diff --git a/R/pairwise_rf.R b/R/pairwise_rf.R
index e65b0a8e..37a6a7e2 100755
--- a/R/pairwise_rf.R
+++ b/R/pairwise_rf.R
@@ -467,7 +467,7 @@ est_pairwise_rf2 <- function(input.seq,
                                          count.matrix.number = count.matrix.number,
                                          count.matrix.pos = count.matrix.pos,
                                          count.matrix.length = count.matrix.length,
-                                         tol = tol, threads = ncpus)
+                                         tol = tol)
   res[res == -1] = NA
   colnames(res) = c("Sh_P1","Sh_P2","rf","LOD_rf","LOD_ph")
   if (verbose) {
@@ -508,8 +508,7 @@ paralell_pairwise_discrete_rcpp <- function(mrk.pairs,
                                             count.matrix.number,
                                             count.matrix.pos,
                                             count.matrix.length,
-                                            tol = .Machine$double.eps^0.25,
-                                            threads)
+                                            tol = .Machine$double.eps^0.25)
 {
   res <- .Call("pairwise_rf_estimation_disc_rcpp",
                as.matrix(mrk.pairs),
@@ -524,7 +523,6 @@ paralell_pairwise_discrete_rcpp <- function(mrk.pairs,
                count.matrix.pos,
                count.matrix.length,
                tol = tol,
-               threads = threads,
                PACKAGE = "mappoly")
   return(res)
   ## return(lapply(res, format_rf))
diff --git a/man/add_md_markers.Rd b/man/add_md_markers.Rd
index cf7bba54..302fd827 100644
--- a/man/add_md_markers.Rd
+++ b/man/add_md_markers.Rd
@@ -15,7 +15,7 @@ add_md_markers(
   thresh = 500,
   extend.tail = 50,
   method = c("hmm", "wMDS_to_1D_pc"),
-  verbose = T
+  verbose = TRUE
 )
 }
 \arguments{
diff --git a/man/paralell_pairwise_discrete_rcpp.Rd b/man/paralell_pairwise_discrete_rcpp.Rd
index bfe703b4..48c894f1 100644
--- a/man/paralell_pairwise_discrete_rcpp.Rd
+++ b/man/paralell_pairwise_discrete_rcpp.Rd
@@ -16,8 +16,7 @@ paralell_pairwise_discrete_rcpp(
   count.matrix.number,
   count.matrix.pos,
   count.matrix.length,
-  tol = .Machine$double.eps^0.25,
-  threads
+  tol = .Machine$double.eps^0.25
 )
 }
 \arguments{
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index 7e21fe7e..f10427fb 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -72,7 +72,7 @@ RcppExport SEXP est_map_hmm_highprec(void *, void *, void *, void *, void *, voi
 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_disc_rcpp(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 *);
 
@@ -94,7 +94,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"get_counts_single_parent_cpp",     (DL_FUNC) &get_counts_single_parent_cpp,      6},
     {"loglike_hmm",                      (DL_FUNC) &loglike_hmm,                       6},
     {"pairwise_rf_estimation_disc",      (DL_FUNC) &pairwise_rf_estimation_disc,       7},
-    {"pairwise_rf_estimation_disc_rcpp", (DL_FUNC) &pairwise_rf_estimation_disc_rcpp, 13},
+    {"pairwise_rf_estimation_disc_rcpp", (DL_FUNC) &pairwise_rf_estimation_disc_rcpp, 12},
     {"pairwise_rf_estimation_prob",      (DL_FUNC) &pairwise_rf_estimation_prob,       8},
     {"poly_hmm_est_CPP",                 (DL_FUNC) &poly_hmm_est_CPP,                 13},
     {NULL, NULL, 0}
diff --git a/src/pairwise_estimation_rcppparallel.cpp b/src/pairwise_estimation_rcppparallel.cpp
index c586bd49..1ec3dcc8 100755
--- a/src/pairwise_estimation_rcppparallel.cpp
+++ b/src/pairwise_estimation_rcppparallel.cpp
@@ -416,8 +416,7 @@ RcppExport SEXP pairwise_rf_estimation_disc_rcpp(SEXP mrk_pairs_R,
                                                  SEXP count_matrix_number_R,
                                                  SEXP count_matrix_pos_R,
                                                  SEXP count_matrix_length_R,
-                                                 SEXP tol_R,
-                                                 SEXP threads_R)
+                                                 SEXP tol_R)
 {
   NumericMatrix mrk_pairs = mrk_pairs_R;
   NumericMatrix geno = geno_R;
@@ -432,7 +431,6 @@ RcppExport SEXP pairwise_rf_estimation_disc_rcpp(SEXP mrk_pairs_R,
   NumericMatrix out(mrk_pairs.ncol(), 5);
   int m = as<int>(m_R);
   double tol = as<double>(tol_R);
-  int threads = as<int>(threads_R);
   int n_ind = geno.ncol();
 
   rf_two_point_parallel RF_two_point_parallel(mrk_pairs, geno, dP, dQ, count_vector,