vignette update

Author: Matt Secrest

vignettes/OLE_analysis_workflow.Rmd

@@ -25,169 +25,107 @@ switches to treatment.
 
 ### 1 DID methods
 
-#### 1.1 IPW
+#### 1.1 DID-EC-IPW
 ```{r message=FALSE, warning=FALSE}
-bootstrap_obj <- setup_bootstrap(
-  replicates = 50,
-  bootstrap_CI_type = "perc"
+method <- did_ec_ipw(
+  ps_formula = "S ~ x1 + x2 + x3 + x4 + x5",
+  trt_formula = "A ~ x1 + x2 + x3 + x4 + x5",
+  bootstrap = 50
 )
 
-method_DID_obj <- setup_method_DID(
-  method_name = "IPW",
-  bootstrap_flag = TRUE,
-  bootstrap_obj = bootstrap_obj,
-  model_form_piS = "S ~ x1 + x2 + x3 + x4 + x5",
-  model_form_piA = "A ~ x1 + x2 + x3 + x4 + x5"
-)
-
-analysis_OLE_obj <- setup_analysis_OLE(
+analysis <- setup_analysis_OLE(
   data = SyntheticData,
   trial_status_col_name = "S",
   treatment_col_name = "A",
   outcome_col_name = c("y1", "y2", "y3", "y4"),
   covariates_col_name = c("x1", "x2", "x3", "x4", "x5"),
   T_cross = 2,
-  method_OLE_obj = method_DID_obj
+  method_OLE_obj = method
 )
 
-res <- run_analysis(analysis_OLE_obj)
+run_analysis(analysis)
 ```
 
-#### 1.2 AIPW
+#### 1.2 DID-EC-AIPW
 ```{r message=FALSE, warning=FALSE}
-bootstrap_obj <- setup_bootstrap(
-  replicates = 50,
-  bootstrap_CI_type = "perc"
-)
-
-model_form_mu <- c(
+model_forms <- c(
   "y1 ~ x1 + x2 + x3 + x4 + x5",
   "y2 ~ x1 + x2 + x3 + x4 + x5",
   "y3 ~ x1 + x2 + x3 + x4 + x5",
   "y4 ~ x1 + x2 + x3 + x4 + x5"
 )
 
-method_DID_obj <- setup_method_DID(
-  method_name = "AIPW",
-  bootstrap_flag = TRUE,
-  bootstrap_obj = bootstrap_obj,
-  model_form_piS = "S ~ x1 + x2 + x3 + x4 + x5",
-  model_form_piA = "A ~ x1 + x2 + x3 + x4 + x5",
-  model_form_mu0_ext = model_form_mu
+method <- did_ec_aipw(
+  ps_formula = "S ~ x1 + x2 + x3 + x4 + x5",
+  trt_formula = "A ~ x1 + x2 + x3 + x4 + x5",
+  outcome_formula = model_forms,
+  bootstrap = 50
 )
 
-analysis_OLE_obj <- setup_analysis_OLE(
+analysis <- setup_analysis_OLE(
   data = SyntheticData,
   trial_status_col_name = "S",
   treatment_col_name = "A",
   outcome_col_name = c("y1", "y2", "y3", "y4"),
   covariates_col_name = c("x1", "x2", "x3", "x4", "x5"),
   T_cross = 2,
-  method_OLE_obj = method_DID_obj
+  method_OLE_obj = method
 )
 
-res <- run_analysis(analysis_OLE_obj)
+run_analysis(analysis)
 ```
 
-
-#### 1.3 OR
+#### 1.3 DID-EC-OR
 ```{r message=FALSE, warning=FALSE}
-bootstrap_obj <- setup_bootstrap(
-  replicates = 50,
-  bootstrap_CI_type = "perc"
-)
-
-model_form_mu <- c(
+model_forms <- c(
   "y1 ~ x1 + x2 + x3 + x4 + x5",
   "y2 ~ x1 + x2 + x3 + x4 + x5",
   "y3 ~ x1 + x2 + x3 + x4 + x5",
   "y4 ~ x1 + x2 + x3 + x4 + x5"
 )
 
-method_DID_obj <- setup_method_DID(
-  method_name = "OR",
-  bootstrap_flag = TRUE,
-  bootstrap_obj = bootstrap_obj,
-  model_form_mu0_ext = model_form_mu,
-  model_form_mu0_rct = model_form_mu,
-  model_form_mu1_rct = model_form_mu
-)
-
-analysis_OLE_obj <- setup_analysis_OLE(
-  data = SyntheticData,
-  trial_status_col_name = "S",
-  treatment_col_name = "A",
-  outcome_col_name = c("y1", "y2", "y3", "y4"),
-  covariates_col_name = c("x1", "x2", "x3", "x4", "x5"),
-  T_cross = 2,
-  method_OLE_obj = method_DID_obj
-)
-
-res <- run_analysis(analysis_OLE_obj)
-res
-```
-
-
-### 2 SCM method: with parallel computing
-```{r}
-bootstrap_obj <- setup_bootstrap(
-  replicates = 50,
-  bootstrap_CI_type = "perc"
-)
-
-method_SCM_obj <- setup_method_SCM(
-  method_name = "SCM",
-  bootstrap_flag = TRUE,
-  bootstrap_obj = bootstrap_obj,
-  lambda.min = 0,
-  lambda.max = 1e-3,
-  nlambda = 10,
-  parallel = "no",
-  ncpus = 1
+method <- did_ec_or(
+  outcome_formula_ext = model_forms,
+  outcome_formula_rct_ctrl = model_forms,
+  outcome_formula_rct_trt = model_forms,
+  bootstrap = 50
 )
 
-analysis_OLE_obj <- setup_analysis_OLE(
+analysis <- setup_analysis_OLE(
   data = SyntheticData,
   trial_status_col_name = "S",
   treatment_col_name = "A",
   outcome_col_name = c("y1", "y2", "y3", "y4"),
   covariates_col_name = c("x1", "x2", "x3", "x4", "x5"),
   T_cross = 2,
-  method_OLE_obj = method_SCM_obj
+  method_OLE_obj = method
 )
 
-run_analysis(analysis_OLE_obj)
+run_analysis(analysis)
 ```
 
 
-### 3 SCM method: without parallel computing
+### 2 Synthetic control method
 ```{r}
-bootstrap_obj <- setup_bootstrap(
-  replicates = 50,
-  bootstrap_CI_type = "perc"
-)
-
-method_SCM_obj <- setup_method_SCM(
-  method_name = "SCM",
-  bootstrap_flag = TRUE,
-  bootstrap_obj = bootstrap_obj,
-  lambda.min = 0,
-  lambda.max = 1e-3,
+method <- scm(
+  lambda_min = 0,
+  lambda_max = 1e-3,
   nlambda = 10,
-  parallel = "no"
+  bootstrap = 50,
+  bootstrap_ci_type = "perc"
 )
 
-analysis_OLE_obj <- setup_analysis_OLE(
+analysis <- setup_analysis_OLE(
   data = SyntheticData,
   trial_status_col_name = "S",
   treatment_col_name = "A",
   outcome_col_name = c("y1", "y2", "y3", "y4"),
   covariates_col_name = c("x1", "x2", "x3", "x4", "x5"),
   T_cross = 2,
-  method_OLE_obj = method_SCM_obj
+  method_OLE_obj = method
 )
 
-run_analysis(analysis_OLE_obj)
+run_analysis(analysis)
 ```
 
 ## References