pre match check
test <- all %>% na.omit()
m.out0 <- matchit(group ~ Gender_Legal_Sex +age_bl+htn+dm+cad+
chf+copd+cancer+nsaid+beta_blockers+statins+ace_arb+ppi+diur+immunosuppressant+
vaccine+pre_cre_freq+pre_inpt_freq+pre_outpt_freq+renal_group2+
prior_infection, data = test,
method = NULL, distance = "glm")
summary(m.out0)
##
## Call:
## matchit(formula = group ~ Gender_Legal_Sex + age_bl + htn + dm +
## cad + chf + copd + cancer + nsaid + beta_blockers + statins +
## ace_arb + ppi + diur + immunosuppressant + vaccine + pre_cre_freq +
## pre_inpt_freq + pre_outpt_freq + renal_group2 + prior_infection,
## data = test, method = NULL, distance = "glm")
##
## Summary of Balance for All Data:
## Means Treated Means Control Std. Mean Diff.
## distance 0.4814 0.2696 0.9409
## Gender_Legal_SexFemale 0.5011 0.5785 -0.1550
## Gender_Legal_SexMale 0.4989 0.4215 0.1550
## age_bl 72.7977 76.4126 -0.2693
## htn0 0.1926 0.0957 0.2457
## htn1 0.8074 0.9043 -0.2457
## dm0 0.5309 0.5990 -0.1366
## dm1 0.4691 0.4010 0.1366
## cad0 0.5085 0.5077 0.0015
## cad1 0.4915 0.4923 -0.0015
## chf0 0.9011 0.9281 -0.0905
## chf1 0.0989 0.0719 0.0905
## copd0 0.8372 0.8473 -0.0274
## copd1 0.1628 0.1527 0.0274
## cancer0 0.5702 0.3910 0.3619
## cancer1 0.4298 0.6090 -0.3619
## nsaid0 0.8138 0.8247 -0.0278
## nsaid1 0.1862 0.1753 0.0278
## beta_blockers0 0.5947 0.5785 0.0329
## beta_blockers1 0.4053 0.4215 -0.0329
## statins0 0.5362 0.3639 0.3454
## statins1 0.4638 0.6361 -0.3454
## ace_arb0 0.6181 0.4663 0.3125
## ace_arb1 0.3819 0.5337 -0.3125
## ppi0 0.6957 0.7024 -0.0145
## ppi1 0.3043 0.2976 0.0145
## diur0 0.6415 0.5885 0.1105
## diur1 0.3585 0.4115 -0.1105
## immunosuppressant0 0.9500 0.9441 0.0269
## immunosuppressant1 0.0500 0.0559 -0.0269
## vaccine0 0.6383 0.3280 0.6458
## vaccine1 0.3617 0.6720 -0.6458
## pre_cre_freq 6.5819 4.5846 0.1737
## pre_inpt_freq 0.8362 0.3551 0.2367
## pre_outpt_freq 48.5894 43.5393 0.0981
## renal_group2eGFR <30, no ESKD 0.0787 0.0183 0.2245
## renal_group2eGFR 30-44.9, no ESKD 0.2309 0.1831 0.1134
## renal_group2eGFR 45-59.9, no ESKD 0.5840 0.7611 -0.3591
## renal_group2ESKD 0.1064 0.0376 0.2230
## prior_infection0 0.9713 0.9840 -0.0759
## prior_infection1 0.0287 0.0160 0.0759
## Var. Ratio eCDF Mean eCDF Max
## distance 1.6862 0.2688 0.4118
## Gender_Legal_SexFemale . 0.0775 0.0775
## Gender_Legal_SexMale . 0.0775 0.0775
## age_bl 1.5496 0.0767 0.1336
## htn0 . 0.0969 0.0969
## htn1 . 0.0969 0.0969
## dm0 . 0.0682 0.0682
## dm1 . 0.0682 0.0682
## cad0 . 0.0008 0.0008
## cad1 . 0.0008 0.0008
## chf0 . 0.0270 0.0270
## chf1 . 0.0270 0.0270
## copd0 . 0.0101 0.0101
## copd1 . 0.0101 0.0101
## cancer0 . 0.1792 0.1792
## cancer1 . 0.1792 0.1792
## nsaid0 . 0.0108 0.0108
## nsaid1 . 0.0108 0.0108
## beta_blockers0 . 0.0161 0.0161
## beta_blockers1 . 0.0161 0.0161
## statins0 . 0.1722 0.1722
## statins1 . 0.1722 0.1722
## ace_arb0 . 0.1518 0.1518
## ace_arb1 . 0.1518 0.1518
## ppi0 . 0.0067 0.0067
## ppi1 . 0.0067 0.0067
## diur0 . 0.0530 0.0530
## diur1 . 0.0530 0.0530
## immunosuppressant0 . 0.0059 0.0059
## immunosuppressant1 . 0.0059 0.0059
## vaccine0 . 0.3103 0.3103
## vaccine1 . 0.3103 0.3103
## pre_cre_freq 0.9546 0.0333 0.1049
## pre_inpt_freq 2.4329 0.0281 0.1174
## pre_outpt_freq 2.4387 0.0655 0.2057
## renal_group2eGFR <30, no ESKD . 0.0605 0.0605
## renal_group2eGFR 30-44.9, no ESKD . 0.0478 0.0478
## renal_group2eGFR 45-59.9, no ESKD . 0.1770 0.1770
## renal_group2ESKD . 0.0688 0.0688
## prior_infection0 . 0.0127 0.0127
## prior_infection1 . 0.0127 0.0127
##
## Sample Sizes:
## Control Treated
## All 1808 940
## Matched 1808 940
## Unmatched 0 0
## Discarded 0 0
plot(m.out0, type = "jitter", interactive = FALSE)
plot(summary(m.out0), abs = FALSE)
a <- test %>% group_by(group) %>% summarise(mean=mean(age_bl))
post match check
m.out1 <- matchit(group ~ Gender_Legal_Sex +age_bl+htn+dm+cad+
chf+copd+cancer+nsaid+beta_blockers+statins+ace_arb+ppi+diur+immunosuppressant+
vaccine+pre_cre_freq+pre_inpt_freq+pre_outpt_freq+renal_group2+
prior_infection, data = test,
method = "nearest", distance = "glm", ratio =2,caliper = .15)
## Warning: Not all treated units will get 2 matches.
summary(m.out1)
##
## Call:
## matchit(formula = group ~ Gender_Legal_Sex + age_bl + htn + dm +
## cad + chf + copd + cancer + nsaid + beta_blockers + statins +
## ace_arb + ppi + diur + immunosuppressant + vaccine + pre_cre_freq +
## pre_inpt_freq + pre_outpt_freq + renal_group2 + prior_infection,
## data = test, method = "nearest", distance = "glm", caliper = 0.15,
## ratio = 2)
##
## Summary of Balance for All Data:
## Means Treated Means Control Std. Mean Diff.
## distance 0.4814 0.2696 0.9409
## Gender_Legal_SexFemale 0.5011 0.5785 -0.1550
## Gender_Legal_SexMale 0.4989 0.4215 0.1550
## age_bl 72.7977 76.4126 -0.2693
## htn0 0.1926 0.0957 0.2457
## htn1 0.8074 0.9043 -0.2457
## dm0 0.5309 0.5990 -0.1366
## dm1 0.4691 0.4010 0.1366
## cad0 0.5085 0.5077 0.0015
## cad1 0.4915 0.4923 -0.0015
## chf0 0.9011 0.9281 -0.0905
## chf1 0.0989 0.0719 0.0905
## copd0 0.8372 0.8473 -0.0274
## copd1 0.1628 0.1527 0.0274
## cancer0 0.5702 0.3910 0.3619
## cancer1 0.4298 0.6090 -0.3619
## nsaid0 0.8138 0.8247 -0.0278
## nsaid1 0.1862 0.1753 0.0278
## beta_blockers0 0.5947 0.5785 0.0329
## beta_blockers1 0.4053 0.4215 -0.0329
## statins0 0.5362 0.3639 0.3454
## statins1 0.4638 0.6361 -0.3454
## ace_arb0 0.6181 0.4663 0.3125
## ace_arb1 0.3819 0.5337 -0.3125
## ppi0 0.6957 0.7024 -0.0145
## ppi1 0.3043 0.2976 0.0145
## diur0 0.6415 0.5885 0.1105
## diur1 0.3585 0.4115 -0.1105
## immunosuppressant0 0.9500 0.9441 0.0269
## immunosuppressant1 0.0500 0.0559 -0.0269
## vaccine0 0.6383 0.3280 0.6458
## vaccine1 0.3617 0.6720 -0.6458
## pre_cre_freq 6.5819 4.5846 0.1737
## pre_inpt_freq 0.8362 0.3551 0.2367
## pre_outpt_freq 48.5894 43.5393 0.0981
## renal_group2eGFR <30, no ESKD 0.0787 0.0183 0.2245
## renal_group2eGFR 30-44.9, no ESKD 0.2309 0.1831 0.1134
## renal_group2eGFR 45-59.9, no ESKD 0.5840 0.7611 -0.3591
## renal_group2ESKD 0.1064 0.0376 0.2230
## prior_infection0 0.9713 0.9840 -0.0759
## prior_infection1 0.0287 0.0160 0.0759
## Var. Ratio eCDF Mean eCDF Max
## distance 1.6862 0.2688 0.4118
## Gender_Legal_SexFemale . 0.0775 0.0775
## Gender_Legal_SexMale . 0.0775 0.0775
## age_bl 1.5496 0.0767 0.1336
## htn0 . 0.0969 0.0969
## htn1 . 0.0969 0.0969
## dm0 . 0.0682 0.0682
## dm1 . 0.0682 0.0682
## cad0 . 0.0008 0.0008
## cad1 . 0.0008 0.0008
## chf0 . 0.0270 0.0270
## chf1 . 0.0270 0.0270
## copd0 . 0.0101 0.0101
## copd1 . 0.0101 0.0101
## cancer0 . 0.1792 0.1792
## cancer1 . 0.1792 0.1792
## nsaid0 . 0.0108 0.0108
## nsaid1 . 0.0108 0.0108
## beta_blockers0 . 0.0161 0.0161
## beta_blockers1 . 0.0161 0.0161
## statins0 . 0.1722 0.1722
## statins1 . 0.1722 0.1722
## ace_arb0 . 0.1518 0.1518
## ace_arb1 . 0.1518 0.1518
## ppi0 . 0.0067 0.0067
## ppi1 . 0.0067 0.0067
## diur0 . 0.0530 0.0530
## diur1 . 0.0530 0.0530
## immunosuppressant0 . 0.0059 0.0059
## immunosuppressant1 . 0.0059 0.0059
## vaccine0 . 0.3103 0.3103
## vaccine1 . 0.3103 0.3103
## pre_cre_freq 0.9546 0.0333 0.1049
## pre_inpt_freq 2.4329 0.0281 0.1174
## pre_outpt_freq 2.4387 0.0655 0.2057
## renal_group2eGFR <30, no ESKD . 0.0605 0.0605
## renal_group2eGFR 30-44.9, no ESKD . 0.0478 0.0478
## renal_group2eGFR 45-59.9, no ESKD . 0.1770 0.1770
## renal_group2ESKD . 0.0688 0.0688
## prior_infection0 . 0.0127 0.0127
## prior_infection1 . 0.0127 0.0127
##
## Summary of Balance for Matched Data:
## Means Treated Means Control Std. Mean Diff.
## distance 0.4099 0.3958 0.0624
## Gender_Legal_SexFemale 0.5280 0.5431 -0.0301
## Gender_Legal_SexMale 0.4720 0.4569 0.0301
## age_bl 74.2588 74.0221 0.0176
## htn0 0.1491 0.1430 0.0156
## htn1 0.8509 0.8570 -0.0156
## dm0 0.5390 0.5575 -0.0370
## dm1 0.4610 0.4425 0.0370
## cad0 0.5048 0.4802 0.0493
## cad1 0.4952 0.5198 -0.0493
## chf0 0.9070 0.9029 0.0137
## chf1 0.0930 0.0971 -0.0137
## copd0 0.8345 0.8242 0.0278
## copd1 0.1655 0.1758 -0.0278
## cancer0 0.5144 0.4938 0.0415
## cancer1 0.4856 0.5062 -0.0415
## nsaid0 0.8126 0.8051 0.0193
## nsaid1 0.1874 0.1949 -0.0193
## beta_blockers0 0.5800 0.5759 0.0084
## beta_blockers1 0.4200 0.4241 -0.0084
## statins0 0.4815 0.4535 0.0562
## statins1 0.5185 0.5465 -0.0562
## ace_arb0 0.5677 0.5622 0.0113
## ace_arb1 0.4323 0.4378 -0.0113
## ppi0 0.6854 0.6888 -0.0074
## ppi1 0.3146 0.3112 0.0074
## diur0 0.6252 0.5937 0.0656
## diur1 0.3748 0.4063 -0.0656
## immunosuppressant0 0.9466 0.9473 -0.0031
## immunosuppressant1 0.0534 0.0527 0.0031
## vaccine0 0.5622 0.5595 0.0057
## vaccine1 0.4378 0.4405 -0.0057
## pre_cre_freq 5.5910 5.6963 -0.0092
## pre_inpt_freq 0.5705 0.5705 0.0000
## pre_outpt_freq 48.9562 49.0055 -0.0010
## renal_group2eGFR <30, no ESKD 0.0438 0.0397 0.0152
## renal_group2eGFR 30-44.9, no ESKD 0.2298 0.2155 0.0341
## renal_group2eGFR 45-59.9, no ESKD 0.6525 0.6751 -0.0458
## renal_group2ESKD 0.0739 0.0698 0.0133
## prior_infection0 0.9795 0.9767 0.0164
## prior_infection1 0.0205 0.0233 -0.0164
## Var. Ratio eCDF Mean eCDF Max Std. Pair Dist.
## distance 1.1352 0.0127 0.0561 0.0473
## Gender_Legal_SexFemale . 0.0150 0.0150 0.9938
## Gender_Legal_SexMale . 0.0150 0.0150 0.9938
## age_bl 1.1324 0.0144 0.0328 0.8829
## htn0 . 0.0062 0.0062 0.5284
## htn1 . 0.0062 0.0062 0.5284
## dm0 . 0.0185 0.0185 0.9082
## dm1 . 0.0185 0.0185 0.9082
## cad0 . 0.0246 0.0246 1.0349
## cad1 . 0.0246 0.0246 1.0349
## chf0 . 0.0041 0.0041 0.5607
## chf1 . 0.0041 0.0041 0.5607
## copd0 . 0.0103 0.0103 0.7671
## copd1 . 0.0103 0.0103 0.7671
## cancer0 . 0.0205 0.0205 0.9120
## cancer1 . 0.0205 0.0205 0.9120
## nsaid0 . 0.0075 0.0075 0.7824
## nsaid1 . 0.0075 0.0075 0.7824
## beta_blockers0 . 0.0041 0.0041 0.9831
## beta_blockers1 . 0.0041 0.0041 0.9831
## statins0 . 0.0280 0.0280 0.9285
## statins1 . 0.0280 0.0280 0.9285
## ace_arb0 . 0.0055 0.0055 0.9805
## ace_arb1 . 0.0055 0.0055 0.9805
## ppi0 . 0.0034 0.0034 0.9406
## ppi1 . 0.0034 0.0034 0.9406
## diur0 . 0.0315 0.0315 0.9563
## diur1 . 0.0315 0.0315 0.9563
## immunosuppressant0 . 0.0007 0.0007 0.4535
## immunosuppressant1 . 0.0007 0.0007 0.4535
## vaccine0 . 0.0027 0.0027 0.6690
## vaccine1 . 0.0027 0.0027 0.6690
## pre_cre_freq 0.7607 0.0065 0.0650 0.5372
## pre_inpt_freq 0.7027 0.0070 0.0294 0.8068
## pre_outpt_freq 1.5394 0.0333 0.1525 0.8422
## renal_group2eGFR <30, no ESKD . 0.0041 0.0041 0.2248
## renal_group2eGFR 30-44.9, no ESKD . 0.0144 0.0144 0.8242
## renal_group2eGFR 45-59.9, no ESKD . 0.0226 0.0226 0.8076
## renal_group2ESKD . 0.0041 0.0041 0.3206
## prior_infection0 . 0.0027 0.0027 0.2292
## prior_infection1 . 0.0027 0.0027 0.2292
##
## Sample Sizes:
## Control Treated
## All 1808. 940
## Matched (ESS) 998.81 731
## Matched 1123. 731
## Unmatched 685. 209
## Discarded 0. 0
plot(m.out1, type = "jitter", interactive = FALSE)
plot(summary(m.out1), abs = FALSE)
m.data1 <- match.data(m.out1, data = test,
distance = "prop.score") %>% select(EMPI,prop.score,weights,subclass)
m.data1 <- m.data1 %>% mutate_at(c("EMPI","prop.score","weights","subclass"),as.numeric)
matched <- all %>% merge(m.data1,by="EMPI",all.y = T)
write_xlsx(matched,"C:\\Users\\to909\\Dropbox (Partners HealthCare)\\Merck COVID-19 project\\FOR TIANQI TO MATCH\\Matched_updated.xlsx")