move core DES stuff out of SpaDES

part of PredictiveEcology/SpaDES#198

.Rbuildignore

@@ -0,0 +1,14 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+.*\.tar\.gz$
+.*\.toc$
+.*\.zip$
+^_ignore$
+^\.lintr$
+^\.travis\.yml$
+^appveyor\.yml$
+CONTRIBUTING\.md
+cran-comments\.md
+LICENSE
+vignettes/.*_cache$
+vignettes/.*\.log$

.aspell/defaults.R

@@ -0,0 +1,4 @@
+vignettes <- list(control = c("--master=en_US", "--add-extra-dicts=en_GB"), personal = "words.pws")
+Rd_files <- list(control = c("--master=en_US", "--add-extra-dicts=en_GB"), personal = "words.pws")
+R_files <- list(control = c("--master=en_US", "--add-extra-dicts=en_GB"), personal = "words.pws")
+C_files <- list(control = c("--master=en_US", "--add-extra-dicts=en_GB"), personal = "words.pws")

.gitattributes

@@ -0,0 +1,22 @@
+# Auto detect text files and perform LF normalization
+* text=auto
+
+# Custom for Visual Studio
+*.cs     diff=csharp
+*.sln    merge=union
+*.csproj merge=union
+*.vbproj merge=union
+*.fsproj merge=union
+*.dbproj merge=union
+
+# Standard to msysgit
+*.doc	 diff=astextplain
+*.DOC	 diff=astextplain
+*.docx diff=astextplain
+*.DOCX diff=astextplain
+*.dot  diff=astextplain
+*.DOT  diff=astextplain
+*.pdf  diff=astextplain
+*.PDF	 diff=astextplain
+*.rtf	 diff=astextplain
+*.RTF	 diff=astextplain

.gitignore

@@ -31,3 +31,4 @@ vignettes/*.pdf
 # Temporary files created by R markdown
 *.utf8.md
 *.knit.md
+.Rproj.user

.lintr

@@ -0,0 +1 @@
+linters: with_defaults(line_length_linter(100), object_name_linter("lowerCamelCase"))

.travis.yml

@@ -0,0 +1,83 @@
+# Sample .travis.yml for R projects.
+#
+# See README.md for instructions, or for more configuration options,
+# see the wiki:
+#   https://github.com/craigcitro/r-travis/wiki
+
+sudo: required
+
+language: r
+
+cache: packages
+
+cran: https://cran.rstudio.com/
+
+matrix:
+  include:
+
+  - os: linux
+    dist: trusty
+    r: oldrel
+    addons:
+      apt:
+        packages:
+          - libgdal1-dev
+          - libproj-dev
+    before_install:
+    - export DISPLAY=:99.0
+    - sh -e /etc/init.d/xvfb start
+
+  - os: linux
+    dist: trusty
+    r: release
+    addons:
+      apt:
+        packages:
+          - libgdal1-dev
+          - libproj-dev
+    before_install:
+      - export DISPLAY=:99.0
+      - sh -e /etc/init.d/xvfb start
+      - Rscript -e 'install.packages("dplyr", dependencies = TRUE)'
+    after_success:
+      - Rscript -e 'library(covr); coveralls(coverage = print(package_coverage(quiet = FALSE)))'
+      - Rscript -e 'library(lintr); lint_package()'
+
+  - os: linux
+    dist: trusty
+    r: devel
+    addons:
+      apt:
+        packages:
+          - libgdal1-dev
+          - libproj-dev
+    before_install:
+      - export DISPLAY=:99.0
+      - sh -e /etc/init.d/xvfb start
+      - Rscript -e 'install.packages("dplyr", dependencies = TRUE)'
+
+  - os: osx
+    osx_image: xcode8
+    latex: false
+    r_build_args: '--no-build-vignettes'
+    r_check_args: '--as-cran --ignore-vignettes --no-examples'
+    before_script:
+      - Rscript -e "install.packages('rgdal', type = 'source')"
+
+r_build_args: " "
+
+r_check_args: "--as-cran"
+
+warnings_are_errors: true
+
+notifications:
+  email:
+    on_success: change
+    on_failure: change
+
+branches:
+  only:
+    - master
+    - development
+    - testing
+

CONTRIBUTING.md

@@ -0,0 +1,24 @@
+We welcome contributions to `SpaDES.core`, both as bug reports or package enhancements.
+
+## Report a bug
+
+1. Use the [issue tracker](https://github.com/PredictiveEcology/SpaDES.core/issues) to report a bug.
+
+2. Please include a minimum reproducible example that triggers the bug.
+
+3. Please include the output of `devtools::session_info()`.
+
+## Submit an enhancement
+
+1. [Fork](https://github.com/rstudio/rstudio/fork) the repository and make your changes.
+
+2. Please follow our code [style guide](https://github.com/PredictiveEcology/SpaDES/wiki/Dev-Docs---Code-Style-Guide) and make your code as easy to follow as possible.
+
+3. If adding new functionality, please include instructional examples and/or [unit tests](http://r-pkgs.had.co.nz/tests.html).
+
+3. Submit a [pull request](https://help.github.com/articles/using-pull-requests) against the development branch.
+
+We'll try to review your pull request and provide feedback / merge improvements as quickly as possible.
+
+Thank you!
+

DESCRIPTION

@@ -0,0 +1,114 @@
+Package: SpaDES.core
+Type: Package
+Title: Develop and Run Spatially Explicit Discrete Event Simulation Models
+Description: Provide the core discrete event simulation (DES) framework for
+    implementing spatially explicit simulation models. The core DES components 
+    facilitate modularity, and easily enable the user to include additional
+    functionality by running user-built simulation modules. This code was split
+    from the 'SpaDES' package in June 2017. Plotting functionality is provided
+    by 'quickPlot'.
+URL:
+    http://spades.predictiveecology.org,
+    https://github.com/PredictiveEcology/SpaDES.core
+Date: 2017-06-28
+Version: 0.1.0
+Authors@R: c(
+    person(c("Alex", "M"), "Chubaty", email = "alexander.chubaty@canada.ca",
+    role = c("aut", "cre")),
+    person(c("Eliot", "J", "B"), "McIntire", email = "eliot.mcintire@canada.ca",
+    role = c("aut")),
+    person("Yong", "Luo", email = "yluo1@lakeheadu.ca",
+    role = c("ctb")),
+    person("Steve", "Cumming", email = "Steve.Cumming@sbf.ulaval.ca",
+    role = c("ctb")),
+    person("Her Majesty the Queen in Right of Canada, as represented by the Minister of Natural Resources Canada",
+    role = "cph")
+    )
+Additional_repositories: http://rforge.net
+Depends:
+    R (>= 3.3.2),
+    quickPlot,
+    reproducible
+Imports:
+    checkmate (>= 1.8.2),
+    chron (>= 2.3-50),
+    CircStats (>= 0.2-4),
+    data.table (>= 1.10.4),
+    DEoptim (>= 2.2-4),
+    DiagrammeR (>= 0.8.2),
+    digest (>= 0.6.12),
+    dplyr (>= 0.5.0),
+    fastdigest,
+    fpCompare (>= 0.2.1),
+    grDevices,
+    httr (>= 1.2.1),
+    igraph (>= 1.0.1),
+    lazyeval (>= 0.2.0),
+    lubridate (>= 1.3.3),
+    methods,
+    parallel,
+    R.utils (>= 2.5.0),
+    RandomFields (>= 3.1.24),
+    raster (>= 2.5-8),
+    stats,
+    sp (>= 1.2-4),
+    stringi (>= 1.1.3),
+    tcltk,
+    utils
+Suggests:
+    covr,
+    hunspell,
+    knitr,
+    Matrix,
+    png,
+    RColorBrewer (>= 1.1-2),
+    rgdal,
+    rgenoud,
+    rmarkdown,
+    snow,
+    SpaDES.tools,
+    testthat (>= 1.0.2),
+    tkrplot
+Remotes:
+    PredictiveEcology/reproducible,
+    PredictiveEcology/quickPlot,
+    PredictiveEcology/SpaDES.tools,
+    MangoTheCat/visualTest
+License: GPL-3
+VignetteBuilder: knitr, rmarkdown
+BugReports: https://github.com/PredictiveEcology/SpaDES.core/issues
+ByteCompile: yes
+Collate: 
+    'priority.R'
+    'environment.R'
+    'module-dependencies-class.R'
+    'misc-methods.R'
+    'helpers.R'
+    'simList-class.R'
+    'POM.R'
+    'cache.R'
+    'check.R'
+    'checkpoint.R'
+    'copy.R'
+    'experiment.R'
+    'simulation-parseModule.R'
+    'simulation-simInit.R'
+    'load.R'
+    'module-define.R'
+    'module-dependencies-methods.R'
+    'moduleMetadata.R'
+    'module-repository.R'
+    'module-template.R'
+    'moduleCoverage.R'
+    'times.R'
+    'simList-accessors.R'
+    'plotting-diagrams.R'
+    'plotting.R'
+    'probability.R'
+    'progress.R'
+    'save.R'
+    'simulation-spades.R'
+    'spades-classes.R'
+    'spades-core-package.R'
+    'zzz.R'
+RoxygenNote: 6.0.1