restore basic functionality

.Rbuildignore

@@ -1,2 +1,8 @@
 ^landscapetools\.Rproj$
 ^\.Rproj\.user$
+^appveyor\.yml$
+^README\.Rmd$
+^\.travis\.yml$
+^CODE_OF_CONDUCT\.md$
+^LICENSE\.md$
+^CONTRIBUTING\.md$

.travis.yml

@@ -0,0 +1,5 @@
+# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
+
+language: R
+sudo: false
+cache: packages

CODE_OF_CONDUCT.md

@@ -0,0 +1,25 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who 
+contribute through reporting issues, posting feature requests, updating documentation,
+submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for
+everyone, regardless of level of experience, gender, gender identity and expression,
+sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or
+imagery, derogatory comments or personal attacks, trolling, public or private harassment,
+insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this 
+Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
+from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by 
+opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the Contributor Covenant 
+(http://contributor-covenant.org), version 1.0.0, available at 
+http://contributor-covenant.org/version/1/0/0/

CONTRIBUTING.md

@@ -0,0 +1,24 @@
+# CONTRIBUTING #
+
+### Please contribute!
+
+We love collaboration.
+
+### Bugs?
+
+* Submit an issue on the Issues page [here](https://github.com/marcosci/nlmr/issues)
+
+### Code contributions
+
+* Fork this repo to your Github account
+* Clone your version on your account down to your machine from your account, e.g,. `git clone https://github.com/<yourgithubusername>/nlmr.git`
+* Make sure to track progress upstream (i.e., on our version of `scrubr` at `ropensci/scrubr`) by doing `git remote add upstream https://github.com/ropensci/nlmr.git`. Before making changes make sure to pull changes in from upstream by doing either `git fetch upstream` then merge later or `git pull upstream` to fetch and merge in one step
+* Make your changes (bonus points for making changes on a new branch)
+* If you alter package functionality at all (e.g., the code itself, not just documentation)
+please do write some tests to cover the new functionality.
+* Push up to your account
+* Submit a pull request to home base at `ropensci/nlmr`
+
+### Questions? Get in touch: [[email protected]](mailto:[email protected])
+
+### Thanks for contributing!

DESCRIPTION

@@ -1,11 +1,29 @@
 Package: landscapetools
-Version: 0.0.0.9000
+Version: 0.1
 Title: What the Package Does (One Line, Title Case)
 Description: What the package does (one paragraph).
-Authors@R: person("First", "Last", , "[email protected]", c("aut", "cre"))
-License: What license it uses
+Authors@R: c(person("Marco", "Sciaini", email = "[email protected]", role = c("aut", "cre")), 
+    person("Matthias", "Fritsch", email = "[email protected]", role =  c("aut")))
+License: GPL-3
 Encoding: UTF-8
 LazyData: true
 ByteCompile: true
 Suggests: 
-    testthat
+    testthat,
+    nlmr
+URL: https://github.com/marcosci/landscapetools
+BugReports: https://github.com/marcosci/landscapetools/issues
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 6.0.1
+Imports: 
+    magrittr,
+    checkmate,
+    dplyr,
+    extrafont,
+    ggplot2,
+    purrr,
+    raster,
+    rasterVis,
+    tibble,
+    tidyr,
+    viridis

NAMESPACE

@@ -1,2 +1,20 @@
-# Generated by roxygen2: fake comment so roxygen2 overwrites silently.
-exportPattern("^[^\\.]")
+# Generated by roxygen2: do not edit by hand
+
+export("%>%")
+export(theme_nlm)
+export(theme_nlm_discrete)
+export(theme_nlm_grey)
+export(theme_nlm_grey_discrete)
+export(util_binarize)
+export(util_calc_boundaries)
+export(util_classify)
+export(util_facetplot)
+export(util_import_roboto_condensed)
+export(util_merge)
+export(util_plot)
+export(util_plot_grey)
+export(util_raster2tibble)
+export(util_rescale)
+export(util_tibble2raster)
+export(util_w2cp)
+importFrom(magrittr,"%>%")

R/landscapetools.R

@@ -0,0 +1,15 @@
+#' landscapetools
+#'
+#' \emph{landscapetools} is
+#'
+#' @details ...
+#'
+
+# nocov start
+# nolint start
+"_PACKAGE"
+
+globalVariables(c("value", "."))
+
+# nolint end
+# nocov end

R/theme_nlm.R

@@ -2,38 +2,37 @@
 #'
 #' @description Opinionated ggplot2 theme to visualize NLM raster.
 #'
-#' @param base_family [\code{character}()]  base font family size
-#' @param base_size [\code{numeric}(1)] base font size
-#' @param plot_title_family [\code{character}()] plot title family
-#' @param plot_title_face [\code{character}()] plot title face
-#' @param plot_title_size [\code{character}()] plot title size
-#' @param plot_title_margin [\code{numeric}(1)] plot title margin
-#' @param plot_margin [\code{character}()]
-#' plot margin (specify with \code{ggplot2::margin})
-#' @param subtitle_family [\code{character}()] plot subtitle family
-#' @param subtitle_face [\code{character}()]` plot subtitle face
-#' @param subtitle_size [\code{numeric}(1)] plot subtitle size
-#' @param subtitle_margin [\code{numeric}(1)]
+#' @param base_family  base font family size
+#' @param base_size  base font size
+#' @param plot_title_family plot title family
+#' @param plot_title_face  plot title face
+#' @param plot_title_size  plot title size
+#' @param plot_title_margin plot title margin
+#' @param plot_margin plot margin (specify with `ggplot2::margin``)
+#' @param subtitle_family plot subtitle family
+#' @param subtitle_face  plot subtitle face
+#' @param subtitle_size plot subtitle size
+#' @param subtitle_margin
 #' plot subtitle margin bottom (single numeric value)
-#' @param strip_text_family [\code{character}()] facet facet label font family
-#' @param strip_text_face [\code{character}()] facet facet label font face
-#' @param strip_text_size [\code{numeric}(1)]
-#' facet label font family, face and size
-#' @param caption_family [\code{character}()] plot caption family
-#' @param caption_face [\code{character}()] plot caption face
-#' @param caption_size [\code{numeric}(1)] plot caption size
-#' @param caption_margin [\code{numeric}(1)] plot caption margin
-#' @param legend_title [\code{character}()] Title of the legend (default "Z")
-#' @param legend_labels [\code{character}()] Labels for the legend ticks, if
+#' @param strip_text_family facet facet label font family
+#' @param strip_text_face  facet facet label font face
+#' @param strip_text_size facet label font family, face and size
+#' @param caption_family plot caption family
+#' @param caption_face plot caption face
+#' @param caption_size plot caption size
+#' @param caption_margin plot caption margin
+#' @param legend_title Title of the legend (default `"Z"`)
+#' @param legend_labels Labels for the legend ticks, if
 #' used with \code{\link{util_plot}} they are automatically derived.
-#' @param ratio [\code{character}()]
+#' @param ratio
 #' ratio for tiles (default 1, if your raster is not a square the ratio should
 #' be \code{raster::nrow(x) / raster::ncol(x)})
-#' @param viridis_scale [\code{character}(1)]
+#' @param viridis_scale
 #' Five options are available: "viridis - magma" (= "A"),
 #'                             "viridis - inferno" (= "B"),
 #'                             "viridis - plasma" (= "C"),
-#'                             "viridis - viridis" (= "D",  the default option)
+#'                             "viridis - viridis" (= "D",  the default option),
+#'                             "viridis - cividis" (= "E")
 #'
 #' @details
 #' A focused theme to visualize raster data that sets a lot of defaults for the
@@ -55,7 +54,7 @@
 #' # nolint start
 #' \dontrun{
 #' # simulate NLM
-#' x <- nlm_random(ncol = 75,
+#' x <- nlmr::nlm_random(ncol = 75,
 #'                 nrow = 75)
 #' # classify
 #' y <- c(0.5, 0.15, 0.25)
@@ -111,20 +110,20 @@ NULL
 
 #' @rdname theme_nlm
 #' @export
-theme_nlm <- function(base_family = "serif",
+theme_nlm <- function(base_family = "plain",
                       base_size = 11.5,
-                      plot_title_family = "serif",
+                      plot_title_family = "plain",
                       plot_title_size = 18,
                       plot_title_face = "bold",
                       plot_title_margin = 10,
-                      subtitle_family = "serif",
+                      subtitle_family = "plain",
                       subtitle_size = 13,
                       subtitle_face = "plain",
                       subtitle_margin = 15,
                       strip_text_family = base_family,
                       strip_text_size = 12,
                       strip_text_face = "plain",
-                      caption_family = "serif",
+                      caption_family = "plain",
                       caption_size = 9,
                       caption_face = "plain",
                       caption_margin = 10,
@@ -197,20 +196,20 @@ theme_nlm <- function(base_family = "serif",
 #' @rdname theme_nlm
 #' @export
 theme_nlm_discrete <- function(
-  base_family = "serif",
+  base_family = "plain",
   base_size = 11.5,
   plot_title_family = base_family,
   plot_title_size = 18,
   plot_title_face = "bold",
   plot_title_margin = 10,
-  subtitle_family = "serif",
+  subtitle_family = "plain",
   subtitle_size = 13,
   subtitle_face = "plain",
   subtitle_margin = 15,
   strip_text_family = base_family,
   strip_text_size = 12,
   strip_text_face = "plain",
-  caption_family = "serif",
+  caption_family = "plain",
   caption_size = 9,
   caption_face = "plain",
   caption_margin = 10,
@@ -289,20 +288,20 @@ theme_nlm_discrete <- function(
 
 #' @rdname theme_nlm
 #' @export
-theme_nlm_grey <- function(base_family = "serif",
+theme_nlm_grey <- function(base_family = "plain",
                            base_size = 11.5,
                            plot_title_family = base_family,
                            plot_title_size = 18,
                            plot_title_face = "bold",
                            plot_title_margin = 10,
-                           subtitle_family = "serif",
+                           subtitle_family = "plain",
                            subtitle_size = 13,
                            subtitle_face = "plain",
                            subtitle_margin = 15,
                            strip_text_family = base_family,
                            strip_text_size = 12,
                            strip_text_face = "plain",
-                           caption_family = "serif",
+                           caption_family = "plain",
                            caption_size = 9,
                            caption_face = "plain",
                            caption_margin = 10,
@@ -375,20 +374,20 @@ theme_nlm_grey <- function(base_family = "serif",
 #' @rdname theme_nlm
 #' @export
 theme_nlm_grey_discrete <-
-  function(base_family = "serif",
+  function(base_family = "plain",
            base_size = 11.5,
            plot_title_family = base_family,
            plot_title_size = 18,
            plot_title_face = "bold",
            plot_title_margin = 10,
-           subtitle_family = "serif",
+           subtitle_family = "plain",
            subtitle_size = 13,
            subtitle_face = "plain",
            subtitle_margin = 15,
            strip_text_family = base_family,
            strip_text_size = 12,
            strip_text_face = "plain",
-           caption_family = "serif",
+           caption_family = "plain",
            caption_size = 9,
            caption_face = "plain",
            caption_margin = 10,

R/util_binarize.R

@@ -1,20 +1,19 @@
 #' Binarize continuous raster values
 #'
 #' @description Classify continuous raster values into binary map cells based upon given
-#' break(s).
+#' break(`s`).
 #'
-#' @details Breaks are considered to be habitat percentages (p). If more than
+#' @details Breaks are considered to be habitat percentages (`p`). If more than
 #' one percentage is given multiple layers are written in the same brick.
 #'
-#' @param x [\code{Raster* object}]
-#'
-#' @param breaks a vector with one or more break percentages
+#' @param x Raster* object
 #'
+#' @param breaks Vector with one or more break percentages
 #'
 #' @return RasterLayer / RasterBrick
 #'
 #' @examples
-#' rndMap <- nlm_random(10, 10)
+#' rndMap <- nlmr::nlm_random(10, 10)
 #' breaks <- c(0.3, 0.5, 0.7, 0.9)
 #' rnd_bin <- util_binarize(rndMap, breaks)
 #' util_plot(rnd_bin)

R/util_calcboundaries.R

@@ -3,8 +3,8 @@
 #' @description Determine upper class boundaries for classification of a matrix with values ranging 0-1 based upon an
 #' vector of cumulative proportions.
 #'
-#' @param x [\code{matrix(x,y)}]\cr 2D matrix of data values.
-#' @param cumulative_proportions [\code{numerical}]\cr Vector of class cumulative proportions, as generated by \code{w2cp}.
+#' @param x 2D matrix of data values.
+#' @param cumulative_proportions Vector of class cumulative proportions, as generated by `w2cp`.
 #'
 #'
 #' @return Numerical vector with boundaries for matrix classification

R/util_classify.R

@@ -10,17 +10,14 @@
 #' If the numerical vector of weightings does not sum up to 1, the sum of the
 #' weightings is divided by the number of elements in the weightings vector and this is then used for the classification.
 #'
-#' @param x [\code{matrix(x,y)}]\cr
-#' 2D matrix of data values.
-#' @param weighting [\code{numerical}]\cr
-#' Vector of numeric values.
-#' @param level_names [\code{character}]\cr
-#' Vector of names for the factor levels.
+#' @param x 2D matrix
+#' @param weighting Vector of numeric values.
+#' @param level_names Vector of names for the factor levels.
 #'
 #' @return RasterLayer
 #'
 #' @examples
-#' x <- nlm_random(10, 10)
+#' x <- nlmr::nlm_random(10, 10)
 #' y <- c(0.5, 0.25, 0.25)
 #' util_classify(x, y, level_names = c("Land Use 1", "Land Use 2", "Land Use 3"))
 #'

R/util_facetplot.R

@@ -10,17 +10,17 @@
 #' size of the maps it is advisable to store the plot in an object and print it to
 #' a file. This will help with compressing and rendering the image.
 #'
-#' @param x [\code{Raster* object}] (Layer, Stack, Brick) or a list of rasterLayers.
+#' @param x Raster* Layer, Stack, Brick or a list of rasterLayers.
 #' @param nrow,ncol Number of rows and columns.
 #'
 #' @return ggplot
 #'
 #' @examples
 #' \dontrun{
-#' l1 <- nlm_fBm(64, 64)
-#' l2 <- nlm_planargradient(64, 64)
-#' l3 <- nlm_randomrectangularcluster(ncol = 60, nrow = 60, minl = 5, maxl = 10)
-#' l4 <- nlm_random(64, 64)
+#' l1 <- nlmr::nlm_fBm(64, 64)
+#' l2 <- nlmr::nlm_planargradient(64, 64)
+#' l3 <- nlmr::nlm_randomrectangularcluster(ncol = 60, nrow = 60, minl = 5, maxl = 10)
+#' l4 <- nlmr::nlm_random(64, 64)
 #'
 #' bri1 <- raster::brick(l1, l2)
 #' util_facetplot(bri1)