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@ehsanx
ehsanx committed Sep 30, 2020
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14 changes: 7 additions & 7 deletions slidePS.Rmd
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Expand Up @@ -274,7 +274,7 @@ baselinevars <- c("age","sex", "race","Disease.category",
"Respiratory.rate", "WBC.count",
"PaO2.by.FIO2","PaCO2","pH",
"Creatinine","Albumin","GComa.Score")
out.formula <- as.formula(paste("I(Death=='Yes')", "~",
out.formula <- as.formula(paste("I(Death=='Yes')", "~ RHC +",
paste(baselinevars,
collapse = "+")))
out.formula
Expand Down Expand Up @@ -343,7 +343,7 @@ require(MatchIt)
m.out = matchit (RHC=="RHC" ~ sex + race,
data = analytic.data,
method = "exact")
m.out$nn
m.out
```

## [2] Exact Matching: 3 variables
Expand All @@ -363,7 +363,7 @@ table(analytic.data$RHC,var.comb=="otherFemale[80, Inf)")
m.out = matchit (RHC=="RHC" ~ age + sex + race,
data = analytic.data,
method = "exact")
m.out$nn
m.out
```

## [2] Exact Matching: 3 variables
Expand All @@ -385,7 +385,7 @@ m.out = matchit (RHC=="RHC" ~ age + sex + race +
Disease.category + DNR.status,
data = analytic.data,
method = "exact")
m.out$nn
m.out
```

## [2] Exact Matching: many categorical variables
Expand All @@ -406,7 +406,7 @@ m.out = matchit (RHC=="RHC" ~ age + sex + race +
Heart.rate, # continuous
data = analytic.data,
method = "exact")
m.out$nn
m.out
```

## [2] Exact Matching: including more continuous variables
Expand All @@ -418,7 +418,7 @@ m.out = matchit (RHC=="RHC" ~ age + sex + race +
Temperature,
data = analytic.data,
method = "exact")
m.out$nn
m.out
```

## [2] Exact Matching: including more continuous variables
Expand Down Expand Up @@ -664,7 +664,7 @@ summary(match.obj$distance)
### Step 2

```{r ps7b, cache=TRUE, echo = TRUE}
match.obj$nn
match.obj
```

## [3] Propensity Score Matching
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371 changes: 209 additions & 162 deletions slidePS.html
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201 changes: 124 additions & 77 deletions slidePS.md
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Expand Up @@ -297,15 +297,15 @@ baselinevars <- c("age","sex", "race","Disease.category",
"Respiratory.rate", "WBC.count",
"PaO2.by.FIO2","PaCO2","pH",
"Creatinine","Albumin","GComa.Score")
out.formula <- as.formula(paste("I(Death=='Yes')", "~",
out.formula <- as.formula(paste("I(Death=='Yes')", "~ RHC +",
paste(baselinevars,
collapse = "+")))
out.formula
```

```
## I(Death == "Yes") ~ age + sex + race + Disease.category + DNR.status +
## APACHE.III.score + Pr.2mo.survival + No.of.comorbidity +
## I(Death == "Yes") ~ RHC + age + sex + race + Disease.category +
## DNR.status + APACHE.III.score + Pr.2mo.survival + No.of.comorbidity +
## DASI.2wk.prior + Temperature + Heart.rate + Blood.pressure +
## Respiratory.rate + WBC.count + PaO2.by.FIO2 + PaCO2 + pH +
## Creatinine + Albumin + GComa.Score
Expand All @@ -322,37 +322,39 @@ publish(fit2)

```
## Variable Units OddsRatio CI.95 p-value
## RHC No RHC Ref
## RHC 2.55 [2.18;2.97] < 1e-04
## age [-Inf,50) Ref
## [50,60) 1.54 [1.27;1.87] < 1e-04
## [60,70) 0.73 [0.62;0.87] 0.0002517
## [70,80) 1.13 [0.97;1.32] 0.1142952
## [80, Inf) 1.12 [0.97;1.29] 0.1117607
## [50,60) 1.70 [1.39;2.07] < 1e-04
## [60,70) 0.77 [0.65;0.91] 0.0019296
## [70,80) 1.18 [1.01;1.38] 0.0396871
## [80, Inf) 1.13 [0.98;1.30] 0.0957860
## sex Male Ref
## Female 0.48 [0.42;0.55] < 1e-04
## Female 0.43 [0.38;0.50] < 1e-04
## race white Ref
## black 1.12 [0.93;1.36] 0.2314302
## other 1.00 [0.74;1.35] 0.9881736
## black 1.14 [0.94;1.38] 0.1917093
## other 0.91 [0.67;1.24] 0.5634739
## Disease.category ARF Ref
## CHF 1.64 [1.24;2.16] 0.0004557
## MOSF 1.06 [0.89;1.26] 0.4986705
## Other 1.14 [0.93;1.41] 0.2070459
## CHF 1.30 [0.98;1.73] 0.0702401
## MOSF 0.94 [0.79;1.12] 0.4786581
## Other 1.29 [1.04;1.59] 0.0196439
## DNR.status No Ref
## Yes 2.20 [1.67;2.89] < 1e-04
## APACHE.III.score 1.01 [1.00;1.01] 0.0115427
## Yes 2.44 [1.85;3.22] < 1e-04
## APACHE.III.score 1.01 [1.00;1.01] 0.0903495
## Pr.2mo.survival 0.01 [0.01;0.02] < 1e-04
## No.of.comorbidity 1.20 [1.13;1.29] < 1e-04
## DASI.2wk.prior 0.96 [0.94;0.97] < 1e-04
## Temperature 0.94 [0.90;0.98] 0.0038857
## Heart.rate 1.00 [1.00;1.00] 0.0191355
## Blood.pressure 1.00 [1.00;1.00] 0.5000114
## Respiratory.rate 1.00 [0.99;1.00] 0.7569105
## WBC.count 1.01 [1.00;1.01] 0.0360557
## PaO2.by.FIO2 1.00 [1.00;1.00] 0.2173154
## PaCO2 0.99 [0.99;1.00] 0.0902647
## pH 0.88 [0.39;1.94] 0.7433254
## Creatinine 1.03 [1.00;1.07] 0.0874115
## Albumin 0.98 [0.90;1.07] 0.6650240
## GComa.Score 1.00 [0.99;1.00] 0.0260942
## No.of.comorbidity 1.22 [1.14;1.30] < 1e-04
## DASI.2wk.prior 0.95 [0.94;0.97] < 1e-04
## Temperature 0.94 [0.90;0.99] 0.0095914
## Heart.rate 1.00 [1.00;1.00] 0.0975692
## Blood.pressure 1.00 [1.00;1.00] 0.5146500
## Respiratory.rate 1.00 [1.00;1.01] 0.1459102
## WBC.count 1.01 [1.00;1.01] 0.0259773
## PaO2.by.FIO2 1.00 [1.00;1.00] 0.0003039
## PaCO2 1.00 [0.99;1.00] 0.5339307
## pH 1.03 [0.46;2.33] 0.9407749
## Creatinine 1.03 [0.99;1.07] 0.1781145
## Albumin 1.00 [0.92;1.10] 0.9337588
## GComa.Score 1.00 [0.99;1.00] 0.0441504
```
## [1] Adjusted regression (v2)

Expand Down Expand Up @@ -447,15 +449,22 @@ require(MatchIt)
m.out = matchit (RHC=="RHC" ~ sex + race,
data = analytic.data,
method = "exact")
m.out$nn
m.out
```

```
##
## Call:
## matchit(formula = RHC == "RHC" ~ sex + race, data = analytic.data,
## method = "exact")
##
## Exact Subclasses: 6
##
## Sample sizes:
## Control Treated
## All 2583 2184
## Matched 2583 2184
## Unmatched 0 0
## Discarded 0 0
```

## [2] Exact Matching: 3 variables
Expand Down Expand Up @@ -501,15 +510,22 @@ table(analytic.data$RHC,var.comb=="otherFemale[80, Inf)")
m.out = matchit (RHC=="RHC" ~ age + sex + race,
data = analytic.data,
method = "exact")
m.out$nn
m.out
```

```
##
## Call:
## matchit(formula = RHC == "RHC" ~ age + sex + race, data = analytic.data,
## method = "exact")
##
## Exact Subclasses: 29
##
## Sample sizes:
## Control Treated
## All 2583 2184
## Matched 2581 2184
## Unmatched 0 0
## Discarded 0 0
## Unmatched 2 0
```

## [2] Exact Matching: 3 variables
Expand Down Expand Up @@ -553,15 +569,22 @@ m.out = matchit (RHC=="RHC" ~ age + sex + race +
Disease.category + DNR.status,
data = analytic.data,
method = "exact")
m.out$nn
m.out
```

```
##
## Call:
## matchit(formula = RHC == "RHC" ~ age + sex + race + Disease.category +
## DNR.status, data = analytic.data, method = "exact")
##
## Exact Subclasses: 137
##
## Sample sizes:
## Control Treated
## All 2583 2184
## Matched 2524 2150
## Unmatched 0 0
## Discarded 0 0
## Unmatched 59 34
```

## [2] Exact Matching: many categorical variables
Expand Down Expand Up @@ -597,15 +620,22 @@ m.out = matchit (RHC=="RHC" ~ age + sex + race +
Heart.rate, # continuous
data = analytic.data,
method = "exact")
m.out$nn
m.out
```

```
##
## Call:
## matchit(formula = RHC == "RHC" ~ age + sex + race + Disease.category +
## DNR.status + Heart.rate, data = analytic.data, method = "exact")
##
## Exact Subclasses: 504
##
## Sample sizes:
## Control Treated
## All 2583 2184
## Matched 929 947
## Unmatched 0 0
## Discarded 0 0
## Unmatched 1654 1237
```

## [2] Exact Matching: including more continuous variables
Expand All @@ -618,15 +648,23 @@ m.out = matchit (RHC=="RHC" ~ age + sex + race +
Temperature,
data = analytic.data,
method = "exact")
m.out$nn
m.out
```

```
##
## Call:
## matchit(formula = RHC == "RHC" ~ age + sex + race + Disease.category +
## DNR.status + Heart.rate + Blood.pressure + Temperature, data = analytic.data,
## method = "exact")
##
## Exact Subclasses: 3
##
## Sample sizes:
## Control Treated
## All 2583 2184
## Matched 3 3
## Unmatched 0 0
## Discarded 0 0
## Unmatched 2580 2181
```

## [2] Exact Matching: including more continuous variables
Expand Down Expand Up @@ -975,10 +1013,17 @@ summary(match.obj$distance)


```r
match.obj$nn
match.obj
```

```
##
## Call:
## matchit(formula = ps.formula, data = analytic.data, method = "nearest",
## distance = analytic.data$PS, replace = FALSE, caliper = 0.1 *
## sd(logitPS), ratio = 1)
##
## Sample sizes:
## Control Treated
## All 2583 2184
## Matched 1519 1519
Expand Down Expand Up @@ -1367,8 +1412,8 @@ out.formula
```

```
## I(Death == "Yes") ~ age + sex + race + Disease.category + DNR.status +
## APACHE.III.score + Pr.2mo.survival + No.of.comorbidity +
## I(Death == "Yes") ~ RHC + age + sex + race + Disease.category +
## DNR.status + APACHE.III.score + Pr.2mo.survival + No.of.comorbidity +
## DASI.2wk.prior + Temperature + Heart.rate + Blood.pressure +
## Respiratory.rate + WBC.count + PaO2.by.FIO2 + PaCO2 + pH +
## Creatinine + Albumin + GComa.Score
Expand All @@ -1381,38 +1426,40 @@ publish(fit3b)
```

```
## Variable Units OddsRatio CI.95 p-value
## age [-Inf,50) Ref
## [50,60) 1.62 [1.26;2.09] 0.0001639
## [60,70) 0.76 [0.61;0.94] 0.0131863
## [70,80) 1.14 [0.94;1.38] 0.1935493
## [80, Inf) 1.26 [1.06;1.51] 0.0084480
## sex Male Ref
## Female 0.45 [0.38;0.54] < 1e-04
## race white Ref
## black 1.13 [0.89;1.44] 0.3224165
## other 0.87 [0.59;1.28] 0.4779060
## Disease.category ARF Ref
## CHF 1.47 [1.05;2.06] 0.0251017
## MOSF 1.02 [0.83;1.26] 0.8354884
## Other 1.28 [0.94;1.73] 0.1134749
## DNR.status No Ref
## Yes 2.51 [1.69;3.75] < 1e-04
## APACHE.III.score 1.00 [1.00;1.01] 0.2170832
## Pr.2mo.survival 0.01 [0.00;0.01] < 1e-04
## No.of.comorbidity 1.18 [1.09;1.28] < 1e-04
## DASI.2wk.prior 0.95 [0.94;0.97] < 1e-04
## Temperature 0.95 [0.90;1.00] 0.0594218
## Heart.rate 1.00 [1.00;1.00] 0.0802537
## Blood.pressure 1.00 [1.00;1.00] 0.3146312
## Respiratory.rate 1.00 [1.00;1.01] 0.3492897
## WBC.count 1.00 [0.99;1.01] 0.5707415
## PaO2.by.FIO2 1.00 [1.00;1.00] 0.0128897
## PaCO2 1.00 [0.99;1.01] 0.8801280
## pH 0.92 [0.33;2.54] 0.8731477
## Creatinine 1.03 [0.98;1.08] 0.1897378
## Albumin 1.01 [0.91;1.13] 0.8175665
## GComa.Score 1.00 [0.99;1.00] 0.0123163
## Variable Units OddsRatio CI.95 p-value
## RHC No RHC Ref
## RHC 2.55 [2.14;3.03] < 1e-04
## age [-Inf,50) Ref
## [50,60) 1.72 [1.33;2.23] < 1e-04
## [60,70) 0.76 [0.61;0.95] 0.015909
## [70,80) 1.12 [0.92;1.37] 0.263369
## [80, Inf) 1.27 [1.06;1.52] 0.008216
## sex Male Ref
## Female 0.43 [0.36;0.52] < 1e-04
## race white Ref
## black 1.14 [0.89;1.46] 0.310211
## other 0.86 [0.57;1.29] 0.460330
## Disease.category ARF Ref
## CHF 1.49 [1.05;2.10] 0.025167
## MOSF 1.00 [0.81;1.24] 0.981457
## Other 1.34 [0.98;1.82] 0.068593
## DNR.status No Ref
## Yes 2.60 [1.73;3.90] < 1e-04
## APACHE.III.score 1.00 [1.00;1.01] 0.297336
## Pr.2mo.survival 0.01 [0.00;0.01] < 1e-04
## No.of.comorbidity 1.19 [1.10;1.30] < 1e-04
## DASI.2wk.prior 0.95 [0.93;0.96] < 1e-04
## Temperature 0.95 [0.90;1.01] 0.081292
## Heart.rate 1.00 [1.00;1.00] 0.089442
## Blood.pressure 1.00 [1.00;1.00] 0.207696
## Respiratory.rate 1.00 [1.00;1.01] 0.175634
## WBC.count 1.00 [1.00;1.01] 0.417667
## PaO2.by.FIO2 1.00 [1.00;1.00] 0.005573
## PaCO2 1.00 [0.99;1.01] 0.907590
## pH 0.86 [0.30;2.43] 0.770447
## Creatinine 1.03 [0.99;1.08] 0.155861
## Albumin 1.02 [0.91;1.15] 0.699519
## GComa.Score 1.00 [0.99;1.00] 0.013497
```


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