Update package index

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dsmextra
 Title: A Toolkit for Extrapolation Assessments in Density Surface Models
-Version: 1.0.2
+Version: 1.1.0
 Authors@R: c(person("Phil", "Bouchet", email = "pjbouchet@gmail.com", role = c("aut", "cre")), person("David", "Miller", email = "dlm22@st-andrews.ac.uk", role = c("aut")), person("Laura", "Mannocci", email = "laura.mannocci@duke.edu", role = c("aut")), person("Jason", "Roberts", email = "jason.roberts@duke.edu", role = c("ctb")), person("Catriona", "Harris", email = "Catriona.Harris@st-andrews.ac.uk", role = c("ctb")), person("Len", "Thomas", email = "len.thomas@st-andrews.ac.uk", role = c("ctb")))
 Description: User-friendly tools for the detection and assessment of extrapolation in multivariate environmental space (Bouchet et al. 2019), with applications to density surface models of line transect data. Provides convenience functions for summarising and visualising extrapolation in prediction areas.
 License: GPL-3 + file LICENSE

R/ExDet.R

@@ -12,7 +12,8 @@
 #' @references Mesgaran, M.B., Cousens, R.D. & Webber, B.L. (2014) \href{https://onlinelibrary.wiley.com/doi/full/10.1111/ddi.12209}{Here be dragons: a tool for quantifying novelty due to covariate range and correlation change when projecting species distribution models}. Diversity & Distributions, 20: 1147-1159, DOI: 10.1111/ddi.12209
 #'
 #' Broennimann O, Di Cola V, Guisan A (2016). ecospat: Spatial Ecology Miscellaneous Methods. R package version 2.1.1. \href{https://CRAN.R-project.org/package=ecospat}{https://CRAN.R-project.org/package=ecospat}.
-#'
+#' @keywords internal
+
 ExDet <- function(ref, tg, xp){
 
   #---------------------------------------------

R/print.extrapolation_results_summary.R

@@ -8,6 +8,8 @@
 #' @param digits precision of results
 #' @param \dots for S3 compatability
 #' @return invisibly returns the summary part of the object only, printing the results
+#' @keywords internal
+
 print.extrapolation_results_summary <- function(x, digits=2, ...){
 
   class(x) <- class(x)[-1]

R/summarise_extrapolation.R

@@ -12,7 +12,7 @@
 #' @references Bouchet PJ, Miller DL, Roberts JJ, Mannocci L, Harris CM and Thomas L (2019). From here and now to there and then: Practical recommendations for extrapolating cetacean density surface models to novel conditions. CREEM Technical Report 2019-01, 59 p. \href{https://research-repository.st-andrews.ac.uk/handle/10023/18509}{https://research-repository.st-andrews.ac.uk/handle/10023/18509}
 #'
 #' Mesgaran MB, Cousens RD, Webber BL (2014). Here be dragons: a tool for quantifying novelty due to covariate range and correlation change when projecting species distribution models. Diversity & Distributions, 20: 1147-1159, DOI: \href{https://onlinelibrary.wiley.com/doi/full/10.1111/ddi.12209}{10.1111/ddi.12209}
-#'
+#' @keywords internal
 
 summarise_extrapolation <- function(extrapolation.object,
                                     covariate.names = NULL,

R/summary.extrapolation_results.R

@@ -8,6 +8,8 @@
 #' @param digits precision of results
 #' @param \dots for S3 compatability
 #' @return invisibly returns the summary part of the object only, printing the results
+#' @keywords internal
+
 summary.extrapolation_results <- function(object, digits, ...){
 
   object$summary

R/whatif.opt.R

@@ -29,7 +29,8 @@
 #' King G, Zeng L (2007). When can history be our guide? The pitfalls of counterfactual inference. International Studies Quarterly 51, 183–210. DOI: \href{https://www.jstor.org/stable/pdf/4621707.pdf?seq=1#page_scan_tab_contents}{10.1111/j.1468-2478.2007.00445.x}
 #'
 #' Henry L, Wickham H (2019). purrr: Functional Programming Tools. R package version 0.3.2. \href{https://CRAN.R-project.org/package=purrr}{https://CRAN.R-project.org/package=purrr}.
-#'
+#'@keywords internal
+
 whatif.opt <- function (formula = NULL,
                         data, cfact,
                         nearby = 1,

R/zzz.R

@@ -1,8 +1,8 @@
 .onAttach <- function(libname, pkgname) {
   packageStartupMessage("-----------------------------------------------\n",
-                        "dsmextra: version 1.0.2:\n",
+                        "dsmextra: version 1.1.0:\n",
                         "-----------------------------------------------\n",
-                        "* Please cite as:\nBouchet PJ, Miller DL, Mannocci L (2020). A Toolkit for Extrapolation Assessments\nin Density Surface Models. R package version 1.0.2.\n",
+                        "* Please cite as:\nBouchet PJ, Miller DL, Mannocci L (2020). A Toolkit for Extrapolation Assessments\nin Density Surface Models. R package version 1.1.0.\n",
                         "\n* Quick start guide:\nA vignette is available at:\nhttps://densitymodelling.github.io/dsmextra/\n",
                         "\n* Further information:\ndsmextra is an output of the DenMod project. For more details, please visit:\nhttps://synergy.st-andrews.ac.uk/denmod/")
 }