+
-[](https://github.com/USEPA/spsurvey/actions/workflows/R-CMD-check.yaml)
+[](https://www.repostatus.org/#active)
[](https://cran.r-project.org/package=spsurvey)
[](https://cran.r-project.org/web/checks/check_results_spsurvey.html)
+[](https://github.com/USEPA/spsurvey/actions/workflows/R-CMD-check.yaml)
[](https://cran.r-project.org/package=spsurvey)
+
-# spsurvey
+# Overview
-spsurvey is an R package that implements a design-based approach to statistical inference,
+`spsurvey` is an R package that implements a design-based approach to statistical inference,
with a focus on spatial data.
Spatially balanced samples are selected using the
Generalized Random Tessellation Stratified (GRTS) algorithm.
@@ -20,7 +24,7 @@ sites, and two options for replacement sites (reverse hierarchical order and
nearest neighbor). Data are analyzed using a wide
range of analysis functions that perform categorical variable analysis, continuous
variable analysis, attributable risk analysis, risk difference analysis, relative
-risk analysis, change analysis, and trend analysis. spsurvey can also be used to
+risk analysis, change analysis, and trend analysis. `spsurvey` can also be used to
summarize objects, visualize objects, select samples that are not spatially balanced,
select panel samples, measure the amount of spatial balance in a sample,
adjust design weights, and more. For additional details, see Dumelle et al. (2023) 17. Interpretation of Sectio
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.
-<one line to give the program's name and a brief idea of what it does.>
-Copyright (C) <year> <name of author>
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.<one line to give the program's name and a brief idea of what it does.>
+Copyright (C) <year> <name of author>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program. If not, see <http://www.gnu.org/licenses/>.Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:
-<program> Copyright (C) <year> <name of author>
-This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
-This is free software, and you are welcome to redistribute it
-under certain conditions; type 'show c' for details.<program> Copyright (C) <year> <name of author>
+This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+This is free software, and you are welcome to redistribute it
+under certain conditions; type 'show c' for details.The hypothetical commands show w and show c should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.
You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <http://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <http://www.gnu.org/philosophy/why-not-lgpl.html>.
@@ -277,7 +277,7 @@How to Apply These Terms
diff --git a/docs/apple-touch-icon-120x120.png b/docs/apple-touch-icon-120x120.png
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new file mode 100644
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diff --git a/docs/articles/EDA.html b/docs/articles/EDA.html
index 2b44289..745ed73 100644
--- a/docs/articles/EDA.html
+++ b/docs/articles/EDA.html
@@ -6,13 +6,20 @@
Summarizing and Visualizing Sampling Frames, Design Sites, and Analysis Data • spsurvey
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
Articles • spsurvey Articles • spsurvey
@@ -32,7 +32,7 @@
Articles
-
@@ -87,7 +87,7 @@ All vignettes
+Articles
-All vignettes
diff --git a/docs/articles/sampling.html b/docs/articles/sampling.html index 77edef8..87e8039 100644 --- a/docs/articles/sampling.html +++ b/docs/articles/sampling.html @@ -6,13 +6,20 @@
+
+library(spsurvey)
Overview +
+spsurvey is an R package that implements a design-based approach to statistical inference, with a focus on spatial data. Spatially balanced samples are selected using the Generalized Random Tessellation Stratified (GRTS) algorithm. The GRTS algorithm can be applied to finite resources (point geometries) and infinite resources (linear / linestring and areal / polygon geometries) and flexibly accommodates a diverse set of sampling design features, including stratification, unequal inclusion probabilities, proportional (to size) inclusion probabilities, legacy (historical) sites, a minimum distance between sites, and two options for replacement sites (reverse hierarchical order and nearest neighbor). Data are analyzed using a wide range of analysis functions that perform categorical variable analysis, continuous variable analysis, attributable risk analysis, risk difference analysis, relative risk analysis, change analysis, and trend analysis. spsurvey can also be used to summarize objects, visualize objects, select samples that are not spatially balanced, select panel samples, measure the amount of spatial balance in a sample, adjust design weights, and more. For additional details, see Dumelle et al. (2023) doi:10.18637/jss.v105.i03.
Installation
@@ -100,7 +113,7 @@Installation# install the most recent approved version from CRAN install.packages("spsurvey") # load the most recent approved version from CRAN -library(spsurvey)
You can install and load the most recent development version ofspsurvey from GitHub by running:
# Installing from GitHub requires you first install the remotes package
@@ -109,10 +122,10 @@ Installation# install the most recent development version from GitHub
remotes::install_github("USEPA/spsurvey", ref = "main")
# load the most recent development version from GitHub
-library(spsurvey)
You can install the most recent development version of spsurvey from GitHub with package vignettes by running:
install the most recent development version from GitHub with package vignettes
-devtools::install_github("USEPA/spsurvey", build_vignettes=TRUE)install the most recent development version from GitHub with package vignettes
+devtools::install_github("USEPA/spsurvey", build_vignettes=TRUE)To view the vignettes in RStudio, run
vignette("start-here", "spsurvey") # start with this vignette for an spsurvey overview
@@ -120,12 +133,12 @@ Installationvignette("sampling", "spsurvey") # for spatially balanced sampling
vignette("analysis", "spsurvey") # for analyzing data
To view the vignettes in a web format, visit here.
-Further detail regarding spsurvey is contained in the package’s documentation manual available for download here.
+Further detail regarding spsurvey is contained in the package’s documentation manual available for download here.
Citation
-If you used spsurvey in your work, please cite it. You can view the most recent citation by running
+If you used spsurvey in your work, please cite it. You can view the most recent citation by running
citation(package = "spsurvey")#> To cite spsurvey in publications use:
@@ -150,12 +163,13 @@ Citation
Package Contributions
-We encourage users to submit issues and enhancement requests so we may continue to improve spsurvey.
+We encourage users to submit issues and enhancement requests so we may continue to improve spsurvey.
-EPA Disclaimer
+
@@ -224,7 +239,7 @@ Changelog • spsurvey Changelog • spsurvey
@@ -32,7 +32,7 @@
@@ -598,7 +598,7 @@
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index a8007b4..fecfc96 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,10 +1,13 @@
-pandoc: 2.19.2
-pkgdown: 2.0.7
+pandoc: 3.1.11
+pkgdown: 2.0.9
pkgdown_sha: ~
articles:
analysis: analysis.html
EDA: EDA.html
sampling: sampling.html
start-here: start-here.html
-last_built: 2024-01-09T17:57Z
+last_built: 2024-08-29T15:02Z
+urls:
+ reference: https://usepa.github.io/spsurvey/reference
+ article: https://usepa.github.io/spsurvey/articles
diff --git a/docs/reference/Illinois_River.html b/docs/reference/Illinois_River.html
index 69d8327..2ab45fa 100644
--- a/docs/reference/Illinois_River.html
+++ b/docs/reference/Illinois_River.html
@@ -1,6 +1,6 @@
-Illinois River data — Illinois_River • spsurvey Illinois River data — Illinois_River • spsurvey
@@ -33,7 +33,7 @@
@@ -101,7 +101,7 @@
diff --git a/docs/reference/Illinois_River_Legacy.html b/docs/reference/Illinois_River_Legacy.html
index f576a1c..52b73b4 100644
--- a/docs/reference/Illinois_River_Legacy.html
+++ b/docs/reference/Illinois_River_Legacy.html
@@ -1,6 +1,6 @@
-EPA Disclaimer
+Acknowledgements
The United States Environmental Protection Agency (EPA) GitHub project code is provided on an “as is” basis and the user assumes responsibility for its use. EPA has relinquished control of the information and no longer has responsibility to protect the integrity , confidentiality, or availability of the information. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by EPA. The EPA seal and logo shall not be used in any manner to imply endorsement of any commercial product or activity by EPA or the United States Government.
+A special thank you to Virginia Vichi-Miller for creating the spsurvey hex sticker (i.e., graphic identifier). The sticker represents the environmental sampling context for which spsurvey was created, with an emphasis on aquatic resources. The sticker shows a sunny day filled with a fish swimming in water, aquatic vegetation, and rolling hills and trees. The word spsurvey is set against the backdrop of the clear sky.
License
@@ -206,9 +220,10 @@Developers
Dev status
-
-
+
+
Dev status
diff --git a/docs/logo.png b/docs/logo.png new file mode 100644 index 0000000..456a7e0 Binary files /dev/null and b/docs/logo.png differ diff --git a/docs/news/index.html b/docs/news/index.html index 991619b..0f25e02 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,5 +1,5 @@ -New features
Format
Format
diff --git a/docs/reference/Lake_Ontario.html b/docs/reference/Lake_Ontario.html index ab8b57e..9f94a0e 100644 --- a/docs/reference/Lake_Ontario.html +++ b/docs/reference/Lake_Ontario.html @@ -1,6 +1,6 @@ -Format
diff --git a/docs/reference/NE_Lakes.html b/docs/reference/NE_Lakes.html index cabc479..228ae6a 100644 --- a/docs/reference/NE_Lakes.html +++ b/docs/reference/NE_Lakes.html @@ -1,6 +1,6 @@ -Format
diff --git a/docs/reference/NE_Lakes_Legacy.html b/docs/reference/NE_Lakes_Legacy.html index 1315ca5..1dedf7a 100644 --- a/docs/reference/NE_Lakes_Legacy.html +++ b/docs/reference/NE_Lakes_Legacy.html @@ -1,5 +1,5 @@ -Format
diff --git a/docs/reference/NE_Lakes_df.html b/docs/reference/NE_Lakes_df.html index d2102b0..e61ddb9 100644 --- a/docs/reference/NE_Lakes_df.html +++ b/docs/reference/NE_Lakes_df.html @@ -1,6 +1,6 @@ -Format
diff --git a/docs/reference/NLA_PNW.html b/docs/reference/NLA_PNW.html index e9fe902..bf95146 100644 --- a/docs/reference/NLA_PNW.html +++ b/docs/reference/NLA_PNW.html @@ -1,7 +1,7 @@ -Format
diff --git a/docs/reference/NRSA_EPA7.html b/docs/reference/NRSA_EPA7.html index af7b155..a3fd865 100644 --- a/docs/reference/NRSA_EPA7.html +++ b/docs/reference/NRSA_EPA7.html @@ -1,7 +1,7 @@ -Format
diff --git a/docs/reference/adjwgt.html b/docs/reference/adjwgt.html index 7da562d..aee111c 100644 --- a/docs/reference/adjwgt.html +++ b/docs/reference/adjwgt.html @@ -1,8 +1,8 @@ -Examples
framesize <- c(A = 15, B = 10) sites <- rep(rep(c(TRUE, FALSE), c(9, 1)), 5) adjwgt(wgt, wgtcat, framesize, sites) -#> [1] 0.006620736 0.073309846 0.864082196 0.199606423 0.556244620 1.140772402 -#> [7] 1.051511478 0.556287607 0.873322282 0.000000000 1.135491447 0.240088460 -#> [13] 0.301826224 1.170262970 0.485577078 0.823762985 0.025623222 0.239542816 -#> [19] 0.027051464 0.000000000 0.971423261 1.143696090 0.220204810 0.645162024 -#> [25] 0.632857303 0.071818203 0.099662452 0.484398260 0.959793342 0.000000000 -#> [31] 1.057573347 0.709004596 1.039502335 1.030638690 0.114893617 1.184803869 -#> [37] 0.343595618 0.483001105 0.488339185 0.000000000 0.455772868 1.066973356 -#> [43] 0.071710181 1.195244333 0.034006027 0.018601238 0.119242042 0.009342650 -#> [49] 0.577754943 0.000000000 +#> [1] 0.106022955 1.095458863 0.788784344 0.206410837 0.009715285 0.612363250 +#> [7] 0.653569531 0.380457302 0.962256116 0.000000000 1.148329267 0.229692762 +#> [13] 0.044958032 0.420658625 0.528247132 0.256909705 0.529835674 0.083585936 +#> [19] 0.510355313 0.000000000 0.380621490 0.890696902 0.965456641 0.257286396 +#> [25] 1.287424600 0.973599623 0.067547702 0.696155991 0.913599727 0.000000000 +#> [31] 0.031186232 0.225244066 0.300406067 0.635566997 0.478348221 0.431561081 +#> [37] 0.705436433 0.947237293 0.180084150 0.000000000 0.679202604 0.498141297 +#> [43] 0.640773369 0.659352102 0.095888583 0.764519223 0.768588110 0.989313538 +#> [49] 0.969150636 0.000000000 @@ -153,7 +153,7 @@Examples
diff --git a/docs/reference/adjwgtNR.html b/docs/reference/adjwgtNR.html index 3039e27..7f94b00 100644 --- a/docs/reference/adjwgtNR.html +++ b/docs/reference/adjwgtNR.html @@ -1,9 +1,9 @@ -Examples
diff --git a/docs/reference/ash1_wgt.html b/docs/reference/ash1_wgt.html index 7f22841..1593ef7 100644 --- a/docs/reference/ash1_wgt.html +++ b/docs/reference/ash1_wgt.html @@ -1,6 +1,6 @@ -Examples
diff --git a/docs/reference/attrisk_analysis.html b/docs/reference/attrisk_analysis.html index d800b31..31d9a34 100644 --- a/docs/reference/attrisk_analysis.html +++ b/docs/reference/attrisk_analysis.html @@ -1,11 +1,11 @@ -Examples
diff --git a/docs/reference/cat_analysis.html b/docs/reference/cat_analysis.html index b7ea43f..172fa54 100644 --- a/docs/reference/cat_analysis.html +++ b/docs/reference/cat_analysis.html @@ -1,10 +1,10 @@ -Examples
diff --git a/docs/reference/cdf_plot.html b/docs/reference/cdf_plot.html index 19694f4..a2aad1f 100644 --- a/docs/reference/cdf_plot.html +++ b/docs/reference/cdf_plot.html @@ -1,7 +1,7 @@ -Examples
diff --git a/docs/reference/change_analysis.html b/docs/reference/change_analysis.html index b675ff8..ba9329d 100644 --- a/docs/reference/change_analysis.html +++ b/docs/reference/change_analysis.html @@ -1,11 +1,11 @@ -Examples
diff --git a/docs/reference/cont_analysis.html b/docs/reference/cont_analysis.html index e02472e..2bb7a1e 100644 --- a/docs/reference/cont_analysis.html +++ b/docs/reference/cont_analysis.html @@ -1,11 +1,11 @@ -Examples
diff --git a/docs/reference/cont_cdfplot.html b/docs/reference/cont_cdfplot.html index 0758b45..d1131ad 100644 --- a/docs/reference/cont_cdfplot.html +++ b/docs/reference/cont_cdfplot.html @@ -1,9 +1,9 @@ -Examples
diff --git a/docs/reference/cont_cdftest.html b/docs/reference/cont_cdftest.html index 97bfb55..e68f0c0 100644 --- a/docs/reference/cont_cdftest.html +++ b/docs/reference/cont_cdftest.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/cov_panel_dsgn.html b/docs/reference/cov_panel_dsgn.html index 4a4a37a..ea14f8b 100644 --- a/docs/reference/cov_panel_dsgn.html +++ b/docs/reference/cov_panel_dsgn.html @@ -1,9 +1,9 @@ -Author
diff --git a/docs/reference/diffrisk_analysis.html b/docs/reference/diffrisk_analysis.html index f490ef5..8c786d0 100644 --- a/docs/reference/diffrisk_analysis.html +++ b/docs/reference/diffrisk_analysis.html @@ -1,11 +1,11 @@ -Examples
diff --git a/docs/reference/errorprnt.html b/docs/reference/errorprnt.html index 227f1ee..2882b8d 100644 --- a/docs/reference/errorprnt.html +++ b/docs/reference/errorprnt.html @@ -1,5 +1,5 @@ -Author
diff --git a/docs/reference/figures/logo.ong.png b/docs/reference/figures/logo.ong.png new file mode 100644 index 0000000..f9934f4 Binary files /dev/null and b/docs/reference/figures/logo.ong.png differ diff --git a/docs/reference/figures/logo.png b/docs/reference/figures/logo.png new file mode 100644 index 0000000..456a7e0 Binary files /dev/null and b/docs/reference/figures/logo.png differ diff --git a/docs/reference/grts.html b/docs/reference/grts.html index cb0f17f..3f822d0 100644 --- a/docs/reference/grts.html +++ b/docs/reference/grts.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/index.html b/docs/reference/index.html index 7d62c89..9ea3869 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,5 +1,5 @@ -All functions
diff --git a/docs/reference/irs.html b/docs/reference/irs.html
index 2a09689..07b3595 100644
--- a/docs/reference/irs.html
+++ b/docs/reference/irs.html
@@ -1,12 +1,12 @@
-Select an independent random sample (IRS) — irs • spsurvey Select an independent random sample (IRS) — irs • spsurvey
@@ -39,7 +39,7 @@
Examples
diff --git a/docs/reference/localmean_cov.html b/docs/reference/localmean_cov.html index 2a1a46b..72b70aa 100644 --- a/docs/reference/localmean_cov.html +++ b/docs/reference/localmean_cov.html @@ -1,6 +1,6 @@ -Author
diff --git a/docs/reference/localmean_var.html b/docs/reference/localmean_var.html index b77af0a..2dc2eee 100644 --- a/docs/reference/localmean_var.html +++ b/docs/reference/localmean_var.html @@ -1,5 +1,5 @@ -Author
diff --git a/docs/reference/localmean_weight.html b/docs/reference/localmean_weight.html index 3220de9..b2d5d36 100644 --- a/docs/reference/localmean_weight.html +++ b/docs/reference/localmean_weight.html @@ -1,6 +1,6 @@ -Author
diff --git a/docs/reference/pd_summary.html b/docs/reference/pd_summary.html index 6654434..ad6e868 100644 --- a/docs/reference/pd_summary.html +++ b/docs/reference/pd_summary.html @@ -1,9 +1,9 @@ -Examples
diff --git a/docs/reference/plot.html b/docs/reference/plot.html index 3be21f3..4b8fd44 100644 --- a/docs/reference/plot.html +++ b/docs/reference/plot.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/plot.sp_CDF.html b/docs/reference/plot.sp_CDF.html index 3b6bde2..d0ef96b 100644 --- a/docs/reference/plot.sp_CDF.html +++ b/docs/reference/plot.sp_CDF.html @@ -1,8 +1,8 @@ -Examples
diff --git a/docs/reference/power_dsgn.html b/docs/reference/power_dsgn.html index 9f35d7c..b4d76a3 100644 --- a/docs/reference/power_dsgn.html +++ b/docs/reference/power_dsgn.html @@ -1,9 +1,9 @@ -Examples
diff --git a/docs/reference/ppd_plot.html b/docs/reference/ppd_plot.html index 4f84ec8..7ad1c8d 100644 --- a/docs/reference/ppd_plot.html +++ b/docs/reference/ppd_plot.html @@ -1,11 +1,11 @@ -Examples
diff --git a/docs/reference/relrisk_analysis.html b/docs/reference/relrisk_analysis.html index 24e99bd..809a287 100644 --- a/docs/reference/relrisk_analysis.html +++ b/docs/reference/relrisk_analysis.html @@ -1,11 +1,11 @@ -Examples
diff --git a/docs/reference/revisit_bibd.html b/docs/reference/revisit_bibd.html index 338eff9..5e79655 100644 --- a/docs/reference/revisit_bibd.html +++ b/docs/reference/revisit_bibd.html @@ -1,10 +1,10 @@ -Examples
diff --git a/docs/reference/revisit_dsgn.html b/docs/reference/revisit_dsgn.html index ee09069..7fd49cb 100644 --- a/docs/reference/revisit_dsgn.html +++ b/docs/reference/revisit_dsgn.html @@ -1,8 +1,8 @@ -Examples
diff --git a/docs/reference/revisit_rand.html b/docs/reference/revisit_rand.html index ed9bb4c..fdb6d7c 100644 --- a/docs/reference/revisit_rand.html +++ b/docs/reference/revisit_rand.html @@ -1,10 +1,10 @@ -Examples
diff --git a/docs/reference/sp_balance.html b/docs/reference/sp_balance.html index cedf22a..7a892eb 100644 --- a/docs/reference/sp_balance.html +++ b/docs/reference/sp_balance.html @@ -1,7 +1,7 @@ -Examples
diff --git a/docs/reference/sp_frame.html b/docs/reference/sp_frame.html index c803e2b..c43565c 100644 --- a/docs/reference/sp_frame.html +++ b/docs/reference/sp_frame.html @@ -1,6 +1,6 @@ -Examples
diff --git a/docs/reference/sp_plot.html b/docs/reference/sp_plot.html index 9bf265d..8aacc2f 100644 --- a/docs/reference/sp_plot.html +++ b/docs/reference/sp_plot.html @@ -1,5 +1,5 @@ -Examples
diff --git a/docs/reference/sp_rbind.html b/docs/reference/sp_rbind.html index b83d48e..e6e6365 100644 --- a/docs/reference/sp_rbind.html +++ b/docs/reference/sp_rbind.html @@ -1,9 +1,9 @@ -Examples
diff --git a/docs/reference/sp_summary.html b/docs/reference/sp_summary.html index 902a4d6..4b8ce4d 100644 --- a/docs/reference/sp_summary.html +++ b/docs/reference/sp_summary.html @@ -1,11 +1,11 @@ -Examples
diff --git a/docs/reference/spsurvey-package.html b/docs/reference/spsurvey-package.html index cf7e064..2b57e0b 100644 --- a/docs/reference/spsurvey-package.html +++ b/docs/reference/spsurvey-package.html @@ -1,5 +1,5 @@ -spsurvey: Spatial Sampling Design and Analysis
See also
-Useful links:
- +
Useful links: