diff --git a/R/plot_progeny_dosage_change.R b/R/plot_progeny_dosage_change.R
index 24b21910..fcefeb5e 100644
--- a/R/plot_progeny_dosage_change.R
+++ b/R/plot_progeny_dosage_change.R
@@ -11,13 +11,14 @@
 #'
 #' @param error error rate used in global error in the `calc_genoprob_error()`
 #' @param verbose T or F for `calc_genoprob_error()` and `calc_homologprob()`
-#' 
+#' @param output_corrected TRUE or FALSE, if F only the ggplot of the changed dosage is printed, if T then a new corrected dosage matrix is output. 
 #'
 #' @return A ggplot of the changed and imputed genotypic dosages
 #'
 #' @examples
-#'     x<-get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE)
-#'     plot_progeny_dosage_change(list(x), error=0.05)     
+#'       x <- get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE)   # subset to run fast in tests
+#'       plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F)   # no new corrected dosages  
+#'       corrected_matrix <- plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F) #output corrected
 #'
 #' @author Jeekin Lau, \email{jzl0026@tamu.edu}, with optimization by Cristiane Taniguti, \email{chtaniguti@tamu.edu}
 #'
@@ -25,7 +26,7 @@
 #' @import reshape2
 #' @export plot_progeny_dosage_change
 
-plot_progeny_dosage_change <- function(map_list, error, verbose=T){
+plot_progeny_dosage_change <- function(map_list, error, verbose=T, output_corrected=F){
   Var1 <- Var2 <- value <- NULL
   map=map_list
   if(!exists(map[[1]]$info$data.name)) stop("mappoly.data object not here")
@@ -175,8 +176,17 @@ plot_progeny_dosage_change <- function(map_list, error, verbose=T){
     guides(fill=guide_legend(title="Dosage change"))
   print("done")
   
-  return(plot1) 
-  
+  print(plot1)
+  if (output_corrected ==T){
+  mrk_names=rownames(finished)
+  mrk_index=which(dat$mrk.names%in%mrk_names)
+  P1 = dat$dosage.p1[mrk_index]
+  P2 = dat$dosage.p2[mrk_index]
+  sequence = dat$chrom[mrk_index]
+  sequence_position = dat$genome.pos[mrk_index]
+  
+  hmm_imputed = cbind(P1,P2,sequence,sequence_position, finished)
+  return(hmm_imputed)}
 }
 
 
diff --git a/man/plot_progeny_dosage_change.Rd b/man/plot_progeny_dosage_change.Rd
index 03666482..710b8d0f 100644
--- a/man/plot_progeny_dosage_change.Rd
+++ b/man/plot_progeny_dosage_change.Rd
@@ -4,7 +4,7 @@
 \alias{plot_progeny_dosage_change}
 \title{Look at genotypes that were imputed or changed by the HMM chain given a level of global genotypic error}
 \usage{
-plot_progeny_dosage_change(map_list, error, verbose = T)
+plot_progeny_dosage_change(map_list, error, verbose = T, output_corrected = F)
 }
 \arguments{
 \item{map_list}{a list of multiple \code{mappoly.map.list}}
@@ -12,6 +12,8 @@ plot_progeny_dosage_change(map_list, error, verbose = T)
 \item{error}{error rate used in global error in the `calc_genoprob_error()`}
 
 \item{verbose}{T or F for `calc_genoprob_error()` and `calc_homologprob()`}
+
+\item{output_corrected}{TRUE or FALSE, if F only the ggplot of the changed dosage is printed, if T then a new corrected dosage matrix is output.}
 }
 \value{
 A ggplot of the changed and imputed genotypic dosages
@@ -25,8 +27,9 @@ Most recent update 8/29/2023:
    -un-hardcoded linkage groups in maps. previously hard-coded for tetraploid rose.
 }
 \examples{
-    x<-get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE)
-    plot_progeny_dosage_change(list(x), error=0.05)     
+      x <- get_submap(solcap.err.map[[1]], 1:30, reestimate.rf = FALSE)   # subset to run fast in tests
+      plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F)   # no new corrected dosages  
+      corrected_matrix <- plot_progeny_dosage_change(list(x), error=0.05, output_corrected=F) #output corrected
 
 }
 \author{
diff --git a/man/split_and_rephase.Rd b/man/split_and_rephase.Rd
index d45e6731..e97fd16a 100644
--- a/man/split_and_rephase.Rd
+++ b/man/split_and_rephase.Rd
@@ -10,6 +10,9 @@ split_and_rephase(
   gap.threshold = 5,
   size.rem.cluster = 1,
   phase.config = "best",
+  thres.twopt = 3,
+  thres.hmm = "best",
+  tol.merge = 0.001,
   tol.final = 0.001,
   verbose = TRUE
 )
@@ -32,6 +35,18 @@ value is 1}
 \item{phase.config}{which phase configuration should be used. "best" (default) 
 will choose the maximum likelihood phase configuration}
 
+\item{thres.twopt}{the threshold used to determine if the linkage
+phases compared via two-point analysis should be considered 
+for the search space reduction (default = 3)}
+
+\item{thres.hmm}{the threshold used to determine which linkage 
+phase configurations should be returned when merging two maps.
+If "best" (default), returns only the best linkage phase 
+configuration. NOTE: if merging multiple maps, it always uses 
+the "best" linkage phase configuration at each block insertion.}
+
+\item{tol.merge}{the desired accuracy for merging maps (default = 10e-04)}
+
 \item{tol.final}{the desired accuracy for the final map (default = 10e-04)}
 
 \item{verbose}{if \code{TRUE} (default), the current progress is shown; if
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index 7e21fe7e..bf307dcc 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -59,22 +59,22 @@ BEGIN_RCPP
 END_RCPP
 }
 
-RcppExport SEXP calc_genoprob(void *, void *, void *, void *, void *, void *, void *);
-RcppExport SEXP calc_genoprob_prior(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
-RcppExport SEXP calc_genprob_haplo(void *, void *, void *, void *, void *, void *, void *, void *);
-RcppExport SEXP calc_genprob_haplo_highprec(void *, void *, void *, void *, void *, void *, void *, void *);
-RcppExport SEXP calc_genprob_single_parent(void *, void *, void *, void *, void *, void *, void *, void *);
-RcppExport SEXP est_haplotype_map(void *, void *, void *, void *, void *, void *, void *, void *, void *);
-RcppExport SEXP est_haplotype_map_highprec(void *, void *, void *, void *, void *, void *, void *, void *, void *);
-RcppExport SEXP est_hmm_map_single_parent(void *, void *, void *, void *, void *, void *, void *, void *, void *);
-RcppExport SEXP est_map_hmm(void *, void *, void *, void *, void *, void *, void *, void *);
-RcppExport SEXP est_map_hmm_highprec(void *, void *, void *, void *, void *, void *, void *, void *);
-RcppExport SEXP get_counts_single_parent_cpp(void *, void *, void *, void *, void *, void *);
-RcppExport SEXP loglike_hmm(void *, void *, void *, void *, void *, void *);
-RcppExport SEXP pairwise_rf_estimation_disc(void *, void *, void *, void *, void *, void *, void *);
-RcppExport SEXP pairwise_rf_estimation_disc_rcpp(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
-RcppExport SEXP pairwise_rf_estimation_prob(void *, void *, void *, void *, void *, void *, void *, void *);
-RcppExport SEXP poly_hmm_est_CPP(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
+RcppExport SEXP calc_genoprob(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP calc_genoprob_prior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP calc_genprob_haplo(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP calc_genprob_haplo_highprec(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP calc_genprob_single_parent(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP est_haplotype_map(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP est_haplotype_map_highprec(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP est_hmm_map_single_parent(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP est_map_hmm(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP est_map_hmm_highprec(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP get_counts_single_parent_cpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP loglike_hmm(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP pairwise_rf_estimation_disc(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP pairwise_rf_estimation_disc_rcpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP pairwise_rf_estimation_prob(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+RcppExport SEXP poly_hmm_est_CPP(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
 
 static const R_CallMethodDef CallEntries[] = {
     {"_mappoly_vcf_get_probabilities", (DL_FUNC) &_mappoly_vcf_get_probabilities, 2},