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IALSA / ialsa-2016-amsterdam

Multi-study and multivariate evaluation of healthy life expectancy (HLE): An IALSA workshop on multistate modeling using R
GNU General Public License v2.0
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Odds-ratios from submitted models #50

Open andkov opened 7 years ago

andkov commented 7 years ago

LASA

> print_hazards(lasa)
          transition predictor             dense
1  State 1 - State 2       age 1.05 (1.04, 1.06)
2  State 1 - State 4       age 1.09 (1.07, 1.10)
3  State 2 - State 1       age 0.96 (0.95, 0.97)
4  State 2 - State 3       age 1.11 (1.09, 1.13)
5  State 2 - State 4       age 1.06 (1.03, 1.08)
6  State 3 - State 4       age 1.05 (1.04, 1.07)
7  State 1 - State 2      male 1.45 (1.26, 1.67)
8  State 1 - State 4      male 1.80 (1.44, 2.24)
9  State 2 - State 1      male 1.00 (1.00, 1.00)
10 State 2 - State 3      male 1.04 (0.77, 1.39)
11 State 2 - State 4      male 1.95 (1.33, 2.84)
12 State 3 - State 4      male 1.27 (1.02, 1.58)
13 State 1 - State 2    edumed 0.53 (0.45, 0.63)
14 State 1 - State 4    edumed 0.94 (0.73, 1.20)
15 State 2 - State 1    edumed 1.00 (1.00, 1.00)
16 State 2 - State 3    edumed 0.92 (0.62, 1.36)
17 State 2 - State 4    edumed 1.04 (0.66, 1.64)
18 State 3 - State 4    edumed 1.33 (0.97, 1.83)
19 State 1 - State 2   eduhigh 0.40 (0.32, 0.50)
20 State 1 - State 4   eduhigh 0.92 (0.70, 1.20)
21 State 2 - State 1   eduhigh 1.00 (1.00, 1.00)
22 State 2 - State 3   eduhigh 1.09 (0.67, 1.77)
23 State 2 - State 4   eduhigh 0.97 (0.51, 1.84)
24 State 3 - State 4   eduhigh 1.15 (0.76, 1.72)
25 State 1 - State 2   inkomen 0.79 (0.73, 0.86)
26 State 1 - State 4   inkomen 1.00 (1.00, 1.00)
27 State 2 - State 1   inkomen 1.00 (1.00, 1.00)
28 State 2 - State 3   inkomen 0.84 (0.72, 1.00)
29 State 2 - State 4   inkomen 1.00 (1.00, 1.00)
30 State 3 - State 4   inkomen 1.00 (1.00, 1.00)

LBC1921

> print_hazards(lbc)
          transition predictor             dense
1  State 1 - State 2       age 1.14 (1.05, 1.24)
2  State 1 - State 4       age 1.18 (1.10, 1.27)
3  State 2 - State 1       age 0.99 (0.87, 1.12)
4  State 2 - State 3       age 1.22 (0.95, 1.57)
5  State 2 - State 4       age 1.19 (0.99, 1.44)
6  State 3 - State 4       age 1.16 (1.02, 1.31)
7  State 1 - State 2    gender 1.12 (0.63, 1.99)
8  State 1 - State 4    gender 0.51 (0.26, 0.99)
9  State 2 - State 1    gender 1.00 (1.00, 1.00)
10 State 2 - State 3    gender 2.30 (0.54, 9.79)
11 State 2 - State 4    gender 1.25 (0.24, 6.60)
12 State 3 - State 4    gender 1.05 (0.47, 2.37)
13 State 1 - State 2       ses 0.93 (0.61, 1.44)
14 State 1 - State 4       ses 1.00 (1.00, 1.00)
15 State 2 - State 1       ses 1.00 (1.00, 1.00)
16 State 2 - State 3       ses 0.69 (0.29, 1.64)
17 State 2 - State 4       ses 1.00 (1.00, 1.00)
18 State 3 - State 4       ses 1.00 (1.00, 1.00)
19 State 1 - State 2    dummy1 0.70 (0.40, 1.22)
20 State 1 - State 4    dummy1 1.00 (1.00, 1.00)
21 State 2 - State 1    dummy1 1.00 (1.00, 1.00)
22 State 2 - State 3    dummy1 0.87 (0.27, 2.83)
23 State 2 - State 4    dummy1 1.00 (1.00, 1.00)
24 State 3 - State 4    dummy1 1.00 (1.00, 1.00)
25 State 1 - State 2    dummy2 0.68 (0.37, 1.26)
26 State 1 - State 4    dummy2 1.00 (1.00, 1.00)
27 State 2 - State 1    dummy2 1.00 (1.00, 1.00)
28 State 2 - State 3    dummy2 0.39 (0.09, 1.80)
29 State 2 - State 4    dummy2 1.00 (1.00, 1.00)
30 State 3 - State 4    dummy2 1.00 (1.00, 1.00)

MAP

> print_hazards(map)
          transition    predictor             dense
1  State 1 - State 2          age 1.08 (1.07, 1.09)
2  State 1 - State 4          age 1.10 (1.07, 1.13)
3  State 2 - State 1          age 0.98 (0.96, 0.99)
4  State 2 - State 3          age 1.05 (1.02, 1.07)
5  State 2 - State 4          age 1.11 (1.04, 1.18)
6  State 3 - State 4          age 1.06 (1.03, 1.09)
7  State 1 - State 2         male 1.36 (1.17, 1.58)
8  State 1 - State 4         male 1.44 (0.94, 2.20)
9  State 2 - State 1         male 1.00 (1.00, 1.00)
10 State 2 - State 3         male 0.87 (0.65, 1.17)
11 State 2 - State 4         male 1.74 (0.94, 3.25)
12 State 3 - State 4         male 1.30 (0.98, 1.72)
13 State 1 - State 2  edu_low_med 0.50 (0.30, 0.83)
14 State 1 - State 4  edu_low_med 1.31 (0.26, 6.66)
15 State 2 - State 1  edu_low_med 1.00 (1.00, 1.00)
16 State 2 - State 3  edu_low_med 2.39 (0.99, 5.80)
17 State 2 - State 4  edu_low_med 0.84 (0.04,15.75)
18 State 3 - State 4  edu_low_med 1.22 (0.54, 2.75)
19 State 1 - State 2 edu_low_high 0.40 (0.29, 0.54)
20 State 1 - State 4 edu_low_high 0.82 (0.21, 3.15)
21 State 2 - State 1 edu_low_high 1.00 (1.00, 1.00)
22 State 2 - State 3 edu_low_high 1.33 (0.66, 2.66)
23 State 2 - State 4 edu_low_high 1.13 (0.25, 4.97)
24 State 3 - State 4 edu_low_high 0.77 (0.43, 1.39)
25 State 1 - State 2       sescat 0.90 (0.82, 0.99)
26 State 1 - State 4       sescat 1.00 (1.00, 1.00)
27 State 2 - State 1       sescat 1.00 (1.00, 1.00)
28 State 2 - State 3       sescat 0.95 (0.79, 1.13)
29 State 2 - State 4       sescat 1.00 (1.00, 1.00)
30 State 3 - State 4       sescat 1.00 (1.00, 1.00)

Whitehall

> print_hazards(whall)
          transition    predictor             dense
1  State 1 - State 2          age 1.02 (0.95, 1.09)
2  State 1 - State 4          age 1.14 (1.06, 1.22)
3  State 2 - State 1          age 0.91 (0.86, 0.96)
4  State 2 - State 3          age 1.15 (0.98, 1.36)
5  State 2 - State 4          age 1.12 (0.92, 1.36)
6  State 3 - State 2          age 1.00 (1.00, 1.00)
7  State 3 - State 4          age 1.00 (1.00, 1.00)
8  State 1 - State 2         male 0.89 (0.61, 1.29)
9  State 1 - State 4         male 0.99 (0.60, 1.64)
10 State 2 - State 1         male 1.00 (1.00, 1.00)
11 State 2 - State 3         male 2.52 (0.69, 9.21)
12 State 2 - State 4         male 1.00 (1.00, 1.00)
13 State 3 - State 2         male 1.00 (1.00, 1.00)
14 State 3 - State 4         male 1.00 (1.00, 1.00)
15 State 1 - State 2 edu_cat_dum1 0.51 (0.25, 1.02)
16 State 1 - State 4 edu_cat_dum1 1.00 (1.00, 1.00)
17 State 2 - State 1 edu_cat_dum1 1.00 (1.00, 1.00)
18 State 2 - State 3 edu_cat_dum1 1.28 (0.22, 7.34)
19 State 2 - State 4 edu_cat_dum1 1.00 (1.00, 1.00)
20 State 3 - State 2 edu_cat_dum1 1.00 (1.00, 1.00)
21 State 3 - State 4 edu_cat_dum1 1.00 (1.00, 1.00)
22 State 1 - State 2 edu_cat_dum2 0.48 (0.26, 0.91)
23 State 1 - State 4 edu_cat_dum2 1.00 (1.00, 1.00)
24 State 2 - State 1 edu_cat_dum2 1.00 (1.00, 1.00)
25 State 2 - State 3 edu_cat_dum2 0.34 (0.06, 1.99)
26 State 2 - State 4 edu_cat_dum2 1.00 (1.00, 1.00)
27 State 3 - State 2 edu_cat_dum2 1.00 (1.00, 1.00)
28 State 3 - State 4 edu_cat_dum2 1.00 (1.00, 1.00)
andkov commented 7 years ago

LASA - summary

> msm_summary(lasa)

-2loglik = 26253.03 
Convergence code = 0 
          p   se Wald ChiSq Pr>ChiSq
qbase -1.93 0.05    1263.03     0.00
qbase -3.57 0.10    1315.11     0.00
qbase -1.63 0.05     952.66     0.00
qbase -3.00 0.12     606.48     0.00
qbase -3.35 0.17     406.24     0.00
qbase -1.90 0.11     312.93     0.00
qcov   0.05 0.01     101.56     0.00
qcov   0.08 0.01     139.10     0.00
qcov  -0.04 0.01      41.37     0.00
qcov   0.10 0.01     110.29     0.00
qcov   0.06 0.01      19.83     0.00
qcov   0.05 0.01      42.48     0.00
qcov   0.37 0.07      27.19     0.00
qcov   0.59 0.11      27.56     0.00
qcov   0.04 0.15       0.06     0.80
qcov   0.67 0.19      11.92     0.00
qcov   0.24 0.11       4.65     0.03
qcov  -0.64 0.08      56.31     0.00
qcov  -0.06 0.13       0.25     0.62
qcov  -0.09 0.20       0.19     0.67
qcov   0.04 0.23       0.03     0.87
qcov   0.29 0.16       3.15     0.08
qcov  -0.92 0.12      64.08     0.00
qcov  -0.09 0.14       0.39     0.53
qcov   0.09 0.25       0.12     0.73
qcov  -0.03 0.33       0.01     0.93
qcov   0.14 0.21       0.44     0.51
qcov  -0.24 0.04      31.38     0.00
qcov  -0.17 0.08       3.97     0.05
p     -2.18 0.08     676.33     0.00
initp -0.93 0.05     423.15     0.00
initp -3.21 0.15     476.41     0.00
> msm_details(lasa)

 Intensity matrix : 
        State 1                      State 2                     
State 1 -0.15085 (-0.16039,-0.14188)  0.11810 ( 0.10928, 0.12764)
State 2  0.20408 ( 0.18464, 0.22557) -0.29327 (-0.31706,-0.27126)
State 3 0                            0                           
State 4 0                            0                           
        State 3                      State 4                     
State 1 0                             0.03275 ( 0.02906, 0.03691)
State 2  0.04399 ( 0.03583, 0.05400)  0.04520 ( 0.03573, 0.05718)
State 3 -0.17396 (-0.21271,-0.14228)  0.17396 ( 0.14228, 0.21271)
State 4 0                            0                           

 Transition probability matrix for t =  2  : 
          State 1   State 2     State 3    State 4
State 1 0.7723075 0.1544629 0.006949625 0.06628000
State 2 0.2669116 0.5860445 0.056172523 0.09087141
State 3 0.0000000 0.0000000 0.706150777 0.29384922
State 4 0.0000000 0.0000000 0.000000000 1.00000000

 Misclassification matrix : 
        State 1 State 2 State 3                 State 4
State 1 1.0000  0       0                       0      
State 2 0       0       0.1016 (0.08759,0.1176) 0      
State 3 0       0       1.0000                  0      
State 4 0       0       0                       1.0000 

 Mean sojourn times : 
        estimates        SE        L        U
State 1  6.629022 0.2074594 6.234628 7.048364
State 2  3.409841 0.1356902 3.153999 3.686435
State 3  5.748341 0.5897236 4.701295 7.028578

 Probability that each state is next : 
        State 1                State 2                State 3               
State 1 0                      0.7829 (0.7560,0.8071) 0                     
State 2 0.6959 (0.6610,0.7284) 0                      0.1500 (0.1233,0.1815)
State 3 0                      0                      0                     
State 4 0                      0                      0                     
        State 4               
State 1 0.2171 (0.1929,0.2440)
State 2 0.1541 (0.1233,0.1910)
State 3 1.0000 (1.0000,1.0000)
State 4 0                     

  Total length of stay : 
  State 1   State 2   State 3   State 4 
14.563221  5.864769  1.483002       Inf 

 Expected number of visits to the state : 
  State 1   State 2   State 3   State 4 
1.1968884 1.7199541 0.2579879 1.0000000
andkov commented 7 years ago

LBC1921 - summary

> msm_summary(lbc)

-2loglik = 2601.394 
Convergence code = 0 
          p   se Wald ChiSq Pr>ChiSq
qbase -3.11 0.53      35.04     0.00
qbase -2.93 0.54      29.42     0.00
qbase -1.37 0.40      11.57     0.00
qbase -4.68 1.76       7.10     0.01
qbase -3.81 1.67       5.20     0.02
qbase -2.63 1.03       6.46     0.01
qcov   0.13 0.04       9.89     0.00
qcov   0.17 0.04      22.80     0.00
qcov  -0.01 0.06       0.04     0.83
qcov   0.20 0.13       2.48     0.12
qcov   0.18 0.10       3.38     0.07
qcov   0.15 0.06       5.53     0.02
qcov   0.11 0.29       0.15     0.70
qcov  -0.67 0.34       3.95     0.05
qcov   0.83 0.74       1.28     0.26
qcov   0.22 0.85       0.07     0.79
qcov   0.05 0.42       0.01     0.90
qcov  -0.07 0.22       0.09     0.76
qcov  -0.37 0.44       0.70     0.40
qcov  -0.36 0.29       1.59     0.21
qcov  -0.14 0.60       0.05     0.82
qcov  -0.39 0.31       1.50     0.22
qcov  -0.93 0.78       1.44     0.23
> msm_details(lbc)

 Intensity matrix : 
        State 1                      State 2                     
State 1 -0.15446 (-0.18603,-0.12825)  0.10093 ( 0.07072, 0.14406)
State 2  0.23194 ( 0.14355, 0.37474) -0.42344 (-0.57913,-0.30960)
State 3 0                            0                           
State 4 0                            0                           
        State 3                      State 4                     
State 1 0                             0.05353 ( 0.03675, 0.07797)
State 2  0.09133 ( 0.04836, 0.17249)  0.10016 ( 0.04473, 0.22429)
State 3 -0.20238 (-0.38129,-0.10742)  0.20238 ( 0.10742, 0.38129)
State 4 0                            0                           

 Transition probability matrix for t =  2  : 
          State 1   State 2    State 3   State 4
State 1 0.7634192 0.1164219 0.01111756 0.1090414
State 2 0.2675314 0.4531639 0.10007217 0.1792326
State 3 0.0000000 0.0000000 0.66713987 0.3328601
State 4 0.0000000 0.0000000 0.00000000 1.0000000

 Misclassification matrix : 
NULL

 Mean sojourn times : 
        estimates        SE        L        U
State 1  6.474201 0.6142626 5.375582 7.797349
State 2  2.361622 0.3772975 1.726715 3.229982
State 3  4.941254 1.5969400 2.622657 9.309640

 Probability that each state is next : 
        State 1                State 2                State 3               
State 1 0                      0.6535 (0.5041,0.7917) 0                     
State 2 0.5478 (0.3744,0.6784) 0                      0.2157 (0.1003,0.3704)
State 3 0                      0                      0                     
State 4 0                      0                      0                     
        State 4               
State 1 0.3465 (0.2083,0.4959)
State 2 0.2366 (0.1072,0.4760)
State 3 1.0000 (1.0000,1.0000)
State 4 0                     

  Total length of stay : 
  State 1   State 2   State 3   State 4 
10.083388  2.403532  1.084729       Inf 

 Expected number of visits to the state : 
  State 1   State 2   State 3   State 4 
0.5574721 1.0177463 0.2195251 1.0000000
andkov commented 7 years ago

MAP - summary

> msm_summary(map)

-2loglik = 14515.36 
Convergence code = 0 
          p   se Wald ChiSq Pr>ChiSq
qbase -1.34 0.17      63.87     0.00
qbase -4.26 0.69      37.52     0.00
qbase -0.22 0.08       6.83     0.01
qbase -2.40 0.36      44.37     0.00
qbase -4.15 0.90      20.99     0.00
qbase -1.80 0.32      31.55     0.00
qcov   0.08 0.01     154.98     0.00
qcov   0.10 0.01      40.91     0.00
qcov  -0.02 0.01       8.12     0.00
qcov   0.05 0.01      14.97     0.00
qcov   0.10 0.03       8.91     0.00
qcov   0.06 0.01      20.99     0.00
qcov   0.31 0.08      16.07     0.00
qcov   0.36 0.22       2.80     0.09
qcov  -0.14 0.15       0.86     0.35
qcov   0.56 0.32       3.08     0.08
qcov   0.26 0.14       3.38     0.07
qcov  -0.68 0.26       7.11     0.01
qcov   0.27 0.83       0.10     0.75
qcov   0.87 0.45       3.74     0.05
qcov  -0.18 1.50       0.01     0.90
qcov   0.20 0.42       0.22     0.64
qcov  -0.93 0.16      33.52     0.00
qcov  -0.19 0.69       0.08     0.78
qcov   0.28 0.35       0.64     0.42
qcov   0.12 0.76       0.02     0.88
qcov  -0.26 0.30       0.75     0.39
qcov  -0.11 0.05       4.76     0.03
qcov  -0.05 0.09       0.33     0.57
p     -2.26 0.09     600.40     0.00
initp -1.50 0.07     463.71     0.00
initp -3.23 0.16     415.39     0.00
> msm_details(map)

 Intensity matrix : 
        State 1                      State 2                     
State 1 -0.24128 (-0.25962,-0.22423)  0.21381 ( 0.19698, 0.23208)
State 2  0.68009 ( 0.61614, 0.75068) -0.89125 (-0.96787,-0.82070)
State 3 0                            0                           
State 4 0                            0                           
        State 3                      State 4                     
State 1 0                             0.02746 ( 0.02218, 0.03401)
State 2  0.16674 ( 0.14002, 0.19856)  0.04442 ( 0.02330, 0.08465)
State 3 -0.21877 (-0.27441,-0.17442)  0.21877 ( 0.17442, 0.27441)
State 4 0                            0                           

 Transition probability matrix for t =  2  : 
          State 1   State 2    State 3    State 4
State 1 0.7442737 0.1620344 0.03166394 0.06202797
State 2 0.5153958 0.2517030 0.12969384 0.10320734
State 3 0.0000000 0.0000000 0.64561881 0.35438119
State 4 0.0000000 0.0000000 0.00000000 1.00000000

 Misclassification matrix : 
        State 1 State 2 State 3                  State 4
State 1 1.00000 0       0                        0      
State 2 0       0       0.09421 (0.07986,0.1108) 0      
State 3 0       0       1.00000                  0      
State 4 0       0       0                        1.00000

 Mean sojourn times : 
        estimates         SE        L        U
State 1  4.144622 0.15495420 3.851778 4.459731
State 2  1.122017 0.04721055 1.033198 1.218470
State 3  4.570948 0.52840403 3.644239 5.733312

 Probability that each state is next : 
        State 1                   State 2                  
State 1 0                         0.88618 (0.85902,0.90711)
State 2 0.76308 (0.72419,0.79184) 0                        
State 3 0                         0                        
State 4 0                         0                        
        State 3                   State 4                  
State 1 0                         0.11382 (0.09289,0.14098)
State 2 0.18709 (0.15793,0.21958) 0.04984 (0.02697,0.09305)
State 3 0                         1.00000 (1.00000,1.00000)
State 4 0                         0                        

  Total length of stay : 
  State 1   State 2   State 3   State 4 
12.800827  3.070953  2.340572       Inf 

 Expected number of visits to the state : 
  State 1   State 2   State 3   State 4 
2.0885392 2.7369938 0.5120539 1.0000000
andkov commented 7 years ago

Whitehall - summary

> msm_summary(whall)

-2loglik = 2296.963 
Convergence code = 0 
          p   se Wald ChiSq Pr>ChiSq
qbase -2.52 0.57      19.72     0.00
qbase -3.17 0.52      37.12     0.00
qbase -2.50 0.46      30.03     0.00
qbase -1.96 1.32       2.20     0.14
qbase -2.82 1.41       3.97     0.05
qbase -1.29 0.36      13.12     0.00
qbase -2.89 0.68      18.11     0.00
qcov   0.01 0.04       0.17     0.68
qcov   0.13 0.04      12.27     0.00
qcov  -0.09 0.03       9.88     0.00
qcov   0.14 0.08       2.89     0.09
qcov   0.11 0.10       1.30     0.25
qcov  -0.12 0.19       0.40     0.53
qcov  -0.01 0.26       0.00     0.97
qcov   0.92 0.66       1.94     0.16
qcov  -0.67 0.36       3.58     0.06
qcov   0.25 0.89       0.08     0.78
qcov  -0.73 0.32       5.13     0.02
qcov  -1.07 0.89       1.42     0.23
> msm_details(whall)

 Intensity matrix : 
        State 1                         State 2                        
State 1 -0.037613 (-0.045551,-0.031058)  0.030681 ( 0.024343, 0.038670)
State 2  0.310480 ( 0.257491, 0.374375) -0.340353 (-0.407453,-0.284303)
State 3 0                                0.274893 ( 0.136685, 0.552848)
State 4 0                               0                              
        State 3                         State 4                        
State 1 0                                0.006932 ( 0.005268, 0.009121)
State 2  0.017720 ( 0.007664, 0.040972)  0.012153 ( 0.005141, 0.028725)
State 3 -0.330719 (-0.624928,-0.175020)  0.055826 ( 0.014780, 0.210855)
State 4 0                               0                              

 Transition probability matrix for t =  2  : 
          State 1    State 2      State 3    State 4
State 1 0.9421839 0.04308313 0.0006880963 0.01404487
State 2 0.4359854 0.52323263 0.0183094084 0.02247261
State 3 0.1080221 0.28403581 0.5211308598 0.08681121
State 4 0.0000000 0.00000000 0.0000000000 1.00000000

 Misclassification matrix : 
NULL

 Mean sojourn times : 
        estimates        SE         L         U
State 1 26.586652 2.5975942 21.953246 32.197974
State 2  2.938126 0.2697457  2.454272  3.517371
State 3  3.023717 0.9817511  1.600185  5.713632

 Probability that each state is next : 
        State 1                   State 2                  
State 1 0                         0.81570 (0.75822,0.86583)
State 2 0.91223 (0.84577,0.94677) 0                        
State 3 0                         0.83120 (0.54095,0.95407)
State 4 0                         0                        
        State 3                   State 4                  
State 1 0                         0.18430 (0.13417,0.24178)
State 2 0.05206 (0.02192,0.10904) 0.03571 (0.01443,0.08101)
State 3 0                         0.16880 (0.04593,0.45905)
State 4 0                         0                        

  Total length of stay : 
    State 1     State 2     State 3     State 4 
119.6350799  11.2722704   0.6039697         Inf 

 Expected number of visits to the state : 
  State 1   State 2   State 3   State 4 
3.4998174 3.8365498 0.1997454 1.0000000