Nothing
tests/testthat/_snaps/coxreg.md
In tern: Create Common TLGs Used in Clinical Trials
h_coxreg_univar_formulas creates formulas with covariate
Code
res
Output
ref
"survival::Surv(time, status) ~ armcd"
X
"survival::Surv(time, status) ~ armcd + X"
y
"survival::Surv(time, status) ~ armcd + y"
h_coxreg_univar_formulas creates formulas with strata
Code
res
Output
ref
"survival::Surv(time, status) ~ armcd + strata(SITE)"
X
"survival::Surv(time, status) ~ armcd + X + strata(SITE)"
y
"survival::Surv(time, status) ~ armcd + y + strata(SITE)"
h_coxreg_univar_formulas creates formula for reference when treatment is only considered
Code
res
Output
ref
"survival::Surv(time, status) ~ armcd"
h_coxreg_univar_formulas creates formulas with interactions
Code
res
Output
ref
"survival::Surv(time, status) ~ armcd + strata(SITE)"
X
"survival::Surv(time, status) ~ armcd * X + strata(SITE)"
y
"survival::Surv(time, status) ~ armcd * y + strata(SITE)"
h_coxreg_univar_formulas creates formula without treatment arm
Code
res
Output
X
"survival::Surv(time, status) ~ 1 + X + strata(SITE)"
y
"survival::Surv(time, status) ~ 1 + y + strata(SITE)"
h_coxreg_univar_formulas creates formulas with multiple strata
Code
res
Output
ref
"survival::Surv(time, status) ~ armcd + strata(SITE, COUNTRY)"
X
"survival::Surv(time, status) ~ armcd + X + strata(SITE, COUNTRY)"
y
"survival::Surv(time, status) ~ armcd + y + strata(SITE, COUNTRY)"
h_coxreg_multivar_extract extracts correct coxph results when covariate names overlap
Code
res
Output
pval hr lcl ucl level n term term_label
1 0.3062027 1.029677 0.9735821 1.089003 age 8 age age
h_coxreg_multivar_extract extracts correct coxph results when covariate is a factor
Code
res
Output
term pval term_label hr lcl ucl level n
1 stage NA stage (reference = 1) NA NA NA <NA> NA
2 stage 0.1947681 2 4.989564 0.4394003 56.65848 2 8
h_coxreg_multivar_formula creates formula without covariate
Code
res
Output
[1] "survival::Surv(TIME, EVNT) ~ ARMCD"
h_coxreg_multivar_formula creates formulas with a strata
Code
res
Output
[1] "survival::Surv(time, status) ~ armcd + X + y + strata(SITE)"
h_coxreg_multivar_formula creates formulas with multiple strata
Code
res
Output
[1] "survival::Surv(time, status) ~ armcd + X + y + strata(SITE, COUNTRY)"
h_coxreg_multivar_formula creates formula with covariate
Code
res
Output
[1] "survival::Surv(time, status) ~ armcd + covar1 + covar2"
h_coxreg_multivar_formula creates formula without treatment arm
Code
res
Output
[1] "survival::Surv(time, status) ~ 1 + covar1 + covar2"
h_coxreg_multivar_formula creates formulas with multiple strata and without arm
Code
res
Output
[1] "survival::Surv(time, status) ~ 1 + X + y + strata(SITE, COUNTRY)"
control_coxreg returns a standard list of parameters
Code
res
Output
$pval_method
[1] "wald"
$ties
[1] "exact"
$conf_level
[1] 0.95
$interaction
[1] FALSE
fit_coxreg_univar returns model results as expected
Code
res
Output
$mod
$mod$ref
Call:
survival::coxph(formula = stats::as.formula(x), data = data,
ties = control$ties)
coef exp(coef) se(coef) z p
armcd2 -0.4484 0.6386 0.1990 -2.253 0.0242
Likelihood ratio test=5.25 on 1 df, p=0.02191
n= 340, number of events= 112
$mod$covar1
Call:
survival::coxph(formula = stats::as.formula(x), data = data,
ties = control$ties)
coef exp(coef) se(coef) z p
armcd2 -0.4992 0.6070 0.2000 -2.496 0.012573
covar12 -0.8180 0.4413 0.2393 -3.418 0.000631
covar13 -1.1921 0.3036 0.2615 -4.559 5.13e-06
covar14 -1.7264 0.1779 0.3074 -5.615 1.96e-08
Likelihood ratio test=47.85 on 4 df, p=1.015e-09
n= 340, number of events= 112
$data
time status arm armcd covar1 covar2 age
1 1 0 ARM: 1 1 1 M 56
2 1 0 ARM: 1 1 2 M 43
3 1 0 ARM: 1 1 3 F 33
4 1 0 ARM: 1 1 4 M 26
5 4 0 ARM: 1 1 1 F 46
6 4 0 ARM: 1 1 2 M 45
7 4 0 ARM: 1 1 3 M 49
8 4 0 ARM: 1 1 4 F 34
9 7 0 ARM: 1 1 1 F 25
10 7 0 ARM: 1 1 2 F 53
11 7 0 ARM: 1 1 3 M 40
12 7 0 ARM: 1 1 4 F 20
13 10 0 ARM: 1 1 1 M 36
14 10 0 ARM: 1 1 2 F 32
15 10 0 ARM: 1 1 3 F 45
16 10 0 ARM: 1 1 4 F 59
17 6 1 ARM: 1 1 1 F 21
18 10 0 ARM: 1 1 2 F 60
19 10 0 ARM: 1 1 3 F 27
20 10 0 ARM: 1 1 4 F 44
21 14 0 ARM: 1 1 1 F 50
22 14 0 ARM: 1 1 2 F 39
23 14 0 ARM: 1 1 3 M 39
24 14 0 ARM: 1 1 4 M 24
25 18 0 ARM: 1 1 1 M 29
26 18 0 ARM: 1 1 2 F 39
27 18 0 ARM: 1 1 3 F 34
28 18 0 ARM: 1 1 4 M 48
29 5 1 ARM: 1 1 1 M 21
30 18 0 ARM: 1 1 2 F 20
31 18 0 ARM: 1 1 3 M 24
32 18 0 ARM: 1 1 4 F 44
33 12 1 ARM: 1 1 1 M 56
34 16 1 ARM: 1 1 2 F 51
35 18 0 ARM: 1 1 3 M 59
36 18 0 ARM: 1 1 4 M 32
37 23 0 ARM: 1 1 1 F 44
38 23 0 ARM: 1 1 2 F 23
39 23 0 ARM: 1 1 3 F 57
40 23 0 ARM: 1 1 4 F 24
41 10 1 ARM: 1 1 1 F 20
42 15 1 ARM: 1 1 2 F 57
43 23 0 ARM: 1 1 3 F 32
44 23 0 ARM: 1 1 4 M 27
45 3 1 ARM: 1 1 1 M 38
46 16 1 ARM: 1 1 2 F 47
47 23 1 ARM: 1 1 3 M 57
48 23 0 ARM: 1 1 4 F 30
49 3 1 ARM: 1 1 1 M 27
50 9 1 ARM: 1 1 2 M 42
51 21 1 ARM: 1 1 3 M 39
52 23 0 ARM: 1 1 4 F 24
53 7 1 ARM: 1 1 1 M 21
54 10 1 ARM: 1 1 2 F 24
55 16 1 ARM: 1 1 3 F 31
56 24 1 ARM: 1 1 4 M 22
57 3 1 ARM: 1 1 1 F 45
58 15 1 ARM: 1 1 2 M 33
59 25 1 ARM: 1 1 3 F 32
60 25 0 ARM: 1 1 4 F 50
61 26 0 ARM: 1 1 1 F 53
62 26 0 ARM: 1 1 2 F 49
63 26 0 ARM: 1 1 3 F 45
64 26 0 ARM: 1 1 4 F 26
65 1 1 ARM: 1 1 1 M 46
66 26 0 ARM: 1 1 2 M 28
67 26 0 ARM: 1 1 3 M 27
68 26 0 ARM: 1 1 4 F 41
69 2 1 ARM: 1 1 1 M 25
70 26 1 ARM: 1 1 2 M 46
71 26 0 ARM: 1 1 3 F 49
72 26 0 ARM: 1 1 4 F 29
73 25 1 ARM: 1 1 1 M 49
74 28 0 ARM: 1 1 2 F 20
75 28 0 ARM: 1 1 3 M 25
76 28 0 ARM: 1 1 4 M 36
77 29 0 ARM: 1 1 1 M 32
78 29 0 ARM: 1 1 2 F 45
79 29 0 ARM: 1 1 3 F 21
80 29 0 ARM: 1 1 4 F 51
81 29 0 ARM: 1 1 1 M 55
82 29 0 ARM: 1 1 2 M 24
83 29 0 ARM: 1 1 3 F 42
84 29 0 ARM: 1 1 4 M 57
85 29 0 ARM: 1 1 1 F 39
86 29 0 ARM: 1 1 2 F 47
87 29 0 ARM: 1 1 3 M 47
88 29 0 ARM: 1 1 4 M 31
89 28 1 ARM: 1 1 1 M 54
90 30 1 ARM: 1 1 2 F 23
91 30 0 ARM: 1 1 3 F 45
92 30 0 ARM: 1 1 4 F 32
93 2 1 ARM: 1 1 1 F 22
94 17 1 ARM: 1 1 2 F 34
95 22 1 ARM: 1 1 3 M 53
96 30 0 ARM: 1 1 4 F 57
97 3 1 ARM: 1 1 1 M 23
98 6 1 ARM: 1 1 2 M 45
99 8 1 ARM: 1 1 3 M 40
100 12 1 ARM: 1 1 4 M 40
101 12 1 ARM: 1 1 1 M 35
102 15 1 ARM: 1 1 2 M 56
103 24 1 ARM: 1 1 3 F 43
104 31 0 ARM: 1 1 4 F 40
105 32 0 ARM: 1 1 1 M 22
106 32 0 ARM: 1 1 2 M 45
107 32 0 ARM: 1 1 3 F 42
108 32 0 ARM: 1 1 4 F 55
109 34 0 ARM: 1 1 1 M 41
110 34 0 ARM: 1 1 2 M 22
111 34 0 ARM: 1 1 3 F 23
112 34 0 ARM: 1 1 4 F 55
113 36 0 ARM: 1 1 1 F 56
114 36 0 ARM: 1 1 2 M 20
115 36 0 ARM: 1 1 3 M 56
116 36 0 ARM: 1 1 4 F 41
117 29 1 ARM: 1 1 1 M 40
118 36 0 ARM: 1 1 2 M 46
119 36 0 ARM: 1 1 3 M 30
120 36 0 ARM: 1 1 4 M 30
121 37 0 ARM: 1 1 1 F 25
122 37 0 ARM: 1 1 2 F 55
123 37 0 ARM: 1 1 3 M 25
124 37 0 ARM: 1 1 4 F 39
125 9 1 ARM: 1 1 1 F 59
126 17 1 ARM: 1 1 2 M 52
127 22 1 ARM: 1 1 3 F 59
128 24 1 ARM: 1 1 4 F 30
129 16 1 ARM: 1 1 1 F 30
130 19 1 ARM: 1 1 2 M 40
131 23 1 ARM: 1 1 3 F 40
132 29 1 ARM: 1 1 4 F 36
133 41 0 ARM: 1 1 1 M 28
134 41 0 ARM: 1 1 2 M 37
135 41 0 ARM: 1 1 3 M 50
136 41 0 ARM: 1 1 4 F 27
137 3 1 ARM: 1 1 1 F 42
138 43 0 ARM: 1 1 2 M 25
139 43 0 ARM: 1 1 3 M 30
140 43 0 ARM: 1 1 4 M 56
141 6 1 ARM: 1 1 1 F 44
142 43 0 ARM: 1 1 2 F 21
143 43 0 ARM: 1 1 3 M 58
144 43 0 ARM: 1 1 4 M 51
145 3 1 ARM: 1 1 1 F 59
146 6 1 ARM: 1 1 2 M 41
147 9 1 ARM: 1 1 3 M 54
148 44 0 ARM: 1 1 4 F 30
149 9 1 ARM: 1 1 1 M 32
150 11 1 ARM: 1 1 2 M 21
151 20 1 ARM: 1 1 3 M 59
152 26 1 ARM: 1 1 4 F 25
153 18 1 ARM: 1 1 1 M 34
154 48 0 ARM: 1 1 2 F 60
155 48 0 ARM: 1 1 3 F 47
156 48 0 ARM: 1 1 4 M 20
157 49 0 ARM: 1 1 1 M 21
158 49 0 ARM: 1 1 2 M 28
159 49 0 ARM: 1 1 3 F 24
160 49 0 ARM: 1 1 4 F 46
161 35 1 ARM: 1 1 1 M 48
162 51 0 ARM: 1 1 2 F 21
163 51 0 ARM: 1 1 3 F 56
164 51 0 ARM: 1 1 4 M 50
165 17 1 ARM: 1 1 1 M 33
166 53 0 ARM: 1 1 2 F 44
167 53 0 ARM: 1 1 3 M 40
168 53 0 ARM: 1 1 4 M 42
169 3 1 ARM: 1 1 1 F 25
170 15 1 ARM: 1 1 2 F 40
171 46 1 ARM: 1 1 3 F 24
172 51 1 ARM: 1 1 4 M 44
173 59 0 ARM: 1 1 1 F 36
174 59 0 ARM: 1 1 2 F 52
175 59 0 ARM: 1 1 3 F 59
176 59 0 ARM: 1 1 4 M 38
177 2 1 ARM: 1 1 1 M 36
178 15 1 ARM: 1 1 2 M 39
179 24 1 ARM: 1 1 3 F 42
180 30 1 ARM: 1 1 4 F 39
181 5 1 ARM: 1 1 1 M 50
182 14 1 ARM: 1 1 2 F 24
183 19 1 ARM: 1 1 3 F 46
184 27 1 ARM: 1 1 4 M 52
185 2 1 ARM: 1 1 1 F 20
186 8 1 ARM: 1 1 2 F 48
187 12 1 ARM: 1 1 3 M 53
188 13 1 ARM: 1 1 4 M 55
189 1 0 ARM: 2 2 1 M 39
190 1 0 ARM: 2 2 2 F 40
191 1 0 ARM: 2 2 3 M 57
192 1 0 ARM: 2 2 4 M 43
193 1 0 ARM: 2 2 1 F 53
194 1 0 ARM: 2 2 2 M 39
195 1 0 ARM: 2 2 3 M 22
196 1 0 ARM: 2 2 4 F 39
197 5 1 ARM: 2 2 1 F 53
198 5 0 ARM: 2 2 2 F 34
199 5 0 ARM: 2 2 3 F 49
200 5 0 ARM: 2 2 4 M 32
201 9 0 ARM: 2 2 1 M 35
202 9 0 ARM: 2 2 2 F 55
203 9 0 ARM: 2 2 3 F 49
204 9 0 ARM: 2 2 4 F 48
205 10 0 ARM: 2 2 1 M 47
206 10 0 ARM: 2 2 2 M 32
207 10 0 ARM: 2 2 3 M 26
208 10 0 ARM: 2 2 4 F 37
209 13 0 ARM: 2 2 1 F 20
210 13 0 ARM: 2 2 2 M 23
211 13 0 ARM: 2 2 3 F 24
212 13 0 ARM: 2 2 4 M 55
213 3 1 ARM: 2 2 1 M 53
214 14 0 ARM: 2 2 2 M 45
215 14 0 ARM: 2 2 3 M 52
216 14 0 ARM: 2 2 4 M 38
217 1 1 ARM: 2 2 1 F 36
218 3 1 ARM: 2 2 2 F 32
219 5 1 ARM: 2 2 3 F 58
220 7 1 ARM: 2 2 4 M 55
221 18 0 ARM: 2 2 1 F 26
222 18 0 ARM: 2 2 2 F 41
223 18 0 ARM: 2 2 3 F 28
224 18 0 ARM: 2 2 4 F 51
225 17 1 ARM: 2 2 1 M 59
226 18 0 ARM: 2 2 2 F 52
227 18 0 ARM: 2 2 3 M 47
228 18 0 ARM: 2 2 4 F 31
229 2 1 ARM: 2 2 1 M 49
230 19 0 ARM: 2 2 2 M 54
231 19 0 ARM: 2 2 3 F 45
232 19 0 ARM: 2 2 4 F 22
233 17 1 ARM: 2 2 1 M 34
234 19 1 ARM: 2 2 2 M 58
235 21 0 ARM: 2 2 3 F 42
236 21 0 ARM: 2 2 4 M 44
237 22 0 ARM: 2 2 1 F 20
238 22 0 ARM: 2 2 2 F 47
239 22 0 ARM: 2 2 3 F 28
240 22 0 ARM: 2 2 4 M 33
241 25 0 ARM: 2 2 1 F 50
242 25 0 ARM: 2 2 2 F 35
243 25 0 ARM: 2 2 3 M 40
244 25 0 ARM: 2 2 4 M 31
245 25 0 ARM: 2 2 1 M 49
246 25 0 ARM: 2 2 2 F 41
247 25 0 ARM: 2 2 3 M 20
248 25 0 ARM: 2 2 4 F 31
249 25 0 ARM: 2 2 1 F 47
250 25 0 ARM: 2 2 2 F 31
251 25 0 ARM: 2 2 3 M 44
252 25 0 ARM: 2 2 4 F 44
253 6 1 ARM: 2 2 1 F 27
254 12 1 ARM: 2 2 2 M 50
255 13 1 ARM: 2 2 3 M 24
256 26 0 ARM: 2 2 4 F 31
257 6 1 ARM: 2 2 1 M 49
258 27 0 ARM: 2 2 2 M 28
259 27 0 ARM: 2 2 3 M 21
260 27 0 ARM: 2 2 4 M 28
261 2 1 ARM: 2 2 1 F 60
262 29 0 ARM: 2 2 2 F 60
263 29 0 ARM: 2 2 3 M 41
264 29 0 ARM: 2 2 4 M 46
265 26 1 ARM: 2 2 1 F 57
266 35 1 ARM: 2 2 2 M 42
267 36 0 ARM: 2 2 3 F 53
268 36 0 ARM: 2 2 4 F 22
269 38 0 ARM: 2 2 1 F 20
270 38 0 ARM: 2 2 2 M 21
271 38 0 ARM: 2 2 3 M 38
272 38 0 ARM: 2 2 4 M 48
273 22 1 ARM: 2 2 1 M 24
274 23 1 ARM: 2 2 2 F 53
275 27 1 ARM: 2 2 3 F 60
276 32 1 ARM: 2 2 4 M 31
277 4 1 ARM: 2 2 1 F 60
278 16 1 ARM: 2 2 2 F 37
279 23 1 ARM: 2 2 3 M 53
280 27 1 ARM: 2 2 4 M 32
281 24 1 ARM: 2 2 1 F 58
282 26 1 ARM: 2 2 2 M 23
283 29 1 ARM: 2 2 3 M 25
284 40 1 ARM: 2 2 4 M 42
285 41 0 ARM: 2 2 1 M 44
286 41 0 ARM: 2 2 2 M 35
287 41 0 ARM: 2 2 3 M 41
288 41 0 ARM: 2 2 4 M 45
289 41 0 ARM: 2 2 1 F 59
290 41 0 ARM: 2 2 2 M 33
291 41 0 ARM: 2 2 3 F 25
292 41 0 ARM: 2 2 4 M 27
293 1 1 ARM: 2 2 1 M 40
294 27 1 ARM: 2 2 2 F 43
295 43 0 ARM: 2 2 3 M 22
296 43 0 ARM: 2 2 4 F 59
297 44 0 ARM: 2 2 1 M 56
298 44 0 ARM: 2 2 2 F 33
299 44 0 ARM: 2 2 3 M 46
300 44 0 ARM: 2 2 4 F 32
301 2 1 ARM: 2 2 1 F 38
302 20 1 ARM: 2 2 2 M 22
303 23 1 ARM: 2 2 3 M 48
304 27 1 ARM: 2 2 4 F 24
305 45 0 ARM: 2 2 1 F 44
306 45 0 ARM: 2 2 2 M 50
307 45 0 ARM: 2 2 3 F 33
308 45 0 ARM: 2 2 4 M 55
309 2 1 ARM: 2 2 1 M 39
310 46 0 ARM: 2 2 2 F 50
311 46 0 ARM: 2 2 3 F 32
312 46 0 ARM: 2 2 4 F 22
313 46 0 ARM: 2 2 1 M 59
314 46 0 ARM: 2 2 2 F 43
315 46 0 ARM: 2 2 3 M 48
316 46 0 ARM: 2 2 4 F 29
317 49 0 ARM: 2 2 1 M 32
318 49 0 ARM: 2 2 2 M 25
319 49 0 ARM: 2 2 3 M 29
320 49 0 ARM: 2 2 4 M 58
321 50 0 ARM: 2 2 1 F 38
322 50 0 ARM: 2 2 2 F 37
323 50 0 ARM: 2 2 3 F 40
324 50 0 ARM: 2 2 4 M 42
325 4 1 ARM: 2 2 1 F 45
326 24 1 ARM: 2 2 2 M 34
327 47 1 ARM: 2 2 3 M 48
328 50 0 ARM: 2 2 4 M 48
329 54 0 ARM: 2 2 1 F 24
330 54 0 ARM: 2 2 2 F 41
331 54 0 ARM: 2 2 3 M 20
332 54 0 ARM: 2 2 4 F 41
333 38 1 ARM: 2 2 1 M 32
334 54 0 ARM: 2 2 2 F 41
335 54 0 ARM: 2 2 3 M 25
336 54 0 ARM: 2 2 4 M 60
337 59 0 ARM: 2 2 1 M 52
338 59 0 ARM: 2 2 2 F 43
339 59 0 ARM: 2 2 3 M 41
340 59 0 ARM: 2 2 4 F 52
$control
$control$pval_method
[1] "wald"
$control$ties
[1] "exact"
$control$conf_level
[1] 0.91
$control$interaction
[1] FALSE
$vars
$vars$time
[1] "time"
$vars$event
[1] "status"
$vars$arm
[1] "armcd"
$vars$covariates
[1] "covar1"
$at
list()
attr(,"class")
[1] "coxreg.univar"
fit_coxreg_univar works without treatment arm
Code
res
Output
[1] "age"
tidy.summary.coxph method tidies up the Cox regression model
Code
res
Output
Pr(>|z|) exp(coef) exp(-coef) lower .95 upper .95 level n
1 0.2472383 3.846606 0.2599694 0.3926671 37.68173 armcdB 8
h_coxreg_univar_extract extracts coxph results
Code
res
Output
effect term term_label level n hr lcl ucl
1 Treatment: armcd B vs control (A) B 8 3.846606 0.3926671 37.68173
pval
1 0.2472383
tidy.coxreg.univar method tidies up the univariate Cox regression model
Code
res
Output
effect term term_label level n hr lcl
ref Treatment: armcd 2 vs control (1) 2 340 0.6386426 0.4323844
covar1 Covariate: covar1 A Covariate Label 2 340 0.607037 0.4101675
covar2 Covariate: covar2 Sex (F/M) 2 340 0.6242738 0.4222423
ucl pval ci
ref 0.9432911 0.02423805 0.4323844, 0.9432911
covar1 0.8983984 0.01257339 0.4101675, 0.8983984
covar2 0.9229721 0.01818876 0.4222423, 0.9229721
tidy.coxreg.univar method works with only numeric covariates with strata
Code
res
Output
effect term term_label level n hr lcl ucl
ref Treatment: armcd 2 vs control (1) 2 340 0.6208343 0.4164994 0.9254162
age Covariate: age age 2 340 0.6076894 0.4072018 0.9068879
pval ci
ref 0.01925561 0.4164994, 0.9254162
age 0.01475084 0.4072018, 0.9068879
tidy.coxreg.univar method works without treatment arm
Code
res
Output
[1] "age" "covar1" "A Covariate Label"
[4] "A Covariate Label" "A Covariate Label"
fit_coxreg_multivar returns model results as expected
Code
res
Output
Call:
survival::coxph(formula = stats::as.formula(form), data = data,
ties = control$ties)
coef exp(coef) se(coef) z p
armcd2 -0.5004 0.6063 0.2000 -2.503 0.01233
covar12 -0.7842 0.4565 0.2407 -3.258 0.00112
covar13 -1.1810 0.3070 0.2615 -4.516 6.29e-06
covar14 -1.7054 0.1817 0.3078 -5.541 3.01e-08
covar2M 0.2542 1.2894 0.1944 1.307 0.19105
Likelihood ratio test=49.57 on 5 df, p=1.694e-09
n= 340, number of events= 112
tidy.coxreg.multivar method tidies up the multivariate Cox regression model
Code
res
Output
term pval term_label
armcd.1 armcd ARM (reference = 1)
armcd.2 ARM 0.01274101 2
covar1.1 covar1 7.121178e-09 A Covariate Label (reference = 1)
covar1.2 A Covariate Label 0.001145167 2
covar1.3 A Covariate Label 6.519833e-06 3
covar1.4 A Covariate Label 3.296958e-08 4
covar2.1 covar2 Sex (F/M) (reference = F)
covar2.2 Sex (F/M) 0.1979248 M
hr lcl ucl level ci
armcd.1 NA NA <NA>
armcd.2 0.6106495 0.4142327 0.9002013 2 0.4142327, 0.9002013
covar1.1 NA NA <NA>
covar1.2 0.46139 0.2894783 0.7353945 2 0.2894783, 0.7353945
covar1.3 0.3111114 0.1872782 0.5168263 3 0.1872782, 0.5168263
covar1.4 0.1847729 0.1015025 0.3363563 4 0.1015025, 0.3363563
covar2.1 NA NA <NA>
covar2.2 1.28109 0.8786364 1.8678847 M 0.8786364, 1.8678847
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h_coxreg_univar_formulas creates formulas with covariate
Code
res
Output
ref
"survival::Surv(time, status) ~ armcd"
X
"survival::Surv(time, status) ~ armcd + X"
y
"survival::Surv(time, status) ~ armcd + y"
h_coxreg_univar_formulas creates formulas with strata
Code
res
Output
ref
"survival::Surv(time, status) ~ armcd + strata(SITE)"
X
"survival::Surv(time, status) ~ armcd + X + strata(SITE)"
y
"survival::Surv(time, status) ~ armcd + y + strata(SITE)"
h_coxreg_univar_formulas creates formula for reference when treatment is only considered
Code
res
Output
ref
"survival::Surv(time, status) ~ armcd"
h_coxreg_univar_formulas creates formulas with interactions
Code
res
Output
ref
"survival::Surv(time, status) ~ armcd + strata(SITE)"
X
"survival::Surv(time, status) ~ armcd * X + strata(SITE)"
y
"survival::Surv(time, status) ~ armcd * y + strata(SITE)"
h_coxreg_univar_formulas creates formula without treatment arm
Code
res
Output
X
"survival::Surv(time, status) ~ 1 + X + strata(SITE)"
y
"survival::Surv(time, status) ~ 1 + y + strata(SITE)"
h_coxreg_univar_formulas creates formulas with multiple strata
Code
res
Output
ref
"survival::Surv(time, status) ~ armcd + strata(SITE, COUNTRY)"
X
"survival::Surv(time, status) ~ armcd + X + strata(SITE, COUNTRY)"
y
"survival::Surv(time, status) ~ armcd + y + strata(SITE, COUNTRY)"
h_coxreg_multivar_extract extracts correct coxph results when covariate names overlap
Code
res
Output
pval hr lcl ucl level n term term_label
1 0.3062027 1.029677 0.9735821 1.089003 age 8 age age
h_coxreg_multivar_extract extracts correct coxph results when covariate is a factor
Code
res
Output
term pval term_label hr lcl ucl level n
1 stage NA stage (reference = 1) NA NA NA <NA> NA
2 stage 0.1947681 2 4.989564 0.4394003 56.65848 2 8
h_coxreg_multivar_formula creates formula without covariate
Code
res
Output
[1] "survival::Surv(TIME, EVNT) ~ ARMCD"
h_coxreg_multivar_formula creates formulas with a strata
Code
res
Output
[1] "survival::Surv(time, status) ~ armcd + X + y + strata(SITE)"
h_coxreg_multivar_formula creates formulas with multiple strata
Code
res
Output
[1] "survival::Surv(time, status) ~ armcd + X + y + strata(SITE, COUNTRY)"
h_coxreg_multivar_formula creates formula with covariate
Code
res
Output
[1] "survival::Surv(time, status) ~ armcd + covar1 + covar2"
h_coxreg_multivar_formula creates formula without treatment arm
Code
res
Output
[1] "survival::Surv(time, status) ~ 1 + covar1 + covar2"
h_coxreg_multivar_formula creates formulas with multiple strata and without arm
Code
res
Output
[1] "survival::Surv(time, status) ~ 1 + X + y + strata(SITE, COUNTRY)"
control_coxreg returns a standard list of parameters
Code
res
Output
$pval_method
[1] "wald"
$ties
[1] "exact"
$conf_level
[1] 0.95
$interaction
[1] FALSE
fit_coxreg_univar returns model results as expected
Code
res
Output
$mod
$mod$ref
Call:
survival::coxph(formula = stats::as.formula(x), data = data,
ties = control$ties)
coef exp(coef) se(coef) z p
armcd2 -0.4484 0.6386 0.1990 -2.253 0.0242
Likelihood ratio test=5.25 on 1 df, p=0.02191
n= 340, number of events= 112
$mod$covar1
Call:
survival::coxph(formula = stats::as.formula(x), data = data,
ties = control$ties)
coef exp(coef) se(coef) z p
armcd2 -0.4992 0.6070 0.2000 -2.496 0.012573
covar12 -0.8180 0.4413 0.2393 -3.418 0.000631
covar13 -1.1921 0.3036 0.2615 -4.559 5.13e-06
covar14 -1.7264 0.1779 0.3074 -5.615 1.96e-08
Likelihood ratio test=47.85 on 4 df, p=1.015e-09
n= 340, number of events= 112
$data
time status arm armcd covar1 covar2 age
1 1 0 ARM: 1 1 1 M 56
2 1 0 ARM: 1 1 2 M 43
3 1 0 ARM: 1 1 3 F 33
4 1 0 ARM: 1 1 4 M 26
5 4 0 ARM: 1 1 1 F 46
6 4 0 ARM: 1 1 2 M 45
7 4 0 ARM: 1 1 3 M 49
8 4 0 ARM: 1 1 4 F 34
9 7 0 ARM: 1 1 1 F 25
10 7 0 ARM: 1 1 2 F 53
11 7 0 ARM: 1 1 3 M 40
12 7 0 ARM: 1 1 4 F 20
13 10 0 ARM: 1 1 1 M 36
14 10 0 ARM: 1 1 2 F 32
15 10 0 ARM: 1 1 3 F 45
16 10 0 ARM: 1 1 4 F 59
17 6 1 ARM: 1 1 1 F 21
18 10 0 ARM: 1 1 2 F 60
19 10 0 ARM: 1 1 3 F 27
20 10 0 ARM: 1 1 4 F 44
21 14 0 ARM: 1 1 1 F 50
22 14 0 ARM: 1 1 2 F 39
23 14 0 ARM: 1 1 3 M 39
24 14 0 ARM: 1 1 4 M 24
25 18 0 ARM: 1 1 1 M 29
26 18 0 ARM: 1 1 2 F 39
27 18 0 ARM: 1 1 3 F 34
28 18 0 ARM: 1 1 4 M 48
29 5 1 ARM: 1 1 1 M 21
30 18 0 ARM: 1 1 2 F 20
31 18 0 ARM: 1 1 3 M 24
32 18 0 ARM: 1 1 4 F 44
33 12 1 ARM: 1 1 1 M 56
34 16 1 ARM: 1 1 2 F 51
35 18 0 ARM: 1 1 3 M 59
36 18 0 ARM: 1 1 4 M 32
37 23 0 ARM: 1 1 1 F 44
38 23 0 ARM: 1 1 2 F 23
39 23 0 ARM: 1 1 3 F 57
40 23 0 ARM: 1 1 4 F 24
41 10 1 ARM: 1 1 1 F 20
42 15 1 ARM: 1 1 2 F 57
43 23 0 ARM: 1 1 3 F 32
44 23 0 ARM: 1 1 4 M 27
45 3 1 ARM: 1 1 1 M 38
46 16 1 ARM: 1 1 2 F 47
47 23 1 ARM: 1 1 3 M 57
48 23 0 ARM: 1 1 4 F 30
49 3 1 ARM: 1 1 1 M 27
50 9 1 ARM: 1 1 2 M 42
51 21 1 ARM: 1 1 3 M 39
52 23 0 ARM: 1 1 4 F 24
53 7 1 ARM: 1 1 1 M 21
54 10 1 ARM: 1 1 2 F 24
55 16 1 ARM: 1 1 3 F 31
56 24 1 ARM: 1 1 4 M 22
57 3 1 ARM: 1 1 1 F 45
58 15 1 ARM: 1 1 2 M 33
59 25 1 ARM: 1 1 3 F 32
60 25 0 ARM: 1 1 4 F 50
61 26 0 ARM: 1 1 1 F 53
62 26 0 ARM: 1 1 2 F 49
63 26 0 ARM: 1 1 3 F 45
64 26 0 ARM: 1 1 4 F 26
65 1 1 ARM: 1 1 1 M 46
66 26 0 ARM: 1 1 2 M 28
67 26 0 ARM: 1 1 3 M 27
68 26 0 ARM: 1 1 4 F 41
69 2 1 ARM: 1 1 1 M 25
70 26 1 ARM: 1 1 2 M 46
71 26 0 ARM: 1 1 3 F 49
72 26 0 ARM: 1 1 4 F 29
73 25 1 ARM: 1 1 1 M 49
74 28 0 ARM: 1 1 2 F 20
75 28 0 ARM: 1 1 3 M 25
76 28 0 ARM: 1 1 4 M 36
77 29 0 ARM: 1 1 1 M 32
78 29 0 ARM: 1 1 2 F 45
79 29 0 ARM: 1 1 3 F 21
80 29 0 ARM: 1 1 4 F 51
81 29 0 ARM: 1 1 1 M 55
82 29 0 ARM: 1 1 2 M 24
83 29 0 ARM: 1 1 3 F 42
84 29 0 ARM: 1 1 4 M 57
85 29 0 ARM: 1 1 1 F 39
86 29 0 ARM: 1 1 2 F 47
87 29 0 ARM: 1 1 3 M 47
88 29 0 ARM: 1 1 4 M 31
89 28 1 ARM: 1 1 1 M 54
90 30 1 ARM: 1 1 2 F 23
91 30 0 ARM: 1 1 3 F 45
92 30 0 ARM: 1 1 4 F 32
93 2 1 ARM: 1 1 1 F 22
94 17 1 ARM: 1 1 2 F 34
95 22 1 ARM: 1 1 3 M 53
96 30 0 ARM: 1 1 4 F 57
97 3 1 ARM: 1 1 1 M 23
98 6 1 ARM: 1 1 2 M 45
99 8 1 ARM: 1 1 3 M 40
100 12 1 ARM: 1 1 4 M 40
101 12 1 ARM: 1 1 1 M 35
102 15 1 ARM: 1 1 2 M 56
103 24 1 ARM: 1 1 3 F 43
104 31 0 ARM: 1 1 4 F 40
105 32 0 ARM: 1 1 1 M 22
106 32 0 ARM: 1 1 2 M 45
107 32 0 ARM: 1 1 3 F 42
108 32 0 ARM: 1 1 4 F 55
109 34 0 ARM: 1 1 1 M 41
110 34 0 ARM: 1 1 2 M 22
111 34 0 ARM: 1 1 3 F 23
112 34 0 ARM: 1 1 4 F 55
113 36 0 ARM: 1 1 1 F 56
114 36 0 ARM: 1 1 2 M 20
115 36 0 ARM: 1 1 3 M 56
116 36 0 ARM: 1 1 4 F 41
117 29 1 ARM: 1 1 1 M 40
118 36 0 ARM: 1 1 2 M 46
119 36 0 ARM: 1 1 3 M 30
120 36 0 ARM: 1 1 4 M 30
121 37 0 ARM: 1 1 1 F 25
122 37 0 ARM: 1 1 2 F 55
123 37 0 ARM: 1 1 3 M 25
124 37 0 ARM: 1 1 4 F 39
125 9 1 ARM: 1 1 1 F 59
126 17 1 ARM: 1 1 2 M 52
127 22 1 ARM: 1 1 3 F 59
128 24 1 ARM: 1 1 4 F 30
129 16 1 ARM: 1 1 1 F 30
130 19 1 ARM: 1 1 2 M 40
131 23 1 ARM: 1 1 3 F 40
132 29 1 ARM: 1 1 4 F 36
133 41 0 ARM: 1 1 1 M 28
134 41 0 ARM: 1 1 2 M 37
135 41 0 ARM: 1 1 3 M 50
136 41 0 ARM: 1 1 4 F 27
137 3 1 ARM: 1 1 1 F 42
138 43 0 ARM: 1 1 2 M 25
139 43 0 ARM: 1 1 3 M 30
140 43 0 ARM: 1 1 4 M 56
141 6 1 ARM: 1 1 1 F 44
142 43 0 ARM: 1 1 2 F 21
143 43 0 ARM: 1 1 3 M 58
144 43 0 ARM: 1 1 4 M 51
145 3 1 ARM: 1 1 1 F 59
146 6 1 ARM: 1 1 2 M 41
147 9 1 ARM: 1 1 3 M 54
148 44 0 ARM: 1 1 4 F 30
149 9 1 ARM: 1 1 1 M 32
150 11 1 ARM: 1 1 2 M 21
151 20 1 ARM: 1 1 3 M 59
152 26 1 ARM: 1 1 4 F 25
153 18 1 ARM: 1 1 1 M 34
154 48 0 ARM: 1 1 2 F 60
155 48 0 ARM: 1 1 3 F 47
156 48 0 ARM: 1 1 4 M 20
157 49 0 ARM: 1 1 1 M 21
158 49 0 ARM: 1 1 2 M 28
159 49 0 ARM: 1 1 3 F 24
160 49 0 ARM: 1 1 4 F 46
161 35 1 ARM: 1 1 1 M 48
162 51 0 ARM: 1 1 2 F 21
163 51 0 ARM: 1 1 3 F 56
164 51 0 ARM: 1 1 4 M 50
165 17 1 ARM: 1 1 1 M 33
166 53 0 ARM: 1 1 2 F 44
167 53 0 ARM: 1 1 3 M 40
168 53 0 ARM: 1 1 4 M 42
169 3 1 ARM: 1 1 1 F 25
170 15 1 ARM: 1 1 2 F 40
171 46 1 ARM: 1 1 3 F 24
172 51 1 ARM: 1 1 4 M 44
173 59 0 ARM: 1 1 1 F 36
174 59 0 ARM: 1 1 2 F 52
175 59 0 ARM: 1 1 3 F 59
176 59 0 ARM: 1 1 4 M 38
177 2 1 ARM: 1 1 1 M 36
178 15 1 ARM: 1 1 2 M 39
179 24 1 ARM: 1 1 3 F 42
180 30 1 ARM: 1 1 4 F 39
181 5 1 ARM: 1 1 1 M 50
182 14 1 ARM: 1 1 2 F 24
183 19 1 ARM: 1 1 3 F 46
184 27 1 ARM: 1 1 4 M 52
185 2 1 ARM: 1 1 1 F 20
186 8 1 ARM: 1 1 2 F 48
187 12 1 ARM: 1 1 3 M 53
188 13 1 ARM: 1 1 4 M 55
189 1 0 ARM: 2 2 1 M 39
190 1 0 ARM: 2 2 2 F 40
191 1 0 ARM: 2 2 3 M 57
192 1 0 ARM: 2 2 4 M 43
193 1 0 ARM: 2 2 1 F 53
194 1 0 ARM: 2 2 2 M 39
195 1 0 ARM: 2 2 3 M 22
196 1 0 ARM: 2 2 4 F 39
197 5 1 ARM: 2 2 1 F 53
198 5 0 ARM: 2 2 2 F 34
199 5 0 ARM: 2 2 3 F 49
200 5 0 ARM: 2 2 4 M 32
201 9 0 ARM: 2 2 1 M 35
202 9 0 ARM: 2 2 2 F 55
203 9 0 ARM: 2 2 3 F 49
204 9 0 ARM: 2 2 4 F 48
205 10 0 ARM: 2 2 1 M 47
206 10 0 ARM: 2 2 2 M 32
207 10 0 ARM: 2 2 3 M 26
208 10 0 ARM: 2 2 4 F 37
209 13 0 ARM: 2 2 1 F 20
210 13 0 ARM: 2 2 2 M 23
211 13 0 ARM: 2 2 3 F 24
212 13 0 ARM: 2 2 4 M 55
213 3 1 ARM: 2 2 1 M 53
214 14 0 ARM: 2 2 2 M 45
215 14 0 ARM: 2 2 3 M 52
216 14 0 ARM: 2 2 4 M 38
217 1 1 ARM: 2 2 1 F 36
218 3 1 ARM: 2 2 2 F 32
219 5 1 ARM: 2 2 3 F 58
220 7 1 ARM: 2 2 4 M 55
221 18 0 ARM: 2 2 1 F 26
222 18 0 ARM: 2 2 2 F 41
223 18 0 ARM: 2 2 3 F 28
224 18 0 ARM: 2 2 4 F 51
225 17 1 ARM: 2 2 1 M 59
226 18 0 ARM: 2 2 2 F 52
227 18 0 ARM: 2 2 3 M 47
228 18 0 ARM: 2 2 4 F 31
229 2 1 ARM: 2 2 1 M 49
230 19 0 ARM: 2 2 2 M 54
231 19 0 ARM: 2 2 3 F 45
232 19 0 ARM: 2 2 4 F 22
233 17 1 ARM: 2 2 1 M 34
234 19 1 ARM: 2 2 2 M 58
235 21 0 ARM: 2 2 3 F 42
236 21 0 ARM: 2 2 4 M 44
237 22 0 ARM: 2 2 1 F 20
238 22 0 ARM: 2 2 2 F 47
239 22 0 ARM: 2 2 3 F 28
240 22 0 ARM: 2 2 4 M 33
241 25 0 ARM: 2 2 1 F 50
242 25 0 ARM: 2 2 2 F 35
243 25 0 ARM: 2 2 3 M 40
244 25 0 ARM: 2 2 4 M 31
245 25 0 ARM: 2 2 1 M 49
246 25 0 ARM: 2 2 2 F 41
247 25 0 ARM: 2 2 3 M 20
248 25 0 ARM: 2 2 4 F 31
249 25 0 ARM: 2 2 1 F 47
250 25 0 ARM: 2 2 2 F 31
251 25 0 ARM: 2 2 3 M 44
252 25 0 ARM: 2 2 4 F 44
253 6 1 ARM: 2 2 1 F 27
254 12 1 ARM: 2 2 2 M 50
255 13 1 ARM: 2 2 3 M 24
256 26 0 ARM: 2 2 4 F 31
257 6 1 ARM: 2 2 1 M 49
258 27 0 ARM: 2 2 2 M 28
259 27 0 ARM: 2 2 3 M 21
260 27 0 ARM: 2 2 4 M 28
261 2 1 ARM: 2 2 1 F 60
262 29 0 ARM: 2 2 2 F 60
263 29 0 ARM: 2 2 3 M 41
264 29 0 ARM: 2 2 4 M 46
265 26 1 ARM: 2 2 1 F 57
266 35 1 ARM: 2 2 2 M 42
267 36 0 ARM: 2 2 3 F 53
268 36 0 ARM: 2 2 4 F 22
269 38 0 ARM: 2 2 1 F 20
270 38 0 ARM: 2 2 2 M 21
271 38 0 ARM: 2 2 3 M 38
272 38 0 ARM: 2 2 4 M 48
273 22 1 ARM: 2 2 1 M 24
274 23 1 ARM: 2 2 2 F 53
275 27 1 ARM: 2 2 3 F 60
276 32 1 ARM: 2 2 4 M 31
277 4 1 ARM: 2 2 1 F 60
278 16 1 ARM: 2 2 2 F 37
279 23 1 ARM: 2 2 3 M 53
280 27 1 ARM: 2 2 4 M 32
281 24 1 ARM: 2 2 1 F 58
282 26 1 ARM: 2 2 2 M 23
283 29 1 ARM: 2 2 3 M 25
284 40 1 ARM: 2 2 4 M 42
285 41 0 ARM: 2 2 1 M 44
286 41 0 ARM: 2 2 2 M 35
287 41 0 ARM: 2 2 3 M 41
288 41 0 ARM: 2 2 4 M 45
289 41 0 ARM: 2 2 1 F 59
290 41 0 ARM: 2 2 2 M 33
291 41 0 ARM: 2 2 3 F 25
292 41 0 ARM: 2 2 4 M 27
293 1 1 ARM: 2 2 1 M 40
294 27 1 ARM: 2 2 2 F 43
295 43 0 ARM: 2 2 3 M 22
296 43 0 ARM: 2 2 4 F 59
297 44 0 ARM: 2 2 1 M 56
298 44 0 ARM: 2 2 2 F 33
299 44 0 ARM: 2 2 3 M 46
300 44 0 ARM: 2 2 4 F 32
301 2 1 ARM: 2 2 1 F 38
302 20 1 ARM: 2 2 2 M 22
303 23 1 ARM: 2 2 3 M 48
304 27 1 ARM: 2 2 4 F 24
305 45 0 ARM: 2 2 1 F 44
306 45 0 ARM: 2 2 2 M 50
307 45 0 ARM: 2 2 3 F 33
308 45 0 ARM: 2 2 4 M 55
309 2 1 ARM: 2 2 1 M 39
310 46 0 ARM: 2 2 2 F 50
311 46 0 ARM: 2 2 3 F 32
312 46 0 ARM: 2 2 4 F 22
313 46 0 ARM: 2 2 1 M 59
314 46 0 ARM: 2 2 2 F 43
315 46 0 ARM: 2 2 3 M 48
316 46 0 ARM: 2 2 4 F 29
317 49 0 ARM: 2 2 1 M 32
318 49 0 ARM: 2 2 2 M 25
319 49 0 ARM: 2 2 3 M 29
320 49 0 ARM: 2 2 4 M 58
321 50 0 ARM: 2 2 1 F 38
322 50 0 ARM: 2 2 2 F 37
323 50 0 ARM: 2 2 3 F 40
324 50 0 ARM: 2 2 4 M 42
325 4 1 ARM: 2 2 1 F 45
326 24 1 ARM: 2 2 2 M 34
327 47 1 ARM: 2 2 3 M 48
328 50 0 ARM: 2 2 4 M 48
329 54 0 ARM: 2 2 1 F 24
330 54 0 ARM: 2 2 2 F 41
331 54 0 ARM: 2 2 3 M 20
332 54 0 ARM: 2 2 4 F 41
333 38 1 ARM: 2 2 1 M 32
334 54 0 ARM: 2 2 2 F 41
335 54 0 ARM: 2 2 3 M 25
336 54 0 ARM: 2 2 4 M 60
337 59 0 ARM: 2 2 1 M 52
338 59 0 ARM: 2 2 2 F 43
339 59 0 ARM: 2 2 3 M 41
340 59 0 ARM: 2 2 4 F 52
$control
$control$pval_method
[1] "wald"
$control$ties
[1] "exact"
$control$conf_level
[1] 0.91
$control$interaction
[1] FALSE
$vars
$vars$time
[1] "time"
$vars$event
[1] "status"
$vars$arm
[1] "armcd"
$vars$covariates
[1] "covar1"
$at
list()
attr(,"class")
[1] "coxreg.univar"
fit_coxreg_univar works without treatment arm
Code
res
Output
[1] "age"
tidy.summary.coxph method tidies up the Cox regression model
Code
res
Output
Pr(>|z|) exp(coef) exp(-coef) lower .95 upper .95 level n
1 0.2472383 3.846606 0.2599694 0.3926671 37.68173 armcdB 8
h_coxreg_univar_extract extracts coxph results
Code
res
Output
effect term term_label level n hr lcl ucl
1 Treatment: armcd B vs control (A) B 8 3.846606 0.3926671 37.68173
pval
1 0.2472383
tidy.coxreg.univar method tidies up the univariate Cox regression model
Code
res
Output
effect term term_label level n hr lcl
ref Treatment: armcd 2 vs control (1) 2 340 0.6386426 0.4323844
covar1 Covariate: covar1 A Covariate Label 2 340 0.607037 0.4101675
covar2 Covariate: covar2 Sex (F/M) 2 340 0.6242738 0.4222423
ucl pval ci
ref 0.9432911 0.02423805 0.4323844, 0.9432911
covar1 0.8983984 0.01257339 0.4101675, 0.8983984
covar2 0.9229721 0.01818876 0.4222423, 0.9229721
tidy.coxreg.univar method works with only numeric covariates with strata
Code
res
Output
effect term term_label level n hr lcl ucl
ref Treatment: armcd 2 vs control (1) 2 340 0.6208343 0.4164994 0.9254162
age Covariate: age age 2 340 0.6076894 0.4072018 0.9068879
pval ci
ref 0.01925561 0.4164994, 0.9254162
age 0.01475084 0.4072018, 0.9068879
tidy.coxreg.univar method works without treatment arm
Code
res
Output
[1] "age" "covar1" "A Covariate Label"
[4] "A Covariate Label" "A Covariate Label"
fit_coxreg_multivar returns model results as expected
Code
res
Output
Call:
survival::coxph(formula = stats::as.formula(form), data = data,
ties = control$ties)
coef exp(coef) se(coef) z p
armcd2 -0.5004 0.6063 0.2000 -2.503 0.01233
covar12 -0.7842 0.4565 0.2407 -3.258 0.00112
covar13 -1.1810 0.3070 0.2615 -4.516 6.29e-06
covar14 -1.7054 0.1817 0.3078 -5.541 3.01e-08
covar2M 0.2542 1.2894 0.1944 1.307 0.19105
Likelihood ratio test=49.57 on 5 df, p=1.694e-09
n= 340, number of events= 112
tidy.coxreg.multivar method tidies up the multivariate Cox regression model
Code
res
Output
term pval term_label
armcd.1 armcd ARM (reference = 1)
armcd.2 ARM 0.01274101 2
covar1.1 covar1 7.121178e-09 A Covariate Label (reference = 1)
covar1.2 A Covariate Label 0.001145167 2
covar1.3 A Covariate Label 6.519833e-06 3
covar1.4 A Covariate Label 3.296958e-08 4
covar2.1 covar2 Sex (F/M) (reference = F)
covar2.2 Sex (F/M) 0.1979248 M
hr lcl ucl level ci
armcd.1 NA NA <NA>
armcd.2 0.6106495 0.4142327 0.9002013 2 0.4142327, 0.9002013
covar1.1 NA NA <NA>
covar1.2 0.46139 0.2894783 0.7353945 2 0.2894783, 0.7353945
covar1.3 0.3111114 0.1872782 0.5168263 3 0.1872782, 0.5168263
covar1.4 0.1847729 0.1015025 0.3363563 4 0.1015025, 0.3363563
covar2.1 NA NA <NA>
covar2.2 1.28109 0.8786364 1.8678847 M 0.8786364, 1.8678847
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