diff --git a/NAMESPACE b/NAMESPACE
index 22290a3..4fab61f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,18 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
 export(benders)
-export(clean_output_benders)
 export(delete_antares_output)
-export(enable_hurdle_costs)
-export(filter_output_areas)
-export(filter_output_links)
 export(get_whole_simulation_name)
 export(read_candidates)
 export(read_options)
 export(report)
 export(run_simulation)
-export(set_simulation_period)
-export(update_link)
 import(data.table)
 importFrom(antaresEditObject,getPlaylist)
 importFrom(antaresEditObject,setPlaylist)
diff --git a/R/benders_tools.R b/R/benders_tools.R
index ccac71b..2cc3911 100644
--- a/R/benders_tools.R
+++ b/R/benders_tools.R
@@ -16,6 +16,7 @@
 #' @importFrom assertthat assert_that
 #' @importFrom antaresRead simOptions getLinks getAreas
 #' @importFrom antaresEditObject updateGeneralSettings updateOptimizationSettings
+#' @noRd
 #' 
 set_antares_options <- function(benders_options, candidates, opts = antaresRead::simOptions())
 {
diff --git a/R/check.R b/R/check.R
index 73d8a29..b252fc9 100644
--- a/R/check.R
+++ b/R/check.R
@@ -13,7 +13,7 @@
 #' 
 #' @importFrom  antaresRead simOptions readClusterDesc
 #' @importFrom dplyr filter
-#' 
+#' @noRd
 #' 
 benders_check <- function(candidates, opts = antaresRead::simOptions())
 {
diff --git a/R/clean.R b/R/clean.R
index d5630af..b4a9bc6 100644
--- a/R/clean.R
+++ b/R/clean.R
@@ -44,7 +44,7 @@ delete_antares_output <- function(simulation_name, opts = antaresRead::simOption
 #' 
 #' @importFrom antaresRead simOptions 
 #' @importFrom assertthat assert_that
-#' @export
+#' @noRd
 #' 
 clean_output_benders <- function(best_solution, unique_key, opts = antaresRead::simOptions())
 {
diff --git a/R/link.r b/R/link.r
index cc5ca61..deb3610 100644
--- a/R/link.r
+++ b/R/link.r
@@ -6,7 +6,7 @@
 #'   Name of one link
 #' @return 
 #' name of the first area that the link connects
-#' 
+#' @noRd
 #' 
 from <- function(link_name)
 {
@@ -21,7 +21,7 @@ from <- function(link_name)
 #'   Name of one link
 #' @return 
 #' name of the second area that the link connects
-#' 
+#' @noRd
 #' 
 to <- function(link_name)
 {
@@ -48,7 +48,7 @@ to <- function(link_name)
 #' 
 #' @importFrom assertthat assert_that
 #' @importFrom antaresRead simOptions
-#' @export
+#' @noRd
 #' 
 #' 
 
@@ -137,7 +137,7 @@ enable_hurdle_costs <- function(link_names, enable = TRUE, opts = antaresRead::s
 #' @importFrom assertthat assert_that
 #' @importFrom antaresRead simOptions
 #' @importFrom utils write.table
-#' @export
+#' @noRd
 #' 
 #' 
 update_link <- function(link_name, property_name, new_value, opts = antaresRead::simOptions())
diff --git a/R/master.R b/R/master.R
index a34bc81..88c5887 100644
--- a/R/master.R
+++ b/R/master.R
@@ -20,6 +20,7 @@
 #' @importFrom antaresRead simOptions
 #' @importFrom assertthat assert_that
 #' @importFrom antaresEditObject getPlaylist
+#' @noRd
 #' 
 initiate_master <- function(candidates, exp_options , opts = antaresRead::simOptions())
 {
@@ -126,6 +127,7 @@ initiate_master <- function(candidates, exp_options , opts = antaresRead::simOpt
 #' 
 #' @importFrom antaresRead simOptions
 #' @importFrom assertthat assert_that
+#' @noRd
 #' 
 solve_master <- function(opts = antaresRead::simOptions(), relax_integrality = FALSE, ampl_path = NULL)
 {
diff --git a/R/patch_numeric_accuracy.R b/R/patch_numeric_accuracy.R
deleted file mode 100644
index e08c0b3..0000000
--- a/R/patch_numeric_accuracy.R
+++ /dev/null
@@ -1,32 +0,0 @@
-#' This function update the bender cuts so as to deal with the numeric
-#' inaccuracy of the ANTARES output
-#' Not used since v0.3
-#' 
-#' Marginal costs are returned in ANTARES with a 10^0 accuracy (without any decimal).
-#' This can cause numeric imprecisions in the cut of the benders decomposition and
-#' make it converge to a non-optimal solution.
-#' 
-#' This function (tries to) corrects this by updating the constant term of the cuts
-#' 
-#' @param x_current
-#'   vector of current invested capacities
-#' @param x_max
-#'   vector of maximum possible investments
-#' @return 
-#' Return correct term to substract to the b of \code{ax+b}
-#' 
-#' 
-#' 
-numeric_patch_cut <- function(x_current, x_max)
-{
-  # a few checks
-  assert_that(length(x_current) == length(x_max))
-  
-  # compute max distance between current point (x_current) and boundary of the investment space
-  each_max <- function(i,vec1, vec2){max(vec2[i] - vec1[i], vec1[i])}
-  d_max <- norm(sapply(1:length(x_current), FUN = each_max, vec1 = x_current, vec2 = x_max), type = "2")
-  
-  # as error can be up to +/- 0.5 
-  return (d_max * 0.5 + 1)
-}
-
diff --git a/R/read_candidates.R b/R/read_candidates.R
index 462a098..bcf90d4 100644
--- a/R/read_candidates.R
+++ b/R/read_candidates.R
@@ -196,7 +196,7 @@ read_candidates <- function(file, opts = antaresRead::simOptions())
 #'
 #' @return 
 #' Returns a vector of link name
-#' 
+#' @noRd
 #' 
 with_profile <- function(candidates)
 {
@@ -218,7 +218,7 @@ with_profile <- function(candidates)
 #'
 #' @return 
 #' Returns a vector of link name
-#' 
+#' @noRd
 #' 
 without_profile <- function(candidates)
 {
diff --git a/R/report.R b/R/report.R
index 93cc0d0..6dfc3d6 100644
--- a/R/report.R
+++ b/R/report.R
@@ -53,6 +53,7 @@ report <- function(benders_out = "last", file = default_report_file(opts), opts
 #' 
 #' @importFrom antaresRead simOptions
 #' @importFrom lubridate now
+#' @noRd
 #'                                       
 default_report_file <- function(opts = antaresRead::simOptions())
 {
diff --git a/R/simulation_settings.R b/R/simulation_settings.R
index 29f9700..272c507 100644
--- a/R/simulation_settings.R
+++ b/R/simulation_settings.R
@@ -22,7 +22,7 @@
 #' 
 #' @importFrom assertthat assert_that
 #' @importFrom antaresRead simOptions
-#' @export
+#' @noRd
 #' 
 #' 
 filter_output_areas <- function(areas, filter, type, opts = antaresRead::simOptions())
@@ -91,7 +91,7 @@ filter_output_areas <- function(areas, filter, type, opts = antaresRead::simOpti
 #' 
 #' @importFrom assertthat assert_that
 #' @importFrom antaresRead simOptions
-#' @export
+#' @noRd
 #' 
 #' 
 filter_output_links <- function(links, filter, type, opts = antaresRead::simOptions())
@@ -158,7 +158,7 @@ filter_output_links <- function(links, filter, type, opts = antaresRead::simOpti
 #' @importFrom antaresRead simOptions
 #' @importFrom data.table first last
 #' @importFrom antaresEditObject updateGeneralSettings
-#' @export
+#' @noRd
 #' 
 set_simulation_period <- function(weeks, opts = antaresRead::simOptions())
 {
diff --git a/man/benders_check.Rd b/man/benders_check.Rd
deleted file mode 100644
index 521836d..0000000
--- a/man/benders_check.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/check.R
-\name{benders_check}
-\alias{benders_check}
-\title{Check that the ANTARES study is ready for benders decomposition}
-\usage{
-benders_check(candidates, opts = antaresRead::simOptions())
-}
-\arguments{
-\item{candidates}{list of investment candidates, as returned by
-\code{\link{read_candidates}}}
-
-\item{opts}{list of simulation parameters returned by the function
-\code{antaresRead::setSimulationPath}}
-}
-\value{
-boolean, indicating whether or not the test are fullfilled
-}
-\description{
-Check that the ANTARES study is ready for benders decomposition
-}
diff --git a/man/clean_output_benders.Rd b/man/clean_output_benders.Rd
deleted file mode 100644
index c54439a..0000000
--- a/man/clean_output_benders.Rd
+++ /dev/null
@@ -1,24 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/clean.R
-\name{clean_output_benders}
-\alias{clean_output_benders}
-\title{Delete the output of the benders iterations which are not usefull anymore}
-\usage{
-clean_output_benders(best_solution, unique_key,
-  opts = antaresRead::simOptions())
-}
-\arguments{
-\item{best_solution}{identifier of the best solution so far 
-(the output related to this iteration will not be removed)}
-
-\item{unique_key}{unique string to identify the output of the current expansion problem}
-
-\item{opts}{list of simulation parameters returned by the function
-\code{antaresRead::setSimulationPath}}
-}
-\value{
-
-}
-\description{
-Delete the output of the benders iterations which are not usefull anymore
-}
diff --git a/man/default_report_file.Rd b/man/default_report_file.Rd
deleted file mode 100644
index 830b75f..0000000
--- a/man/default_report_file.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/report.R
-\name{default_report_file}
-\alias{default_report_file}
-\title{Return the default file name for the report}
-\usage{
-default_report_file(opts = antaresRead::simOptions())
-}
-\arguments{
-\item{opts}{list of simulation parameters returned by the function
-\code{antaresRead::setSimulationPath}}
-}
-\value{
-name of the first area that the link connects
-}
-\description{
-Return the default file name for the report
-}
diff --git a/man/enable_hurdle_costs.Rd b/man/enable_hurdle_costs.Rd
deleted file mode 100644
index cabdf66..0000000
--- a/man/enable_hurdle_costs.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/link.r
-\name{enable_hurdle_costs}
-\alias{enable_hurdle_costs}
-\title{Enable or disable the hurdle cost of a link or a list of links}
-\usage{
-enable_hurdle_costs(link_names, enable = TRUE,
-  opts = antaresRead::simOptions())
-}
-\arguments{
-\item{link_names}{Name of one link, or vector with several link names}
-
-\item{enable}{Should the hurdle costs be enabled (\code{TRUE}) or disabled (\code{FALSE}) ?}
-
-\item{opts}{list of simulation parameters returned by the function
-\code{antaresRead::setSimulationPath}}
-}
-\value{
-The function does not return anything. It is  used to modify the input of an 
-ANTARES study
-}
-\description{
-\code{enable_hurdle_costs} is a function which modifies the input file of an ANTARES
-study and enable (or disable) the hurdle costs of a link
-}
diff --git a/man/filter_output_areas.Rd b/man/filter_output_areas.Rd
deleted file mode 100644
index ff2ca26..0000000
--- a/man/filter_output_areas.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulation_settings.R
-\name{filter_output_areas}
-\alias{filter_output_areas}
-\title{Modify the filters on the output of the areas}
-\usage{
-filter_output_areas(areas, filter, type, opts = antaresRead::simOptions())
-}
-\arguments{
-\item{areas}{Area, or vector of areas whose filter will be changed.}
-
-\item{filter}{Vector of filters to adopt for the area. Can contain "annual", "monthly", "weekly", 
-"daily", "hourly" or a combination of them.}
-
-\item{type}{On which type of output the filters will applied ? The MC synthesis (\code{type = "synthesis"}) ? The 
-year by year outputs (\code{type = "year-by-year"}) ? Or both(\code{type = c("synthesis", "year-by-year")}) 
-?}
-
-\item{opts}{list of simulation parameters returned by the function
-\code{antaresRead::setSimulationPath}}
-}
-\value{
-The function does not return anything. It is  used to modify the input of an 
-ANTARES study
-}
-\description{
-\code{filter_output_areas} is a function which modifies the input file of an ANTARES
-study by updating the output filters of some areas
-}
diff --git a/man/filter_output_links.Rd b/man/filter_output_links.Rd
deleted file mode 100644
index 3d8ee52..0000000
--- a/man/filter_output_links.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulation_settings.R
-\name{filter_output_links}
-\alias{filter_output_links}
-\title{Modify the filters on the output of the links}
-\usage{
-filter_output_links(links, filter, type, opts = antaresRead::simOptions())
-}
-\arguments{
-\item{links}{Link, or vector of links whose filter will be changed.}
-
-\item{filter}{Vector of filters to adopt for the area. Can contain "annual", "monthly", "weekly", 
-"daily", "hourly" or a combination of them.}
-
-\item{type}{On which type of output the filters will applied ? The MC synthesis (\code{type = "synthesis"}) ? The 
-year by year outputs (\code{type = "year-by-year"}) ? Or both(\code{type = c("synthesis", "year-by-year")}) 
-?}
-
-\item{opts}{list of simulation parameters returned by the function
-\code{antaresRead::setSimulationPath}}
-}
-\value{
-The function does not return anything. It is  used to modify the input of an 
-ANTARES study
-}
-\description{
-\code{filter_output_links} is a function which modifies the input file of an ANTARES
-study by updating the output filters of some links
-}
diff --git a/man/from.Rd b/man/from.Rd
deleted file mode 100644
index 4a54493..0000000
--- a/man/from.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/link.r
-\name{from}
-\alias{from}
-\title{Return the first area that a link connects}
-\usage{
-from(link_name)
-}
-\arguments{
-\item{link_name}{Name of one link}
-}
-\value{
-name of the first area that the link connects
-}
-\description{
-Return the first area that a link connects
-}
diff --git a/man/initiate_master.Rd b/man/initiate_master.Rd
deleted file mode 100644
index 9676ba9..0000000
--- a/man/initiate_master.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/master.R
-\name{initiate_master}
-\alias{initiate_master}
-\title{Initiate master problem}
-\usage{
-initiate_master(candidates, exp_options, opts = antaresRead::simOptions())
-}
-\arguments{
-\item{candidates}{list of investment candidates, as returned by
-\code{\link{read_candidates}}}
-
-\item{exp_options}{list of options related to the expansion planning, as returned
-by the function \code{\link{read_options}}}
-
-\item{opts}{list of simulation parameters returned by the function
-\code{antaresRead::setSimulationPath}}
-}
-\value{
-This function does not return anything.
-}
-\description{
-\code{initiate_master} copy the AMPL files into the temporary 
-folder of the expansion planning optimisation and create the other input
-and output file of the master problem
-}
diff --git a/man/numeric_patch_cut.Rd b/man/numeric_patch_cut.Rd
deleted file mode 100644
index 24ecb5a..0000000
--- a/man/numeric_patch_cut.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/patch_numeric_accuracy.R
-\name{numeric_patch_cut}
-\alias{numeric_patch_cut}
-\title{This function update the bender cuts so as to deal with the numeric
-inaccuracy of the ANTARES output
-Not used since v0.3}
-\usage{
-numeric_patch_cut(x_current, x_max)
-}
-\arguments{
-\item{x_current}{vector of current invested capacities}
-
-\item{x_max}{vector of maximum possible investments}
-}
-\value{
-Return correct term to substract to the b of \code{ax+b}
-}
-\description{
-Marginal costs are returned in ANTARES with a 10^0 accuracy (without any decimal).
-This can cause numeric imprecisions in the cut of the benders decomposition and
-make it converge to a non-optimal solution.
-}
-\details{
-This function (tries to) corrects this by updating the constant term of the cuts
-}
diff --git a/man/set_antares_options.Rd b/man/set_antares_options.Rd
deleted file mode 100644
index b9d13f9..0000000
--- a/man/set_antares_options.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/benders_tools.R
-\name{set_antares_options}
-\alias{set_antares_options}
-\title{Set ANTARES study options related to the current benders decomposition}
-\usage{
-set_antares_options(benders_options, candidates,
-  opts = antaresRead::simOptions())
-}
-\arguments{
-\item{benders_options}{list of benders decomposition options, as returned by
-\code{\link{read_options}}.}
-
-\item{candidates}{list of investment candidates, as returned by
-\code{\link{read_candidates}}}
-
-\item{opts}{list of simulation parameters returned by the function
-\code{antaresRead::setSimulationPath}}
-}
-\value{
-nothing
-}
-\description{
-Set ANTARES study options related to the current benders decomposition
-}
diff --git a/man/set_simulation_period.Rd b/man/set_simulation_period.Rd
deleted file mode 100644
index 6b6344d..0000000
--- a/man/set_simulation_period.Rd
+++ /dev/null
@@ -1,22 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simulation_settings.R
-\name{set_simulation_period}
-\alias{set_simulation_period}
-\title{Set period on which we want the ANTARES simulation to run.
-Update "first day" and "last day" parameters of the ANTARES study.}
-\usage{
-set_simulation_period(weeks, opts = antaresRead::simOptions())
-}
-\arguments{
-\item{weeks}{vector of weeks identiers which should be simulated}
-
-\item{opts}{list of simulation parameters returned by the function
-\code{antaresRead::setSimulationPath}}
-}
-\value{
-
-}
-\description{
-Set period on which we want the ANTARES simulation to run.
-Update "first day" and "last day" parameters of the ANTARES study.
-}
diff --git a/man/solve_master.Rd b/man/solve_master.Rd
deleted file mode 100644
index 14fd5ca..0000000
--- a/man/solve_master.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/master.R
-\name{solve_master}
-\alias{solve_master}
-\title{Solver master problem}
-\usage{
-solve_master(opts = antaresRead::simOptions(), relax_integrality = FALSE,
-  ampl_path = NULL)
-}
-\arguments{
-\item{opts}{list of simulation parameters returned by the function
-\code{antaresRead::setSimulationPath}}
-
-\item{relax_integrality}{logical, indicating whether (TRUE) or not (FALSE) the integer variables
-should be relaxed}
-
-\item{ampl_path}{Character containing the path to the ampl.exe file}
-}
-\value{
-This function does not return anything.
-}
-\description{
-\code{solver_master} execute the AMPL file master_run.ampl
-located in the temporary folder of the current expansion 
-planning optimisation
-}
diff --git a/man/to.Rd b/man/to.Rd
deleted file mode 100644
index aa5041d..0000000
--- a/man/to.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/link.r
-\name{to}
-\alias{to}
-\title{Return the second area that a link connects}
-\usage{
-to(link_name)
-}
-\arguments{
-\item{link_name}{Name of one link}
-}
-\value{
-name of the second area that the link connects
-}
-\description{
-Return the second area that a link connects
-}
diff --git a/man/update_link.Rd b/man/update_link.Rd
deleted file mode 100644
index c4b0987..0000000
--- a/man/update_link.Rd
+++ /dev/null
@@ -1,28 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/link.r
-\name{update_link}
-\alias{update_link}
-\title{Update the properties of a link (capacity, impedance or hurdle costs)}
-\usage{
-update_link(link_name, property_name, new_value,
-  opts = antaresRead::simOptions())
-}
-\arguments{
-\item{link_name}{Name of one link}
-
-\item{property_name}{Name of the propery to change, must be equal to "direct_capacity" or "indirect_capacity" or
-"impedance" or "direct_hurdle_cost" or "indirect_hurdle_cost"}
-
-\item{new_value}{New value of the property}
-
-\item{opts}{list of simulation parameters returned by the function
-\code{antaresRead::setSimulationPath}}
-}
-\value{
-The function does not return anything. It is  used to modify the input of an 
-ANTARES study
-}
-\description{
-\code{update_link} is a function which modifies the input file of an ANTARES
-study and update the properties of a link
-}
diff --git a/man/with_profile.Rd b/man/with_profile.Rd
deleted file mode 100644
index ebe362e..0000000
--- a/man/with_profile.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_candidates.R
-\name{with_profile}
-\alias{with_profile}
-\title{Return vector of candidate names which have a link profile}
-\usage{
-with_profile(candidates)
-}
-\arguments{
-\item{candidates}{list of investment candidates, as returned by
-\code{\link{read_candidates}}}
-}
-\value{
-Returns a vector of link name
-}
-\description{
-Return vector of candidate names which have a link profile
-}
diff --git a/man/without_profile.Rd b/man/without_profile.Rd
deleted file mode 100644
index aa8b7a8..0000000
--- a/man/without_profile.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_candidates.R
-\name{without_profile}
-\alias{without_profile}
-\title{Return vector of candidate names which do not have a link profile}
-\usage{
-without_profile(candidates)
-}
-\arguments{
-\item{candidates}{list of investment candidates, as returned by
-\code{\link{read_candidates}}}
-}
-\value{
-Returns a vector of link name
-}
-\description{
-Return vector of candidate names which do not have a link profile
-}