diff --git a/DESCRIPTION b/DESCRIPTION
index 8a6c1f7..8a31981 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -10,6 +10,7 @@ Description: Provides a framework for generating virtual species distributions,
     models. This package integrates the existing methodological approaches with the
     objective of generating virtual species distributions with increased ecological
     realism.
+Encoding: UTF-8
 License: GPL (>=2.0)
 Depends:
     raster
@@ -23,4 +24,4 @@ Imports:
     stats,
     utils
 URL: http://borisleroy.com/virtualspecies
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
diff --git a/man/convertToPA.Rd b/man/convertToPA.Rd
index 3e14e88..01bb340 100644
--- a/man/convertToPA.Rd
+++ b/man/convertToPA.Rd
@@ -4,9 +4,17 @@
 \alias{convertToPA}
 \title{Convert a virtual species distribution (or a suitability raster) into presence-absence}
 \usage{
-convertToPA(x, PA.method = "probability", prob.method = "logistic",
-  beta = "random", alpha = -0.05, a = NULL, b = NULL,
-  species.prevalence = NULL, plot = TRUE)
+convertToPA(
+  x,
+  PA.method = "probability",
+  prob.method = "logistic",
+  beta = "random",
+  alpha = -0.05,
+  a = NULL,
+  b = NULL,
+  species.prevalence = NULL,
+  plot = TRUE
+)
 }
 \arguments{
 \item{x}{a suitability raster, or the output from functions 
diff --git a/man/generateRandomSp.Rd b/man/generateRandomSp.Rd
index 89b4a94..a4b1954 100644
--- a/man/generateRandomSp.Rd
+++ b/man/generateRandomSp.Rd
@@ -4,13 +4,25 @@
 \alias{generateRandomSp}
 \title{Generate a random virtual species distribution from environmental variables}
 \usage{
-generateRandomSp(raster.stack, approach = "automatic", rescale = TRUE,
-  convert.to.PA = TRUE, relations = c("gaussian", "linear", "logistic",
-  "quadratic"), rescale.each.response = TRUE, realistic.sp = TRUE,
-  species.type = "multiplicative", niche.breadth = "any",
-  sample.points = FALSE, nb.points = 10000,
-  PA.method = "probability", alpha = -0.1, adjust.alpha = TRUE,
-  beta = "random", species.prevalence = NULL, plot = TRUE)
+generateRandomSp(
+  raster.stack,
+  approach = "automatic",
+  rescale = TRUE,
+  convert.to.PA = TRUE,
+  relations = c("gaussian", "linear", "logistic", "quadratic"),
+  rescale.each.response = TRUE,
+  realistic.sp = TRUE,
+  species.type = "multiplicative",
+  niche.breadth = "any",
+  sample.points = FALSE,
+  nb.points = 10000,
+  PA.method = "probability",
+  alpha = -0.1,
+  adjust.alpha = TRUE,
+  beta = "random",
+  species.prevalence = NULL,
+  plot = TRUE
+)
 }
 \arguments{
 \item{raster.stack}{a RasterStack object, in which each layer represent an environmental 
diff --git a/man/generateSpFromBCA.Rd b/man/generateSpFromBCA.Rd
index bfc9fbf..ef63b34 100644
--- a/man/generateSpFromBCA.Rd
+++ b/man/generateSpFromBCA.Rd
@@ -4,10 +4,18 @@
 \alias{generateSpFromBCA}
 \title{Generate a virtual species distribution from a Between Component Analysis of environmental variables}
 \usage{
-generateSpFromBCA(raster.stack.current, raster.stack.future,
-  rescale = TRUE, niche.breadth = "any", means = NULL, sds = NULL,
-  bca = NULL, sample.points = FALSE, nb.points = 10000,
-  plot = TRUE)
+generateSpFromBCA(
+  raster.stack.current,
+  raster.stack.future,
+  rescale = TRUE,
+  niche.breadth = "any",
+  means = NULL,
+  sds = NULL,
+  bca = NULL,
+  sample.points = FALSE,
+  nb.points = 10000,
+  plot = TRUE
+)
 }
 \arguments{
 \item{raster.stack.current}{a RasterStack object, in which each layer represent an environmental 
diff --git a/man/generateSpFromFun.Rd b/man/generateSpFromFun.Rd
index b799eee..8c78159 100644
--- a/man/generateSpFromFun.Rd
+++ b/man/generateSpFromFun.Rd
@@ -4,9 +4,15 @@
 \alias{generateSpFromFun}
 \title{Generate a virtual species distributions with responses to environmental variables}
 \usage{
-generateSpFromFun(raster.stack, parameters, rescale = TRUE,
-  formula = NULL, species.type = "multiplicative",
-  rescale.each.response = TRUE, plot = FALSE)
+generateSpFromFun(
+  raster.stack,
+  parameters,
+  rescale = TRUE,
+  formula = NULL,
+  species.type = "multiplicative",
+  rescale.each.response = TRUE,
+  plot = FALSE
+)
 }
 \arguments{
 \item{raster.stack}{a RasterStack object, in which each layer represent an environmental 
diff --git a/man/generateSpFromPCA.Rd b/man/generateSpFromPCA.Rd
index bc3ff1b..7750bb1 100644
--- a/man/generateSpFromPCA.Rd
+++ b/man/generateSpFromPCA.Rd
@@ -4,9 +4,18 @@
 \alias{generateSpFromPCA}
 \title{Generate a virtual species distribution with a PCA of environmental variables}
 \usage{
-generateSpFromPCA(raster.stack, rescale = TRUE, niche.breadth = "any",
-  axes = c(1, 2), means = NULL, sds = NULL, pca = NULL,
-  sample.points = FALSE, nb.points = 10000, plot = TRUE)
+generateSpFromPCA(
+  raster.stack,
+  rescale = TRUE,
+  niche.breadth = "any",
+  axes = c(1, 2),
+  means = NULL,
+  sds = NULL,
+  pca = NULL,
+  sample.points = FALSE,
+  nb.points = 10000,
+  plot = TRUE
+)
 }
 \arguments{
 \item{raster.stack}{a RasterStack object, in which each layer represent an environmental 
diff --git a/man/limitDistribution.Rd b/man/limitDistribution.Rd
index f8b4194..6f0a128 100644
--- a/man/limitDistribution.Rd
+++ b/man/limitDistribution.Rd
@@ -4,8 +4,7 @@
 \alias{limitDistribution}
 \title{Limit a virtual species distribution to a defined area}
 \usage{
-limitDistribution(x, geographical.limit = "extent", area = NULL,
-  plot = TRUE)
+limitDistribution(x, geographical.limit = "extent", area = NULL, plot = TRUE)
 }
 \arguments{
 \item{x}{a \code{rasterLayer} object composed of 0, 1 and NA, or the output list from 
diff --git a/man/plotResponse.Rd b/man/plotResponse.Rd
index 11d0447..5022814 100644
--- a/man/plotResponse.Rd
+++ b/man/plotResponse.Rd
@@ -4,8 +4,15 @@
 \alias{plotResponse}
 \title{Visualise the response of the virtual species to environmental variables}
 \usage{
-plotResponse(x, parameters = NULL, approach = NULL, rescale = TRUE,
-  axes.to.plot = NULL, no.plot.reset = FALSE, ...)
+plotResponse(
+  x,
+  parameters = NULL,
+  approach = NULL,
+  rescale = TRUE,
+  axes.to.plot = NULL,
+  no.plot.reset = FALSE,
+  ...
+)
 }
 \arguments{
 \item{x}{the output from \code{\link{generateSpFromFun}}, \code{\link{generateSpFromPCA}}, 
diff --git a/man/removeCollinearity.Rd b/man/removeCollinearity.Rd
index f389abd..ec47cf0 100644
--- a/man/removeCollinearity.Rd
+++ b/man/removeCollinearity.Rd
@@ -4,9 +4,15 @@
 \alias{removeCollinearity}
 \title{Remove collinearity among variables of a a raster stack}
 \usage{
-removeCollinearity(raster.stack, multicollinearity.cutoff = 0.7,
-  select.variables = FALSE, sample.points = FALSE, nb.points = 10000,
-  plot = FALSE, method = "pearson")
+removeCollinearity(
+  raster.stack,
+  multicollinearity.cutoff = 0.7,
+  select.variables = FALSE,
+  sample.points = FALSE,
+  nb.points = 10000,
+  plot = FALSE,
+  method = "pearson"
+)
 }
 \arguments{
 \item{raster.stack}{a RasterStack object, in which each layer represent an environmental 
diff --git a/man/sampleOccurrences.Rd b/man/sampleOccurrences.Rd
index f66f00c..340daff 100644
--- a/man/sampleOccurrences.Rd
+++ b/man/sampleOccurrences.Rd
@@ -4,12 +4,23 @@
 \alias{sampleOccurrences}
 \title{Sample occurrences in a virtual species distribution}
 \usage{
-sampleOccurrences(x, n, type = "presence only",
-  extract.probability = FALSE, sampling.area = NULL,
-  detection.probability = 1, correct.by.suitability = FALSE,
-  error.probability = 0, bias = "no.bias", bias.strength = 50,
-  bias.area = NULL, weights = NULL, sample.prevalence = NULL,
-  replacement = FALSE, plot = TRUE)
+sampleOccurrences(
+  x,
+  n,
+  type = "presence only",
+  extract.probability = FALSE,
+  sampling.area = NULL,
+  detection.probability = 1,
+  correct.by.suitability = FALSE,
+  error.probability = 0,
+  bias = "no.bias",
+  bias.strength = 50,
+  bias.area = NULL,
+  weights = NULL,
+  sample.prevalence = NULL,
+  replacement = FALSE,
+  plot = TRUE
+)
 }
 \arguments{
 \item{x}{a \code{rasterLayer} object or the output list from