diff --git a/man/check_file_extension.Rd b/man/check_file_extension.Rd new file mode 100644 index 0000000000000000000000000000000000000000..81991257084f8c17f3cba2e98a950c4ccc0432b7 --- /dev/null +++ b/man/check_file_extension.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_utils.R +\name{check_file_extension} +\alias{check_file_extension} +\title{check_file_extension} +\usage{ +check_file_extension(file, expected_extension) +} +\arguments{ +\item{file}{A file} + +\item{expected_extension}{The expected file extension} +} +\description{ +Helper function to check the extension of a file +} diff --git a/man/generate_as_node_func.Rd b/man/generate_as_node_func.Rd new file mode 100644 index 0000000000000000000000000000000000000000..13aff84a1dbcec3731543f82906ecca2d4bbb34e --- /dev/null +++ b/man/generate_as_node_func.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/generate_functions.R +\name{generate_as_node_func} +\alias{generate_as_node_func} +\title{generate_as_node_func} +\usage{ +generate_as_node_func( + file, + element_name, + subclasses = NULL, + show_result = TRUE +) +} +\arguments{ +\item{file}{The XML file to parse} + +\item{element_name}{The name of the XML element to base the method on} + +\item{subclasses}{Optional: A named vector of subclasses} + +\item{show_result}{Should the generated function be printed to the console?} +} +\description{ +Generates a method for the generic function as_node based on an XML element +} diff --git a/man/generate_as_node_method_content.Rd b/man/generate_as_node_method_content.Rd new file mode 100644 index 0000000000000000000000000000000000000000..c10c7874921233f022dcce42ed2f4b37a435f116 --- /dev/null +++ b/man/generate_as_node_method_content.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/generate_functions.R +\name{generate_as_node_method_content} +\alias{generate_as_node_method_content} +\title{generate_as_node_method_content} +\usage{ +generate_as_node_method_content( + element, + iteration_depth = 0, + subclasses = NULL +) +} +\arguments{ +\item{element}{The XML element to base the method on} + +\item{iteration_depth}{Utility parameter for the recursion, just leave this alone!} + +\item{subclasses}{Optional: A named vector of subclasses} +} +\description{ +... +} diff --git a/man/generate_simple_read_in.Rd b/man/generate_simple_read_in.Rd new file mode 100644 index 0000000000000000000000000000000000000000..13283e7d56ab210f93c1fe986b0054e1215e9c3b --- /dev/null +++ b/man/generate_simple_read_in.Rd @@ -0,0 +1,26 @@ +% 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 new file mode 100644 index 0000000000000000000000000000000000000000..7ffe582287db4564926fdd02a77fb88a0f83d908 --- /dev/null +++ b/man/get_value_types.Rd @@ -0,0 +1,16 @@ +% 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/guess_structure.Rd b/man/guess_structure.Rd new file mode 100644 index 0000000000000000000000000000000000000000..227acea62a0740846dc25ef71817092c56b3f89f --- /dev/null +++ b/man/guess_structure.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_utils.R +\name{guess_structure} +\alias{guess_structure} +\title{guess_structure} +\usage{ +guess_structure(xml_node, subclasses_names = NULL) +} +\arguments{ +\item{xml_node}{An XML node (of class xml2::xml_node)} + +\item{subclasses_names}{Optional: A character vector containing the names of r2ogs6_* +subclasses (r2ogs6_* classes without a method for input_add)} +} +\description{ +Guesses the R representation of an XML node and adds it to parameter list +ASSUMPTIONS: +1) Leaf nodes will have EITHER a value OR attributes (and will not be missing both, e.g. '<a/>'). +2) Leaf nodes will never be r2ogs6_* objects +3) If there are multiple occurrences of r2ogs6_* class (and subclass) elements on the same level, +they have a wrapper node as their parent (e.g. <processes>, <properties>) which +will contain ONLY elements of this type +4) Wrapper nodes are represented as lists +5) Parent nodes whose children have no children are represented as lists +} diff --git a/man/node_to_r2ogs6_obj.Rd b/man/node_to_r2ogs6_obj.Rd new file mode 100644 index 0000000000000000000000000000000000000000..0c15db51bc9e58224bdeab25542514850994b625 --- /dev/null +++ b/man/node_to_r2ogs6_obj.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_utils.R +\name{node_to_r2ogs6_obj} +\alias{node_to_r2ogs6_obj} +\title{node_to_r2ogs6_obj} +\usage{ +node_to_r2ogs6_obj(xml_node, subclasses_names = NULL) +} +\arguments{ +\item{xml_node}{An XML node (of class xml2::xml_node)} + +\item{subclasses_names}{Optional: A character vector containing the names of r2ogs6_* +subclasses (r2ogs6_* classes without a method for input_add)} +} +\description{ +Takes an XML node and turns it into a class object +} diff --git a/man/order_parameters.Rd b/man/order_parameters.Rd new file mode 100644 index 0000000000000000000000000000000000000000..254aeb75c7d69fee12256a45b6edf53aaa6ddc03 --- /dev/null +++ b/man/order_parameters.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_utils.R +\name{order_parameters} +\alias{order_parameters} +\title{order_parameters} +\usage{ +order_parameters(parameter_list, class_name) +} +\arguments{ +\item{parameter_list}{A list of parameters} + +\item{class_name}{The name of a class} +} +\description{ +Orders a list of parameters corresponding to the argument order of a class +} diff --git a/man/pick_vtu_file.Rd b/man/pick_vtu_file.Rd new file mode 100644 index 0000000000000000000000000000000000000000..1360afd109c3a23d1da406f7a79bd593fc4f7eee --- /dev/null +++ b/man/pick_vtu_file.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_vtu.R +\name{pick_vtu_file} +\alias{pick_vtu_file} +\title{pick_vtu_file} +\usage{ +pick_vtu_file(ogs6_obj) +} +\arguments{ +\item{ogs6_obj}{A OGS6 class object} +} +\description{ +Lets the user pick a .vtu file and adds it to the specified OGS6 class object +} diff --git a/man/read_in.Rd b/man/read_in.Rd new file mode 100644 index 0000000000000000000000000000000000000000..6b4016346263aa58e9b70f9e18d40fe36ef2fdf3 --- /dev/null +++ b/man/read_in.Rd @@ -0,0 +1,34 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_utils.R +\name{read_in} +\alias{read_in} +\title{read_in} +\usage{ +read_in( + ogs6_obj, + prj_path, + element_name, + child_name, + selection_vector = NULL, + subclasses_names = NULL +) +} +\arguments{ +\item{ogs6_obj}{A OGS6 class object} + +\item{prj_path}{The path to the project file the elements should be read from} + +\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 child elements (e.g. 'process')} + +\item{selection_vector}{Optional: Either a character vector containing the names of the children +OR a numeric vector containing their wanted indices} + +\item{subclasses_names}{Optional: A named character vector containing the names of r2ogs6_* +subclasses (r2ogs6_* classes without a method for input_add) +e.g. c(process = "r2ogs6_tl_process") if child_name would be time_loop} +} +\description{ +Reads in elements from a .prj file +} diff --git a/man/read_in_curves.Rd b/man/read_in_curves.Rd new file mode 100644 index 0000000000000000000000000000000000000000..29c7e6cf81a72c95287b2ae6e1d3272f2318c659 --- /dev/null +++ b/man/read_in_curves.Rd @@ -0,0 +1,18 @@ +% 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_gml.Rd b/man/read_in_gml.Rd new file mode 100644 index 0000000000000000000000000000000000000000..afb696c76b6a298e4d4dc6826215bcd8d74e9ef7 --- /dev/null +++ b/man/read_in_gml.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_gml.R +\name{read_in_gml} +\alias{read_in_gml} +\title{read_in_gml} +\usage{ +read_in_gml(ogs6_obj, gml_path) +} +\arguments{ +\item{ogs6_obj}{A OGS6 class object} + +\item{gml_path}{The path to the geometry file that should be read in} +} +\description{ +Wrapper function to read in a whole .gml file +} diff --git a/man/read_in_linear_solvers.Rd b/man/read_in_linear_solvers.Rd new file mode 100644 index 0000000000000000000000000000000000000000..584247b7d755ded6f916afeac6c658113af4f903 --- /dev/null +++ b/man/read_in_linear_solvers.Rd @@ -0,0 +1,18 @@ +% 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 new file mode 100644 index 0000000000000000000000000000000000000000..ee48fdc835e65465ad5864677fb1b16fa92b17d9 --- /dev/null +++ b/man/read_in_media.Rd @@ -0,0 +1,18 @@ +% 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 new file mode 100644 index 0000000000000000000000000000000000000000..bbdfc1b8f107dbc98ee952967bd643efb6d36f96 --- /dev/null +++ b/man/read_in_nonlinear_solvers.Rd @@ -0,0 +1,18 @@ +% 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 new file mode 100644 index 0000000000000000000000000000000000000000..8fd76faea7f239d3d90ea20d4894386d9973aa5e --- /dev/null +++ b/man/read_in_parameters.Rd @@ -0,0 +1,18 @@ +% 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_points.Rd b/man/read_in_points.Rd new file mode 100644 index 0000000000000000000000000000000000000000..e0956b9ccb297636f9404e61780cb1b704cf399e --- /dev/null +++ b/man/read_in_points.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_gml.R +\name{read_in_points} +\alias{read_in_points} +\title{read_in_points} +\usage{ +read_in_points(xml_doc) +} +\arguments{ +\item{xml_doc}{A parsed XML document (of class 'xml2::xml_document')} +} +\description{ +Reads points from a .gml file +} diff --git a/man/read_in_polylines.Rd b/man/read_in_polylines.Rd new file mode 100644 index 0000000000000000000000000000000000000000..242ac2a1d728666c394b8247f55a3b895d7d89c1 --- /dev/null +++ b/man/read_in_polylines.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_gml.R +\name{read_in_polylines} +\alias{read_in_polylines} +\title{read_in_polylines} +\usage{ +read_in_polylines(xml_doc) +} +\arguments{ +\item{xml_doc}{A parsed XML document (of class 'xml2::xml_document')} +} +\description{ +Reads polylines from a .gml file +} diff --git a/man/read_in_prj.Rd b/man/read_in_prj.Rd new file mode 100644 index 0000000000000000000000000000000000000000..3bda7d9f7523a02c488715f15c3a89a5e5b2e337 --- /dev/null +++ b/man/read_in_prj.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_prj.R +\name{read_in_prj} +\alias{read_in_prj} +\title{read_in_prj} +\usage{ +read_in_prj(ogs6_obj, prj_path) +} +\arguments{ +\item{ogs6_obj}{A OGS6 class object} + +\item{prj_path}{The path to the project file that should be read in} +} +\description{ +Wrapper function to read in a whole .prj file +} diff --git a/man/read_in_process_variables.Rd b/man/read_in_process_variables.Rd new file mode 100644 index 0000000000000000000000000000000000000000..92c255e11af162858c4962c18b8dab8bcfabad34 --- /dev/null +++ b/man/read_in_process_variables.Rd @@ -0,0 +1,18 @@ +% 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 new file mode 100644 index 0000000000000000000000000000000000000000..cbb060cf7ae567abdfab4551a50ddd905cb708ee --- /dev/null +++ b/man/read_in_processes.Rd @@ -0,0 +1,18 @@ +% 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_surfaces.Rd b/man/read_in_surfaces.Rd new file mode 100644 index 0000000000000000000000000000000000000000..f197240d1f0d7cdbf3142a1b1aae83b5144725d3 --- /dev/null +++ b/man/read_in_surfaces.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_gml.R +\name{read_in_surfaces} +\alias{read_in_surfaces} +\title{read_in_surfaces} +\usage{ +read_in_surfaces(xml_doc) +} +\arguments{ +\item{xml_doc}{A parsed XML document (of class 'xml2::xml_document')} +} +\description{ +Reads surfaces from a .gml file +} diff --git a/man/read_in_test_definition.Rd b/man/read_in_test_definition.Rd new file mode 100644 index 0000000000000000000000000000000000000000..e0c538a365582d6efc5a47b71c94ca5758afe629 --- /dev/null +++ b/man/read_in_test_definition.Rd @@ -0,0 +1,18 @@ +% 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 new file mode 100644 index 0000000000000000000000000000000000000000..5f325422509c0ffa36ca06f30f947596eaff572f --- /dev/null +++ b/man/read_in_time_loop.Rd @@ -0,0 +1,16 @@ +% 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 +} diff --git a/man/read_in_vtu.Rd b/man/read_in_vtu.Rd new file mode 100644 index 0000000000000000000000000000000000000000..7de06c79b21da6f934a974972fe9e00007ae628e --- /dev/null +++ b/man/read_in_vtu.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_vtu.R +\name{read_in_vtu} +\alias{read_in_vtu} +\title{read_in_vtu} +\usage{ +read_in_vtu(ogs6_obj, vtu_path) +} +\arguments{ +\item{ogs6_obj}{A OGS6 class object} + +\item{vtu_path}{The path to the mesh file that should be read in} +} +\description{ +Wrapper function to read in a whole .vtu file +} diff --git a/man/strings_equal.Rd b/man/strings_equal.Rd new file mode 100644 index 0000000000000000000000000000000000000000..4043eb0453381e463ea913d2c670f02226eb52f1 --- /dev/null +++ b/man/strings_equal.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/generate_functions.R +\name{strings_equal} +\alias{strings_equal} +\title{strings_equal} +\usage{ +strings_equal(strings_vector) +} +\arguments{ +\item{strings_vector}{A vector or a list of strings} +} +\description{ +Checks if all strings in a vector or list are equal +} diff --git a/man/validate_read_in_xml.Rd b/man/validate_read_in_xml.Rd new file mode 100644 index 0000000000000000000000000000000000000000..cabc846de0ca59e3df792bf3a71628f920541299 --- /dev/null +++ b/man/validate_read_in_xml.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_utils.R +\name{validate_read_in_xml} +\alias{validate_read_in_xml} +\title{validate_read_in_xml} +\usage{ +validate_read_in_xml(file) +} +\arguments{ +\item{file}{A file to be parsed as XML} +} +\value{ +The parsed XML file (as class object of type xml2::xml_document) +} +\description{ +Utility function, tries parsing the provided file as an XML document +} diff --git a/man/vector_from_nodeset.Rd b/man/vector_from_nodeset.Rd new file mode 100644 index 0000000000000000000000000000000000000000..0b54312a01108173ead724c5fdaaa2dd87512a63 --- /dev/null +++ b/man/vector_from_nodeset.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/read_in_utils.R +\name{vector_from_nodeset} +\alias{vector_from_nodeset} +\title{vector_from_nodeset} +\usage{ +vector_from_nodeset(xml_nodeset) +} +\arguments{ +\item{xml_nodeset}{An XML nodeset (of class xml2::xml_nodeset)} +} +\description{ +Creates a named vector from a nodeset +}