---
title: "psrwe: Propensity Score-Integrated Methods for Incorporating Real-World Evidence in Clinical Studies"
author: "Chenguang Wang"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{psrwe: Propensity Score-Integrated Methods for Incorporating Real-World Evidence in Clinical Studies}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---


```{r, eval=T, echo=FALSE}
require(psrwe)
set.seed(1000)
```

# Introduction

In the *R* package **psrwe**, we implement a series of approaches for leveraging
real-world evidence in clinical study design and analysis.

# Propensity score estimation

The approaches implemented in **psrwe** are mostly based on propensity score
adjustment. Estimation of propensity scores can be done by using the function
**psrwe_est**.

```{r, eval=T, echo=TRUE}
data(ex_dta)
dta_ps <- psrwe_est(ex_dta,
                     v_covs = paste("V", 1:7, sep = ""),
                     v_grp = "Group",
                     cur_grp_level = "current",
                     nstrata = 5,
                     ps_method = "logistic")
dta_ps
```

It is extremely important to evaluate the propensity score adjustment results.
In **psrwe**, functions are provided to visualize the balance in covariate
distributions and propensity score distributions based on propensity score
stratification.

```{r, echo=TRUE, fig.width=6, fig.height=5}
plot(dta_ps, plot_type = "balance")
```

```{r, echo=TRUE, fig.width=6, fig.height=5}
plot(dta_ps, plot_type = "ps")
```

# PS-integrated power prior approach for single arm studies

For single arm studies when there is one external data source, the function
**psrwe_powerp** allows one to conduct the analysis proposed in Wang et. al.
(2019). The method uses propensity score to pre-select a subset of real-world
data containing patients that are similar to those in the current study in terms
of covariates, and to stratify the selected patients together with those in the
current study into more homogeneous strata. The power prior approach is then
applied in each stratum to obtain stratum-specific posterior distributions,
which are combined to complete the Bayesian inference for the parameters of
interest.

```{r, eval=T, echo=TRUE}
ps_bor <- psrwe_borrow(dta_ps, total_borrow = 40,
                        method = "distance")
rst_pp <- psrwe_powerp(ps_bor, v_outcome = "Y_Bin",
                        outcome_type = "binary",
                        seed = 1234)
```

Results can be further summarized as:
```{r, eval=T, echo=TRUE}
summary(rst_pp)
```

# PS-integrated composite likelihood approach for single arm studies

For single arm studies when there is one external data source, the function
**psrwe_cl** allows one to conduct the analysis proposed in Wang et. al.
(2020). In this approach, within each propensity score stratum, a composite
likelihood function is specified and utilized to down-weight the information
contributed by the external data source. Estimates of the stratum-specific
parameters are obtained by maximizing the composite likelihood function. These
stratum-specific estimates are then combined to obtain an overall
population-level estimate of the parameter of interest.

```{r, eval=T, echo=TRUE}
rst_cl <- psrwe_compl(ps_bor, v_outcome = "Y_Bin",
                       outcome_type = "binary")
summary(rst_cl)
```

# PS-integrated composite likelihood approach for randomized studies

For randomized studies when there is one external data source that contains
*control* subjects, the function **psrwe_cl2arm** allows one to conduct the
analysis proposed in Chen et. al. (2020). In this approach, a propensity
score-integrated composite likelihood approach is developed for augmenting the
control arm of the two-arm randomized controlled trial with patients from
the external data source. An example is given below.

```{r, eval=T, echo=TRUE}
data(ex_dta_rct)
dta_ps_rct <- psrwe_est(ex_dta_rct, v_covs = paste("V", 1:7, sep = ""),
                         v_grp = "Group", cur_grp_level = "current",
                         v_arm = "Arm", ctl_arm_level = "control")
dta_ps_rct

ps_bor_rct <- psrwe_borrow(dta_ps_rct, total_borrow = 30,
                            method = "distance")
ps_bor_rct

rst_cl_rct <- psrwe_compl(ps_bor_rct, v_outcome = "Y_Con",
                           outcome_type = "continuous")

rst_cl_rct$Effect
```

# Demo examples

The full examples for the PSPP and PSCL approaches can be found via
the script `demo("sec_4_1_ex", package = "psrwe")` and
`demo("sec_4_2_ex", package = "psrwe")`.


# Reference

Chen, W.C., Wang, C., Li, H., Lu, N., Tiwari, R., Xu, Y. and Yue, L.Q., 2020.
Propensity score-integrated composite likelihood approach for augmenting the
control arm of a randomized controlled trial by incorporating real-world
data. Journal of Biopharmaceutical Statistics, 30(3), pp.508-520.

Wang, C., Lu, N., Chen, W. C., Li, H., Tiwari, R., Xu, Y., & Yue, L. Q.
(2020). Propensity score-integrated composite likelihood approach for
incorporating real-world evidence in single-arm clinical studies. Journal of
biopharmaceutical statistics, 30(3), 495-507.

Wang, C., Li, H., Chen, W. C., Lu, N., Tiwari, R., Xu, Y., & Yue, L. Q.
(2019). Propensity score-integrated power prior approach for incorporating
real-world evidence in single-arm clinical studies. Journal of
biopharmaceutical statistics, 29(5), 731-748.