diff --git a/CRAN-RELEASE b/CRAN-RELEASE deleted file mode 100644 index c772351..0000000 --- a/CRAN-RELEASE +++ /dev/null @@ -1,2 +0,0 @@ -This package was submitted to CRAN on 2018-02-16. -Once it is accepted, delete this file and tag the release (commit e23d5fe100). diff --git a/R/nlm_edgegradient.R b/R/nlm_edgegradient.R index 0dba755..7c4c55b 100755 --- a/R/nlm_edgegradient.R +++ b/R/nlm_edgegradient.R @@ -63,7 +63,9 @@ nlm_edgegradient <- function(ncol, } # Create planar gradient ---- - gradient_raster <- nlm_planargradient(ncol, nrow, direction) + gradient_raster <- nlm_planargradient(ncol, nrow, + resolution = resolution, + direction = direction) # Transform to a central gradient ---- edgegradient_raster <- diff --git a/R/util_facetplot.R b/R/util_facetplot.R old mode 100644 new mode 100755 index 2ce6317..6e13a2c --- a/R/util_facetplot.R +++ b/R/util_facetplot.R @@ -1,6 +1,6 @@ #' util_facetplot() for visual overview #' -#' @description Plot multiple maps side by side for visual inspection. +#' @description Plot multiple raster (RasterStack, -brick or list of raster) side by side as facets. #' #' @details The output uses ggplots faceting and beforehand raster2tibble. #' Thus you will loose any spatial information (resolution, extent or reference system). diff --git a/man/NLMR-package.Rd b/man/NLMR-package.Rd index d5a8b39..78f7c64 100644 --- a/man/NLMR-package.Rd +++ b/man/NLMR-package.Rd @@ -13,12 +13,12 @@ This package contains vignettes that introduce NLM and basic usage of the \emph{NLMR} package. The vignettes in this package are listed below. \describe{ -\item{\href{https://marcosci.github.io/NLMR/articles/background.html}{NLM +\item{\href{https://marcosci.github.io/NLMR/articles/background.html/}{NLM Concepts + Terminology}}{Background information on the concepts and terminology that underpin the simulation of neutral landscape models.} -\item{\href{https://marcosci.github.io/NLMR/articles/bestiary.html}{NLMR +\item{\href{https://marcosci.github.io/NLMR/articles/bestiary.html/}{NLMR Bestiary}}{Bestiary of the available neutral landscape models.} -\item{\href{https://marcosci.github.io/NLMR/articles/getstarted.html}{ +\item{\href{https://marcosci.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/man/nlm_distancegradient.Rd b/man/nlm_distancegradient.Rd index 947663c..18a37e5 100644 --- a/man/nlm_distancegradient.Rd +++ b/man/nlm_distancegradient.Rd @@ -27,7 +27,7 @@ Otherwise, the distance in raster units is calculated.} RasterLayer } \description{ -Simulate a distance gradient neutral landscape model. +Simulates a distance gradient neutral landscape model. } \details{ The function takes the number of columns and rows as input and creates a diff --git a/man/nlm_edgegradient.Rd b/man/nlm_edgegradient.Rd index 30f1b7b..0f7e20d 100644 --- a/man/nlm_edgegradient.Rd +++ b/man/nlm_edgegradient.Rd @@ -32,7 +32,7 @@ Simulates an edge gradient neutral landscape model. } \details{ Simulates a linear gradient orientated on a specified or random direction -that has a central peak. which runs perpendicular to the gradient direction. +that has a central peak, which runs perpendicular to the gradient direction. } \examples{ diff --git a/man/nlm_fBm.Rd b/man/nlm_fBm.Rd index 35d3980..9ec596f 100644 --- a/man/nlm_fBm.Rd +++ b/man/nlm_fBm.Rd @@ -37,8 +37,7 @@ Neutral landscapes are generated using fractional Brownian motion, an extension of Brownian motion in which the amount of correlation between steps is controlled by the Hurst coefficient H. An H of 1 produces a relatively smooth surface while an H of 0 produces a rough, uncorrelated, - surface. Implementation of this method is limited to landscapes with - extents less than 90 by 90 cells. + surface. } \examples{ # simulate fractional brownian motion @@ -50,7 +49,6 @@ util_plot(fBm_raster) } \references{ Martin Schlather, Alexander Malinowski, Peter J. Menck, Marco Oesting, -Kirstin Strokorb (2015). Analysis, Simulation and Prediction of Multivariate -Random Fields with Package RandomFields. \emph{Journal of Statistical +Kirstin Strokorb (2015). nlm_fBm. \emph{Journal of Statistical Software}, 63(8), 1-25. URL http://www.jstatsoft.org/v63/i08/. } diff --git a/man/nlm_mosaicfield.Rd b/man/nlm_mosaicfield.Rd index 4b752b1..a030252 100644 --- a/man/nlm_mosaicfield.Rd +++ b/man/nlm_mosaicfield.Rd @@ -39,7 +39,7 @@ If \code{TRUE} (default), the values are rescaled between 0-1.} RasterLayer or List with RasterLayer(s) and/or RasterBrick } \description{ -Simulate a mosaic random field neutral landscape model. +Simulates a mosaic random field neutral landscape model. } \examples{ diff --git a/man/nlm_mpd.Rd b/man/nlm_mpd.Rd index 155ad8a..5844cc1 100644 --- a/man/nlm_mpd.Rd +++ b/man/nlm_mpd.Rd @@ -18,7 +18,7 @@ Number of rows for the raster.} Resolution of the raster.} \item{roughness}{[\code{numerical(1)}]\cr -Controls the level of spatial autocorrelation (!= hurst index)} +Controls the level of spatial autocorrelation (!= hurst exponent)} \item{rand_dev}{[\code{numerical(1)}]\cr Initial standard deviation for the displacement step (default == 1)} @@ -34,7 +34,7 @@ the algorithm.} RasterLayer } \description{ -Simulate a midpoint displacement neutral landscape model. +Simulates a midpoint displacement neutral landscape model. } \details{ The algorithm is a direct implementation of the midpoint displacement @@ -53,7 +53,7 @@ It performs the following steps: diamond.} } -At each iteration the roughness, an approximation to common hurst index, +At each iteration the roughness, an approximation to common hurst exponent, is reduced. The image below shows the steps involved in running the diamond-square diff --git a/man/nlm_percolation.Rd b/man/nlm_percolation.Rd index 4bad0fa..f42cced 100644 --- a/man/nlm_percolation.Rd +++ b/man/nlm_percolation.Rd @@ -23,7 +23,7 @@ Probability value for setting a cell either to 0 or 1.} RasterLayer } \description{ -Create a random percolation neutral landscape model. +Simulates a random percolation neutral landscape model. } \details{ The simulation of a random percolation map is accomplished in two steps: diff --git a/man/nlm_planargradient.Rd b/man/nlm_planargradient.Rd index 932641d..100fc8f 100644 --- a/man/nlm_planargradient.Rd +++ b/man/nlm_planargradient.Rd @@ -28,7 +28,7 @@ If \code{TRUE} (default), the values are rescaled between 0-1.} RasterLayer } \description{ -Create a planar gradient neutral landscape model. +Simulates a planar gradient neutral landscape model. } \details{ Simulates a linear gradient sloping in a specified or random direction. diff --git a/man/nlm_random.Rd b/man/nlm_random.Rd index 96bbcc5..a04a523 100644 --- a/man/nlm_random.Rd +++ b/man/nlm_random.Rd @@ -23,7 +23,7 @@ If \code{TRUE} (default), the values are rescaled between 0-1.} RasterLayer } \description{ -Simulate a spatially random neutral landscape model with values +Simulates a spatially random neutral landscape model with values drawn a uniform distribution. } \details{ diff --git a/man/nlm_randomrectangularcluster.Rd b/man/nlm_randomrectangularcluster.Rd index c86d9f6..5994515 100644 --- a/man/nlm_randomrectangularcluster.Rd +++ b/man/nlm_randomrectangularcluster.Rd @@ -24,7 +24,7 @@ nlm_randomrectangularcluster(ncol, nrow, resolution = 1, minl, maxl, RasterLayer with random values ranging from 0-1. } \description{ -Create a random rectangular cluster neutral landscape model with values ranging 0-1. +Simulates a random rectangular cluster neutral landscape model with values ranging 0-1. } \examples{ # simulate random rectangular cluster @@ -38,3 +38,8 @@ util_plot(randomrectangular_cluster) } } +\references{ +Gustafson, E.J. & Parker, G.R. (1992). Relationships between landcover +proportion and indices of landscape spatial pattern. \emph{Landscape ecology}, +7, 101–110. +} diff --git a/man/util_facetplot.Rd b/man/util_facetplot.Rd index 2d63c60..bba0067 100644 --- a/man/util_facetplot.Rd +++ b/man/util_facetplot.Rd @@ -13,7 +13,7 @@ util_facetplot(x) ggplot } \description{ -Plot multiple maps side by side for visual inspection. +Plot multiple raster (RasterStack, -brick or list of raster) side by side as facets. } \details{ The output uses ggplots faceting and beforehand raster2tibble.