diff --git a/R/accepted_input.R b/R/accepted_input.R
deleted file mode 100644
index 9e119bac922554365c62c354ae89757ac020cbb8..0000000000000000000000000000000000000000
--- a/R/accepted_input.R
+++ /dev/null
@@ -1,8 +0,0 @@
-#This is a helper script providing an overview of some accepted input parameters.
-
-#============================== .vtu ================================
-vtu_appended_data_valid_encoding_types <- list("binary", "base64")
-
-
-#============================== .prj ================================
-prj_medium_phase_types <- c("Gas", "Solid", "AqueousLiquid", "NonAqueousLiquid")
\ No newline at end of file
diff --git a/R/generate_functions.R b/R/generate_functions.R
deleted file mode 100644
index 09559677c74250b96f6ecf4c06ce7268d357f076..0000000000000000000000000000000000000000
--- a/R/generate_functions.R
+++ /dev/null
@@ -1,132 +0,0 @@
-#This is a script containing experimental functions which generate other
-# functions.
-#These will not be exported, but in the best case developers can use them to
-# make their workflow more efficient.
-
-generate_class_from_element <- function(element, export = TRUE) {
-
- children <- xml2::xml_children(element)
- attrs <- xml2::xml_attrs(element)
- element_name <- xml2::xml_name(element)
-
- #Generate name of new class from element name if class_name is not specified
- if(is.null(class_name)){
- class_name <- snakecase::to_any_case(element_name, "snake")
- }
-
-
- #Start of description
- class_str <- paste0("#'r2ogs6_", element_name, "\n",
- "#'@description r2ogs6 class representing a ",
- element_name, " element \n")
-
- #Add parameter documentation tag(s)
- parameters <- list()
-
- for(i in seq_len(length(children))){
- parameters <- c(parameters, xml2::xml_name(children[[i]]))
-
- class_str <- paste0(class_str, "#'@param ",
- xml2::xml_name(children[[i]]),
- " (Auto generated)\n")
- }
-
- #Add export documentation tag if class should be exported
- if(export){
- class_str <- paste0(class_str, "#'@export\n")
- }
-
- #Start of declaration
- class_str <- paste0(class_str, "r2ogs6_", element_name, " <- function(\n")
-
- #ADD PARAMETERS HERE
-
- class_str <- paste0(class_str, ") {\n")
-
- #ADD FUNCTION CONTENTS
-
- class_str <- paste0(class_str, "}\n")
-
-
- generated_class <- structure(list(), class = element_name)
-
- return(generated_class)
-}
-
-
-#============================== READ_IN FUNCTION GENERATOR =====================
-
-#'generate_simple_read_in
-#'@description Assuming function read_in gets good enough results, this could
-#' save code later.
-#'@param element_name The name of the .prj element to be read from
-#' (wrapper element, e.g. 'processes')
-#'@param child_name The name of the element children (e.g. 'process')
-#'@param has_name_tag Do the child elements have a child element with the
-#' name 'name'?
-#'@param subclasses_names Optional: A character vector containing the names
-#' of r2ogs6_*
-#' subclasses (r2ogs6_* classes without a method for input_add)
-generate_simple_read_in <- function(element_name,
- child_name,
- has_name_tag = TRUE,
- subclasses_names = NULL) {
-
- assertthat::assert_that(assertthat::is.string(element_name))
- assertthat::assert_that(assertthat::is.string(child_name))
- assertthat::assert_that(assertthat::is.flag(has_name_tag))
-
- if(!is.null(subclasses_names)){
- assertthat::assert_that(is.character(subclasses_names))
- }
-
- func_str <- paste0("#'read_in_", element_name, "\n",
- "#'@description Reads in ", child_name,
- " elements from a .prj file\n",
- "#'@param ogs6_obj A OGS6 class object\n",
- "#'@param prj_path The path to the project file the ",
- child_name, " elements should be read from\n")
-
- if(has_name_tag){
- func_str <- paste0(func_str, "#'@param ", child_name,
- "_names Optional: The names of the ",
- child_name, " elements to be read in\n")
- }else{
- func_str <- paste0(func_str, "#'@param ", child_name,
- "_indices Optional: The indices of the ",
- child_name, " elements to be read in\n")
- }
-
- func_str <- paste0(func_str, "#'@export\n",
- "read_in_", element_name,
- " <- function(ogs6_obj, prj_path, ")
-
- if(has_name_tag){
- func_str <- paste0(func_str, child_name, "_names = NULL) {\n")
- }else{
- func_str <- paste0(func_str, child_name, "_indices = NULL) {\n")
- }
-
- func_str <- paste0(func_str, "read_in(ogs6_obj, prj_path, \"", element_name,
- "\", \"", child_name, "\", selection_vector = ")
-
- if(has_name_tag){
- func_str <- paste0(func_str, child_name, "_names")
- }else{
- func_str <- paste0(func_str, child_name, "_indices")
- }
-
- if(!is.null(subclasses_names)){
- subclasses_str <- utils::capture.output(
- invisible(dput(subclasses_names)))
- subclasses_str <- paste(subclasses_str, collapse = "")
- func_str <- paste0(func_str, ", subclasses_names = ", subclasses_str)
- }
-
- func_str <- paste0(func_str,
- ")\n",
- "}\n")
-
- cat(func_str)
- return(invisible(func_str))
-}
\ No newline at end of file
diff --git a/R/utils-pipe.R b/R/utils-pipe.R
deleted file mode 100644
index e79f3d80856576d6db32c9fb05cdbc02b28f4ff8..0000000000000000000000000000000000000000
--- a/R/utils-pipe.R
+++ /dev/null
@@ -1,11 +0,0 @@
-#' Pipe operator
-#'
-#' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details.
-#'
-#' @name %>%
-#' @rdname pipe
-#' @keywords internal
-#' @export
-#' @importFrom magrittr %>%
-#' @usage lhs \%>\% rhs
-NULL
diff --git a/man/generate_simple_read_in.Rd b/man/generate_simple_read_in.Rd
deleted file mode 100644
index 13283e7d56ab210f93c1fe986b0054e1215e9c3b..0000000000000000000000000000000000000000
--- a/man/generate_simple_read_in.Rd
+++ /dev/null
@@ -1,26 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/generate_functions.R
-\name{generate_simple_read_in}
-\alias{generate_simple_read_in}
-\title{generate_simple_read_in}
-\usage{
-generate_simple_read_in(
- element_name,
- child_name,
- has_name_tag = TRUE,
- subclasses_names = NULL
-)
-}
-\arguments{
-\item{element_name}{The name of the .prj element to be read from (wrapper element, e.g. 'processes')}
-
-\item{child_name}{The name of the element children (e.g. 'process')}
-
-\item{has_name_tag}{Do the child elements have a child element with the name 'name'?}
-
-\item{subclasses_names}{Optional: A character vector containing the names of r2ogs6_*
-subclasses (r2ogs6_* classes without a method for input_add)}
-}
-\description{
-Assuming function read_in gets good enough results, this could save code later.
-}
diff --git a/man/get_value_types.Rd b/man/get_value_types.Rd
deleted file mode 100644
index 7ffe582287db4564926fdd02a77fb88a0f83d908..0000000000000000000000000000000000000000
--- a/man/get_value_types.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_value_types}
-\alias{get_value_types}
-\title{get_value_types}
-\usage{
-get_value_types(xml_node)
-}
-\arguments{
-\item{xml_node}{An XML node (of class xml2::xml_node)}
-}
-\description{
-Gets the type of an XML value based on the documentation
-(per default, XML values are read in as a string, but for many elements,
-we want to coerce them to double)
-}
diff --git a/man/new_r2ogs6_curve.Rd b/man/new_r2ogs6_curve.Rd
deleted file mode 100644
index cec545b7c3048c2bda18a2dd138479c13edab9b5..0000000000000000000000000000000000000000
--- a/man/new_r2ogs6_curve.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/prj_curve.R
-\name{new_r2ogs6_curve}
-\alias{new_r2ogs6_curve}
-\title{new_r2ogs6_curve}
-\usage{
-new_r2ogs6_curve(name, coords, values)
-}
-\arguments{
-\item{name}{The name of the curve}
-
-\item{coords}{Coordinates at which the curve's values are given}
-
-\item{values}{Values of the curve at the given coordinates}
-}
-\description{
-Constructor for S3 class r2ogs6_curve
-}
diff --git a/man/r2ogs6_medium_phase.Rd b/man/r2ogs6_medium_phase.Rd
deleted file mode 100644
index f92afb7a2c1cb0ca952a74573181fdabae18e4af..0000000000000000000000000000000000000000
--- a/man/r2ogs6_medium_phase.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/prj_medium.R
-\name{r2ogs6_medium_phase}
-\alias{r2ogs6_medium_phase}
-\title{r2ogs6_medium_phase}
-\usage{
-r2ogs6_medium_phase(type, properties)
-}
-\arguments{
-\item{type}{A string specifying the medium type (one of "Gas", "Solid", "AqueousLiquid" and "NonAqueousLiquid")}
-
-\item{properties}{A list of properties (see ?r2ogs6_medium_property for more info)}
-}
-\description{
-S3 class describing a .prj medium phase (a coherent material with homogeneous properties)
-}
diff --git a/man/r2ogs6_medium_property.Rd b/man/r2ogs6_medium_property.Rd
deleted file mode 100644
index ef8583652190ee70fdbb8663d8e58021ed0c38c4..0000000000000000000000000000000000000000
--- a/man/r2ogs6_medium_property.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/prj_medium.R
-\name{r2ogs6_medium_property}
-\alias{r2ogs6_medium_property}
-\title{r2ogs6_medium_property}
-\usage{
-r2ogs6_medium_property(name, type, value = NULL, ...)
-}
-\arguments{
-\item{name}{A string specifying the property name}
-
-\item{type}{A string specifying the property type}
-
-\item{value}{A string ...}
-
-\item{...}{...}
-}
-\description{
-S3 class describing a .prj medium property (a constitutive property) (WIP!)
-}
diff --git a/man/r2ogs6_tl_output.Rd b/man/r2ogs6_tl_output.Rd
deleted file mode 100644
index dbd327dfcd3843dbf84b032bfc86195df10ae25a..0000000000000000000000000000000000000000
--- a/man/r2ogs6_tl_output.Rd
+++ /dev/null
@@ -1,31 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/prj_time_loop.R
-\name{r2ogs6_tl_output}
-\alias{r2ogs6_tl_output}
-\title{r2ogs6_tl_output}
-\usage{
-r2ogs6_tl_output(
- type,
- prefix,
- suffix,
- timesteps,
- variables,
- compress_output = NULL
-)
-}
-\arguments{
-\item{type}{...}
-
-\item{prefix}{...}
-
-\item{suffix}{...}
-
-\item{timesteps}{...}
-
-\item{variables}{...}
-
-\item{compress_output}{Optional: Should the output be compressed?}
-}
-\description{
-S3 class describing a .prj time_loop output
-}
diff --git a/man/read_in_curves.Rd b/man/read_in_curves.Rd
deleted file mode 100644
index 29c7e6cf81a72c95287b2ae6e1d3272f2318c659..0000000000000000000000000000000000000000
--- a/man/read_in_curves.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_prj.R
-\name{read_in_curves}
-\alias{read_in_curves}
-\title{read_in_curves}
-\usage{
-read_in_curves(ogs6_obj, prj_path, curve_names = NULL)
-}
-\arguments{
-\item{ogs6_obj}{A OGS6 class object}
-
-\item{prj_path}{The path to the project file the curve elements should be read from}
-
-\item{curve_names}{Optional: The names of the curve elements to be read in}
-}
-\description{
-Reads in curve elements from a .prj file
-}
diff --git a/man/read_in_linear_solvers.Rd b/man/read_in_linear_solvers.Rd
deleted file mode 100644
index 584247b7d755ded6f916afeac6c658113af4f903..0000000000000000000000000000000000000000
--- a/man/read_in_linear_solvers.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_prj.R
-\name{read_in_linear_solvers}
-\alias{read_in_linear_solvers}
-\title{read_in_linear_solvers}
-\usage{
-read_in_linear_solvers(ogs6_obj, prj_path, linear_solver_names = NULL)
-}
-\arguments{
-\item{ogs6_obj}{A OGS6 class object}
-
-\item{prj_path}{The path to the project file the linear_solver elements should be read from}
-
-\item{linear_solver_names}{Optional: The names of the linear_solver elements to be read in}
-}
-\description{
-Reads in linear_solver elements from a .prj file
-}
diff --git a/man/read_in_media.Rd b/man/read_in_media.Rd
deleted file mode 100644
index ee48fdc835e65465ad5864677fb1b16fa92b17d9..0000000000000000000000000000000000000000
--- a/man/read_in_media.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_prj.R
-\name{read_in_media}
-\alias{read_in_media}
-\title{read_in_media}
-\usage{
-read_in_media(ogs6_obj, prj_path, medium_indices = NULL)
-}
-\arguments{
-\item{ogs6_obj}{A OGS6 class object}
-
-\item{prj_path}{The path to the project file the medium elements should be read from}
-
-\item{medium_indices}{Optional: The indices of the medium elements to be read in}
-}
-\description{
-Reads in medium elements from a .prj file
-}
diff --git a/man/read_in_nonlinear_solvers.Rd b/man/read_in_nonlinear_solvers.Rd
deleted file mode 100644
index bbdfc1b8f107dbc98ee952967bd643efb6d36f96..0000000000000000000000000000000000000000
--- a/man/read_in_nonlinear_solvers.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_prj.R
-\name{read_in_nonlinear_solvers}
-\alias{read_in_nonlinear_solvers}
-\title{read_in_nonlinear_solvers}
-\usage{
-read_in_nonlinear_solvers(ogs6_obj, prj_path, nonlinear_solver_names = NULL)
-}
-\arguments{
-\item{ogs6_obj}{A OGS6 class object}
-
-\item{prj_path}{The path to the project file the nonlinear_solver elements should be read from}
-
-\item{nonlinear_solver_names}{Optional: The names of the nonlinear_solver elements to be read in}
-}
-\description{
-Reads in nonlinear_solver elements from a .prj file
-}
diff --git a/man/read_in_parameters.Rd b/man/read_in_parameters.Rd
deleted file mode 100644
index 8fd76faea7f239d3d90ea20d4894386d9973aa5e..0000000000000000000000000000000000000000
--- a/man/read_in_parameters.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_prj.R
-\name{read_in_parameters}
-\alias{read_in_parameters}
-\title{read_in_parameters}
-\usage{
-read_in_parameters(ogs6_obj, prj_path, parameter_names = NULL)
-}
-\arguments{
-\item{ogs6_obj}{A OGS6 class object}
-
-\item{prj_path}{The path to the project file the parameter elements should be read from}
-
-\item{parameter_names}{Optional: The names of the parameter elements to be read in}
-}
-\description{
-Reads in parameter elements from a .prj file
-}
diff --git a/man/read_in_process_variables.Rd b/man/read_in_process_variables.Rd
deleted file mode 100644
index 92c255e11af162858c4962c18b8dab8bcfabad34..0000000000000000000000000000000000000000
--- a/man/read_in_process_variables.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_prj.R
-\name{read_in_process_variables}
-\alias{read_in_process_variables}
-\title{read_in_process_variables}
-\usage{
-read_in_process_variables(ogs6_obj, prj_path, process_variable_names = NULL)
-}
-\arguments{
-\item{ogs6_obj}{A OGS6 class object}
-
-\item{prj_path}{The path to the project file the process_variable elements should be read from}
-
-\item{process_variable_names}{Optional: The names of the process_variable elements to be read in}
-}
-\description{
-Reads in process_variable elements from a .prj file
-}
diff --git a/man/read_in_processes.Rd b/man/read_in_processes.Rd
deleted file mode 100644
index cbb060cf7ae567abdfab4551a50ddd905cb708ee..0000000000000000000000000000000000000000
--- a/man/read_in_processes.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_prj.R
-\name{read_in_processes}
-\alias{read_in_processes}
-\title{read_in_processes}
-\usage{
-read_in_processes(ogs6_obj, prj_path, process_names = NULL)
-}
-\arguments{
-\item{ogs6_obj}{A OGS6 class object}
-
-\item{prj_path}{The path to the project file the process elements should be read from}
-
-\item{process_names}{Optional: The names of the process elements to be read in}
-}
-\description{
-Reads in process elements from a .prj file
-}
diff --git a/man/read_in_test_definition.Rd b/man/read_in_test_definition.Rd
deleted file mode 100644
index e0c538a365582d6efc5a47b71c94ca5758afe629..0000000000000000000000000000000000000000
--- a/man/read_in_test_definition.Rd
+++ /dev/null
@@ -1,18 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_prj.R
-\name{read_in_test_definition}
-\alias{read_in_test_definition}
-\title{read_in_test_definition}
-\usage{
-read_in_test_definition(ogs6_obj, prj_path, vtkdiff_indices = NULL)
-}
-\arguments{
-\item{ogs6_obj}{A OGS6 class object}
-
-\item{prj_path}{The path to the project file the vtkdiff elements should be read from}
-
-\item{vtkdiff_indices}{Optional: The indices of the vtkdiff elements to be read in}
-}
-\description{
-Reads in vtkdiff elements from a .prj file
-}
diff --git a/man/read_in_time_loop.Rd b/man/read_in_time_loop.Rd
deleted file mode 100644
index 5f325422509c0ffa36ca06f30f947596eaff572f..0000000000000000000000000000000000000000
--- a/man/read_in_time_loop.Rd
+++ /dev/null
@@ -1,16 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/read_in_prj.R
-\name{read_in_time_loop}
-\alias{read_in_time_loop}
-\title{read_in_time_loop}
-\usage{
-read_in_time_loop(ogs6_obj, prj_path)
-}
-\arguments{
-\item{ogs6_obj}{A OGS6 class object}
-
-\item{prj_path}{The path to the project file the time_loop element should be read from}
-}
-\description{
-Reads in time_loop element from a .prj file
-}