diff --git a/.github/workflows/R-CMD-check-windows.yaml b/.github/workflows/R-CMD-check-windows.yaml index c1d05d7..8073a1d 100644 --- a/.github/workflows/R-CMD-check-windows.yaml +++ b/.github/workflows/R-CMD-check-windows.yaml @@ -79,7 +79,7 @@ jobs: remotes::install_deps(dependencies = TRUE) remotes::install_cran("rcmdcheck") remotes::install_cran("covr") - remotes::install_github("jeffreyhanson/surveyvoi") + remotes::install_github("prioritizr/surveyvoi") shell: Rscript {0} - name: Session information diff --git a/DESCRIPTION b/DESCRIPTION index 9ad3287..b00fafb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: surveyvoi Type: Package -Version: 1.0.3.8 +Version: 1.0.3.9 Title: Survey Value of Information Description: Decision support tool for prioritizing sites for ecological surveys based on their potential to improve plans for conserving @@ -83,10 +83,10 @@ SystemRequirements: pkg-config (>= 0.29.2), autoconf (>= 2.69), automake (>= 1.16.5) -URL: https://github.com/jeffreyhanson/surveyvoi -BugReports: https://github.com/jeffreyhanson/surveyvoi/issues +URL: https://github.com/prioritizr/surveyvoi, https://prioritizr.github.io/surveyvoi +BugReports: https://github.com/prioritizr/surveyvoi/issues VignetteBuilder: knitr -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.0 Encoding: UTF-8 Biarch: true Collate: @@ -116,3 +116,5 @@ Collate: 'validate.R' 'weighted_survey_scheme.R' Roxygen: list(markdown = TRUE) +Remotes: + cran/RandomFields diff --git a/Makefile b/Makefile index 73c73cf..f354d18 100644 --- a/Makefile +++ b/Makefile @@ -4,6 +4,9 @@ initc: R --slave -e "Rcpp::compileAttributes()" R --slave -e "tools::package_native_routine_registration_skeleton('.', 'src/init.c', character_only = FALSE)" +conf: + autoconf + docs: man readme vigns data: @@ -84,4 +87,4 @@ sancheck: vgcheck: R --slave -e "rhub::check(platform = 'ubuntu-gcc-devel', valgrind = TRUE, email = 'jeffrey.hanson@uqconnect.edu.au', show_status = FALSE)" -.PHONY: initc docs data site test check checkwb build install man readme vigns site quicksite benchmark examples solarischeck wbcheck sancheck vgcheck +.PHONY: initc docs data site test check checkwb build install man readme vigns site quicksite benchmark examples solarischeck wbcheck sancheck vgcheck conf diff --git a/NEWS.md b/NEWS.md index 6649ac7..ed35560 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# surveyvoi 1.0.3.9 + +- Update documentation for new code repository location. +- Add remote for RandomFields package to facilitate installation. + # surveyvoi 1.0.3.8 - Standardize spelling (en-US). diff --git a/README.Rmd b/README.Rmd index 12f870a..6cc8794 100644 --- a/README.Rmd +++ b/README.Rmd @@ -9,11 +9,11 @@ output: # surveyvoi: Survey Value of Information [![lifecycle](https://img.shields.io/badge/Lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html) -[![R-CMD-check-Ubuntu](https://img.shields.io/github/workflow/status/jeffreyhanson/surveyvoi/Ubuntu/master.svg?label=Ubuntu)](https://github.com/jeffreyhanson/surveyvoi/actions) -[![R-CMD-check-Windows](https://img.shields.io/github/workflow/status/jeffreyhanson/surveyvoi/Windows/master.svg?label=Windows)](https://github.com/jeffreyhanson/surveyvoi/actions) -[![R-CMD-check-macOS](https://img.shields.io/github/workflow/status/jeffreyhanson/surveyvoi/macOS/master.svg?label=macOS)](https://github.com/jeffreyhanson/surveyvoi/actions) -[![Documentation](https://img.shields.io/github/workflow/status/jeffreyhanson/surveyvoi/Documentation/master.svg?label=Documentation)](https://github.com/jeffreyhanson/surveyvoi/actions) -[![Coverage Status](https://codecov.io/github/jeffreyhanson/surveyvoi/coverage.svg?branch=master)](https://codecov.io/github/jeffreyhanson/surveyvoi?branch=master) +[![R-CMD-check-Ubuntu](https://img.shields.io/github/workflow/status/prioritizr/surveyvoi/Ubuntu/master.svg?label=Ubuntu)](https://github.com/prioritizr/surveyvoi/actions) +[![R-CMD-check-Windows](https://img.shields.io/github/workflow/status/prioritizr/surveyvoi/Windows/master.svg?label=Windows)](https://github.com/prioritizr/surveyvoi/actions) +[![R-CMD-check-macOS](https://img.shields.io/github/workflow/status/prioritizr/surveyvoi/macOS/master.svg?label=macOS)](https://github.com/prioritizr/surveyvoi/actions) +[![Documentation](https://img.shields.io/github/workflow/status/prioritizr/surveyvoi/Documentation/master.svg?label=Documentation)](https://github.com/prioritizr/surveyvoi/actions) +[![Coverage Status](https://codecov.io/github/prioritizr/surveyvoi/coverage.svg?branch=master)](https://codecov.io/github/prioritizr/surveyvoi?branch=master) [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/surveyvoi)](https://CRAN.R-project.org/package=surveyvoi) ```{r, include = FALSE} @@ -31,11 +31,11 @@ The _surveyvoi_ package is a decision support tool for prioritizing sites for ec ## Installation -The development version can be installed from [GitHub](https://github.com/jeffreyhanson/surveyvoi) using the following code. +The development version can be installed from [GitHub](https://github.com/prioritizr/surveyvoi) using the following code. ```{r, eval = FALSE} if (!require(remotes)) install.packages("remotes") -remotes::install_github("jeffreyhanson/surveyvoi") +remotes::install_github("prioritizr/surveyvoi") ``` #### Windows @@ -75,7 +75,7 @@ Please cite the _surveyvoi R_ package when using it in publications. To cite the ```{r, echo = FALSE, results = "asis", comment = ""} dev_version <- as.character(packageVersion("surveyvoi")) dev_year <- "2022" -cat(paste0("> Hanson JO, Chadès I, Hudgins EJ, Bennett J (", dev_year, "). surveyvoi: Survey Value of Information. R package version ", dev_version, ". Available at https://github.com/jeffreyhanson/surveyvoi.\n")) +cat(paste0("> Hanson JO, Chadès I, Hudgins EJ, Bennett J (", dev_year, "). surveyvoi: Survey Value of Information. R package version ", dev_version, ". Available at https://github.com/prioritizr/surveyvoi.\n")) ``` ## Usage @@ -208,8 +208,8 @@ ggtitle("scheme") + theme(legend.title = element_blank()) ``` -This has just been a taster of the _surveyvoi R_ package. In addition to this functionality, it can be used to evaluate survey schemes using value of information analysis. Furthermore, it can be used to generate survey schemes using conventional approaches (e.g. sampling environmental gradients, and selecting places with highly uncertain information). For more information, see the [package vignette](http://jeffrey-hanson.com/surveyvoi/articles/surveyvoi.html). +This has just been a taster of the _surveyvoi R_ package. In addition to this functionality, it can be used to evaluate survey schemes using value of information analysis. Furthermore, it can be used to generate survey schemes using conventional approaches (e.g. sampling environmental gradients, and selecting places with highly uncertain information). For more information, see the [package vignette](https://prioritizr.github.io/surveyvoi/articles/surveyvoi.html). ## Getting help -If you have any questions about using the _surveyvoi R_ package or suggestions for improving it, please [file an issue at the package's online code repository](https://github.com/jeffreyhanson/surveyvoi/issues/new). +If you have any questions about using the _surveyvoi R_ package or suggestions for improving it, please [file an issue at the package's online code repository](https://github.com/prioritizr/surveyvoi/issues/new). diff --git a/README.md b/README.md index e7541f0..f7abe42 100644 --- a/README.md +++ b/README.md @@ -4,12 +4,12 @@ # surveyvoi: Survey Value of Information [![lifecycle](https://img.shields.io/badge/Lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html) -[![R-CMD-check-Ubuntu](https://img.shields.io/github/workflow/status/jeffreyhanson/surveyvoi/Ubuntu/master.svg?label=Ubuntu)](https://github.com/jeffreyhanson/surveyvoi/actions) -[![R-CMD-check-Windows](https://img.shields.io/github/workflow/status/jeffreyhanson/surveyvoi/Windows/master.svg?label=Windows)](https://github.com/jeffreyhanson/surveyvoi/actions) -[![R-CMD-check-macOS](https://img.shields.io/github/workflow/status/jeffreyhanson/surveyvoi/macOS/master.svg?label=macOS)](https://github.com/jeffreyhanson/surveyvoi/actions) -[![Documentation](https://img.shields.io/github/workflow/status/jeffreyhanson/surveyvoi/Documentation/master.svg?label=Documentation)](https://github.com/jeffreyhanson/surveyvoi/actions) +[![R-CMD-check-Ubuntu](https://img.shields.io/github/workflow/status/prioritizr/surveyvoi/Ubuntu/master.svg?label=Ubuntu)](https://github.com/prioritizr/surveyvoi/actions) +[![R-CMD-check-Windows](https://img.shields.io/github/workflow/status/prioritizr/surveyvoi/Windows/master.svg?label=Windows)](https://github.com/prioritizr/surveyvoi/actions) +[![R-CMD-check-macOS](https://img.shields.io/github/workflow/status/prioritizr/surveyvoi/macOS/master.svg?label=macOS)](https://github.com/prioritizr/surveyvoi/actions) +[![Documentation](https://img.shields.io/github/workflow/status/prioritizr/surveyvoi/Documentation/master.svg?label=Documentation)](https://github.com/prioritizr/surveyvoi/actions) [![Coverage -Status](https://codecov.io/github/jeffreyhanson/surveyvoi/coverage.svg?branch=master)](https://codecov.io/github/jeffreyhanson/surveyvoi?branch=master) +Status](https://codecov.io/github/prioritizr/surveyvoi/coverage.svg?branch=master)](https://codecov.io/github/prioritizr/surveyvoi?branch=master) [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/surveyvoi)](https://CRAN.R-project.org/package=surveyvoi) The *surveyvoi* package is a decision support tool for prioritizing @@ -32,12 +32,12 @@ required to fit hierarchical generalized linear models. ## Installation The development version can be installed from -[GitHub](https://github.com/jeffreyhanson/surveyvoi) using the following +[GitHub](https://github.com/prioritizr/surveyvoi) using the following code. ``` r if (!require(remotes)) install.packages("remotes") -remotes::install_github("jeffreyhanson/surveyvoi") +remotes::install_github("prioritizr/surveyvoi") ``` #### Windows @@ -86,8 +86,8 @@ Please cite the *surveyvoi R* package when using it in publications. To cite the developmental version, please use: > Hanson JO, Chadès I, Hudgins EJ, Bennett J (2022). surveyvoi: Survey -> Value of Information. R package version 1.0.3.8. Available at -> . +> Value of Information. R package version 1.0.3.9. Available at +> . ## Usage @@ -343,11 +343,11 @@ value of information analysis. Furthermore, it can be used to generate survey schemes using conventional approaches (e.g. sampling environmental gradients, and selecting places with highly uncertain information). For more information, see the [package -vignette](http://jeffrey-hanson.com/surveyvoi/articles/surveyvoi.html). +vignette](https://prioritizr.github.io/surveyvoi/articles/surveyvoi.html). ## Getting help If you have any questions about using the *surveyvoi R* package or suggestions for improving it, please [file an issue at the package’s online code -repository](https://github.com/jeffreyhanson/surveyvoi/issues/new). +repository](https://github.com/prioritizr/surveyvoi/issues/new). diff --git a/_pkgdown.yml b/_pkgdown.yml index 033c92a..c3fce5e 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,4 +1,4 @@ -url: https://jeffrey-hanson.com/surveyvoi +url: https://github.com/prioritizr/surveyvoi authors: Jeffrey O Hanson: diff --git a/configure b/configure index a80e34d..edc5b3b 100755 --- a/configure +++ b/configure @@ -2,7 +2,7 @@ # Guess values for system-dependent variables and create Makefiles. # Generated by GNU Autoconf 2.69 for surveyvoi see.DESCRIPTION. # -# Report bugs to . +# Report bugs to . # # # Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc. @@ -266,7 +266,7 @@ fi $as_echo "$0: be upgraded to zsh 4.3.4 or later." else $as_echo "$0: Please tell bug-autoconf@gnu.org and -$0: https://github.com/jeffreyhanson/surveyvoi/issues about +$0: https://github.com/prioritizr/surveyvoi/issues about $0: your system, including any error possibly output before $0: this message. Then install a modern shell, or manually $0: run the script under such a shell if you do have one." @@ -581,7 +581,7 @@ PACKAGE_NAME='surveyvoi' PACKAGE_TARNAME='surveyvoi' PACKAGE_VERSION='see.DESCRIPTION' PACKAGE_STRING='surveyvoi see.DESCRIPTION' -PACKAGE_BUGREPORT='https://github.com/jeffreyhanson/surveyvoi/issues' +PACKAGE_BUGREPORT='https://github.com/prioritizr/surveyvoi/issues' PACKAGE_URL='' ac_subst_vars='LTLIBOBJS @@ -1251,7 +1251,7 @@ if test -n "$ac_init_help"; then esac cat <<\_ACEOF -Report bugs to . +Report bugs to . _ACEOF ac_status=$? fi @@ -2532,7 +2532,7 @@ Usage: $0 [OPTION]... [TAG]... Configuration files: $config_files -Report bugs to ." +Report bugs to ." _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 diff --git a/configure.ac b/configure.ac index 784d1f4..ee1f5b0 100755 --- a/configure.ac +++ b/configure.ac @@ -1,7 +1,7 @@ # Initialization ## setup configure AC_PREREQ([2.69]) -AC_INIT([surveyvoi], [see.DESCRIPTION], [https://github.com/jeffreyhanson/surveyvoi/issues]) +AC_INIT([surveyvoi], [see.DESCRIPTION], [https://github.com/prioritizr/surveyvoi/issues]) ## set GMP variables GMP_NAME="gmp" diff --git a/cran-comments.md b/cran-comments.md index 4616808..91eb495 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -9,11 +9,11 @@ Jeff # Test environments * [Debian (testing), R-release](https://github.com/r-devel/rcheckserver) ([based on rcheckserver](https://statmath.wu.ac.at/AASC/debian/)) -* [Ubuntu 20.04, R-release](https://github.com/jeffreyhanson/surveyvoi/actions?query=workflow%3AUbuntu) -* [Ubuntu 20.04, R-devel](https://github.com/jeffreyhanson/surveyvoi/actions?query=workflow%3AUbuntu) -* [macOS 10.15, R-release](https://github.com/jeffreyhanson/surveyvoi/actions?query=workflow%3A%22Mac+OSX%22) +* [Ubuntu 20.04, R-release](https://github.com/prioritizr/surveyvoi/actions?query=workflow%3AUbuntu) +* [Ubuntu 20.04, R-devel](https://github.com/prioritizr/surveyvoi/actions?query=workflow%3AUbuntu) +* [macOS 10.15, R-release](https://github.com/prioritizr/surveyvoi/actions?query=workflow%3A%22Mac+OSX%22) * [macOS 11.5.2 (arm64), R-release (macOS builder)](https://mac.r-project.org/macbuilder/submit.html) -* [Windows Server 2019, R-release](https://github.com/jeffreyhanson/surveyvoi/actions?query=workflow%3AWindows) +* [Windows Server 2019, R-release](https://github.com/prioritizr/surveyvoi/actions?query=workflow%3AWindows) * [Windows Server 2008 (x64), R-devel (Win-Builder)](https://win-builder.r-project.org/) # R CMD check results diff --git a/docs/404.html b/docs/404.html index 2ccaa24..83508ee 100644 --- a/docs/404.html +++ b/docs/404.html @@ -7,11 +7,11 @@ Page not found (404) • surveyvoi - - + + - - + +