correcting all errors and approved test run

DESCRIPTION

@@ -4,6 +4,7 @@ Title: Bayesian Marginal Structural Models
 Version: 0.1.0
 Author: Kuan Liu, Xiao Yan
 Maintainer: Xiao Yan <[email protected]>
+<<<<<<< HEAD
 Depends:
     R (>= 4.2.0)
 Imports:
@@ -18,7 +19,23 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2
 Suggests: 
+=======
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.3.1
+Imports: 
+    MCMCpack,
+	  doParallel,
+	  foreach,
+	  parallel,
+	  R2jags,
+	  knitr,
+	  coda (>= 0.19-4),
+>>>>>>> c02a61c92d3be0eeca4a22bb0196a74db590a6ec
     testthat (>= 3.0.0)
+NeedsCompilation: no
 Config/testthat/edition: 3
 Description: This package provides tools for estimating causal effects using Bayesian Marginal Structural Models. It includes functions for estimating Bayesian weights using JAGS and for Bayesian non-parametric bootstrap to calculate causal effects.
 URL: https://kuan-liu-lab.github.io/bayesmsm/
+BugReports: https://github.com/Kuan-Liu-Lab/bayesmsm/issues

NAMESPACE

@@ -5,10 +5,13 @@ export(bayesweight)
 export(plot_APO)
 export(plot_ATE)
 export(plot_est_box)
+<<<<<<< HEAD
 export(summary_bayesmsm)
 import(MCMCpack)
+=======
+>>>>>>> c02a61c92d3be0eeca4a22bb0196a74db590a6ec
 import(doParallel)
-import(foreach)
-import(parallel)
+importFrom(MCMCpack,rdirichlet)
 importFrom(R2jags,jags)
 importFrom(coda,mcmc)
+importFrom(foreach,"%dopar%")

R/bayesmsm.R

@@ -27,10 +27,14 @@
 #' * `reference`, the reference intervention level
 #' * `comparator`, the camparison intervention level
 #'
-#' @import foreach
+#' @importFrom foreach "%dopar%"
 #' @import doParallel
+<<<<<<< HEAD
 #' @import parallel
 #' @import MCMCpack
+=======
+#' @importFrom MCMCpack rdirichlet
+>>>>>>> c02a61c92d3be0eeca4a22bb0196a74db590a6ec
 #'
 #' @export
 #'
@@ -67,10 +71,29 @@ bayesmsm <- function(ymodel,
                      ncore = 6){
 
   # load all the required R packages;
+<<<<<<< HEAD
   # require(foreach)
   # require(doParallel)
   # require(MCMCpack)
   # require(parallel)
+=======
+  # if (!require(foreach)){
+  #   install.packages("foreach",repos="http://cran.r-project.org")
+  #   library(foreach)
+  # }
+  # if (!require(doParallel)){
+  #   install.packages("doParallel",repos="http://cran.r-project.org")
+  #   library(doParallel)
+  # }
+  # if (!require(MCMCpack)){
+  #   install.packages("MCMCpack",repos="http://cran.r-project.org")
+  #   library(MCMCpack)
+  # }
+
+  require(foreach)
+  require(doParallel)
+  require(MCMCpack)
+>>>>>>> c02a61c92d3be0eeca4a22bb0196a74db590a6ec
 
   # return error message if the input weight vector has different length comparing to the outcome Y;
   if (length(wmean) != nrow(data)) {
@@ -256,7 +279,7 @@ bayesmsm <- function(ymodel,
         reference = reference,
         comparator = comparator
       ))
-    } else {
+    } else if (family == "gaussian"){
       return(list(
         RD_mean = mean(results[,2]),
         RD_sd = sqrt(var(results[,2])),

R/bayesweight.R

@@ -16,9 +16,15 @@
 #'
 #' @importFrom R2jags jags
 #' @importFrom coda mcmc
+<<<<<<< HEAD
 #' @import parallel
 #' @import doParallel
 #' @import foreach
+=======
+#' @import doParallel
+#' @importFrom foreach "%dopar%"
+#'
+>>>>>>> c02a61c92d3be0eeca4a22bb0196a74db590a6ec
 #' @export
 #'
 #' @examples
@@ -47,12 +53,32 @@ bayesweight <- function(trtmodel.list,
                         parallel = TRUE){
 
   # Load all the required R packages;
+<<<<<<< HEAD
   # require(foreach)
   # require(doParallel)
   # require(MCMCpack)
   # require(parallel)
   # require(R2jags)
   # require(coda)
+=======
+  # if (!require(R2jags)){
+  #   install.packages("R2jags",repos="http://cran.r-project.org")
+  #   library(R2jags)
+  # }
+  # if (!require(coda)){
+  #   install.packages("coda",repos="http://cran.r-project.org")
+  #   library(coda)
+  # }
+  # if (!require(parallel)){
+  #   install.packages("parallel",repos="http://cran.r-project.org")
+  #   library(parallel)
+  # }
+
+  require(R2jags)
+  require(coda)
+  require(doParallel)
+  require(foreach)
+>>>>>>> c02a61c92d3be0eeca4a22bb0196a74db590a6ec
 
   create_marginal_treatment_models <- function(trtmodel.list) {
     # Initialize the list for the marginal treatment models
@@ -266,9 +292,15 @@ bayesweight <- function(trtmodel.list,
     if (n.chains >= available_cores) {
       stop(paste("Parallel MCMC requires 1 core per chain. You have", available_cores, "cores. We recommend using", available_cores - 2, "cores."))
     }
+<<<<<<< HEAD
     # Run JAGS model in parallel
     cl <- parallel::makeCluster(n.chains)
     doParallel::registerDoParallel(cl)
+=======
+    # Run JAGS model in parallel;
+    cl <- makeCluster(n.chains)
+    registerDoParallel(cl)
+>>>>>>> c02a61c92d3be0eeca4a22bb0196a74db590a6ec
     jags.model.wd <- paste(getwd(), '/treatment_model.txt',sep='')
 
     posterior <- foreach::foreach(i=1:n.chains, .packages=c('R2jags'),