diff --git a/DESCRIPTION b/DESCRIPTION index 85500e1..b234838 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: raptr Type: Package Title: Representative and Adequate Prioritization Toolkit in R -Version: 1.0.0 +Version: 1.0.1 Authors@R: c(person(c("Jeffrey", "O"), "Hanson", email="jeffrey.hanson@uqconnect.edu.au", role = c("aut", "cre")), person(c("Jonathan", "R"), "Rhodes", role = c("aut")), @@ -90,6 +90,6 @@ Collate: 'sim.species.R' 'urap.proportion.held.R' 'zzz.R' -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 NeedsCompilation: yes Roxygen: list(markdown = TRUE) diff --git a/NEWS.md b/NEWS.md index 1f2e524..e71d10f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# raptr 1.0.1 + +- Fix usage sections in documentation. +- Fix missing braces in documentation. +- Fix aliasing for package manual entry (#15). + # raptr 1.0.0 - The package has been overhauled to support modern spatial data structures. diff --git a/R/generics.R b/R/generics.R index c678688..4375a10 100644 --- a/R/generics.R +++ b/R/generics.R @@ -718,7 +718,7 @@ amount.held <- function(x, y, species) UseMethod("amount.held") #' #' @param value `numeric` new target. #' -#' @return code{numeric} vector. +#' @return `numeric` vector. #' #' @seealso [RapData()], [RapResults()], #' [RapSolved()]. @@ -769,7 +769,7 @@ amount.target <- function(x, species) UseMethod("amount.target") #' @param space `NULL` for all spaces or `integer` indicating a #' specific space. #' -#' @return code{matrix} object. +#' @return `matrix` object. #' #' @seealso [RapResults()], [RapSolved()]. #' diff --git a/R/package.R b/R/package.R index f9f2f83..f14cc40 100644 --- a/R/package.R +++ b/R/package.R @@ -52,6 +52,7 @@ NULL #' **9**: 320--330. DOI: 10.1111/2041-210X.12862. #' #' @docType package +#' @aliases raptr-package #' @name raptr NULL diff --git a/R/raptr-internal.R b/R/raptr-internal.R index 1c0336e..4c1f577 100644 --- a/R/raptr-internal.R +++ b/R/raptr-internal.R @@ -460,6 +460,8 @@ basemap <- function(x, basemap = "hybrid", grayscale = FALSE, #' @keywords internal #' #' @name is.cached +#' +#' @aliases is.cached,RapData,character-method is.cached,RapResults,character-method methods::setGeneric("is.cached", function(x, name) methods::standardGeneric("is.cached")) @@ -482,6 +484,8 @@ methods::setGeneric("is.cached", #' @keywords internal #' #' @name cache +#' +#' @aliases cache,RapData,character,ANY-method cache,RapData,character,missing-method cache,RapResults,character,ANY-method cache,RapResults,character,missing-method methods::setGeneric("cache", function(x, name, y) methods::standardGeneric("cache")) diff --git a/README.md b/README.md index f91e807..7732da4 100644 --- a/README.md +++ b/README.md @@ -75,7 +75,6 @@ vignette("raptr", package = "raptr") citation("raptr") ``` - ## ## To cite the raptr package in publications, use: ## ## Hanson JO, Rhodes JR, Possingham HP & Fuller RA (2018) raptr: diff --git a/cran-comments.md b/cran-comments.md index b8fbc2a..c24721b 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,10 +1,6 @@ Dear CRAN volunteers, -Thank you very much for reviewing this submission. - -This submission contains an update for the raptr package that is currently available on CRAN. It aims to address several of the NOTES and the ERROR detected by CRAN's automated checks on the CRAN's Fedora-clang platform (i.e., `r-devel-linux-x86_64-fedora-clang`). Specifically, it has updates that (i) replace dependencies for the rgdal and rgeos packages in anticipation of their retirement, (ii) fix package startup message issues, (iii) fix the CITATION file format, and (iv) removes the C++ specification because it is compatible with C++14 (following advice on R-pkg-devel emailing list, ). Additionally, it has updated examples and unit tests to address failing checks on CRAN's Fedora-clang platform. - -In case it is helpful, I will explain the steps and rationale taken to address the failing checks on CRAN's Fedora-clang platform. Although I have attempted to reproduce the failed check on a comparable platform (i.e., the R-hub Fedora Clang docker image, ) and other platforms (see test environments below), I am unable to reproduce the specific error detected on CRAN's Fedora-clang platform. As such, I have (i) encapsulated all examples within `dontrun{}` and (ii) ensured that unit tests are not run on Fedora platforms. This approach ensures that the examples and unit tests will not throw an error on CRAN's Fedora-clang platform. This approach also ensures that all unit tests are still run on other platforms (e.g., Windows, Debian, macOS). It is also worth noting that I cannot simply encapsulate the failing example and unit test detected on CRAN's Fedora-clang platform, because I cannot guarantee that there are not other examples that fail on this platform (since I cannot reproduce the error). Although this approach is not ideal, I believe that the CRAN volunteers' time is the most precious resource and this approach is the only way that I can think of that would avoid wasting their time with the possibility of multiple submissions. I hope that my explanation and approach is satisfactory. +Thank you for reviewing this submission. This submission contains updates for the raptr package. Specifically, these updates include documentation fixes to address the NOTEs on CRAN's checks and the aliasing for the package overview help file. Cheers, @@ -22,7 +18,7 @@ Jeff # R CMD check results -0 errors | 0 warnings | 3 notes +0 errors | 0 warnings | 2 notes # Notes diff --git a/docs/404.html b/docs/404.html index 7e6fe9b..2b85378 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/articles/index.html b/docs/articles/index.html index 1b20d79..63a894d 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/articles/raptr.html b/docs/articles/raptr.html index e17d746..913ff07 100644 --- a/docs/articles/raptr.html +++ b/docs/articles/raptr.html @@ -33,7 +33,7 @@ raptr - 1.0.0 + 1.0.1 @@ -884,7 +884,7 @@

Analysis## Run_Number Status Score Cost Planning_Units Connectivity_Total ## 1 1 OPTIMAL 137 137 137 91758023 ## Connectivity_In Connectivity_Edge Connectivity_Out Connectivity_In_Fraction -## 1 9824052 74050879 7883092 0.1070648 +## 1 9472518 73701258 8584247 0.1032337 diff --git a/docs/articles/raptr_files/figure-html/unnamed-chunk-58-1.png b/docs/articles/raptr_files/figure-html/unnamed-chunk-58-1.png index a39f768..84e60c3 100644 Binary files a/docs/articles/raptr_files/figure-html/unnamed-chunk-58-1.png and b/docs/articles/raptr_files/figure-html/unnamed-chunk-58-1.png differ diff --git a/docs/articles/raptr_files/figure-html/unnamed-chunk-62-1.png b/docs/articles/raptr_files/figure-html/unnamed-chunk-62-1.png index 73c403d..855be2b 100644 Binary files a/docs/articles/raptr_files/figure-html/unnamed-chunk-62-1.png and b/docs/articles/raptr_files/figure-html/unnamed-chunk-62-1.png differ diff --git a/docs/articles/raptr_files/figure-html/unnamed-chunk-63-1.png b/docs/articles/raptr_files/figure-html/unnamed-chunk-63-1.png index ce4024f..a1e021f 100644 Binary files a/docs/articles/raptr_files/figure-html/unnamed-chunk-63-1.png and b/docs/articles/raptr_files/figure-html/unnamed-chunk-63-1.png differ diff --git a/docs/articles/raptr_files/figure-html/unnamed-chunk-64-1.png b/docs/articles/raptr_files/figure-html/unnamed-chunk-64-1.png index 4e3108b..f93decd 100644 Binary files a/docs/articles/raptr_files/figure-html/unnamed-chunk-64-1.png and b/docs/articles/raptr_files/figure-html/unnamed-chunk-64-1.png differ diff --git a/docs/articles/raptr_files/figure-html/unnamed-chunk-66-1.png b/docs/articles/raptr_files/figure-html/unnamed-chunk-66-1.png index c04e6dc..f2893ee 100644 Binary files a/docs/articles/raptr_files/figure-html/unnamed-chunk-66-1.png and b/docs/articles/raptr_files/figure-html/unnamed-chunk-66-1.png differ diff --git a/docs/articles/raptr_files/figure-html/unnamed-chunk-7-1.png b/docs/articles/raptr_files/figure-html/unnamed-chunk-7-1.png index 7cf3779..b76d28f 100644 Binary files a/docs/articles/raptr_files/figure-html/unnamed-chunk-7-1.png and b/docs/articles/raptr_files/figure-html/unnamed-chunk-7-1.png differ diff --git a/docs/authors.html b/docs/authors.html index 92dab73..b6660b0 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/index.html b/docs/index.html index d1d324f..84225c3 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ raptr - 1.0.0 + 1.0.1 @@ -112,27 +112,26 @@

Citation 
 citation("raptr")
-
## 
-## To cite the raptr package in publications, use:
-## 
-##   Hanson JO, Rhodes JR, Possingham HP & Fuller RA (2018) raptr:
-##   Representative and Adequate Prioritization Toolkit in R. Methods in
-##   Ecology & Evolution, 9: 320--330. DOI: 10.1111/2041-210X.12862
-## 
-## A BibTeX entry for LaTeX users is
-## 
-##   @Article{,
-##     author = {Jeffrey O Hanson and Jonathan R Rhodes and Hugh P Possingham and Richard A Fuller},
-##     title = {raptr: Representative and adequate prioritization toolkit in R},
-##     journal = {Methods in Ecology and Evolution},
-##     year = {2018},
-##     volume = {9},
-##     pages = {320--330},
-##     doi = {10.1111/2041-210X.12862},
-##   }
-## 
-## You may also want to cite the package version. Find it with
-## "help(package=raptr)".
+
## To cite the raptr package in publications, use:
+## 
+##   Hanson JO, Rhodes JR, Possingham HP & Fuller RA (2018) raptr:
+##   Representative and Adequate Prioritization Toolkit in R. Methods in
+##   Ecology & Evolution, 9: 320--330. DOI: 10.1111/2041-210X.12862
+## 
+## A BibTeX entry for LaTeX users is
+## 
+##   @Article{,
+##     author = {Jeffrey O Hanson and Jonathan R Rhodes and Hugh P Possingham and Richard A Fuller},
+##     title = {raptr: Representative and adequate prioritization toolkit in R},
+##     journal = {Methods in Ecology and Evolution},
+##     year = {2018},
+##     volume = {9},
+##     pages = {320--330},
+##     doi = {10.1111/2041-210X.12862},
+##   }
+## 
+## You may also want to cite the package version. Find it with
+## "help(package=raptr)".
diff --git a/docs/news/index.html b/docs/news/index.html index fbc7656..9a3be53 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 @@ -51,7 +51,13 @@

Changelog

-

raptr 1.0.0

+

raptr 1.0.1

+
  • Fix usage sections in documentation.
    • +
  • Fix missing braces in documentation.
    • +
  • Fix aliasing for package manual entry (#15).
    • +
+
+

raptr 1.0.02023-03-14

  • The package has been overhauled to support modern spatial data structures. Specifically, sf package objects (sf::st_sf()) are now use for vector data and terra package objects (terra::rast()) for raster data. These updates impact many of the user-facing functions (e.g., calcBoundaryData(), sim.species(), sim.space(), calcSpeciesAverageInPus(), rap()), so users will likely need to update their code.
  • The cs_pus, cs_spp, and cs_spaces built-in datasets have been removed. This is because terra::rast() objects cannot be distributed as built-in datasets for packages. These datasets can now be manually imported from external files distributed with the package (see ?cs_pus for more details).
  • Remove rgdal and rgeos packages as dependencies (#13).
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 610687e..81eec19 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: raptr: raptr.html -last_built: 2023-03-14T03:26Z +last_built: 2024-01-26T00:56Z urls: reference: https://jeffrey-hanson.com/raptr/reference article: https://jeffrey-hanson.com/raptr/articles diff --git a/docs/reference/AttributeSpace-class.html b/docs/reference/AttributeSpace-class.html index a9f34f6..54c89e2 100644 --- a/docs/reference/AttributeSpace-class.html +++ b/docs/reference/AttributeSpace-class.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1
diff --git a/docs/reference/AttributeSpace.html b/docs/reference/AttributeSpace.html index a635b89..f487352 100644 --- a/docs/reference/AttributeSpace.html +++ b/docs/reference/AttributeSpace.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/AttributeSpaces-class.html b/docs/reference/AttributeSpaces-class.html index 59a7581..1c33b49 100644 --- a/docs/reference/AttributeSpaces-class.html +++ b/docs/reference/AttributeSpaces-class.html @@ -20,7 +20,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/AttributeSpaces.html b/docs/reference/AttributeSpaces.html index f96053d..96f9152 100644 --- a/docs/reference/AttributeSpaces.html +++ b/docs/reference/AttributeSpaces.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/DemandPoints-class.html b/docs/reference/DemandPoints-class.html index c758cb8..7cce036 100644 --- a/docs/reference/DemandPoints-class.html +++ b/docs/reference/DemandPoints-class.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/DemandPoints.html b/docs/reference/DemandPoints.html index 5b8a9ef..9c99f5b 100644 --- a/docs/reference/DemandPoints.html +++ b/docs/reference/DemandPoints.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 @@ -93,68 +93,68 @@

Examples

print(dps) #> An object of class "DemandPoints" #> Slot "coords": -#> [,1] [,2] -#> [1,] 1.47073203 -1.258018766 -#> [2,] 0.33366123 -1.332680870 -#> [3,] 1.13611968 -0.832239487 -#> [4,] 1.17919925 -1.353292397 -#> [5,] 0.63157306 -0.393176375 -#> [6,] -1.88270851 1.171874830 -#> [7,] 0.18757829 -0.006887564 -#> [8,] 1.12796118 1.284925119 -#> [9,] 0.53471390 -1.025075340 -#> [10,] -0.82085270 0.227347974 -#> [11,] 1.17541526 0.495358342 -#> [12,] 0.35879898 -1.524380509 -#> [13,] -0.13852087 0.217900158 -#> [14,] -0.63629149 0.704308207 -#> [15,] -0.57720226 -0.751992375 -#> [16,] -1.18694775 0.785776414 -#> [17,] -1.36514061 -0.055205115 -#> [18,] -0.16790986 -0.414880583 -#> [19,] 0.57037504 -0.184065453 -#> [20,] -0.01518033 -0.810975339 -#> [21,] -2.03234214 -1.566672264 -#> [22,] 1.87315052 -0.392646716 -#> [23,] 0.38788201 0.004858200 -#> [24,] 1.10628317 0.965011766 -#> [25,] 0.63434750 -1.312012816 -#> [26,] 0.51302944 -1.918013703 -#> [27,] -0.16015063 0.093832010 -#> [28,] 0.56062405 -1.076149483 -#> [29,] 0.20452969 2.200127302 -#> [30,] -0.17630018 -0.005071820 -#> [31,] -1.16687235 -1.602550243 -#> [32,] -0.87506108 -0.003713870 -#> [33,] 0.40671129 1.940001439 -#> [34,] -0.61199550 0.232542318 -#> [35,] -0.94199232 -0.653319147 -#> [36,] 0.75895377 0.511247243 -#> [37,] -1.43957235 1.790971027 -#> [38,] -0.46082657 -0.602038436 -#> [39,] 1.25034476 -2.060321384 -#> [40,] 0.33285069 -1.543311814 -#> [41,] -1.58280576 -0.050266381 -#> [42,] -0.38496189 0.774456939 -#> [43,] -0.66045568 1.378186654 -#> [44,] 0.85612181 -2.024294882 -#> [45,] 0.03994205 -0.350415784 -#> [46,] -2.28752220 -0.521105521 -#> [47,] -0.47208936 0.118951478 -#> [48,] 1.55625271 -0.036027174 -#> [49,] 1.15045509 1.214186053 -#> [50,] -0.45332157 -0.380823535 +#> [,1] [,2] +#> [1,] 0.416942847 -0.10921759 +#> [2,] -0.632587542 0.26466174 +#> [3,] 1.150146673 0.30384826 +#> [4,] -0.235475907 -0.18338848 +#> [5,] -1.643107386 0.55964967 +#> [6,] -1.503382146 -0.18655384 +#> [7,] -2.050584847 -0.81227537 +#> [8,] -0.753198229 -1.64058167 +#> [9,] -0.134141958 0.50792248 +#> [10,] 1.005782847 1.75433696 +#> [11,] 2.167186798 0.59240020 +#> [12,] 2.322556540 1.01671329 +#> [13,] -1.020423391 0.12162059 +#> [14,] 0.048814436 -1.07806726 +#> [15,] -0.771888628 -1.14356572 +#> [16,] -0.785235068 -0.52964368 +#> [17,] -0.726603031 -0.68127316 +#> [18,] 0.681878032 -0.20244756 +#> [19,] -0.229843287 1.68449572 +#> [20,] -1.510601724 -1.03377324 +#> [21,] -0.583727687 -0.15597667 +#> [22,] -2.022918454 -0.04640064 +#> [23,] 0.403504676 -0.95362873 +#> [24,] 0.550015549 0.41626080 +#> [25,] 0.028357122 0.11402961 +#> [26,] 0.893165020 0.06391875 +#> [27,] -0.376555496 -0.91933224 +#> [28,] 0.605884808 0.90133529 +#> [29,] -0.004874726 -0.79772830 +#> [30,] -0.520796373 0.66822120 +#> [31,] -0.639018598 0.15521430 +#> [32,] -0.635894137 0.12868809 +#> [33,] 0.106586975 -1.53306545 +#> [34,] 1.176914248 0.20236067 +#> [35,] 0.447391153 -0.71753865 +#> [36,] 2.272954766 0.36169476 +#> [37,] 0.136058206 1.39900429 +#> [38,] -1.999039133 0.37269896 +#> [39,] -0.420500870 -1.56564429 +#> [40,] -0.378407395 -0.05169454 +#> [41,] 1.220774789 0.51408210 +#> [42,] -1.541030292 0.54989952 +#> [43,] -0.310310122 0.86781691 +#> [44,] -0.020108184 0.68436008 +#> [45,] -2.390200336 -0.16267998 +#> [46,] 0.889865359 -1.78436472 +#> [47,] -1.482813325 -1.03714557 +#> [48,] 0.445750348 0.83014772 +#> [49,] 1.369775856 0.60734694 +#> [50,] -0.020110027 -0.12218636 #> #> Slot "weights": -#> [1] 0.02721305 0.48958724 0.99499331 0.93060837 0.46788487 0.29207875 -#> [7] 0.41057292 0.15333049 0.49687816 0.37071024 0.70375219 0.95706132 -#> [13] 0.67041750 0.53405550 0.92381556 0.46644003 0.98437345 0.21427925 -#> [19] 0.04642168 0.19822015 0.58173241 0.39944537 0.95886370 0.23000955 -#> [25] 0.11466910 0.03061763 0.72477981 0.15822648 0.78181034 0.57540717 -#> [31] 0.44643628 0.11877352 0.68460706 0.61563837 0.67630997 0.39455456 -#> [37] 0.48096725 0.30485306 0.23352605 0.27429248 0.70524684 0.09099607 -#> [43] 0.05443510 0.90300795 0.38210081 0.05637002 0.25011004 0.89465186 -#> [49] 0.22081772 0.68882898 +#> [1] 0.82462233 0.20905156 0.16820653 0.98027422 0.60067001 0.15167630 +#> [7] 0.29273868 0.44806062 0.82390783 0.96940433 0.29540916 0.23268974 +#> [13] 0.32548104 0.10037212 0.33022536 0.19259870 0.26887364 0.88352934 +#> [19] 0.67062316 0.07432107 0.68530920 0.60081559 0.70614048 0.46816601 +#> [25] 0.01098793 0.78329569 0.62185330 0.86605874 0.91985234 0.32539892 +#> [31] 0.91576207 0.08054491 0.85551768 0.30502898 0.73636304 0.94096257 +#> [37] 0.86102324 0.36417012 0.91252348 0.75292220 0.64148241 0.79545033 +#> [43] 0.98497173 0.62236924 0.55532649 0.96106650 0.91563972 0.60327560 +#> [49] 0.31155411 0.55515212 #> # } diff --git a/docs/reference/GurobiOpts-class.html b/docs/reference/GurobiOpts-class.html index f159c51..e037c3a 100644 --- a/docs/reference/GurobiOpts-class.html +++ b/docs/reference/GurobiOpts-class.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/GurobiOpts.html b/docs/reference/GurobiOpts.html index 267678b..ffc76fb 100644 --- a/docs/reference/GurobiOpts.html +++ b/docs/reference/GurobiOpts.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/ManualOpts-class.html b/docs/reference/ManualOpts-class.html index 04e2506..6848588 100644 --- a/docs/reference/ManualOpts-class.html +++ b/docs/reference/ManualOpts-class.html @@ -19,7 +19,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/ManualOpts.html b/docs/reference/ManualOpts.html index eb64061..0b53646 100644 --- a/docs/reference/ManualOpts.html +++ b/docs/reference/ManualOpts.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/PlanningUnitPoints-class.html b/docs/reference/PlanningUnitPoints-class.html index f131516..1ba0f4b 100644 --- a/docs/reference/PlanningUnitPoints-class.html +++ b/docs/reference/PlanningUnitPoints-class.html @@ -19,7 +19,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/PlanningUnitPoints.html b/docs/reference/PlanningUnitPoints.html index 239e117..9fb8bae 100644 --- a/docs/reference/PlanningUnitPoints.html +++ b/docs/reference/PlanningUnitPoints.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 @@ -90,157 +90,157 @@

Examples

print(x) #> An object of class "PlanningUnitPoints" #> Slot "coords": -#> [,1] -#> [1,] -0.398183215 -#> [2,] 1.345963326 -#> [3,] -0.456933906 -#> [4,] -0.552581695 -#> [5,] 1.237734493 -#> [6,] -1.432532727 -#> [7,] 0.846318792 -#> [8,] 0.705637805 -#> [9,] 0.181161078 -#> [10,] 1.190033360 -#> [11,] 1.091976682 -#> [12,] 0.428545568 -#> [13,] 0.079687362 -#> [14,] -0.387659575 -#> [15,] -1.271489837 -#> [16,] 0.058149939 -#> [17,] 1.535147467 -#> [18,] -0.847571567 -#> [19,] 0.622449597 -#> [20,] 2.937113054 -#> [21,] 0.339376789 -#> [22,] -0.737600455 -#> [23,] 1.746466453 -#> [24,] -0.535912105 -#> [25,] -0.860500276 -#> [26,] -0.356628200 -#> [27,] -0.534357617 -#> [28,] 0.944437851 -#> [29,] -0.159460270 -#> [30,] 0.717010049 -#> [31,] -0.949679580 -#> [32,] -2.102386525 -#> [33,] -1.286628385 -#> [34,] 0.136924533 -#> [35,] -1.336616067 -#> [36,] -0.930328563 -#> [37,] 0.026078937 -#> [38,] -0.131181320 -#> [39,] 0.238862698 -#> [40,] 0.852670724 -#> [41,] -0.009607844 -#> [42,] -0.603657878 -#> [43,] -0.563383040 -#> [44,] -0.940472743 -#> [45,] 0.943069854 -#> [46,] 0.684553315 -#> [47,] 0.520040692 -#> [48,] 1.723493599 -#> [49,] 0.652816336 -#> [50,] 2.820056903 -#> [51,] -0.464987033 -#> [52,] -0.240881514 -#> [53,] 0.448729266 -#> [54,] -0.324781560 -#> [55,] -0.458258440 -#> [56,] -0.677329907 -#> [57,] 1.215005588 -#> [58,] 0.183561994 -#> [59,] -0.619650458 -#> [60,] -1.205476310 -#> [61,] 0.284576203 -#> [62,] -0.254787529 -#> [63,] 0.206273194 -#> [64,] 0.674128711 -#> [65,] 0.639147942 -#> [66,] 1.569398582 -#> [67,] -1.677056384 -#> [68,] 0.127942811 -#> [69,] 0.549142152 -#> [70,] -1.157995321 -#> [71,] 0.503313773 -#> [72,] -0.922745575 -#> [73,] -1.472938134 -#> [74,] -0.833748717 -#> [75,] -1.113358606 -#> [76,] 1.625405819 -#> [77,] 0.141993925 -#> [78,] 0.098941455 -#> [79,] 0.212589566 -#> [80,] 0.832848554 -#> [81,] 1.554311172 -#> [82,] -2.105177114 -#> [83,] -1.530185027 -#> [84,] -0.727075532 -#> [85,] -0.743137819 -#> [86,] 0.094783437 -#> [87,] -1.085469306 -#> [88,] 0.870780177 -#> [89,] -1.325292709 -#> [90,] 0.382346441 -#> [91,] 0.547391852 -#> [92,] 0.795453021 -#> [93,] -1.017830775 -#> [94,] 0.687238891 -#> [95,] 0.718672473 -#> [96,] 1.087617534 -#> [97,] -0.083684886 -#> [98,] 0.909112243 -#> [99,] -1.029450176 -#> [100,] -0.713103583 -#> [101,] 0.132429804 -#> [102,] -0.817251755 -#> [103,] -2.639254554 -#> [104,] -0.627987134 -#> [105,] 1.157584269 -#> [106,] 0.808436331 -#> [107,] 0.128690751 -#> [108,] -1.338993651 -#> [109,] 0.280314432 -#> [110,] -0.510402703 -#> [111,] -1.077106846 -#> [112,] -0.431682630 -#> [113,] 0.978235696 -#> [114,] 0.198851427 -#> [115,] -1.309903934 -#> [116,] -0.911978165 -#> [117,] -1.171877677 -#> [118,] -1.559275924 -#> [119,] 1.420636194 -#> [120,] -1.570893709 -#> [121,] 0.836220020 -#> [122,] 1.024407314 -#> [123,] 0.296882544 -#> [124,] -0.307013464 -#> [125,] -1.966917655 -#> [126,] 0.497430248 -#> [127,] 1.011969351 -#> [128,] -0.526850047 -#> [129,] 0.414225049 -#> [130,] -1.024613385 -#> [131,] -0.596238642 -#> [132,] 0.227064620 -#> [133,] 0.024418171 -#> [134,] 0.396144104 -#> [135,] -0.817405762 -#> [136,] 1.905439876 -#> [137,] 1.155966088 -#> [138,] 0.777272715 -#> [139,] 1.351717652 -#> [140,] 2.163923940 -#> [141,] 0.485586976 -#> [142,] 0.945791607 -#> [143,] 0.179615962 -#> [144,] 0.670394537 -#> [145,] 0.866223740 -#> [146,] 0.722502255 -#> [147,] -0.186018622 -#> [148,] 0.013324073 -#> [149,] -1.697339376 -#> [150,] 0.799303263 +#> [,1] +#> [1,] 1.53491576 +#> [2,] -0.41619872 +#> [3,] -0.52054380 +#> [4,] 0.85058387 +#> [5,] 0.33449657 +#> [6,] -0.82935177 +#> [7,] -0.21869594 +#> [8,] -1.54508372 +#> [9,] 0.23322978 +#> [10,] 0.03106964 +#> [11,] 0.35786565 +#> [12,] 1.60862422 +#> [13,] 1.42985426 +#> [14,] -0.94833964 +#> [15,] 1.01570554 +#> [16,] 0.03773461 +#> [17,] -1.74423940 +#> [18,] -0.97007381 +#> [19,] -0.22902736 +#> [20,] -0.97484568 +#> [21,] 2.69237242 +#> [22,] 1.39239386 +#> [23,] 1.36007615 +#> [24,] -0.36541588 +#> [25,] -0.86893720 +#> [26,] -0.50655673 +#> [27,] 1.21470730 +#> [28,] 0.50695868 +#> [29,] -2.09497131 +#> [30,] 0.03407924 +#> [31,] 0.85272870 +#> [32,] 0.74322814 +#> [33,] 0.55715361 +#> [34,] -1.24858322 +#> [35,] -0.20787431 +#> [36,] 0.42396946 +#> [37,] -0.50669744 +#> [38,] -0.61152331 +#> [39,] 2.41165945 +#> [40,] -0.16495814 +#> [41,] -0.44040605 +#> [42,] 0.52197617 +#> [43,] -1.91832225 +#> [44,] -1.98264996 +#> [45,] 0.52120016 +#> [46,] 0.77778320 +#> [47,] -0.81211887 +#> [48,] 0.91074832 +#> [49,] 0.94875395 +#> [50,] -1.34804945 +#> [51,] 0.35417586 +#> [52,] 0.53026393 +#> [53,] -0.31097493 +#> [54,] -0.24415553 +#> [55,] -0.29187819 +#> [56,] -1.12808616 +#> [57,] -1.12288159 +#> [58,] 2.05393864 +#> [59,] -0.90951843 +#> [60,] 0.45837916 +#> [61,] -0.04661845 +#> [62,] -0.68095460 +#> [63,] -1.48882940 +#> [64,] -0.39251301 +#> [65,] -1.74968202 +#> [66,] -0.03866763 +#> [67,] -0.79715324 +#> [68,] -0.91592054 +#> [69,] 0.07326746 +#> [70,] 1.23817132 +#> [71,] 0.71837134 +#> [72,] 0.53946650 +#> [73,] -1.06123399 +#> [74,] -0.54073787 +#> [75,] -0.71520471 +#> [76,] -0.17892009 +#> [77,] 0.16497028 +#> [78,] -0.72740817 +#> [79,] -0.53783713 +#> [80,] -0.59966490 +#> [81,] 1.18208775 +#> [82,] 0.18921288 +#> [83,] 0.24894911 +#> [84,] 1.04664341 +#> [85,] -1.28930094 +#> [86,] 0.37511557 +#> [87,] -0.55691839 +#> [88,] 0.30242663 +#> [89,] 0.22226647 +#> [90,] -0.96216696 +#> [91,] 0.05203237 +#> [92,] 0.90004038 +#> [93,] -0.39490088 +#> [94,] 0.95414600 +#> [95,] -0.58821435 +#> [96,] -1.47658453 +#> [97,] -1.37777577 +#> [98,] -1.34567231 +#> [99,] -0.73663796 +#> [100,] -0.47011150 +#> [101,] 1.38060934 +#> [102,] 1.67501093 +#> [103,] 1.17690663 +#> [104,] -0.14889834 +#> [105,] -0.17782336 +#> [106,] 0.80312186 +#> [107,] -0.41579535 +#> [108,] 1.21248959 +#> [109,] 1.24036003 +#> [110,] 0.68567588 +#> [111,] -0.02679868 +#> [112,] 0.30958051 +#> [113,] 0.24986433 +#> [114,] -1.35646087 +#> [115,] 0.59937977 +#> [116,] 0.00864779 +#> [117,] 0.09071661 +#> [118,] -0.65705741 +#> [119,] -0.48178225 +#> [120,] 0.01775788 +#> [121,] -0.85953576 +#> [122,] 1.35770498 +#> [123,] 1.21506118 +#> [124,] 1.45391292 +#> [125,] -0.08591198 +#> [126,] -0.61756875 +#> [127,] -0.21826025 +#> [128,] -1.32600521 +#> [129,] -2.36220890 +#> [130,] -1.40996955 +#> [131,] 0.25439714 +#> [132,] 0.29587030 +#> [133,] 0.05678979 +#> [134,] -0.10265486 +#> [135,] 1.95192303 +#> [136,] 0.87856596 +#> [137,] -1.30661693 +#> [138,] 0.09034427 +#> [139,] 0.90235804 +#> [140,] 0.54942132 +#> [141,] -0.86983920 +#> [142,] -0.03921465 +#> [143,] -0.51845168 +#> [144,] -0.91184962 +#> [145,] 0.15031364 +#> [146,] 0.44035545 +#> [147,] 1.31978206 +#> [148,] 0.24656113 +#> [149,] 0.94182660 +#> [150,] -0.34215133 #> #> Slot "ids": #> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 diff --git a/docs/reference/PolySet-class.html b/docs/reference/PolySet-class.html index 1ab6faa..bf8d4a8 100644 --- a/docs/reference/PolySet-class.html +++ b/docs/reference/PolySet-class.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/RapData-class.html b/docs/reference/RapData-class.html index 4533210..e730be3 100644 --- a/docs/reference/RapData-class.html +++ b/docs/reference/RapData-class.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/RapData.html b/docs/reference/RapData.html index 5fd6bce..216a33c 100644 --- a/docs/reference/RapData.html +++ b/docs/reference/RapData.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/RapOpts-class.html b/docs/reference/RapOpts-class.html index 05757b2..346ec62 100644 --- a/docs/reference/RapOpts-class.html +++ b/docs/reference/RapOpts-class.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/RapReliableOpts-class.html b/docs/reference/RapReliableOpts-class.html index c2e0fe5..1bff6ae 100644 --- a/docs/reference/RapReliableOpts-class.html +++ b/docs/reference/RapReliableOpts-class.html @@ -20,7 +20,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/RapReliableOpts.html b/docs/reference/RapReliableOpts.html index 6ff6d91..c425ced 100644 --- a/docs/reference/RapReliableOpts.html +++ b/docs/reference/RapReliableOpts.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/RapResults-class.html b/docs/reference/RapResults-class.html index 9e07bf7..d430c00 100644 --- a/docs/reference/RapResults-class.html +++ b/docs/reference/RapResults-class.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/RapResults.html b/docs/reference/RapResults.html index 5ea3969..c1a8cad 100644 --- a/docs/reference/RapResults.html +++ b/docs/reference/RapResults.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/RapSolved-class.html b/docs/reference/RapSolved-class.html index d0f82f8..aa5fabb 100644 --- a/docs/reference/RapSolved-class.html +++ b/docs/reference/RapSolved-class.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/RapSolved.html b/docs/reference/RapSolved.html index 712bd87..515fcf8 100644 --- a/docs/reference/RapSolved.html +++ b/docs/reference/RapSolved.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/RapUnreliableOpts-class.html b/docs/reference/RapUnreliableOpts-class.html index a46e452..8377f65 100644 --- a/docs/reference/RapUnreliableOpts-class.html +++ b/docs/reference/RapUnreliableOpts-class.html @@ -20,7 +20,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/RapUnreliableOpts.html b/docs/reference/RapUnreliableOpts.html index d3c511d..40573e7 100644 --- a/docs/reference/RapUnreliableOpts.html +++ b/docs/reference/RapUnreliableOpts.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/RapUnsolved-class.html b/docs/reference/RapUnsolved-class.html index 318f90d..1500e17 100644 --- a/docs/reference/RapUnsolved-class.html +++ b/docs/reference/RapUnsolved-class.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/RapUnsolved.html b/docs/reference/RapUnsolved.html index 02af7c9..27b16ff 100644 --- a/docs/reference/RapUnsolved.html +++ b/docs/reference/RapUnsolved.html @@ -19,7 +19,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/SolverOpts-class.html b/docs/reference/SolverOpts-class.html index 9f94826..1ac5ec5 100644 --- a/docs/reference/SolverOpts-class.html +++ b/docs/reference/SolverOpts-class.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/amount.held.html b/docs/reference/amount.held.html index 5a63666..c2a4eef 100644 --- a/docs/reference/amount.held.html +++ b/docs/reference/amount.held.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/amount.target.html b/docs/reference/amount.target.html index 469f791..7cdd0fd 100644 --- a/docs/reference/amount.target.html +++ b/docs/reference/amount.target.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 @@ -93,7 +93,7 @@

Arguments

Value

-

codenumeric vector.

+

numeric vector.

See also

diff --git a/docs/reference/as.list.html b/docs/reference/as.list.html index e8f597a..7c31391 100644 --- a/docs/reference/as.list.html +++ b/docs/reference/as.list.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1
diff --git a/docs/reference/basemap.html b/docs/reference/basemap.html index 47b56f8..0c8911a 100644 --- a/docs/reference/basemap.html +++ b/docs/reference/basemap.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/blank.raster.html b/docs/reference/blank.raster.html index 2691ecb..cde82e6 100644 --- a/docs/reference/blank.raster.html +++ b/docs/reference/blank.raster.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/cache.html b/docs/reference/cache.html index 6900712..f65422c 100644 --- a/docs/reference/cache.html +++ b/docs/reference/cache.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/calcBoundaryData.html b/docs/reference/calcBoundaryData.html index eabf5b4..b1ad246 100644 --- a/docs/reference/calcBoundaryData.html +++ b/docs/reference/calcBoundaryData.html @@ -20,7 +20,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/calcSpeciesAverageInPus.html b/docs/reference/calcSpeciesAverageInPus.html index 006eedb..c50db1a 100644 --- a/docs/reference/calcSpeciesAverageInPus.html +++ b/docs/reference/calcSpeciesAverageInPus.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/casestudy_data.html b/docs/reference/casestudy_data.html index e19a1f5..d26dbd0 100644 --- a/docs/reference/casestudy_data.html +++ b/docs/reference/casestudy_data.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/convert2PolySet.html b/docs/reference/convert2PolySet.html index a21c5eb..d4ed513 100644 --- a/docs/reference/convert2PolySet.html +++ b/docs/reference/convert2PolySet.html @@ -19,7 +19,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/dp.subset.html b/docs/reference/dp.subset.html index c04139c..7fd3bbd 100644 --- a/docs/reference/dp.subset.html +++ b/docs/reference/dp.subset.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/index.html b/docs/reference/index.html index 4d36ed7..bc6fa3f 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 @@ -255,7 +255,7 @@

All functions

Deprecation notice

-

raptr

+

raptr raptr-package

raptr: Representative and Adequate Prioritization Toolkit in R

diff --git a/docs/reference/is.GurobiInstalled.html b/docs/reference/is.GurobiInstalled.html index e253c97..b6a88eb 100644 --- a/docs/reference/is.GurobiInstalled.html +++ b/docs/reference/is.GurobiInstalled.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/is.cached.html b/docs/reference/is.cached.html index bf98f64..87b1231 100644 --- a/docs/reference/is.cached.html +++ b/docs/reference/is.cached.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/is.comparable.html b/docs/reference/is.comparable.html index 41f1f6e..22cb653 100644 --- a/docs/reference/is.comparable.html +++ b/docs/reference/is.comparable.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/logging.file.html b/docs/reference/logging.file.html index 4247e3c..fac5dad 100644 --- a/docs/reference/logging.file.html +++ b/docs/reference/logging.file.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/make.DemandPoints.html b/docs/reference/make.DemandPoints.html index f44608a..0ab429c 100644 --- a/docs/reference/make.DemandPoints.html +++ b/docs/reference/make.DemandPoints.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/make.RapData.html b/docs/reference/make.RapData.html index 16f92a5..3822165 100644 --- a/docs/reference/make.RapData.html +++ b/docs/reference/make.RapData.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/maximum.targets.html b/docs/reference/maximum.targets.html index f8d3216..6dbcdb4 100644 --- a/docs/reference/maximum.targets.html +++ b/docs/reference/maximum.targets.html @@ -21,7 +21,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/names.html b/docs/reference/names.html index 6282d72..1cdb62f 100644 --- a/docs/reference/names.html +++ b/docs/reference/names.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/plot.html b/docs/reference/plot.html index 1fe74ea..559859c 100644 --- a/docs/reference/plot.html +++ b/docs/reference/plot.html @@ -21,7 +21,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/print.html b/docs/reference/print.html index d62a5d7..3c2c56d 100644 --- a/docs/reference/print.html +++ b/docs/reference/print.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/prob.subset.html b/docs/reference/prob.subset.html index 154d3d8..3effe99 100644 --- a/docs/reference/prob.subset.html +++ b/docs/reference/prob.subset.html @@ -19,7 +19,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/pu.subset.html b/docs/reference/pu.subset.html index 4397ebe..c590c35 100644 --- a/docs/reference/pu.subset.html +++ b/docs/reference/pu.subset.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/randomPoints.html b/docs/reference/randomPoints.html index 37cd37b..4f2f856 100644 --- a/docs/reference/randomPoints.html +++ b/docs/reference/randomPoints.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/rap.html b/docs/reference/rap.html index 6f6f681..c2ea29e 100644 --- a/docs/reference/rap.html +++ b/docs/reference/rap.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/raptr-deprecated.html b/docs/reference/raptr-deprecated.html index c15b7aa..c07f60d 100644 --- a/docs/reference/raptr-deprecated.html +++ b/docs/reference/raptr-deprecated.html @@ -27,7 +27,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/raptr.html b/docs/reference/raptr.html index 4701259..b274a62 100644 --- a/docs/reference/raptr.html +++ b/docs/reference/raptr.html @@ -27,7 +27,7 @@ raptr - 1.0.0 + 1.0.1 @@ -122,6 +122,20 @@

References

Toolkit in R. Methods in Ecology & Evolution,", 9: 320--330. DOI: 10.1111/2041-210X.12862.

+ +
+

Author

+

Maintainer: Jeffrey O Hanson jeffrey.hanson@uqconnect.edu.au

+

Authors:

  • Jonathan R Rhodes

    • +

  • Hugh P Possingham

    • +

  • Richard A Fuller

    • +
diff --git a/docs/reference/rrap.proportion.held.html b/docs/reference/rrap.proportion.held.html index 3fdbb8d..e246926 100644 --- a/docs/reference/rrap.proportion.held.html +++ b/docs/reference/rrap.proportion.held.html @@ -19,7 +19,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/score.html b/docs/reference/score.html index f48ba41..38c0927 100644 --- a/docs/reference/score.html +++ b/docs/reference/score.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/selections.html b/docs/reference/selections.html index 6b61161..53c5e34 100644 --- a/docs/reference/selections.html +++ b/docs/reference/selections.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/show.html b/docs/reference/show.html index da2c816..fa8aaf4 100644 --- a/docs/reference/show.html +++ b/docs/reference/show.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/sim.pus.html b/docs/reference/sim.pus.html index 11a5be1..d8678cf 100644 --- a/docs/reference/sim.pus.html +++ b/docs/reference/sim.pus.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/sim.space.html b/docs/reference/sim.space.html index e753750..f51c262 100644 --- a/docs/reference/sim.space.html +++ b/docs/reference/sim.space.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/sim.species-1.png b/docs/reference/sim.species-1.png index f074144..8e97cb0 100644 Binary files a/docs/reference/sim.species-1.png and b/docs/reference/sim.species-1.png differ diff --git a/docs/reference/sim.species.html b/docs/reference/sim.species.html index 0d2be3f..a3b7028 100644 --- a/docs/reference/sim.species.html +++ b/docs/reference/sim.species.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/simulated_data.html b/docs/reference/simulated_data.html index 9cc872c..982aaac 100644 --- a/docs/reference/simulated_data.html +++ b/docs/reference/simulated_data.html @@ -23,7 +23,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/solve.html b/docs/reference/solve.html index d13d8ee..3412eb4 100644 --- a/docs/reference/solve.html +++ b/docs/reference/solve.html @@ -19,7 +19,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/space.held.html b/docs/reference/space.held.html index cc50317..77325c1 100644 --- a/docs/reference/space.held.html +++ b/docs/reference/space.held.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 @@ -90,7 +90,7 @@

Arguments

Value

-

codematrix object.

+

matrix object.

See also

diff --git a/docs/reference/space.plot.html b/docs/reference/space.plot.html index fee8208..365e426 100644 --- a/docs/reference/space.plot.html +++ b/docs/reference/space.plot.html @@ -20,7 +20,7 @@ raptr - 1.0.0 + 1.0.1
diff --git a/docs/reference/space.target.html b/docs/reference/space.target.html index 9187ed4..8258546 100644 --- a/docs/reference/space.target.html +++ b/docs/reference/space.target.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/spp.plot.html b/docs/reference/spp.plot.html index 8c78aae..d1df123 100644 --- a/docs/reference/spp.plot.html +++ b/docs/reference/spp.plot.html @@ -17,7 +17,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/spp.subset.html b/docs/reference/spp.subset.html index 4020c7c..d5ec5dc 100644 --- a/docs/reference/spp.subset.html +++ b/docs/reference/spp.subset.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/summary.html b/docs/reference/summary.html index 5830f1f..335bf76 100644 --- a/docs/reference/summary.html +++ b/docs/reference/summary.html @@ -18,7 +18,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/update.html b/docs/reference/update.html index d4b1e74..e1494e2 100644 --- a/docs/reference/update.html +++ b/docs/reference/update.html @@ -20,7 +20,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/docs/reference/urap.proportion.held.html b/docs/reference/urap.proportion.held.html index 3119c70..0063069 100644 --- a/docs/reference/urap.proportion.held.html +++ b/docs/reference/urap.proportion.held.html @@ -19,7 +19,7 @@ raptr - 1.0.0 + 1.0.1 diff --git a/inst/doc/raptr.html b/inst/doc/raptr.html index c203f58..962fc48 100644 --- a/inst/doc/raptr.html +++ b/inst/doc/raptr.html @@ -283,7 +283,7 @@

Data

main = c("Uniform species", "Normal species", "Bimodal species") )
-_Distribution of three simulated species. Each square represents a planning unit. The color of each square denotes the probability that individuals from each species occupy it._ +_Distribution of three simulated species. Each square represents a planning unit. The color of each square denotes the probability that individuals from each species occupy it._

Distribution of three simulated species. Each square represents a planning unit. The color of each square denotes the probability that individuals from each species occupy it.

@@ -875,7 +875,7 @@

Analysis

# plot prioritization
 plot(cs_rs_amount, 1)
-_Multi-species prioritization generated for four bird species using amount-based targets (20\%). See Figure 12 captions for conventions._ +_Multi-species prioritization generated for four bird species using amount-based targets (20\%). See Figure 12 captions for conventions._

Multi-species prioritization generated for four bird species using amount-based targets (20%). See Figure 12 captions for conventions.

@@ -913,10 +913,10 @@

Analysis

##   Run_Number  Status Score Cost Planning_Units Connectivity_Total
 ## 1          1 OPTIMAL   137  137            137           91758023
 ##   Connectivity_In Connectivity_Edge Connectivity_Out Connectivity_In_Fraction
-## 1         9824052          74050879          7883092                0.1070648
+## 1 9472518 73701258 8584247 0.1032337 
# plot prioritization
 plot(cs_rs_space, 1)
-

+

# plot prioritization in geographic attribute space
 p1 <- space.plot(cs_rs_space, 1, 2, main = "Blue-winged\nkookaburra")
 p2 <- space.plot(cs_rs_space, 2, 2, main = "Brown-backed\nhoneyeater")
@@ -924,7 +924,7 @@ 
Analysis

 p4 <- space.plot(cs_rs_space, 4, 2, main = "Pale-headed\nrosella")
 gridExtra::grid.arrange(p1, p2, p3, p4, ncol = 2)
-_Distribution of the amount- and space-based prioritization in the geographic attribute space. See Figure 28 caption for conventions._ +_Distribution of the amount- and space-based prioritization in the geographic attribute space. See Figure 28 caption for conventions._

Distribution of the amount- and space-based prioritization in the geographic attribute space. See Figure 28 caption for conventions.

@@ -936,7 +936,7 @@

Analysis

p4 <- space.plot(cs_rs_space, 4, 1, main = "Pale-headed\nrosella") gridExtra::grid.arrange(p1, p2, p3, p4, ncol = 2)
-_Distribution of the amount- and space-based prioritization in the environmental attribute space. See Figure 28 caption for conventions._ +_Distribution of the amount- and space-based prioritization in the environmental attribute space. See Figure 28 caption for conventions._

Distribution of the amount- and space-based prioritization in the environmental attribute space. See Figure 28 caption for conventions.

@@ -1003,7 +1003,7 @@

Analysis

axis.line.x = element_line(), axis.line.y = element_line() )
-_Prioritizations were generated using amount-based targets (20\%), and with additional space-based targets (85\%). These are compared to the Queensland reserve network. Data represent means and standard errors for the four species in each prioritization._ +_Prioritizations were generated using amount-based targets (20\%), and with additional space-based targets (85\%). These are compared to the Queensland reserve network. Data represent means and standard errors for the four species in each prioritization._

Prioritizations were generated using amount-based targets (20%), and with additional space-based targets (85%). These are compared to the Queensland reserve network. Data represent means and standard errors for the four species in each prioritization.

diff --git a/man/amount.target.Rd b/man/amount.target.Rd index 6c1c15c..5e91f07 100644 --- a/man/amount.target.Rd +++ b/man/amount.target.Rd @@ -31,7 +31,7 @@ species.} \item{value}{\code{numeric} new target.} } \value{ -code{numeric} vector. +\code{numeric} vector. } \description{ This function sets or returns the target amounts for each species. diff --git a/man/cache.Rd b/man/cache.Rd index c345147..32eabf2 100644 --- a/man/cache.Rd +++ b/man/cache.Rd @@ -2,6 +2,10 @@ % Please edit documentation in R/raptr-internal.R, R/RapData.R, R/RapResults.R \name{cache} \alias{cache} +\alias{cache,RapData,character,ANY-method} +\alias{cache,RapData,character,missing-method} +\alias{cache,RapResults,character,ANY-method} +\alias{cache,RapResults,character,missing-method} \title{Get and set cache methods} \usage{ cache(x, name, y) diff --git a/man/is.cached.Rd b/man/is.cached.Rd index 450fa14..65644ab 100644 --- a/man/is.cached.Rd +++ b/man/is.cached.Rd @@ -2,6 +2,8 @@ % Please edit documentation in R/raptr-internal.R, R/RapData.R, R/RapResults.R \name{is.cached} \alias{is.cached} +\alias{is.cached,RapData,character-method} +\alias{is.cached,RapResults,character-method} \title{Test if hash is cached in a Rap object} \usage{ is.cached(x, name) diff --git a/man/raptr.Rd b/man/raptr.Rd index d8aad51..e84fd04 100644 --- a/man/raptr.Rd +++ b/man/raptr.Rd @@ -3,6 +3,7 @@ \docType{package} \name{raptr} \alias{raptr} +\alias{raptr-package} \title{raptr: Representative and Adequate Prioritization Toolkit in R} \description{ Biodiversity is in crisis. The overarching aim of conservation is to preserve @@ -50,3 +51,23 @@ raptr: Representative and Adequate Prioritization", Toolkit in R. \emph{Methods in Ecology & Evolution},", \strong{9}: 320--330. DOI: 10.1111/2041-210X.12862. } +\seealso{ +Useful links: +\itemize{ + \item \url{https://jeffrey-hanson.com/raptr/} + \item \url{https://github.com/jeffreyhanson/raptr} + \item Report bugs at \url{https://github.com/jeffreyhanson/raptr/issues} +} + +} +\author{ +\strong{Maintainer}: Jeffrey O Hanson \email{jeffrey.hanson@uqconnect.edu.au} + +Authors: +\itemize{ + \item Jonathan R Rhodes + \item Hugh P Possingham + \item Richard A Fuller +} + +} diff --git a/man/space.held.Rd b/man/space.held.Rd index 9c1067e..c56204f 100644 --- a/man/space.held.Rd +++ b/man/space.held.Rd @@ -23,7 +23,7 @@ species.} specific space.} } \value{ -code{matrix} object. +\code{matrix} object. } \description{ This function returns the attribute space held for each species in a