Merge pull request #41 from ropensci/develop

ready for CRAN
ropensci · Apr 3, 2018 · bccd4b5 · bccd4b5
2 parents cea0459 + 6360dd2
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diff --git a/CRAN-RELEASE b/CRAN-RELEASE
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,4 +1,4 @@
-Package: nlmr
+Package: NLMR
 Type: Package
 Title: Simulating Neutral Landscape Models
 Version: 0.3.0
@@ -15,7 +15,7 @@ Authors@R: c(person("Marco", "Sciaini", email = "[email protected]", role
        comment = "Jeffrey reviewed the package for rOpenSci, see 
                   https://github.com/ropensci/onboarding/issues/188"))
 Maintainer: Marco Sciaini <[email protected]>
-Description: Provides neutral landscape models (<https://doi.org/10.1007/BF02275262>,
+Description: Provides neutral landscape models (<doi:10.1007/BF02275262>,
     <http://sci-hub.tw/10.1007/bf02275262>).  
     Neutral landscape models range from "hard" 
     neutral models (completely random distributed), to "soft" neutral models 
@@ -46,8 +46,8 @@ Imports:
     tibble,
     fasterize,
     sf
-URL: https://ropensci.github.io/nlmr/
-BugReports: https://github.com/ropensci/nlmr/issues/
+URL: https://ropensci.github.io/NLMR/
+BugReports: https://github.com/ropensci/NLMR/issues/
 Suggests:
     testthat,
     covr,

diff --git a/NEWS.md b/NEWS.md
@@ -7,9 +7,8 @@ v0.3.0 was released on 26/03/2018
 ### Changes
 
 - successful review through rOpenSci
-- rename the package into lowercase: `nlmr`
 - split package into two packages:
-  - `nlmr` 
+  - `NLMR` 
     - contains now only the neutral landscape models, minimal dependencies
   - [`landscapetools`](https://github.com/marcosci/landscapetools)
     - contains now only utility functions

diff --git a/R/nlmr.R → R/NLMR.R b/R/nlmr.R → R/NLMR.R
@@ -1,13 +1,13 @@
 #' Simulating Neutral Landscape Models
 #'
-#' \emph{nlmr} is an R package for simulating neutral landscape models (NLMs).
+#' \emph{NLMR} is an R package for simulating neutral landscape models (NLMs).
 #'
 #' @details This package contains vignettes that introduce NLM and basic usage
-#' of the \emph{nlmr} package. The vignettes in this package are listed below.
+#' of the \emph{NLMR} package. The vignettes in this package are listed below.
 #'
 #' \describe{
-#' \item{\href{https://ropensci.github.io/nlmr/articles/getstarted/}{
-#' Quickstart Guide}}{Short walk-through of the \emph{nlmr} package and how to
+#' \item{\href{https://ropensci.github.io/NLMR/articles/getstarted.html}{
+#' Quickstart Guide}}{Short walk-through of the \emph{NLMR} package and how to
 #' handle the simulations.}
 #' }
 #'

diff --git a/R/nlm_mosaictess.R b/R/nlm_mosaictess.R
@@ -40,10 +40,10 @@
 #'
 
 nlm_mosaictess <- function(ncol,
-                            nrow,
-                            resolution = 1,
-                            germs,
-                            rescale = TRUE) {
+                           nrow,
+                           resolution = 1,
+                           germs,
+                           rescale = TRUE) {
 
   # Check function arguments ----
   checkmate::assert_count(ncol, positive = TRUE)

diff --git a/README.Rmd b/README.Rmd
@@ -15,16 +15,16 @@ knitr::opts_chunk$set(
 )
 ```
 
-[![Build Status](https://travis-ci.org/ropensci/nlmr.svg?branch=develop)](https://travis-ci.org/ropensci/nlmr)[![Build status](https://ci.appveyor.com/api/projects/status/djw840fitcvolbxg?svg=true)](https://ci.appveyor.com/project/ropensci/nlmr)
-[![codecov](https://codecov.io/gh/ropensci/nlmr/branch/develop/graph/badge.svg?token=MKCm2fVrDa)](https://codecov.io/gh/ropensci/nlmr)
+[![Build Status](https://travis-ci.org/ropensci/NLMR.svg?branch=develop)](https://travis-ci.org/ropensci/NLMR)[![Build status](https://ci.appveyor.com/api/projects/status/djw840fitcvolbxg?svg=true)](https://ci.appveyor.com/project/ropensci/NLMR)
+[![codecov](https://codecov.io/gh/ropensci/NLMR/branch/develop/graph/badge.svg?token=MKCm2fVrDa)](https://codecov.io/gh/ropensci/NLMR)
 [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/NLMR)](https://cran.r-project.org/package=NLMR) 
-[![Join the chat at  https://gitter.im/nlmr_landscapegenerator](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/nlmr_landscapegenerator) 
+[![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
 [![](http://cranlogs.r-pkg.org/badges/grand-total/NLMR)](http://cran.rstudio.com/web/packages/NLMR/index.html) 
 [![](https://badges.ropensci.org/188_status.svg)](https://github.com/ropensci/onboarding/issues/188)
 
 
-`nlmr` is an ``R`` package for simulating **n**eutral **l**andscape **m**odels (NLM). Designed to be a generic framework like [NLMpy](https://pypi.python.org/pypi/nlmpy), it leverages the ability to simulate the most common NLM that are described in the ecological literature. 
-`nlmr` builds on the advantages of the ``raster`` package and returns all simulation as ``RasterLayer`` objects, thus ensuring a direct compability to common GIS tasks and a flexible and simple usage.
+`NLMR` is an ``R`` package for simulating **n**eutral **l**andscape **m**odels (NLM). Designed to be a generic framework like [NLMpy](https://pypi.python.org/pypi/nlmpy), it leverages the ability to simulate the most common NLM that are described in the ecological literature. 
+`NLMR` builds on the advantages of the ``raster`` package and returns all simulation as ``RasterLayer`` objects, thus ensuring a direct compability to common GIS tasks and a flexible and simple usage.
 Furthermore, it simulates NLMs within a self-contained, reproducible framework.
 
 ## Installation
@@ -38,29 +38,29 @@ install.packages("NLMR")
 __NOTE__: The version on CRAN is pre-rOpenSci review, so it still contains the
 utility functions you find now in [`landscapetools`](https://github.com/ropensci/landscapetools).
 
-To install the developmental version of ``nlmr``, use the following R code:
+To install the developmental version of ``NLMR``, use the following R code:
 
 ```{r eval = FALSE}
 # install.packages("devtools")
-devtools::install_github("ropensci/nlmr", ref = "develop")
+devtools::install_github("ropensci/NLMR", ref = "develop")
 ```
 
 ## Example
 
-Each neutral landscape models is simulated with a single function (all starting with `nlm_`) in `nlmr`, e.g.:
+Each neutral landscape models is simulated with a single function (all starting with `nlm_`) in `NLMR`, e.g.:
 
 ```{r message=FALSE}
-random_cluster <- nlmr::nlm_randomcluster(nrow = 100,
+random_cluster <- NLMR::nlm_randomcluster(nrow = 100,
                                       ncol = 100,
                                       p    = 0.5,
                                       ai   = c(0.3, 0.6, 0.1),
                                       rescale = FALSE)
 
-random_curdling <- nlmr::nlm_curds(curds = c(0.5, 0.3, 0.6),
+random_curdling <- NLMR::nlm_curds(curds = c(0.5, 0.3, 0.6),
                               recursion_steps = c(32, 6, 2))
 
 
-midpoint_displacememt <- nlmr::nlm_mpd(ncol = 100,
+midpoint_displacememt <- NLMR::nlm_mpd(ncol = 100,
                                  nrow = 100,
                                  roughness = 0.61)
 ```
@@ -69,7 +69,7 @@ midpoint_displacememt <- nlmr::nlm_mpd(ncol = 100,
 
 ## Overview
 
-`nlmr` supplies 14 NLM algorithms, with several options to simulate derivates of
+`NLMR` supplies 14 NLM algorithms, with several options to simulate derivates of
 them. The algorithms differ from each other in spatial auto-correlation, from 
 no auto-correlation (random NLM) to a constant gradient (planar gradients):  
 
@@ -159,18 +159,18 @@ kable(function_tibble) %>%
 
 ## See also
 
-`nlmr` was split during its development process - to have a minimal dependency version
+`NLMR` was split during its development process - to have a minimal dependency version
 for simulating neutral landscape models and an utility toolbox to facilate workflows
 with raster data.
 If you are interested in merging, visualizing or further handling neutral landscape models
 have a look at the [landscapetools](https://github.com/ropensci/landscapetools/) package.
 
 ## Meta
 
-* Please [report any issues or bugs](https://github.com/ropensci/nlmr/issues/new/).
+* Please [report any issues or bugs](https://github.com/ropensci/NLMR/issues/new/).
 * License: GPL3
-* Get citation information for `nlmr` in R doing `citation(package = 'nlmr')`
-    * Additionally, we keep a [record of publications](https://ropensci.github.io/nlmr/articles/publication_record.html/) that use`nlmr`. Hence, if you used `nlmr` please [file an issue on GitHub](https://github.com/ropensci/nlmr/issues/new/) so we can add it to the list.
+* Get citation information for `NLMR` in R doing `citation(package = 'NLMR')`
+    * Additionally, we keep a [record of publications](https://ropensci.github.io/NLMR/articles/publication_record.html/) that use`NLMR`. Hence, if you used `NLMR` please [file an issue on GitHub](https://github.com/ropensci/NLMR/issues/new/) so we can add it to the list.
 * We are very open to contributions - if you are interested check out our [Contributor Guidelines](CONTRIBUTING.md).
     * Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
 

diff --git a/README.md b/README.md
@@ -1,8 +1,8 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
-[![Build Status](https://travis-ci.org/ropensci/nlmr.svg?branch=develop)](https://travis-ci.org/ropensci/nlmr)[![Build status](https://ci.appveyor.com/api/projects/status/djw840fitcvolbxg?svg=true)](https://ci.appveyor.com/project/ropensci/nlmr) [![codecov](https://codecov.io/gh/ropensci/nlmr/branch/develop/graph/badge.svg?token=MKCm2fVrDa)](https://codecov.io/gh/ropensci/nlmr) [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/NLMR)](https://cran.r-project.org/package=NLMR) [![Join the chat at https://gitter.im/nlmr\_landscapegenerator](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/nlmr_landscapegenerator) [![](http://cranlogs.r-pkg.org/badges/grand-total/NLMR)](http://cran.rstudio.com/web/packages/NLMR/index.html) [![](https://badges.ropensci.org/188_status.svg)](https://github.com/ropensci/onboarding/issues/188)
+[![Build Status](https://travis-ci.org/ropensci/NLMR.svg?branch=develop)](https://travis-ci.org/ropensci/NLMR)[![Build status](https://ci.appveyor.com/api/projects/status/djw840fitcvolbxg?svg=true)](https://ci.appveyor.com/project/ropensci/NLMR) [![codecov](https://codecov.io/gh/ropensci/NLMR/branch/develop/graph/badge.svg?token=MKCm2fVrDa)](https://codecov.io/gh/ropensci/NLMR) [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/NLMR)](https://cran.r-project.org/package=NLMR) [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) [![](http://cranlogs.r-pkg.org/badges/grand-total/NLMR)](http://cran.rstudio.com/web/packages/NLMR/index.html) [![](https://badges.ropensci.org/188_status.svg)](https://github.com/ropensci/onboarding/issues/188)
 
-`nlmr` is an `R` package for simulating **n**eutral **l**andscape **m**odels (NLM). Designed to be a generic framework like [NLMpy](https://pypi.python.org/pypi/nlmpy), it leverages the ability to simulate the most common NLM that are described in the ecological literature. `nlmr` builds on the advantages of the `raster` package and returns all simulation as `RasterLayer` objects, thus ensuring a direct compability to common GIS tasks and a flexible and simple usage. Furthermore, it simulates NLMs within a self-contained, reproducible framework.
+`NLMR` is an `R` package for simulating **n**eutral **l**andscape **m**odels (NLM). Designed to be a generic framework like [NLMpy](https://pypi.python.org/pypi/nlmpy), it leverages the ability to simulate the most common NLM that are described in the ecological literature. `NLMR` builds on the advantages of the `raster` package and returns all simulation as `RasterLayer` objects, thus ensuring a direct compability to common GIS tasks and a flexible and simple usage. Furthermore, it simulates NLMs within a self-contained, reproducible framework.
 
 Installation
 ------------
@@ -15,30 +15,30 @@ install.packages("NLMR")
 
 **NOTE**: The version on CRAN is pre-rOpenSci review, so it still contains the utility functions you find now in [`landscapetools`](https://github.com/ropensci/landscapetools).
 
-To install the developmental version of `nlmr`, use the following R code:
+To install the developmental version of `NLMR`, use the following R code:
 
 ``` r
 # install.packages("devtools")
-devtools::install_github("ropensci/nlmr", ref = "develop")
+devtools::install_github("ropensci/NLMR", ref = "develop")
 ```
 
 Example
 -------
 
-Each neutral landscape models is simulated with a single function (all starting with `nlm_`) in `nlmr`, e.g.:
+Each neutral landscape models is simulated with a single function (all starting with `nlm_`) in `NLMR`, e.g.:
 
 ``` r
-random_cluster <- nlmr::nlm_randomcluster(nrow = 100,
+random_cluster <- NLMR::nlm_randomcluster(nrow = 100,
                                       ncol = 100,
                                       p    = 0.5,
                                       ai   = c(0.3, 0.6, 0.1),
                                       rescale = FALSE)
 
-random_curdling <- nlmr::nlm_curds(curds = c(0.5, 0.3, 0.6),
+random_curdling <- NLMR::nlm_curds(curds = c(0.5, 0.3, 0.6),
                               recursion_steps = c(32, 6, 2))
 
 
-midpoint_displacememt <- nlmr::nlm_mpd(ncol = 100,
+midpoint_displacememt <- NLMR::nlm_mpd(ncol = 100,
                                  nrow = 100,
                                  roughness = 0.61)
 ```
@@ -48,7 +48,7 @@ midpoint_displacememt <- nlmr::nlm_mpd(ncol = 100,
 Overview
 --------
 
-`nlmr` supplies 14 NLM algorithms, with several options to simulate derivates of them. The algorithms differ from each other in spatial auto-correlation, from no auto-correlation (random NLM) to a constant gradient (planar gradients):
+`NLMR` supplies 14 NLM algorithms, with several options to simulate derivates of them. The algorithms differ from each other in spatial auto-correlation, from no auto-correlation (random NLM) to a constant gradient (planar gradients):
 
 | Function                      | Description                                                                                                                                                                                                                                                                                                                                                                                                               | Reference                                                           |
 |:------------------------------|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:--------------------------------------------------------------------|
@@ -72,15 +72,15 @@ Overview
 See also
 --------
 
-`nlmr` was split during its development process - to have a minimal dependency version for simulating neutral landscape models and an utility toolbox to facilate workflows with raster data. If you are interested in merging, visualizing or further handling neutral landscape models have a look at the [landscapetools](https://github.com/ropensci/landscapetools/) package.
+`NLMR` was split during its development process - to have a minimal dependency version for simulating neutral landscape models and an utility toolbox to facilate workflows with raster data. If you are interested in merging, visualizing or further handling neutral landscape models have a look at the [landscapetools](https://github.com/ropensci/landscapetools/) package.
 
 Meta
 ----
 
--   Please [report any issues or bugs](https://github.com/ropensci/nlmr/issues/new/).
+-   Please [report any issues or bugs](https://github.com/ropensci/NLMR/issues/new/).
 -   License: GPL3
--   Get citation information for `nlmr` in R doing `citation(package = 'nlmr')`
-    -   Additionally, we keep a [record of publications](https://ropensci.github.io/nlmr/articles/publication_record.html/) that use`nlmr`. Hence, if you used `nlmr` please [file an issue on GitHub](https://github.com/ropensci/nlmr/issues/new/) so we can add it to the list.
+-   Get citation information for `NLMR` in R doing `citation(package = 'NLMR')`
+    -   Additionally, we keep a [record of publications](https://ropensci.github.io/NLMR/articles/publication_record.html/) that use`NLMR`. Hence, if you used `NLMR` please [file an issue on GitHub](https://github.com/ropensci/NLMR/issues/new/) so we can add it to the list.
 -   We are very open to contributions - if you are interested check out our [Contributor Guidelines](CONTRIBUTING.md).
     -   Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,17 +1,6 @@
-## New submission/Updated package
+## Resubmission
 
-nlmr replaces NLMR. 
-
-This update is the development of a review process through 
-rOpenSci. During that, we were encouraged to split the package into two distinct 
-packages and rename it - hence this package is now a slender version that
-is focused only on simulating the data and not handling it. 
-The renaming was done to meet the requirements of rOpenSci and ensure a long-term
-compliance to their software standards.
-
-The package itself keeps its main functionality, so none of the users should 
-have major difficulties. Since there are no reverse depencies, the renaming of
-the package should have only minor drawbacks in general.
+Fixed invalid URL in documentation.
 
 ## Test environments
 

diff --git a/docs/CONDUCT.html b/docs/CONDUCT.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html