234680e+01
70 6.734997e+00
71 3.237662e+01
72 1.508299e+01
73 1.838954e+00
74 2.822783e+01
75 2.099879e+01
76 2.266680e+01
77 2.257850e+01
78 1.013264e+01
79 2.775749e+01
80 2.385303e+01
81 2.435383e+01
82 2.910584e+01
83 2.958993e+01
84 2.130638e+01
85 1.731492e+01
86 8.918666e+00
87 1.972054e+01
88 1.746225e+01
89 7.560886e+00
90 1.898087e+01
91 1.565773e+01
92 1.826795e+01
93 6.256132e+00
94 2.756669e+01
95 2.271502e+01
96 2.592081e+01
97 2.319719e+01
98 2.172389e+01
99 2.816861e+01
100 1.700014e+01
101 1.298786e+01
102 1.564080e+01
103 1.700014e+01
104 3.635995e+01
105 1.865924e+01
106 2.176944e+01
107 1.355231e+01
108 1.965870e+01
109 2.587456e+01
110 2.490290e+01
111 2.996283e+01
112 2.831342e+01
113 2.341833e+01
114 2.190965e+01
115 3.452451e+01
116 2.804580e+01
117 2.682330e+00
118 2.238101e+01
119 4.606828e+01
120 4.040758e+01
121 1.672018e+01
122 5.056074e+01
123 2.261905e+01
124 3.009042e+01
125 2.483527e+01
126 5.760310e+01
127 1.580188e+01
128 2.122569e+01
129 3.408236e+01
130 1.713534e+01
131 2.673318e+01
132 5.165843e+01
133 3.669188e+01
134 7.740770e+01
135 3.379181e+00
136 4.104403e+01
137 8.735827e+01
138 2.511312e+01
139 9.219516e+01
140 2.504228e+01
141 8.135884e+00
142 3.209020e+01
143 3.373807e+00
144 2.724482e+01
145 3.004171e+01
146 2.272260e+01
147 3.351499e+01
148 2.476240e+01
149 2.800526e+01
150 2.777463e+01
151 2.706936e+01
152 1.352939e+02
153 7.239505e+01
154 7.919085e+01
155 3.720940e+01
156 5.231306e+01
157 1.440342e+02
158 1.838501e+02
159 6.559607e+01
160 7.769277e+01
161 4.030050e+01
162 3.428421e+01
163 3.091422e+01
164 3.774964e+00
165 4.820581e+00
166 3.774964e+00
167 4.890087e+00
168 9.902095e-01
169 4.992254e+00
170 2.063432e+01
171 1.492843e-04
172 7.118737e+00
173 6.321833e+00
174 1.475209e+01
175 4.466678e+00
176 4.890087e+00
177 4.970625e+00
178 1.398589e+01
179 3.828381e-03
180 1.370852e+01
181 6.113632e+00
182 2.381519e+01
183 5.415926e+00
184 1.152380e+00
185 1.364167e+00
186 5.778762e+00
187 4.890087e+00
188 4.890087e+00
189 4.890087e+00
190 3.269787e+00
191 5.532035e+00
192 4.473081e+00
193 4.890087e+00
194 1.119380e+01
195 6.394347e+00
196 1.597881e+01
197 9.202013e+00
198 1.239613e+01
199 4.890087e+00
200 6.769727e+00
201 1.183935e+01
202 7.118737e+00
203 1.924177e+01
> summary(ed1, stat="mean")
mean
25.18
> summary(ed1, stat="median")
median
19.121
>
> ed1 <- coxed(mv.cox, method="npsf", bootstrap = TRUE)
Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) :
cannot coerce class '"coxph"' to a data.frame
Calls: coxed ... <Anonymous> -> as.data.frame -> as.data.frame.default
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.3.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'coxed.Rmd' using rmarkdown
Loading required package: rms
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2
Attaching package: 'Hmisc'
The following objects are masked from 'package:base':
format.pval, units
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.
Attaching package: 'dplyr'
The following object is masked from 'package:nlme':
collapse
The following objects are masked from 'package:Hmisc':
src, summarize
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Quitting from lines 88-89 (coxed.Rmd)
Error: processing vignette 'coxed.Rmd' failed with diagnostics:
cannot coerce class '"coxph"' to a data.frame
--- failed re-building 'coxed.Rmd'
--- re-building 'simulating_survival_data.Rmd' using rmarkdown
Loading required package: rms
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2
Attaching package: 'Hmisc'
The following objects are masked from 'package:base':
format.pval, units
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.
--- finished re-building 'simulating_survival_data.Rmd'
SUMMARY: processing the following file failed:
'coxed.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.3.2
Check: Rd cross-references
Result: NOTE
Undeclared package ‘mediation’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.2
Check: examples
Result: ERROR
Running examples in ‘coxed-Ex.R’ failed
The error most likely occurred in:
> ### Name: summary.coxedExpdur
> ### Title: The mean or median expected duration
> ### Aliases: summary.coxedExpdur
>
> ### ** Examples
>
> require(survival)
> mv.surv <- Surv(martinvanberg$formdur, event = rep(1, nrow(martinvanberg)))
> mv.cox <- coxph(mv.surv ~ postel + prevdef + cont + ident + rgovm + pgovno + tpgovno +
+ minority, method = "breslow", data = martinvanberg)
> summary(mv.cox)
Call:
coxph(formula = mv.surv ~ postel + prevdef + cont + ident + rgovm +
pgovno + tpgovno + minority, data = martinvanberg, method = "breslow")
n= 203, number of events= 203
coef exp(coef) se(coef) z Pr(>|z|)
postel -0.57665 0.56177 0.16862 -3.420 0.000627 ***
prevdef -0.10000 0.90484 0.22987 -0.435 0.663543
cont 1.10047 3.00556 0.23970 4.591 4.41e-06 ***
ident 0.14579 1.15695 0.11859 1.229 0.218938
rgovm -0.21312 0.80806 0.12036 -1.771 0.076625 .
pgovno 1.19057 3.28894 0.12405 9.598 < 2e-16 ***
tpgovno -0.43189 0.64928 0.03476 -12.425 < 2e-16 ***
minority -0.42759 0.65208 0.20793 -2.056 0.039740 *
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
exp(coef) exp(-coef) lower .95 upper .95
postel 0.5618 1.7801 0.4037 0.7818
prevdef 0.9048 1.1052 0.5766 1.4198
cont 3.0056 0.3327 1.8789 4.8079
ident 1.1570 0.8643 0.9170 1.4597
rgovm 0.8081 1.2375 0.6382 1.0231
pgovno 3.2889 0.3040 2.5791 4.1942
tpgovno 0.6493 1.5402 0.6065 0.6951
minority 0.6521 1.5336 0.4338 0.9801
Concordance= 0.903 (se = 0.007 )
Likelihood ratio test= 277.2 on 8 df, p=<2e-16
Wald test = 218.1 on 8 df, p=<2e-16
Score (logrank) test = 279.3 on 8 df, p=<2e-16
>
> # NPSF method
> ed1 <- coxed(mv.cox, method="npsf")
> ed1$baseline.functions
time cbh survivor
1 1 0.01631230 9.838200e-01
2 2 0.03587341 9.647624e-01
3 3 0.04746259 9.536462e-01
4 4 0.07651484 9.263392e-01
5 5 0.09169880 9.123799e-01
6 6 0.12573075 8.818522e-01
7 7 0.16500990 8.478853e-01
8 8 0.18849681 8.282031e-01
9 9 0.20530921 8.143955e-01
10 10 0.24089191 7.859266e-01
11 11 0.29960997 7.411072e-01
12 12 0.33587336 7.147136e-01
13 13 0.34926287 7.052077e-01
14 14 0.44435177 6.412398e-01
15 15 0.47494715 6.219179e-01
16 16 0.52282119 5.928457e-01
17 17 0.55688241 5.729926e-01
18 18 0.64587601 5.242031e-01
19 19 0.78113579 4.578857e-01
20 20 0.85884119 4.236527e-01
21 21 0.94180170 3.899247e-01
22 22 1.00021359 3.678009e-01
23 23 1.09362425 3.350002e-01
24 24 1.22638118 2.933522e-01
25 26 1.33308790 2.636618e-01
26 27 1.44872000 2.348707e-01
27 30 1.81954923 1.620988e-01
28 31 1.92420399 1.459919e-01
29 33 2.14527897 1.170354e-01
30 34 2.26179451 1.041634e-01
31 35 2.44667759 8.658077e-02
32 36 2.80857821 6.029065e-02
33 37 3.14057906 4.325774e-02
34 38 3.24639408 3.891428e-02
35 39 3.80762820 2.220077e-02
36 40 4.19431539 1.508106e-02
37 41 4.34335299 1.299289e-02
38 43 4.49999388 1.110906e-02
39 45 5.02209242 6.590722e-03
40 46 6.18711444 2.055750e-03
41 47 6.69153421 1.241377e-03
42 48 6.95267245 9.560767e-04
43 50 7.23110969 7.237173e-04
44 51 7.51952425 5.423905e-04
45 54 7.84412949 3.920467e-04
46 56 8.19637535 2.756509e-04
47 57 8.62252803 1.800046e-04
48 58 9.08135198 1.137677e-04
49 59 9.60651686 6.728879e-05
50 62 10.19614217 3.731399e-05
51 63 10.91531958 1.817762e-05
52 65 13.20281335 1.845402e-06
53 66 14.19298696 6.855894e-07
54 68 15.37610331 2.100116e-07
55 69 16.63672681 5.953349e-08
56 71 17.97187127 1.566446e-08
57 75 19.77397017 2.583889e-09
58 79 21.86806564 3.182876e-10
59 83 24.35851132 2.637746e-11
60 100 27.07612214 1.741765e-12
61 107 29.88395991 1.050899e-13
62 108 32.74677576 6.001447e-15
63 122 36.04174427 2.224689e-16
64 129 39.49973708 7.006194e-18
65 148 45.31343822 2.092299e-20
66 163 51.28404525 5.340995e-23
67 166 57.37242611 1.211914e-25
68 205 73.48754160 1.215531e-32
> ed1$exp.dur
exp.dur
1 3.462066e+01
2 3.163998e+01
3 3.950909e+01
4 1.471754e+01
5 2.473799e+00
6 4.734767e+01
7 2.232690e+01
8 2.190967e+01
9 2.779519e+01
10 1.485610e+01
11 1.912067e+01
12 1.242269e+01
13 3.007997e+01
14 3.659978e+01
15 3.773806e+01
16 1.357897e+01
17 8.751686e+00
18 1.053473e+01
19 1.988052e+01
20 2.559284e+01
21 4.019031e+00
22 2.829087e+01
23 4.055814e+01
24 2.373287e+01
25 5.878934e+01
26 5.823483e+01
27 5.395568e+01
28 6.511424e+01
29 1.764696e-06
30 8.357956e+01
31 1.650684e+02
32 8.599634e+00
33 8.315060e+01
34 2.249185e+01
35 7.087216e+00
36 4.747175e+01
37 5.046366e+01
38 1.767727e+02
39 1.009101e+01
40 1.779990e+00
41 1.015981e+01
42 9.100677e+00
43 2.514407e+00
44 1.117863e+01
45 2.756237e-01
46 4.211441e+00
47 5.151383e-01
48 7.904575e+00
49 8.942254e+00
50 7.001254e+00
51 1.376298e+01
52 3.955364e+00
53 1.275698e+01
54 1.584214e+01
55 1.141698e+01
56 8.059208e-01
57 8.023809e+00
58 1.408503e+01
59 4.794977e+00
60 2.833782e-03
61 2.192574e+01
62 6.931307e+00
63 5.025603e+00
64 6.672316e+00
65 4.422389e+01
66 5.637958e-01
67 4.790266e+00
68 1.316113e+01
69 3.234680e+01
70 6.734997e+00
71 3.237662e+01
72 1.508299e+01
73 1.838954e+00
74 2.822783e+01
75 2.099879e+01
76 2.266680e+01
77 2.257850e+01
78 1.013264e+01
79 2.775749e+01
80 2.385303e+01
81 2.435383e+01
82 2.910584e+01
83 2.958993e+01
84 2.130638e+01
85 1.731492e+01
86 8.918666e+00
87 1.972054e+01
88 1.746225e+01
89 7.560886e+00
90 1.898087e+01
91 1.565773e+01
92 1.826795e+01
93 6.256132e+00
94 2.756669e+01
95 2.271502e+01
96 2.592081e+01
97 2.319719e+01
98 2.172389e+01
99 2.816861e+01
100 1.700014e+01
101 1.298786e+01
102 1.564080e+01
103 1.700014e+01
104 3.635995e+01
105 1.865924e+01
106 2.176944e+01
107 1.355231e+01
108 1.965870e+01
109 2.587456e+01
110 2.490290e+01
111 2.996283e+01
112 2.831342e+01
113 2.341833e+01
114 2.190965e+01
115 3.452451e+01
116 2.804580e+01
117 2.682330e+00
118 2.238101e+01
119 4.606828e+01
120 4.040758e+01
121 1.672018e+01
122 5.056074e+01
123 2.261905e+01
124 3.009042e+01
125 2.483527e+01
126 5.760310e+01
127 1.580188e+01
128 2.122569e+01
129 3.408236e+01
130 1.713534e+01
131 2.673318e+01
132 5.165843e+01
133 3.669188e+01
134 7.740770e+01
135 3.379181e+00
136 4.104403e+01
137 8.735827e+01
138 2.511312e+01
139 9.219516e+01
140 2.504228e+01
141 8.135884e+00
142 3.209020e+01
143 3.373807e+00
144 2.724482e+01
145 3.004171e+01
146 2.272260e+01
147 3.351499e+01
148 2.476240e+01
149 2.800526e+01
150 2.777463e+01
151 2.706936e+01
152 1.352939e+02
153 7.239505e+01
154 7.919085e+01
155 3.720940e+01
156 5.231306e+01
157 1.440342e+02
158 1.838501e+02
159 6.559607e+01
160 7.769277e+01
161 4.030050e+01
162 3.428421e+01
163 3.091422e+01
164 3.774964e+00
165 4.820581e+00
166 3.774964e+00
167 4.890087e+00
168 9.902095e-01
169 4.992254e+00
170 2.063432e+01
171 1.492843e-04
172 7.118737e+00
173 6.321833e+00
174 1.475209e+01
175 4.466678e+00
176 4.890087e+00
177 4.970625e+00
178 1.398589e+01
179 3.828381e-03
180 1.370852e+01
181 6.113632e+00
182 2.381519e+01
183 5.415926e+00
184 1.152380e+00
185 1.364167e+00
186 5.778762e+00
187 4.890087e+00
188 4.890087e+00
189 4.890087e+00
190 3.269787e+00
191 5.532035e+00
192 4.473081e+00
193 4.890087e+00
194 1.119380e+01
195 6.394347e+00
196 1.597881e+01
197 9.202013e+00
198 1.239613e+01
199 4.890087e+00
200 6.769727e+00
201 1.183935e+01
202 7.118737e+00
203 1.924177e+01
> summary(ed1, stat="mean")
mean
25.18
> summary(ed1, stat="median")
median
19.121
>
> ed1 <- coxed(mv.cox, method="npsf", bootstrap = TRUE)
Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) :
cannot coerce class ‘"coxph"’ to a data.frame
Calls: coxed ... <Anonymous> -> as.data.frame -> as.data.frame.default
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 0.3.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘coxed.Rmd’ using rmarkdown
Loading required package: rms
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2
Attaching package: 'Hmisc'
The following objects are masked from 'package:base':
format.pval, units
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.
Attaching package: 'dplyr'
The following object is masked from 'package:nlme':
collapse
The following objects are masked from 'package:Hmisc':
src, summarize
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Quitting from lines 88-89 (coxed.Rmd)
Error: processing vignette 'coxed.Rmd' failed with diagnostics:
cannot coerce class '"coxph"' to a data.frame
--- failed re-building ‘coxed.Rmd’
--- re-building ‘simulating_survival_data.Rmd’ using rmarkdown
Loading required package: rms
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2
Attaching package: 'Hmisc'
The following objects are masked from 'package:base':
format.pval, units
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.
--- finished re-building ‘simulating_survival_data.Rmd’
SUMMARY: processing the following file failed:
‘coxed.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64
Version: 0.3.2
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘coxed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: rms
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2
Attaching package: 'Hmisc'
The following objects are masked from 'package:base':
format.pval, units
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.
Attaching package: 'dplyr'
The following object is masked from 'package:nlme':
collapse
The following objects are masked from 'package:Hmisc':
src, summarize
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Quitting from lines 88-89 (coxed.Rmd)
Error: processing vignette 'coxed.Rmd' failed with diagnostics:
cannot coerce class '"coxph"' to a data.frame
--- failed re-building ‘coxed.Rmd’
--- re-building ‘simulating_survival_data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: rms
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2
Attaching package: 'Hmisc'
The following objects are masked from 'package:base':
format.pval, units
Loading required package: SparseM
Attaching package: 'SparseM'
The following object is masked from 'package:base':
backsolve
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.
--- finished re-building ‘simulating_survival_data.Rmd’
SUMMARY: processing the following file failed:
‘coxed.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86