Merge branch 'release/v0.5.0'

.Rbuildignore

@@ -5,3 +5,4 @@
 ^NEWS\.md$
 ^inst/code/
 ^data-raw$
+^README\.Rmd$

DESCRIPTION

@@ -1,13 +1,18 @@
 Package: RMODFLOW
 Type: Package
-Title: Pre- and post-processing of MODFLOW files in R
-Version: 0.4.1
-Date: 2016-06-27
+Title: Pre- and post-processing of MODFLOW files
+Version: 0.5.0
+Date: 2021-10-12
 Authors@R: c(
-    person("Bart", "Rogiers", role = c("aut", "cre"), email = "brogiers@sckcen.be"),
+    person(
+    given = "Bart",
+    family = "Rogiers",
+    email = "bart.rogiers@sckcen.be",
+    role = c("cre", "aut"),
+    comment = c(ORCID = "0000-0002-8836-0988")),
     person("Cas", "Neyens", role = "aut", email = "cas.neyens@vub.be"))
 Description: The RMODFLOW package provides a set of tools for groundwater flow
-    modelling with MODFLOW.
+    modelling with the MODFLOW-2005 family of codes.
 License: GPL (>= 2)
 Imports: 
     ggplot2,
@@ -40,7 +45,7 @@ Imports:
 Remotes:
     rogiersbart/spectralscale,
     rogiersbart/rui
-URL: https://github.com/rogiersbart/RMODFLOW
+URL: https://rogiersbart.github.io/RMODFLOW/
 BugReports: https://github.com/rogiersbart/RMODFLOW/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)

NEWS.md

@@ -1,23 +1,30 @@
-# RMODFLOW 0.5.0 [WIP]
-
+# RMODFLOW 0.5.0
+
+* Version presented by [Neyens and Rogiers (2021)](https://drive.google.com/file/d/1KC1geIZ4PoauFP00fkcxtEqD3jxAfP4L/).
+* New functionality for converting between {[RMODFLOW](https://rogiersbart.github.io/RMODFLOW/)} and {[sf](https://rspatial.github.io/sf/)}, {[stars](https://rspatial.github.io/stars/)} and {[raster](https://rspatial.github.io/raster/)} objects ([#20](https://github.com/rogiersbart/RMODFLOW/pull/20)).
+* New model-level functionality with `rmf_read()`, `rmf_write()`, `rmf_create()` ([#8](https://github.com/rogiersbart/RMODFLOW/pull/8)).
+* Reworked model execution UI, resulting in the new `rmf_execute()`, `rmf_analyze()` and `rmf_optimize()` ([#7](https://github.com/rogiersbart/RMODFLOW/issues/7)).
+* Updated input data processing and representation ([#8](https://github.com/rogiersbart/RMODFLOW/pull/8)).
+* Extended MODFLOW package support for the `rmf_read_*()`, `rmf_write_*()` and `rmf_create_*()` families of functions ([#3](https://github.com/rogiersbart/RMODFLOW/pull/3)).
 * Added automatic installation of MODFLOW variants ([#2](https://github.com/rogiersbart/RMODFLOW/issues/2)).
 * Added automatic finding of paths to MODFLOW executables.
 * Added function prefixes `rmf_`, and `rmfi_` for internal functions.
 * Added a [pkgdown site](https://rogiersbart.github.io/RMODFLOW/).
 * Added example models for function documentation examples and vignettes.
+* First developments presented by [Rogiers (2017)](https://drive.google.com/file/d/0B4xr2UZeAf_mZVJHSGhYek52bm8/).
 
 # RMODFLOW 0.4.0
 
-* Version used by [Neyens (2016)](https://rogiersbart.github.io/science-output.html#13416953).
+* Version used by [Neyens (2016)](https://drive.google.com/file/d/0B4xr2UZeAf_mY2lzLU1xbDBWeHc/).
 
 # RMODFLOW 0.3.0
 
-* Version presented by [Rogiers (2015)](https://rogiersbart.github.io/science-output.html#26516586).
+* Version presented by [Rogiers (2015)](https://drive.google.com/file/d/0B4xr2UZeAf_mUEJuRUhCM3JtQlE/).
 
 # RMODFLOW 0.2.0
 
-* Version presented by [Rogiers (2015)](https://rogiersbart.github.io/science-output.html#25516537).
+* Version presented by [Rogiers (2015)](https://drive.google.com/file/d/1-UlcwQzaSI-VIrp7A5KpYjM9WLOmuMZT/).
 
 # RMODFLOW 0.1.0
 
-* Different modifications to the code for use in reproducible reporting. 
+* Different modifications to the code for use in reproducible reporting.

R/execute.R

@@ -394,7 +394,8 @@ rmf_optimize <- function(
       rui::error("Issue with optimization.")
     }
     start <- readr::read_tsv(export, lazy = FALSE) %>%
-      dplyr::select(-1, -2) %>%
+      dplyr::filter(is.finite(cost)) %>% 
+      dplyr::select(-cost, -converged) %>%
       dplyr::slice(nrow(.)) %>%
       unlist()
   }

README.Rmd

@@ -0,0 +1,68 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# The {RMODFLOW} R package<br><small><font color="#999">Pre- and post-processing of MODFLOW files</font></small>
+
+<!-- badges: start -->
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
+[![CRAN status](https://www.r-pkg.org/badges/version/RMODFLOW.svg)](https://CRAN.R-project.org/package=RMODFLOW)
+<!-- badges: end -->
+
+The {[RMODFLOW](https://rogiersbart.github.io/RMODFLOW/)} R package provides a set
+of tools for groundwater flow modelling with
+[MODFLOW](https://www.usgs.gov/mission-areas/water-resources/science/modflow-and-related-programs).
+The functionality is targeted at feature-parity with that of the
+[ModelMuse](https://www.usgs.gov/software/modelmuse-a-graphical-user-interface-groundwater-models)
+GUI and friends, albeit restricted to the
+[MODFLOW-2005](https://www.usgs.gov/software/modflow-2005-usgs-three-dimensional-finite-difference-ground-water-model)
+family of codes. Related developments are the
+{[RMT3DMS](https://rogiersbart.github.io/RMT3DMS/)} package for solute transport
+modelling, and {[RMODPATH](https://github.com/cneyens/RMODPATH)} for particle
+tracking.
+
+# Install
+
+You can install the latest version of
+{[RMODFLOW](https://rogiersbart.github.io/RMODFLOW/)} with any of the following:
+
+```{r eval = FALSE}
+renv::install("rogiersbart/RMODFLOW")
+pak::pkg_install("rogiersbart/RMODFLOW")
+remotes::install_github("rogiersbart/RMODFLOW")
+```
+
+If you don't have {[renv](https://rstudio.github.io/renv/)},
+{[pak](https://pak.r-lib.org/)}, or {[remotes](https://remotes.r-lib.org/)}
+installed, try this instead:
+
+```{r eval = FALSE}
+install.packages("remotes")
+remotes::install_github("rogiersbart/RMODFLOW")
+```
+
+# Use
+
+To get started, have a look at the [introduction to
+{RMODFLOW}](https://rogiersbart.github.io/RMODFLOW/docs/articles/RMODFLOW.html).
+A series of articles is available if you want to dive deeper into the {RMODFLOW}
+functionality:
+
+- [Boundary conditions](https://rogiersbart.github.io/RMODFLOW/articles/boundary_conditions.html)
+- [Structure of input data](https://rogiersbart.github.io/RMODFLOW/articles/input_data_structure.html)
+- [Handling MODFLOW output](https://rogiersbart.github.io/RMODFLOW/articles/output.html)
+- [MODFLOW parameters](https://rogiersbart.github.io/RMODFLOW/articles/parameters.html)
+- [Plotting in RMODFLOW](https://rogiersbart.github.io/RMODFLOW/articles/plotting.html)
+- [Spatial functions](https://rogiersbart.github.io/RMODFLOW/articles/spatial.html)
+- [Top-level functions](https://rogiersbart.github.io/RMODFLOW/articles/top_level.html)

README.md

@@ -1,8 +1,67 @@
-RMODFLOW<br><small><font color="#333333">Pre- and post-processing of MODFLOW files in R</font></small>
-======================================================================================================
 
-[![Travis-CI Build Status](https://travis-ci.org/rogiersbart/RMODFLOW.svg?branch=master)](https://travis-ci.org/rogiersbart/RMODFLOW)
-[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/RMODFLOW)](https://cran.r-project.org/package=RMODFLOW)
-[![Coverage Status](https://img.shields.io/codecov/c/github/rogiersbart/RMODFLOW/master.svg)](https://codecov.io/github/rogiersbart/RMODFLOW?branch=master)
+<!-- README.md is generated from README.Rmd. Please edit that file -->
 
-The [RMODFLOW](https://rogiersbart.github.io/RMODFLOW/) package provides a set of tools for groundwater flow modelling with [MODFLOW](https://water.usgs.gov/ogw/modflow/). A related package is the [RMT3DMS](https://rogiersbart.github.io/RMT3DMS/) package for solute transport modelling. The latest development version can be installed as follows: `devtools::install_github("rogiersbart/RMODFLOW")`. For more information, visit the [RMODFLOW website](https://rogiersbart.github.io/RMODFLOW).
+# The {RMODFLOW} R package<br><small><font color="#999">Pre- and post-processing of MODFLOW files</font></small>
+
+<!-- badges: start -->
+
+[![Lifecycle:
+experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
+[![CRAN
+status](https://www.r-pkg.org/badges/version/RMODFLOW.svg)](https://CRAN.R-project.org/package=RMODFLOW)
+<!-- badges: end -->
+
+The {[RMODFLOW](https://rogiersbart.github.io/RMODFLOW/)} R package
+provides a set of tools for groundwater flow modelling with
+[MODFLOW](https://www.usgs.gov/mission-areas/water-resources/science/modflow-and-related-programs).
+The functionality is targeted at feature-parity with that of the
+[ModelMuse](https://www.usgs.gov/software/modelmuse-a-graphical-user-interface-groundwater-models)
+GUI and friends, albeit restricted to the
+[MODFLOW-2005](https://www.usgs.gov/software/modflow-2005-usgs-three-dimensional-finite-difference-ground-water-model)
+family of codes. Related developments are the
+{[RMT3DMS](https://rogiersbart.github.io/RMT3DMS/)} package for solute
+transport modelling, and
+{[RMODPATH](https://github.com/cneyens/RMODPATH)} for particle tracking.
+
+# Install
+
+You can install the latest version of
+{[RMODFLOW](https://rogiersbart.github.io/RMODFLOW/)} with any of the
+following:
+
+``` r
+renv::install("rogiersbart/RMODFLOW")
+pak::pkg_install("rogiersbart/RMODFLOW")
+remotes::install_github("rogiersbart/RMODFLOW")
+```
+
+If you don’t have {[renv](https://rstudio.github.io/renv/)},
+{[pak](https://pak.r-lib.org/)}, or
+{[remotes](https://remotes.r-lib.org/)} installed, try this instead:
+
+``` r
+install.packages("remotes")
+remotes::install_github("rogiersbart/RMODFLOW")
+```
+
+# Use
+
+To get started, have a look at the [introduction to
+{RMODFLOW}](https://rogiersbart.github.io/RMODFLOW/docs/articles/RMODFLOW.html).
+A series of articles is available if you want to dive deeper into the
+{RMODFLOW} functionality:
+
+-   [Boundary
+    conditions](https://rogiersbart.github.io/RMODFLOW/articles/boundary_conditions.html)
+-   [Structure of input
+    data](https://rogiersbart.github.io/RMODFLOW/articles/input_data_structure.html)
+-   [Handling MODFLOW
+    output](https://rogiersbart.github.io/RMODFLOW/articles/output.html)
+-   [MODFLOW
+    parameters](https://rogiersbart.github.io/RMODFLOW/articles/parameters.html)
+-   [Plotting in
+    RMODFLOW](https://rogiersbart.github.io/RMODFLOW/articles/plotting.html)
+-   [Spatial
+    functions](https://rogiersbart.github.io/RMODFLOW/articles/spatial.html)
+-   [Top-level
+    functions](https://rogiersbart.github.io/RMODFLOW/articles/top_level.html)

_pkgdown.yml

@@ -1,13 +1,37 @@
+home:
+  title: The {RMODFLOW} R package
+  description: Pre- and post-processing of MODFLOW files
+url: https://rogiersbart.github.io/RMODFLOW/
 authors:
   Bart Rogiers:
     href: https://rogiersbart.github.io/
-
-template:
-  params:
-    bootswatch: united
-    ganalytics: UA-32706734-4
-
 reference:
+  - title: "Model-level functionality"
+    desc: "Work with complete models"
+    contents:
+      - rmf_read
+      - rmf_write
+      - rmf_create
+  - title: "Execute, analyze and optimize models"
+    desc: "Run MODFLOW, perform sensitivity analysis and local optimization"
+    contents:
+      - rmf_execute
+      - rmf_analyze
+      - rmf_optimize
+      - rmf_performance
+  - title: "Install the MODFLOW-2005 family of codes"
+    desc: "Download the MODFLOW codes and put them in a known location"
+    contents:
+      - starts_with("rmf_install")
+  - title: "Work with a coordinate reference system"
+    desc: ""
+    contents:
+      - matches("prj")
+      - ends_with("reference")
+  - title: "Work with example models"
+    desc: ""
+    contents:
+      - starts_with("rmf_example")
   - title: "Read MODFLOW files"
     desc: "Functions to read MODFLOW files and return RMODFLOW objects"
     contents: 
@@ -20,17 +44,22 @@ reference:
     desc: "Functions to create RMODFLOW objects"
     contents: 
       - starts_with("rmf_create_")
-  - title: "Convert"
-    desc: "Convert"
+  - title: "Convert RMODFLOW objects"
+    desc: "Convert between object types, coordinates, ..."
     contents:
       - starts_with("rmf_convert_")
+      - starts_with("rmf_as_")
   - title: "Other"
-    desc: "Other"
+    desc: ""
     contents:
-      - starts_with("rmf_animate_")
-      - starts_with("rmf_cell")
-      - rmf_example_file
-      - starts_with("rmf_export")
-      - starts_with("rmf_performance")
+      - rmf_guide
+      - rmf_gradient
+      - rmf_interpolate
       - starts_with("rmf_plot")
-      - starts_with("rmf_run")
+      - rmf_saturated_thickness
+      - rmf_time_steps
+      - rmf_copy_to_wd
+      - rmf_browse
+      - matches("cell")
+      - starts_with("rmf_calculate")
+      - rmf_animate