From 71e4d03dd31daa8c8efe4304752758e34efb9584 Mon Sep 17 00:00:00 2001
From: aheinri5 <Anna@netzkritzler.de>
Date: Mon, 15 Feb 2021 23:17:08 +0100
Subject: [PATCH] [docs] added examples for OGS6 class
---
R/ogs6.R | 190 +++++++++++++++++++++++++++++++------------------------
1 file changed, 106 insertions(+), 84 deletions(-)
diff --git a/R/ogs6.R b/R/ogs6.R
index 6d8a5c7..c05732b 100644
--- a/R/ogs6.R
+++ b/R/ogs6.R
@@ -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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