TotalPoints.rms: Caculate Total Points for nomogram Picture
In nomogramFormula: Calculate Total Points and Probabilities for Nomogram
Description
Usage
Arguments
Value
Examples
View source: R/TotalPoints.rms.R
Description
Compared with points_cal() command, TotalPoints.rms() is suit
for more complexed condition. Since this command is based on formula
from 'rms' package, it may be also more accurate. However, formula for
each variable can not be caculated.
Usage
1
TotalPoints.rms(rd, fit, nom, kint = NULL)
Arguments
rd
raw data
fit
regression result in 'rma' package
nom
nomoram() command result
kint
number of intercept. Default is to use fit$interceptRef if it
exists, or 1.
Value
a dataframe contains rawdata and total points
Examples
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
library(rms)
n <- 1000
set.seed(17)
d <- data.frame(age = rnorm(n, 50, 10),
blood.pressure = rnorm(n, 120, 15),
cholesterol = rnorm(n, 200, 25),
sex = factor(sample(c('female','male'), n,TRUE)))
d <- upData(d,
L = .4*(sex=='male') + .045*(age-50) +
(log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male')),
y = ifelse(runif(n) < plogis(L), 1, 0))
ddist <- datadist(d); options(datadist='ddist')
f <- lrm(y ~ lsp(age,50) + sex * rcs(cholesterol, 4) + blood.pressure,
data=d)
nom <- nomogram(f)
TotalPoints.rms(rd = d,fit = f,nom = nom)
Example output
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
Input object size: 29616 bytes; 4 variables 1000 observations
Added variable L
Added variable y
New object size: 41856 bytes; 6 variables 1000 observations
age sex cholesterol blood.pressure total points
1 39.84991 male 191.6668 98.37248 72.37029
2 49.20363 male 168.1024 112.99815 81.43506
3 47.67013 female 196.4870 100.90785 70.53558
4 41.82732 female 197.8634 122.22211 62.47700
5 57.72091 female 200.2004 125.38972 78.91130
6 48.34388 male 231.3853 118.71428 98.06697
7 59.72874 female 217.1354 125.00913 81.30797
8 67.16534 female 215.5950 95.61015 86.75973
9 52.55237 male 175.6908 126.21661 85.92205
10 53.66581 male 197.0684 112.12832 87.63523
11 61.80789 female 189.1410 113.59159 80.13437
12 56.43192 female 218.6268 115.39797 79.17059
13 62.95322 female 224.7456 138.64789 81.80828
14 51.87918 male 209.8016 123.38761 86.21882
15 65.91205 male 240.1214 118.03400 120.16451
16 49.44821 male 201.3340 136.55724 83.60887
17 58.38471 female 232.5283 96.39998 77.44069
18 51.59370 female 179.7718 135.65666 73.32360
19 56.25954 male 194.6000 137.19306 89.18210
20 56.33585 male 195.8520 125.85966 89.27195
21 56.81028 male 213.6618 136.15947 90.47297
22 43.17967 female 217.2580 124.94794 65.77589
23 42.76743 male 202.9612 114.72142 74.82082
24 66.73526 female 214.9434 117.24793 86.14756
25 44.04244 female 182.3234 122.71212 64.26122
26 61.59844 male 227.9575 150.11641 103.78343
27 51.17422 female 162.4534 110.43721 76.47135
28 52.59221 female 250.4253 137.84058 66.83585
29 53.82362 male 209.7332 141.53884 87.13513
30 42.88518 male 196.6625 98.14596 75.92030
31 38.22430 female 194.0338 133.02617 56.75100
32 40.39833 female 210.8321 129.55811 62.20033
33 41.21048 female 186.6302 114.53614 60.48440
34 14.43864 male 184.4276 110.65898 37.65911
35 35.83250 male 215.8029 109.48929 68.38242
36 45.51231 female 199.7717 89.00088 68.41279
37 42.24032 male 217.8165 97.66564 78.46388
38 41.68172 male 241.7264 102.84821 100.71897
39 50.51830 male 209.4910 105.35082 85.59068
40 43.83449 male 230.1793 121.06453 90.66615
41 52.54397 male 221.5995 103.11464 93.20114
42 46.68480 male 192.2245 115.77981 81.28948
43 47.93681 male 207.2510 101.84303 82.16211
44 62.15337 female 205.6877 131.10155 82.57550
45 68.92056 female 152.5611 134.12809 89.71839
46 50.74194 male 215.2521 116.45792 87.67047
47 67.51696 female 187.9607 131.18112 83.43794
48 47.68513 male 152.5440 99.64838 74.59181
49 55.43452 male 205.6408 107.41441 88.24728
50 40.10999 female 204.7385 117.56270 61.43172
51 53.15531 female 192.7313 130.78399 74.61629
52 74.42327 male 180.7205 132.69549 100.82798
53 55.49693 female 192.7975 102.87920 76.62513
54 49.70757 female 234.9685 140.61031 70.07523
55 41.69217 female 188.4530 126.18153 60.99552
56 62.46434 male 154.9905 119.32882 86.21689
57 36.24245 male 192.9221 115.44524 67.05840
58 46.68892 male 206.2719 132.02659 79.85348
59 59.80911 male 207.5063 88.17980 91.54812
60 71.90771 male 195.2808 113.22137 99.59672
61 50.30546 female 221.1495 130.57501 74.55535
62 42.14483 female 216.8751 120.32933 64.49438
63 53.25441 male 198.5605 108.72838 87.23953
64 41.19156 female 224.7812 127.77045 61.69792
65 52.09326 male 191.5176 93.75516 87.58403
66 51.51033 male 183.0139 123.32588 86.52914
67 46.56521 male 215.9976 132.96535 82.63755
68 59.05878 male 210.6436 132.75066 90.89350
69 59.18955 female 172.3430 104.89470 79.73857
70 44.44013 female 180.0211 94.74611 65.45295
71 55.60235 female 211.9951 140.90890 78.65461
72 32.07582 female 193.3880 116.24679 48.60966
73 34.34583 female 200.4600 104.48238 53.11436
74 16.79681 male 178.7811 116.60531 40.01455
75 51.54722 female 186.7461 134.63356 73.05495
76 46.35373 male 194.7787 141.74536 80.10104
77 25.66316 male 183.3357 113.97735 52.73245
78 53.36464 male 252.4105 142.42112 125.60500
79 43.59547 female 266.4948 140.29488 50.82340
80 68.21120 female 230.4323 143.76430 83.57733
81 31.53277 female 227.9089 101.41723 48.26028
82 56.41717 male 181.8737 114.28983 89.71501
83 61.85525 female 200.2828 112.45521 81.81697
84 48.22312 male 212.8090 123.92027 83.53676
85 37.13874 female 174.8951 107.82255 55.91427
86 54.63451 female 228.1492 82.69460 76.56698
87 58.80666 female 161.7869 134.11060 81.11806
88 51.39422 female 175.7233 123.18211 73.87533
89 46.24945 female 160.7844 108.03340 71.04282
90 50.42539 female 217.0939 102.59418 75.71645
91 56.33880 male 197.9094 127.87864 88.96995
92 32.92512 male 219.3503 137.48091 66.13551
93 50.19687 male 182.7063 120.17301 85.70519
94 47.01204 male 180.9520 89.39197 81.84243
95 45.58237 male 227.6790 95.62920 91.01239
96 55.90975 male 214.7232 113.62969 90.78279
97 38.65679 female 233.4938 124.49784 55.84635
98 45.61255 male 211.0458 122.53741 79.40364
99 53.44901 female 215.9364 90.73557 77.98463
100 45.50600 female 267.3507 121.75343 53.44396
101 50.43820 female 194.3606 94.34574 73.74341
102 44.32008 male 232.9010 146.28607 93.71772
103 68.24860 male 196.6942 156.17277 96.29885
104 54.33003 female 174.3399 121.35805 75.99780
105 36.46034 female 218.7881 115.72095 56.62866
106 61.54466 male 195.4254 135.18378 92.51717
107 59.20737 female 225.3490 134.47916 79.32561
108 45.51343 male 223.5890 112.68471 86.91896
109 70.70574 female 185.2261 100.46659 85.98517
110 48.00444 male 179.9149 120.88050 82.47625
111 38.70872 male 189.9283 143.65987 70.12877
112 37.04445 male 199.6546 117.56241 67.27974
113 62.40419 male 221.3726 104.23296 99.35608
114 66.95059 male 180.6526 114.86667 96.31998
115 55.02301 male 248.3332 128.02826 122.29764
116 53.33632 female 167.7674 114.77484 76.65047
117 44.91797 female 196.1169 87.22843 66.97845
118 46.29368 male 194.8776 136.30063 80.10323
119 65.08643 male 250.0630 128.09253 130.74127
120 49.50374 female 243.8592 93.13831 67.57355
121 63.81757 female 201.8325 136.69104 82.93288
122 54.48932 male 211.6901 116.54671 88.55940
123 48.47690 female 226.0799 106.21418 71.64726
124 52.59294 male 153.7504 142.39782 79.04535
125 33.88598 female 216.8342 93.20081 53.77071
126 29.91044 male 191.1337 128.47947 58.39254
127 30.00629 female 190.3424 137.63467 45.06869
128 51.21041 female 188.4116 115.45788 73.23478
129 47.70005 female 170.5817 129.10710 70.58435
130 28.00898 female 167.3284 105.07015 44.92303
131 32.89591 female 204.5946 104.97136 51.84340
132 52.26259 male 158.2069 140.45820 80.33160
133 59.50850 male 180.3840 109.37154 91.58381
134 71.08416 male 221.5865 121.22582 104.81147
135 43.78774 male 140.2354 116.69177 64.95721
136 60.54647 female 224.3943 106.70137 80.90324
137 33.60991 male 170.8583 115.68396 61.01802
138 58.40983 female 196.0090 119.60233 78.70070
139 44.74525 female 238.9512 113.35766 62.47065
140 50.63859 male 171.5354 109.83466 83.95576
141 45.36348 male 218.1990 116.39966 82.61494
142 56.61045 female 203.2630 111.43041 78.98281
143 45.60014 female 274.0808 126.95666 51.13056
144 47.11840 female 225.8230 96.55812 70.03846
145 36.84052 female 192.9442 123.33057 54.88831
146 67.10227 male 174.7096 144.19242 94.75160
147 46.72460 male 195.2265 141.03513 80.56038
148 31.61542 female 207.3669 136.08595 49.92192
149 63.19412 female 198.2440 119.69188 82.17722
150 53.48882 female 188.8464 104.55116 74.91819
151 79.16072 female 209.5653 121.95875 94.08449
152 50.99916 male 199.7379 141.04811 85.07895
153 63.13161 female 200.1357 122.88272 82.42811
154 56.89424 female 212.0526 124.75931 79.77143
155 45.98274 female 155.6184 95.37448 72.07365
156 60.36309 female 200.1866 113.91551 80.81266
157 38.89748 male 221.8621 141.30292 76.02967
158 48.42273 female 190.5183 108.21581 70.59227
159 65.76608 male 155.9526 119.89339 88.64947
160 38.19165 male 237.3224 135.17872 90.43893
161 40.70018 male 168.9288 121.09251 69.99709
162 43.09108 male 212.6594 131.41979 76.38240
163 25.45227 female 204.0095 127.49400 41.25528
164 38.30148 male 224.4614 139.72684 77.40442
165 40.31481 male 213.0700 96.91998 73.38705
166 55.00603 female 232.5741 102.32738 75.14586
167 68.38355 female 259.2984 97.48492 74.61961
168 50.13434 female 208.2179 104.75498 75.59180
169 49.35124 male 172.1086 104.15080 82.91669
170 48.21001 female 200.5042 119.85173 71.66348
171 45.09528 male 209.7749 138.69903 78.07731
172 45.00974 female 195.5428 128.11750 66.28472
173 60.92964 male 138.5056 124.88010 79.71218
174 49.97333 male 209.5231 136.52106 84.67801
175 42.61789 female 207.1354 104.74396 65.37809
176 53.57214 male 200.1483 109.34220 87.25077
177 59.97497 female 187.3772 106.80670 78.98931
178 54.07237 male 213.5994 102.91080 89.26885
179 39.46020 male 262.0089 130.59053 120.24303
180 37.77512 male 202.2525 111.57387 68.14181
181 35.99933 male 146.4978 113.89021 56.49706
182 37.81473 male 182.6263 122.42804 68.99562
183 37.99364 female 182.6047 130.25644 55.90652
184 73.93216 male 205.7570 137.96875 99.62573
185 31.11745 male 190.5399 113.74009 60.32699
186 55.44037 male 164.7706 116.17702 84.93954
187 42.15128 female 247.3559 137.19787 55.59952
188 63.98375 male 136.1323 119.65965 80.99101
189 58.36235 male 189.0102 100.58002 91.62145
190 38.13302 female 245.2851 129.59711 51.00412
191 37.53780 male 192.4080 95.16781 69.22448
192 39.64434 male 211.3889 109.06217 71.64991
193 35.95791 female 185.2157 118.82538 53.27362
194 44.44913 female 226.6344 109.08914 65.98988
195 46.48444 male 201.5119 124.75365 79.78084
196 56.66832 female 139.8480 134.72320 84.69690
197 45.83863 female 171.4680 130.32483 67.87729
198 44.09856 female 184.6968 120.19042 64.30105
199 37.22521 male 197.4119 118.01755 67.79192
200 52.49431 male 214.6837 90.90859 88.96462
201 46.19954 female 160.3498 114.72435 70.95521
202 58.14106 female 204.6412 111.79250 80.18122
203 47.33294 female 207.4202 120.93303 71.52172
204 63.66916 female 190.4443 125.35117 81.22640
205 53.47493 male 209.2136 106.30930 87.41989
206 53.40397 female 213.0926 123.61372 77.53178
207 62.77533 male 188.3531 92.57846 94.61160
208 46.39728 female 172.1786 104.14102 68.97339
209 55.84699 male 195.0682 109.38916 89.34830
210 62.56603 female 187.5040 149.86112 79.90284
211 46.55472 male 229.5983 114.81762 93.88000
212 37.37735 female 224.3945 152.53333 56.17564
213 56.86841 male 214.3533 131.64817 90.90459
214 49.52093 female 168.1623 123.86106 73.61229
215 46.38928 female 194.3021 141.87692 67.71468
216 61.42558 female 178.2199 119.49575 80.09320
217 61.07806 male 224.4818 114.90035 100.86772
218 51.75732 female 172.7961 103.29451 74.90448
219 51.65830 male 231.3732 124.27908 101.27144
220 49.61923 female 215.0006 111.86197 74.94474
221 64.68078 female 190.7287 144.74881 81.56231
222 46.69996 male 194.4647 129.09361 80.83261
223 45.17915 male 256.3300 121.71505 121.71201
224 45.17796 female 212.4570 133.52345 68.63233
225 73.79524 female 188.6040 125.47113 87.61280
226 63.02396 female 183.6349 104.09310 81.00502
227 45.22677 female 169.3317 116.84250 67.67991
228 59.59923 female 228.1329 130.54056 78.92500
229 52.07470 male 235.1985 116.16671 105.77892
230 32.90904 female 202.8160 145.65047 50.85672
231 46.95887 male 183.4721 91.19602 82.04352
232 33.23434 female 182.6870 137.97229 49.30872
233 54.07193 female 177.1207 148.12733 74.97900
234 34.51059 male 185.6030 155.19190 64.18899
235 65.84956 male 187.4074 133.20116 95.86814
236 33.81719 female 239.7145 130.91733 47.06822
237 38.68427 female 247.0316 121.43532 51.28635
238 41.90329 female 187.0393 137.02521 61.03673
239 69.58569 female 236.6017 113.41942 83.01769
240 40.30140 female 206.4677 109.24537 62.07630
241 48.38010 female 172.9489 105.22649 71.51548
242 42.34927 male 216.2577 124.45497 77.21142
243 49.00274 male 192.6199 126.19806 84.21344
244 50.39129 female 170.2644 87.67800 74.74635
245 43.60238 male 199.8725 107.66737 76.32854
246 44.33646 female 230.0940 100.58371 65.02650
247 39.99658 female 222.7052 129.42362 60.50486
248 63.52706 female 159.6115 135.29536 84.62761
249 51.29197 female 243.0307 116.87119 68.94964
250 45.78155 male 163.4849 150.63054 74.69476
251 61.66081 male 188.5697 105.60884 93.66282
252 51.61467 female 202.4935 106.97041 75.71387
253 44.74623 female 209.4460 103.08973 68.50166
254 63.23157 female 208.5155 137.85006 83.46900
255 70.94325 female 208.9205 128.38452 88.63486
256 44.97496 female 209.8373 129.51241 68.36925
257 52.40340 female 222.8960 91.20047 76.26069
258 48.70724 female 164.7383 123.89133 73.22177
259 42.44227 female 192.1826 118.02891 62.48417
260 43.04590 female 209.9186 117.20196 65.97317
261 50.13571 male 214.6353 110.26534 87.08082
262 61.67776 female 193.7371 118.21079 80.46683
263 42.67988 female 205.7689 121.49795 64.99665
264 61.02352 female 237.0336 136.28768 76.95385
265 50.01485 male 174.7748 145.44735 83.74048
266 49.48657 female 153.4040 130.57736 76.70869
267 53.94725 male 189.1545 127.55936 88.29950
268 60.49769 male 190.5756 126.88031 92.47518
269 63.08166 male 248.9445 140.01160 127.97010
270 49.46041 male 171.5281 126.28794 82.52025
271 56.85371 female 180.0786 110.22392 77.13300
272 54.57734 female 213.4084 140.37485 77.98327
273 68.46792 male 212.8495 114.03903 98.03131
274 15.98776 male 136.6671 134.26380 25.75314
275 50.26442 male 204.9800 102.61619 84.98419
276 53.70320 female 183.1033 113.85156 74.84976
277 41.98659 male 211.1344 109.05406 74.74835
278 50.02312 female 225.2290 102.99862 73.99513
279 39.24705 female 176.1587 129.32801 58.21990
280 59.22104 male 200.9490 110.44836 90.79022
281 51.80184 male 254.6010 105.87123 127.73001
282 72.63697 male 208.9649 108.24013 99.67760
283 53.09739 male 194.7203 126.90105 87.31233
284 59.74529 male 229.0013 109.32244 104.33179
285 47.16618 female 211.0328 104.03780 71.83902
286 50.45696 male 164.4497 113.49032 81.67599
287 57.06693 female 150.2635 107.33864 83.07752
288 55.42263 male 212.4558 134.12986 89.12358
289 57.77911 male 205.1776 133.11201 89.28961
290 49.90823 female 251.7878 147.06404 64.40368
291 34.57463 female 184.3033 129.56997 51.21998
292 53.42366 male 199.4679 109.07994 87.23440
293 47.04443 female 193.5026 100.60448 69.21250
294 60.47260 male 174.8766 108.99888 91.14164
295 46.30484 female 230.7075 125.77268 67.07038
296 51.95196 male 171.0747 141.71917 84.11465
297 40.64255 male 185.9436 133.31958 72.91295
298 56.70419 female 224.6790 94.56718 78.57685
299 48.98040 male 196.8245 150.86554 83.23986
300 35.55739 male 151.4721 133.59168 57.18501
301 54.35901 male 229.7038 102.13249 101.69188
302 50.21576 female 212.4664 113.36215 75.66968
303 46.77232 male 191.2142 134.37780 81.16252
304 69.69414 female 223.0253 140.77916 86.49452
305 49.91519 female 206.2109 155.59360 74.27127
306 51.42589 female 200.8777 99.78891 75.43229
307 63.61635 female 233.9737 112.13019 80.06942
308 50.71093 male 191.3628 107.02127 86.47159
309 57.66070 female 200.4891 129.94243 78.84503
310 54.48897 female 199.5283 105.64448 77.05467
311 67.86128 male 206.1746 113.30220 96.17292
312 51.71603 male 190.5544 153.50983 86.35141
313 53.85655 male 158.2589 137.35544 81.42992
314 48.58626 male 236.8295 136.19350 103.97518
315 61.76749 male 191.1887 133.37017 93.13987
316 37.76280 female 204.6543 102.50710 58.49968
317 46.69275 female 216.0496 141.44727 70.37192
318 59.31041 male 212.2948 130.11776 91.63804
319 42.91934 male 168.5168 109.02912 73.10045
320 43.58483 male 156.4368 124.97382 69.86113
321 33.87611 female 193.3108 140.27570 50.61778
322 49.48637 male 216.0674 115.97655 86.93922
323 53.88888 male 189.9606 111.57496 88.51864
324 30.40513 female 170.0484 107.25295 47.60158
325 47.15579 male 224.1429 101.75487 89.81237
326 48.10084 female 203.5942 126.85715 71.93122
327 38.71597 male 216.2422 112.72993 72.47951
328 55.78552 male 245.0296 83.92589 119.81575
329 48.36811 female 195.8601 130.27733 70.85692
330 49.50641 male 199.4607 136.42646 83.87841
331 34.68969 female 198.6477 127.11311 52.84899
332 37.78393 male 232.0338 117.21120 84.44325
333 47.46049 female 191.1110 100.12053 69.48732
334 46.22302 female 205.0770 119.26445 69.74639
335 35.17996 male 204.2209 138.22492 64.07482
336 52.66579 male 188.0378 122.89646 87.56639
337 66.28626 female 192.2207 134.31812 82.94485
338 52.17923 male 191.3588 99.90900 87.54289
339 52.80179 female 239.9691 122.42305 70.89205
340 34.91685 male 201.9232 109.36112 64.32496
341 47.90907 male 179.4281 133.11922 82.05107
342 59.59021 female 215.5963 86.11430 82.04874
343 41.75614 female 212.4223 134.29153 63.97608
344 62.45752 male 181.8803 97.81909 93.89627
345 43.19393 female 248.7084 103.12853 57.14293
346 48.83752 female 201.2186 103.03210 72.94107
347 42.68946 female 212.2458 136.98063 65.19616
348 40.81053 male 251.0243 116.22202 109.85738
349 56.35702 male 229.3014 117.86620 102.29762
350 52.85871 female 182.8873 127.10627 74.08129
351 53.65170 male 165.1538 108.38156 84.04588
352 50.71484 female 178.6960 135.71262 72.85937
353 47.10088 male 248.1249 110.49056 115.20186
354 49.73246 male 212.2459 107.61446 85.65805
355 47.40992 female 209.4181 92.11581 72.30770
356 47.35448 male 210.4736 107.48013 81.86884
357 51.51098 female 209.1602 124.57622 76.20534
358 51.38726 female 218.8430 121.01004 75.79281
359 50.30766 male 212.6639 100.00918 86.51081
360 46.34957 female 183.9102 110.77680 67.53832
361 64.34832 female 163.2983 106.48325 84.83776
362 62.01889 male 233.0893 128.38243 109.68158
363 55.98876 female 184.9139 120.86799 76.15051
364 58.06182 male 177.9785 104.65348 90.32211
365 57.82339 female 216.9502 114.94540 80.27825
366 50.71609 female 148.6579 147.39029 78.64497
367 39.92700 male 201.0320 132.78109 70.78267
368 44.43085 female 193.5740 146.29233 64.87078
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772 39.26008 male 230.1572 104.88320 84.72204
773 47.68556 male 229.4304 127.45641 95.02316
774 57.75547 male 195.3653 135.60076 90.07730
775 32.40722 female 233.0091 108.28666 47.80756
776 37.64600 female 191.3524 119.28042 55.85792
777 54.69159 female 217.6100 130.62964 77.91107
778 42.78120 female 195.1390 107.52935 63.55732
779 38.82606 male 165.3455 102.80350 66.69100
780 57.69218 female 180.9845 95.49322 77.86194
781 56.23105 female 136.9724 125.15091 85.23540
782 47.48175 female 187.6303 110.76034 69.08733
783 48.41339 female 193.7845 104.18519 71.04787
784 41.27154 female 177.4806 108.67574 61.16592
785 55.18422 male 197.6595 120.59957 88.38685
786 44.08620 male 146.0678 116.96808 67.27437
787 57.91512 female 189.3148 114.40590 77.62460
788 44.84700 female 217.0262 116.69499 68.20909
789 42.31007 male 220.5887 107.94299 80.27708
790 53.06560 male 163.6351 122.43271 82.93839
791 45.41095 male 253.5807 106.02019 119.18184
792 42.83515 female 214.0232 118.19821 65.68157
793 75.94994 male 216.6224 97.54948 104.98615
794 59.93307 male 201.7641 116.69946 91.07021
795 61.89603 male 247.0367 114.84322 125.48435
796 70.27934 male 176.6557 124.68701 97.57283
797 56.54219 female 200.8289 92.95821 78.83877
798 41.03907 female 202.3857 115.23223 62.35077
799 53.65224 male 168.4687 122.95429 84.80041
800 52.10734 male 214.7839 146.03270 87.79245
801 57.38427 female 202.9758 114.80454 79.37359
802 43.41624 male 218.2838 135.87482 79.68416
803 58.40234 male 182.1896 104.98038 91.19694
804 51.60598 female 192.9600 118.15627 73.87183
805 63.86294 female 185.5186 112.48256 81.36544
806 49.08805 female 187.0940 112.02345 71.22791
807 79.66487 female 243.9822 113.27884 86.95282
808 59.89731 female 222.7800 112.17137 80.74098
809 53.55515 male 213.8771 101.74473 89.07899
810 40.73266 female 204.6085 100.97508 62.54954
811 56.84838 male 187.3805 117.06849 90.35543
812 67.86741 female 220.4280 121.05696 86.15920
813 46.84813 male 197.4643 129.99112 80.63115
814 44.95121 female 213.4993 119.96529 68.54189
815 56.08369 female 183.4098 111.77022 76.40780
816 66.01224 male 175.6750 104.82765 94.96382
817 35.57402 male 147.9227 116.07660 56.34974
818 43.79087 female 214.3093 128.06582 66.79076
819 69.22378 male 203.3426 125.49308 96.80883
820 48.12650 female 208.1076 116.96277 72.73768
821 39.74480 male 216.6408 109.55284 74.15841
822 51.00437 female 211.6948 113.81004 76.16981
823 42.94480 female 230.1440 133.46291 62.54361
824 59.49921 female 220.3629 144.38439 80.36972
825 48.44751 male 200.6038 126.58089 82.49361
826 58.58877 female 183.1325 113.10716 78.00800
827 62.93580 male 188.2664 165.47772 93.42961
828 41.35515 female 195.2355 121.13557 61.39817
829 50.26992 male 221.1230 111.42825 91.22423
830 61.28684 male 250.2300 107.60005 128.84530
831 57.40883 male 218.5856 119.35653 93.87768
832 41.75427 male 178.6914 132.94974 73.57463
833 48.60878 male 186.2520 103.06034 84.26993
834 43.49882 male 146.6413 130.57040 66.42602
835 33.95923 male 198.9766 113.90786 63.23640
836 50.43620 male 226.5307 117.40784 95.81769
837 34.82324 female 229.1750 116.19098 52.11021
838 68.78285 male 182.8660 98.65326 98.07166
839 40.13228 male 191.7448 118.25622 72.39645
840 47.55877 female 147.0025 99.29509 76.09441
841 23.88745 male 158.2637 107.09021 44.04992
842 43.08004 male 200.4810 124.60319 75.25757
843 66.14604 male 209.2390 119.60094 95.35076
844 54.37748 female 203.0426 116.97358 77.41022
845 53.64862 female 194.8740 112.48150 75.57192
846 66.30091 female 186.8044 139.66901 82.46866
847 56.19261 female 157.4227 136.29851 80.38229
848 55.63602 female 243.6854 138.85072 71.13104
849 41.47367 male 211.9308 123.68184 74.05578
850 57.26530 male 194.8191 125.93856 90.00113
851 49.71384 male 183.6030 121.75856 85.25543
852 46.95597 female 198.0523 126.37542 69.39708
853 27.90421 male 191.2682 143.40793 55.39759
854 65.51514 female 185.0408 140.09440 81.94509
855 54.80597 male 176.1016 122.50502 87.52875
856 51.04022 female 203.7625 128.24171 75.18091
857 56.03171 female 205.8898 137.58909 78.54611
858 43.39035 male 188.0101 124.16701 76.85859
859 39.20505 female 205.8413 114.99648 60.40614
860 63.12020 male 152.4987 131.12728 85.61216
861 51.67307 male 200.8440 94.97341 86.21199
862 57.07285 female 170.8406 145.92795 77.91605
863 48.79300 female 151.7320 93.68327 76.79689
864 35.87513 male 219.7513 115.25761 70.81078
865 47.29440 male 179.0038 113.16571 81.49616
866 77.27456 female 185.2217 148.60548 89.36658
867 40.66271 male 224.9058 106.76325 81.57964
868 57.77127 male 164.5587 126.71003 86.18782
869 53.95885 female 221.4599 153.49711 76.44699
870 52.36737 female 227.2752 122.58326 74.64032
871 43.63828 male 213.4117 129.04544 77.47255
872 65.67994 male 186.0165 115.99336 96.01678
873 56.81726 male 197.2479 124.13185 89.42964
874 48.08501 female 197.8945 113.53362 71.12682
875 43.48864 male 182.2439 125.40091 76.59720
876 35.25851 male 199.2668 103.98829 65.14006
877 52.64640 female 188.6924 126.19020 73.98524
878 56.62083 female 179.4439 124.70887 76.78382
879 50.38931 female 206.6232 119.99778 75.31641
880 53.56164 male 230.6518 120.11704 101.82507
881 53.73560 male 237.0031 146.68782 108.30771
882 48.83069 female 239.5380 133.50827 67.45540
883 37.44385 male 185.2825 123.41689 68.71038
884 43.51905 male 200.3888 101.84878 76.26378
885 37.62085 female 127.5679 100.02128 66.99874
886 54.19335 male 157.3906 115.34125 81.74961
887 39.47749 male 197.7297 140.56261 70.40935
888 32.48813 female 212.4089 122.91853 51.60113
889 52.57396 male 196.4317 108.88428 87.07282
890 38.77485 male 201.8741 127.03972 69.25162
891 54.54032 female 212.5543 111.55098 78.48571
892 51.86916 female 199.8874 107.05031 75.40876
893 40.35714 male 202.4310 114.77647 71.57771
894 50.73840 male 210.5981 101.64925 86.07100
895 59.93747 female 209.3982 120.29774 81.72356
896 50.01351 female 218.7571 80.83158 75.62870
897 45.86158 female 239.1690 129.41923 63.62673
898 40.96717 male 219.2599 126.61010 77.17695
899 56.71988 male 165.9006 107.54483 86.26985
900 36.27838 male 188.4302 121.51243 67.25515
901 58.39919 female 178.5290 125.75529 78.00094
902 50.31709 female 233.8078 110.24517 71.59184
903 52.26459 female 198.6006 130.15625 75.01937
904 52.81671 female 204.2491 114.80945 76.63898
905 43.89484 male 200.0140 113.28387 76.61105
906 45.89054 female 220.6348 126.25706 68.94963
907 44.42435 male 241.0143 125.83026 103.22683
908 65.35628 female 165.8078 109.55055 84.88929
909 46.57083 female 200.4882 115.18831 69.51860
910 38.68762 male 178.6127 108.10686 69.83747
911 57.71760 female 221.4279 94.51659 79.91362
912 38.51459 male 190.7425 104.10707 70.52233
913 49.84405 female 229.5011 108.09212 72.54062
914 76.81381 male 200.8561 118.27276 101.99050
915 49.36245 female 166.4736 96.91508 74.21763
916 46.33561 male 224.3081 107.42175 88.74224
917 57.66171 male 215.5384 94.38717 92.66524
918 58.21994 male 203.2045 128.11267 89.68148
919 67.99287 female 249.2724 111.92633 77.61323
920 60.62276 male 177.8534 108.21014 91.88471
921 49.12915 female 205.0081 110.23699 73.83881
922 33.57334 female 210.5381 136.65825 52.80459
923 49.35266 male 209.6973 124.57479 84.08532
924 50.69028 male 215.6720 125.38144 87.70004
925 51.67579 male 245.0975 131.03686 116.41536
926 43.33161 male 189.5073 116.97702 76.88675
927 51.13624 female 181.9151 115.77975 73.22154
928 46.98813 male 178.4608 80.39277 81.56138
929 44.04078 male 178.7589 113.65218 77.02955
930 55.77130 female 222.2721 107.08566 78.27642
931 52.69501 female 173.3046 142.59616 74.73216
932 56.33029 female 181.9353 126.19857 76.38158
933 43.66897 female 171.1309 115.83116 65.24899
934 46.99291 female 230.8117 108.54655 68.27640
935 45.97213 male 198.2684 115.19950 79.60058
936 55.71315 male 167.8967 116.09256 86.07907
937 48.86922 male 222.2568 87.32361 90.82485
938 56.61710 male 196.8829 122.31641 89.38050
939 48.48679 female 207.9394 128.77845 73.00214
940 33.22375 male 193.2004 127.65642 62.71777
941 54.90290 female 234.9200 125.19046 73.91742
942 52.90942 male 228.6596 132.55236 99.18237
943 45.31011 male 171.5422 112.85241 77.12949
944 41.22137 male 191.0203 119.08394 73.91350
945 52.97831 female 203.7294 118.37265 76.59773
946 60.09629 male 178.1354 119.01558 91.40868
947 54.53652 female 166.1781 120.40760 77.65183
948 38.75707 female 200.9512 96.95177 59.32204
949 48.70504 male 222.3115 131.09986 89.87389
950 49.40077 female 258.8321 133.35316 61.49785
951 51.16101 male 205.2703 143.67554 84.84356
952 53.32302 male 172.9159 105.70276 86.11837
953 64.10103 female 154.0180 136.32681 86.24589
954 57.67562 female 198.0280 108.40508 78.78299
955 58.78822 female 162.9982 131.72776 80.87827
956 52.04191 female 214.2244 116.67554 76.73589
957 41.97216 female 181.8173 111.69649 61.67476
958 45.40810 female 165.8736 154.22177 67.96759
959 54.45560 female 178.4737 153.53624 74.97718
960 48.69533 female 181.6671 124.37835 70.58284
961 55.30231 female 173.1722 133.05881 76.60086
962 51.38589 female 237.4918 141.73794 70.49488
963 38.98296 male 165.0657 100.53768 66.85598
964 44.45917 male 249.7605 124.52511 113.22688
965 42.53167 female 183.4106 104.23917 62.48906
966 45.86850 male 219.5949 126.89798 84.05513
967 46.51929 female 178.2719 112.89075 68.12312
968 54.95569 female 221.3499 93.21639 78.17231
969 47.46831 male 201.6796 113.38472 81.30306
970 41.39749 male 180.6603 136.26258 73.35512
971 48.42029 female 189.2037 123.19274 70.22144
972 48.52858 male 213.4327 109.22661 84.46657
973 42.61501 female 205.9944 112.41807 65.09893
974 46.74092 female 227.7289 101.50706 68.94335
975 45.03750 female 167.0931 123.70901 67.74831
976 54.69533 male 208.4543 121.20297 87.80506
977 66.33097 male 162.9341 114.06154 91.40330
978 54.95178 male 233.6088 156.36368 105.19425
979 34.88552 male 220.4504 138.47269 69.56260
980 54.28807 female 207.2419 120.41058 77.89188
981 71.30287 male 209.7068 114.28944 98.86617
982 57.74894 female 240.3625 133.47548 73.74616
983 70.68089 female 162.5273 106.02147 89.09496
984 65.32843 female 221.7307 124.90670 84.22218
985 59.33466 female 176.7936 137.55260 78.59503
986 57.59475 female 164.5001 110.07861 80.16205
987 40.76193 female 199.8826 112.04870 61.58103
988 60.62751 female 189.5047 118.92865 79.30485
989 44.01032 female 174.4263 111.78427 65.23777
990 41.83081 male 187.9142 134.45576 74.56051
991 44.65820 female 213.4563 128.93560 67.98751
992 41.17597 male 194.2132 125.60131 73.42912
993 55.21883 male 227.6059 121.47027 99.84165
994 60.15756 female 223.8088 121.11432 80.53069
995 56.38017 male 182.7939 117.00429 89.75286
996 37.44108 male 220.1090 140.47532 72.74644
997 54.42725 female 211.9623 137.93919 77.95015
998 44.58957 female 171.6227 108.59141 66.53845
999 56.34561 female 221.0425 132.59931 78.42875
1000 55.83437 male 238.9407 130.36502 112.12181
nomogramFormula documentation built on Jan. 28, 2020, 5:07 p.m.
R Package Documentation
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Description Usage Arguments Value Examples
View source: R/TotalPoints.rms.R
Description
Compared with points_cal() command, TotalPoints.rms() is suit for more complexed condition. Since this command is based on formula from 'rms' package, it may be also more accurate. However, formula for each variable can not be caculated.
Usage
1 | TotalPoints.rms(rd, fit, nom, kint = NULL)
|
Arguments
rd |
raw data |
fit |
regression result in 'rma' package |
nom |
nomoram() command result |
kint |
number of intercept. Default is to use fit$interceptRef if it exists, or 1. |
Value
a dataframe contains rawdata and total points
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | library(rms)
n <- 1000
set.seed(17)
d <- data.frame(age = rnorm(n, 50, 10),
blood.pressure = rnorm(n, 120, 15),
cholesterol = rnorm(n, 200, 25),
sex = factor(sample(c('female','male'), n,TRUE)))
d <- upData(d,
L = .4*(sex=='male') + .045*(age-50) +
(log(cholesterol - 10)-5.2)*(-2*(sex=='female') + 2*(sex=='male')),
y = ifelse(runif(n) < plogis(L), 1, 0))
ddist <- datadist(d); options(datadist='ddist')
f <- lrm(y ~ lsp(age,50) + sex * rcs(cholesterol, 4) + blood.pressure,
data=d)
nom <- nomogram(f)
TotalPoints.rms(rd = d,fit = f,nom = nom)
|
Example output
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
Input object size: 29616 bytes; 4 variables 1000 observations
Added variable L
Added variable y
New object size: 41856 bytes; 6 variables 1000 observations
age sex cholesterol blood.pressure total points
1 39.84991 male 191.6668 98.37248 72.37029
2 49.20363 male 168.1024 112.99815 81.43506
3 47.67013 female 196.4870 100.90785 70.53558
4 41.82732 female 197.8634 122.22211 62.47700
5 57.72091 female 200.2004 125.38972 78.91130
6 48.34388 male 231.3853 118.71428 98.06697
7 59.72874 female 217.1354 125.00913 81.30797
8 67.16534 female 215.5950 95.61015 86.75973
9 52.55237 male 175.6908 126.21661 85.92205
10 53.66581 male 197.0684 112.12832 87.63523
11 61.80789 female 189.1410 113.59159 80.13437
12 56.43192 female 218.6268 115.39797 79.17059
13 62.95322 female 224.7456 138.64789 81.80828
14 51.87918 male 209.8016 123.38761 86.21882
15 65.91205 male 240.1214 118.03400 120.16451
16 49.44821 male 201.3340 136.55724 83.60887
17 58.38471 female 232.5283 96.39998 77.44069
18 51.59370 female 179.7718 135.65666 73.32360
19 56.25954 male 194.6000 137.19306 89.18210
20 56.33585 male 195.8520 125.85966 89.27195
21 56.81028 male 213.6618 136.15947 90.47297
22 43.17967 female 217.2580 124.94794 65.77589
23 42.76743 male 202.9612 114.72142 74.82082
24 66.73526 female 214.9434 117.24793 86.14756
25 44.04244 female 182.3234 122.71212 64.26122
26 61.59844 male 227.9575 150.11641 103.78343
27 51.17422 female 162.4534 110.43721 76.47135
28 52.59221 female 250.4253 137.84058 66.83585
29 53.82362 male 209.7332 141.53884 87.13513
30 42.88518 male 196.6625 98.14596 75.92030
31 38.22430 female 194.0338 133.02617 56.75100
32 40.39833 female 210.8321 129.55811 62.20033
33 41.21048 female 186.6302 114.53614 60.48440
34 14.43864 male 184.4276 110.65898 37.65911
35 35.83250 male 215.8029 109.48929 68.38242
36 45.51231 female 199.7717 89.00088 68.41279
37 42.24032 male 217.8165 97.66564 78.46388
38 41.68172 male 241.7264 102.84821 100.71897
39 50.51830 male 209.4910 105.35082 85.59068
40 43.83449 male 230.1793 121.06453 90.66615
41 52.54397 male 221.5995 103.11464 93.20114
42 46.68480 male 192.2245 115.77981 81.28948
43 47.93681 male 207.2510 101.84303 82.16211
44 62.15337 female 205.6877 131.10155 82.57550
45 68.92056 female 152.5611 134.12809 89.71839
46 50.74194 male 215.2521 116.45792 87.67047
47 67.51696 female 187.9607 131.18112 83.43794
48 47.68513 male 152.5440 99.64838 74.59181
49 55.43452 male 205.6408 107.41441 88.24728
50 40.10999 female 204.7385 117.56270 61.43172
51 53.15531 female 192.7313 130.78399 74.61629
52 74.42327 male 180.7205 132.69549 100.82798
53 55.49693 female 192.7975 102.87920 76.62513
54 49.70757 female 234.9685 140.61031 70.07523
55 41.69217 female 188.4530 126.18153 60.99552
56 62.46434 male 154.9905 119.32882 86.21689
57 36.24245 male 192.9221 115.44524 67.05840
58 46.68892 male 206.2719 132.02659 79.85348
59 59.80911 male 207.5063 88.17980 91.54812
60 71.90771 male 195.2808 113.22137 99.59672
61 50.30546 female 221.1495 130.57501 74.55535
62 42.14483 female 216.8751 120.32933 64.49438
63 53.25441 male 198.5605 108.72838 87.23953
64 41.19156 female 224.7812 127.77045 61.69792
65 52.09326 male 191.5176 93.75516 87.58403
66 51.51033 male 183.0139 123.32588 86.52914
67 46.56521 male 215.9976 132.96535 82.63755
68 59.05878 male 210.6436 132.75066 90.89350
69 59.18955 female 172.3430 104.89470 79.73857
70 44.44013 female 180.0211 94.74611 65.45295
71 55.60235 female 211.9951 140.90890 78.65461
72 32.07582 female 193.3880 116.24679 48.60966
73 34.34583 female 200.4600 104.48238 53.11436
74 16.79681 male 178.7811 116.60531 40.01455
75 51.54722 female 186.7461 134.63356 73.05495
76 46.35373 male 194.7787 141.74536 80.10104
77 25.66316 male 183.3357 113.97735 52.73245
78 53.36464 male 252.4105 142.42112 125.60500
79 43.59547 female 266.4948 140.29488 50.82340
80 68.21120 female 230.4323 143.76430 83.57733
81 31.53277 female 227.9089 101.41723 48.26028
82 56.41717 male 181.8737 114.28983 89.71501
83 61.85525 female 200.2828 112.45521 81.81697
84 48.22312 male 212.8090 123.92027 83.53676
85 37.13874 female 174.8951 107.82255 55.91427
86 54.63451 female 228.1492 82.69460 76.56698
87 58.80666 female 161.7869 134.11060 81.11806
88 51.39422 female 175.7233 123.18211 73.87533
89 46.24945 female 160.7844 108.03340 71.04282
90 50.42539 female 217.0939 102.59418 75.71645
91 56.33880 male 197.9094 127.87864 88.96995
92 32.92512 male 219.3503 137.48091 66.13551
93 50.19687 male 182.7063 120.17301 85.70519
94 47.01204 male 180.9520 89.39197 81.84243
95 45.58237 male 227.6790 95.62920 91.01239
96 55.90975 male 214.7232 113.62969 90.78279
97 38.65679 female 233.4938 124.49784 55.84635
98 45.61255 male 211.0458 122.53741 79.40364
99 53.44901 female 215.9364 90.73557 77.98463
100 45.50600 female 267.3507 121.75343 53.44396
101 50.43820 female 194.3606 94.34574 73.74341
102 44.32008 male 232.9010 146.28607 93.71772
103 68.24860 male 196.6942 156.17277 96.29885
104 54.33003 female 174.3399 121.35805 75.99780
105 36.46034 female 218.7881 115.72095 56.62866
106 61.54466 male 195.4254 135.18378 92.51717
107 59.20737 female 225.3490 134.47916 79.32561
108 45.51343 male 223.5890 112.68471 86.91896
109 70.70574 female 185.2261 100.46659 85.98517
110 48.00444 male 179.9149 120.88050 82.47625
111 38.70872 male 189.9283 143.65987 70.12877
112 37.04445 male 199.6546 117.56241 67.27974
113 62.40419 male 221.3726 104.23296 99.35608
114 66.95059 male 180.6526 114.86667 96.31998
115 55.02301 male 248.3332 128.02826 122.29764
116 53.33632 female 167.7674 114.77484 76.65047
117 44.91797 female 196.1169 87.22843 66.97845
118 46.29368 male 194.8776 136.30063 80.10323
119 65.08643 male 250.0630 128.09253 130.74127
120 49.50374 female 243.8592 93.13831 67.57355
121 63.81757 female 201.8325 136.69104 82.93288
122 54.48932 male 211.6901 116.54671 88.55940
123 48.47690 female 226.0799 106.21418 71.64726
124 52.59294 male 153.7504 142.39782 79.04535
125 33.88598 female 216.8342 93.20081 53.77071
126 29.91044 male 191.1337 128.47947 58.39254
127 30.00629 female 190.3424 137.63467 45.06869
128 51.21041 female 188.4116 115.45788 73.23478
129 47.70005 female 170.5817 129.10710 70.58435
130 28.00898 female 167.3284 105.07015 44.92303
131 32.89591 female 204.5946 104.97136 51.84340
132 52.26259 male 158.2069 140.45820 80.33160
133 59.50850 male 180.3840 109.37154 91.58381
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950 49.40077 female 258.8321 133.35316 61.49785
951 51.16101 male 205.2703 143.67554 84.84356
952 53.32302 male 172.9159 105.70276 86.11837
953 64.10103 female 154.0180 136.32681 86.24589
954 57.67562 female 198.0280 108.40508 78.78299
955 58.78822 female 162.9982 131.72776 80.87827
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957 41.97216 female 181.8173 111.69649 61.67476
958 45.40810 female 165.8736 154.22177 67.96759
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960 48.69533 female 181.6671 124.37835 70.58284
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965 42.53167 female 183.4106 104.23917 62.48906
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967 46.51929 female 178.2719 112.89075 68.12312
968 54.95569 female 221.3499 93.21639 78.17231
969 47.46831 male 201.6796 113.38472 81.30306
970 41.39749 male 180.6603 136.26258 73.35512
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973 42.61501 female 205.9944 112.41807 65.09893
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977 66.33097 male 162.9341 114.06154 91.40330
978 54.95178 male 233.6088 156.36368 105.19425
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980 54.28807 female 207.2419 120.41058 77.89188
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986 57.59475 female 164.5001 110.07861 80.16205
987 40.76193 female 199.8826 112.04870 61.58103
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989 44.01032 female 174.4263 111.78427 65.23777
990 41.83081 male 187.9142 134.45576 74.56051
991 44.65820 female 213.4563 128.93560 67.98751
992 41.17597 male 194.2132 125.60131 73.42912
993 55.21883 male 227.6059 121.47027 99.84165
994 60.15756 female 223.8088 121.11432 80.53069
995 56.38017 male 182.7939 117.00429 89.75286
996 37.44108 male 220.1090 140.47532 72.74644
997 54.42725 female 211.9623 137.93919 77.95015
998 44.58957 female 171.6227 108.59141 66.53845
999 56.34561 female 221.0425 132.59931 78.42875
1000 55.83437 male 238.9407 130.36502 112.12181
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