From 530ca0b17e95191d8bed678534307725e30a6d0b Mon Sep 17 00:00:00 2001 From: Phil Bouchet Date: Mon, 18 May 2020 10:00:03 +0100 Subject: [PATCH] Update package index --- DESCRIPTION | 2 +- R/ExDet.R | 3 ++- R/print.extrapolation_results_summary.R | 2 ++ R/summarise_extrapolation.R | 2 +- R/summary.extrapolation_results.R | 2 ++ R/whatif.opt.R | 3 ++- R/zzz.R | 4 ++-- man/ExDet.Rd | 1 + man/print.extrapolation_results_summary.Rd | 1 + man/summarise_extrapolation.Rd | 1 + man/summary.extrapolation_results.Rd | 1 + man/whatif.opt.Rd | 1 + 12 files changed, 17 insertions(+), 6 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index bb8dc6f..5dd5715 100644 --- a/DESCRIPTION +++ b/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 diff --git a/R/ExDet.R b/R/ExDet.R index af0752a..cd26709 100644 --- a/R/ExDet.R +++ b/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){ #--------------------------------------------- diff --git a/R/print.extrapolation_results_summary.R b/R/print.extrapolation_results_summary.R index df5fd23..bbdd9e6 100644 --- a/R/print.extrapolation_results_summary.R +++ b/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] diff --git a/R/summarise_extrapolation.R b/R/summarise_extrapolation.R index f1c92d5..5f269c7 100644 --- a/R/summarise_extrapolation.R +++ b/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, diff --git a/R/summary.extrapolation_results.R b/R/summary.extrapolation_results.R index df8fd34..373b247 100644 --- a/R/summary.extrapolation_results.R +++ b/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 diff --git a/R/whatif.opt.R b/R/whatif.opt.R index ac962a2..89fbe28 100644 --- a/R/whatif.opt.R +++ b/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, diff --git a/R/zzz.R b/R/zzz.R index 12361ca..3216369 100644 --- a/R/zzz.R +++ b/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/") } diff --git a/man/ExDet.Rd b/man/ExDet.Rd index 89e7672..12b75e7 100644 --- a/man/ExDet.Rd +++ b/man/ExDet.Rd @@ -27,3 +27,4 @@ Broennimann O, Di Cola V, Guisan A (2016). ecospat: Spatial Ecology Miscellaneou \author{ Phil J. Bouchet } +\keyword{internal} diff --git a/man/print.extrapolation_results_summary.Rd b/man/print.extrapolation_results_summary.Rd index b4f99f2..572dea4 100644 --- a/man/print.extrapolation_results_summary.Rd +++ b/man/print.extrapolation_results_summary.Rd @@ -22,3 +22,4 @@ Print the summary of extrapolation results (already calculated by \code{\link{co \author{ David L Miller } +\keyword{internal} diff --git a/man/summarise_extrapolation.Rd b/man/summarise_extrapolation.Rd index af3d952..cb7746d 100644 --- a/man/summarise_extrapolation.Rd +++ b/man/summarise_extrapolation.Rd @@ -37,3 +37,4 @@ Mesgaran MB, Cousens RD, Webber BL (2014). Here be dragons: a tool for quantifyi \author{ Phil J. Bouchet } +\keyword{internal} diff --git a/man/summary.extrapolation_results.Rd b/man/summary.extrapolation_results.Rd index db705e4..1511186 100644 --- a/man/summary.extrapolation_results.Rd +++ b/man/summary.extrapolation_results.Rd @@ -22,3 +22,4 @@ Print the summary of extrapolation results (already calculated by \code{\link{co \author{ David L Miller } +\keyword{internal} diff --git a/man/whatif.opt.Rd b/man/whatif.opt.Rd index f8192d2..22d3fea 100644 --- a/man/whatif.opt.Rd +++ b/man/whatif.opt.Rd @@ -53,3 +53,4 @@ Henry L, Wickham H (2019). purrr: Functional Programming Tools. R package versio \author{ Phil J. Bouchet } +\keyword{internal}