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Commit 71e4d03d authored by Ruben Heinrich's avatar Ruben Heinrich
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[docs] added examples for OGS6 class

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2 merge requests!12Resolve "format documentation",!11Resolve "Add examples to class and function documentation"
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R/ogs6.R
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......@@ -2,17 +2,19 @@
#===== OGS6 =====
#'OGS6
#'@description Constructor for the OGS6 base class
#'@export
#' OGS6
#' @description Constructor for the \code{OGS6} base class
#' @export
OGS6 <- R6::R6Class("OGS6",
public = list(
#'@description
#'Creates new OGS6 object
#'@param sim_name string: Simulation name
#'@param sim_path string: Path where all files for the simulation will be
#' saved
#' @description
#' Creates new OGS6 object
#' @param sim_name string: Simulation name
#' @param sim_path string: Path where all files for the simulation will be
#' saved
#' @examples
#' ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
initialize = function(sim_name,
sim_path) {
......@@ -30,9 +32,12 @@ OGS6 <- R6::R6Class("OGS6",
#===== Adding components =====
#'@description
#'Adds a .prj simulation component
#'@param x An object of any .prj `r2ogs6` class
#' @description
#' Adds a .prj simulation component
#' @param x An object of any .prj `r2ogs6` class
#' @examples
#' ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
#' ogs6_obj$add(r2ogs6_parameter$new(name = "foo", type = "bar"))
add = function(x){
# Assert that class name is in implemented .prj classes for OGS6
......@@ -66,11 +71,15 @@ OGS6 <- R6::R6Class("OGS6",
invisible(self)
},
#'@description
#'Adds a reference to a .gml file and optionally, a OGS6_gml object
#'@param gml string | r2ogs6_gml: Either a path to a file with extension
#' .gml or a r2ogs6_gml object.
#@examples
#' @description
#' Adds a reference to a file with ending .gml and optionally, a
#' \code{OGS6_gml} object
#' @param gml string | OGS6_gml: Either a path to a file with extension
#' .gml or a OGS6_gml object.
#' @examples
#' ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
#' ogs6_obj$add_gml("this_works.gml")
#' \dontrun{ogs6_obj$add_gml("this_doesnt.oops")}
add_gml = function(gml){
if(assertthat::is.string(gml)){
......@@ -85,11 +94,16 @@ OGS6 <- R6::R6Class("OGS6",
invisible(self)
},
#'@description
#'Adds a reference to a .vtu file and optionally, a OGS6_vtu object
#'@param path string:
#'@param read_in_vtu flag: Optional: Should .vtu file just be copied or
#' read in too?
#' @description
#' Adds a reference to a \code{.vtu} file and optionally, a \code{OGS6_vtu}
#' object
#' @param path string: A path
#' @param read_in_vtu flag: Optional: Should \code{.vtu} file just be
#' copied or read in too?
#' @examples
#' ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
#' ogs6_obj$add_vtu("this_works.vtu")
#' \dontrun{ogs6_obj$add_vtu("this_doesnt.oops")}
add_vtu = function(path,
read_in_vtu = FALSE){
assertthat::assert_that(assertthat::is.string(path))
......@@ -109,10 +123,13 @@ OGS6 <- R6::R6Class("OGS6",
#===== Utility =====
#'@description
#'Checks if the OGS6 object has all necessary parameters for
#' @description
#' Checks if the \code{OGS6} object has all necessary parameters for
#' starting a simulation
#'@param print_status flag: Should the status be printed to the console?
#' @param print_status flag: Should the status be printed to the console?
#' @examples
#' ogs6_obj <- OGS6$new(sim_name = "my_sim", sim_path = "my/path")
#' ogs6_obj$get_status()
get_status = function(print_status = TRUE){
assertthat::assert_that(assertthat::is.flag(print_status))
......@@ -166,8 +183,8 @@ OGS6 <- R6::R6Class("OGS6",
return(invisible(flag))
},
#'@description
#'Overrides default printing behaviour
#' @description
#' Overrides default printing behaviour
print = function(){
cat("OGS6\n")
cat("simulation name: ", self$sim_name, "\n", sep = "")
......@@ -197,8 +214,8 @@ OGS6 <- R6::R6Class("OGS6",
invisible(self)
},
#'print_log
#'@description Prints logfile to console (if it exists)
#' print_log
#' @description Prints logfile to console (if it exists)
print_log = function(){
if(!is.null(self$logfile)){
writeLines(readLines(self$logfile))
......@@ -209,11 +226,11 @@ OGS6 <- R6::R6Class("OGS6",
invisible(self)
},
#'@description
#'Clears components from the OGS6 object
#'@param which character: The names of the components (all by default).
#' @description
#' Clears components from the \code{OGS6} object
#' @param which character: The names of the components (all by default).
#' If you want to delete only some components, run
#' names(prj_top_level_classes()) for the available options.
#' \code{names(prj_top_level_classes())} for the available options.
clear = function(which){
if(missing(which)){
......@@ -254,8 +271,8 @@ OGS6 <- R6::R6Class("OGS6",
active = list(
#'@field sim_name
#'Simulation name. `value` must be string
#' @field sim_name
#' Simulation name. \code{value} must be string
sim_name = function(value) {
if(missing(value)) {
private$.sim_name
......@@ -265,8 +282,8 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field sim_path
#'Simulation path. `value` must be string
#' @field sim_path
#' Simulation path. \code{value} must be string
sim_path = function(value) {
if(missing(value)) {
private$.sim_path
......@@ -275,8 +292,8 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field logfile
#'Logfile path. `value` must be string
#' @field logfile
#' Logfile path. \code{value} must be string
logfile = function(value) {
if(missing(value)) {
private$.logfile
......@@ -286,14 +303,14 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field gml
#'.gml. read-only
#' @field gml
#' \code{.gml}. read-only
gml = function() {
private$.gml
},
#'@field geometry
#'.prj `geometry` tag. `value` must be string
#' @field geometry
#' \code{.prj} \code{geometry} tag. \code{value} must be string
geometry = function(value) {
if(missing(value)) {
private$.geometry
......@@ -303,8 +320,8 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field meshes
#'.prj `meshes` tag. `value` must be list of strings
#' @field meshes
#' \code{.prj} \code{meshes} tag. \code{value} must be list of strings
meshes = function(value) {
if(missing(value)) {
private$.meshes
......@@ -317,8 +334,8 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field vtus
#'.vtus. `value` must be list of `OGS_vtu` objects
#' @field vtus
#' \code{.vtu}s. \code{value} must be list of \code{OGS6_vtu} objects
vtus = function(value) {
if(missing(value)) {
private$.vtus
......@@ -329,8 +346,8 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field python_script
#'.prj `python_script` tag. `value` must be string
#' @field python_script
#' \code{.prj} \code{python_script} tag. \code{value} must be string
python_script = function(value) {
if(missing(value)) {
private$.python_script
......@@ -340,9 +357,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field search_length_algorithm
#'.prj `search_length_algorithm` tag. `value` must be
#' `r2ogs6_search_length_algorithm` object
#' @field search_length_algorithm
#' \code{.prj} \code{search_length_algorithm} tag. \code{value} must be
#' \code{r2ogs6_search_length_algorithm} object
search_length_algorithm = function(value) {
if(missing(value)) {
private$.search_length_algorithm
......@@ -354,8 +371,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field processes
#'.prj `processes` tag. `value` must be list of `r2ogs6_process` objects
#' @field processes
#' \code{.prj} \code{processes} tag. \code{value} must be list of
#' \code{r2ogs6_process} objects
processes = function(value) {
if(missing(value)) {
private$.processes
......@@ -384,8 +402,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field time_loop
#'.prj `time_loop` tag. `value` must be `r2ogs6_time_loop` object
#' @field time_loop
#' \code{.prj} \code{time_loop} tag. \code{value} must be
#' \code{r2ogs6_time_loop} object
time_loop = function(value) {
if(missing(value)) {
private$.time_loop
......@@ -397,9 +416,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field local_coordinate_system
#'.prj `local_coordinate_system` tag. `value` must be
#' `r2ogs6_local_coordinate_system` object
#' @field local_coordinate_system
#' \code{.prj} \code{local_coordinate_system} tag. \code{value} must be
#' \code{r2ogs6_local_coordinate_system} object
local_coordinate_system = function(value) {
if(missing(value)) {
private$.local_coordinate_system
......@@ -411,8 +430,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field media
#'.prj `media` tag. `value` must be list of `r2ogs6_medium` objects
#' @field media
#' \code{.prj} \code{media} tag. \code{value} must be list of
#' \code{r2ogs6_medium} objects
media = function(value) {
if(missing(value)) {
private$.media
......@@ -423,9 +443,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field parameters
#'.prj `parameters` tag. `value` must be list of `r2ogs6_parameter`
#' objects
#' @field parameters
#' \code{.prj} \code{parameters} tag. \code{value} must be list of
#' \code{r2ogs6_parameter} objects
parameters = function(value) {
if(missing(value)) {
private$.parameters
......@@ -436,9 +456,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field chemical_system
#'.prj `chemical_system` tag. `value` must be `r2ogs6_chemical_system`
#' object
#' @field chemical_system
#' \code{.prj} \code{chemical_system} tag. \code{value} must be
#' \code{r2ogs6_chemical_system} object
chemical_system = function(value) {
if(missing(value)) {
private$.chemical_system
......@@ -450,8 +470,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field curves
#'.prj `curves` tag. `value` must be list of `r2ogs6_curve` objects
#' @field curves
#' \code{.prj} \code{curves} tag. \code{value} must be list of
#' \code{r2ogs6_curve} objects
curves = function(value) {
if(missing(value)) {
private$.curves
......@@ -462,9 +483,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field process_variables
#'.prj `process_variables` tag. `value` must be list of
#' `r2ogs6_process_variable` objects
#' @field process_variables
#' \code{.prj} \code{process_variables} tag. \code{value} must be list of
#' \code{r2ogs6_process_variable} objects
process_variables = function(value) {
if(missing(value)) {
private$.process_variables
......@@ -476,9 +497,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field nonlinear_solvers
#'.prj `nonlinear_solvers` tag. `value` must be list of
#' `r2ogs6_nonlinear_solver` objects
#' @field nonlinear_solvers
#' \code{.prj} \code{nonlinear_solvers} tag. \code{value} must be list of
#' \code{r2ogs6_nonlinear_solver} objects
nonlinear_solvers = function(value) {
if(missing(value)) {
private$.nonlinear_solvers
......@@ -490,9 +511,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field linear_solvers
#'.prj `linear_solvers` tag. `value` must be list of
#' `r2ogs6_linear_solver` objects
#' @field linear_solvers
#' \code{.prj} \code{linear_solvers} tag. \code{value} must be list of
#' \code{r2ogs6_linear_solver} objects
linear_solvers = function(value) {
if(missing(value)) {
private$.linear_solvers
......@@ -503,9 +524,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field test_definition
#'.prj `test_definition` tag. `value` must be list of `r2ogs6_vtkdiff`
#' objects
#' @field test_definition
#' \code{.prj} \code{test_definition} tag. \code{value} must be list of
#' \code{r2ogs6_vtkdiff} objects
test_definition = function(value) {
if(missing(value)) {
private$.test_definition
......@@ -516,8 +537,9 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field insitu
#'.prj `insitu` tag. `value` must be `r2ogs6_insitu` object
#' @field insitu
#' \code{.prj} \code{insitu} tag. \code{value} must be
#' \code{r2ogs6_insitu} object
insitu = function(value) {
if(missing(value)) {
private$.insitu
......@@ -529,8 +551,8 @@ OGS6 <- R6::R6Class("OGS6",
}
},
#'@field pvds
#'.pvds. `value` must be list of `OGS6_pvd` objects
#' @field pvds
#' \code{.pvd}s. \code{value} must be list of \code{OGS6_pvd} objects
pvds = function(value) {
if(missing(value)) {
private$.pvds
......
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