From 5af52951489bc879caeec3cfce9ea3c498bcf2d6 Mon Sep 17 00:00:00 2001 From: mitchellmanware Date: Tue, 30 Jul 2024 10:55:45 -0400 Subject: [PATCH 1/4] remove links --- R/calculate_covariates.R | 1 - README.md | 2 +- inst/REFERENCES.bib | 2 +- 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/R/calculate_covariates.R b/R/calculate_covariates.R index d341d950..26627406 100644 --- a/R/calculate_covariates.R +++ b/R/calculate_covariates.R @@ -1136,7 +1136,6 @@ calc_temporal_dummies <- #' @author Insang Song #' @references #' \insertRef{messier2012integrating}{amadeus} -#' \insertRef{web_sedctutorial}{amadeus} #' @examples #' library(terra) #' library(sf) diff --git a/README.md b/README.md index a825a149..080c6a3b 100644 --- a/README.md +++ b/README.md @@ -58,7 +58,7 @@ Utilize [Issues](https://github.com/NIEHS/amadeus/issues) to notify the authors | [US EPA National Emissions Inventory (NEI)](https://www.epa.gov/air-emissions-inventories) | CSV | Emissions | | [US EPA Toxic Release Inventory (TRI) Program](https://www.epa.gov/toxics-release-inventory-tri-program/tri-basic-data-files-calendar-years-1987-present) | CSV | Chemicals
Pollution | | [USGS[^6] Global Multi-resolution Terrain Elevation Data (GMTED2010)](https://www.usgs.gov/coastal-changes-and-impacts/gmted2010) | ESRI ASCII Grid | Elevation | -| [USGS National Hydrography Dataset (NHD)](https://www.sciencebase.gov/catalog/item/4f5545cce4b018de15819ca9) | Geopackage
Geodatabase | Hydrography | +| [USGS National Hydrography Dataset (NHD)](https://www.usgs.gov/national-hydrography) | Geopackage
Geodatabase | Hydrography | See the "[download_data](https://niehs.github.io/amadeus/articles/download_functions.html)" vignette for a detailed description of source-specific download functions. diff --git a/inst/REFERENCES.bib b/inst/REFERENCES.bib index c41db9d4..729ecfcd 100644 --- a/inst/REFERENCES.bib +++ b/inst/REFERENCES.bib @@ -908,7 +908,7 @@ @inproceedings{abstract_simoes2021rstac @misc{data_usgs2023nhd, author = {{U.S. Geological Survey}}, title = {{National Hydrography Dataset (NHD) -- USGS National Map Downloadable Data Collection}}, - url = {https://www.sciencebase.gov/catalog/item/4f5545cce4b018de15819ca9}, + url = {https://www.usgs.gov/national-hydrography}, year = {2023} } From acfb7f1ed3b565c870ac21faedbcd8bf180e2000 Mon Sep 17 00:00:00 2001 From: mitchellmanware Date: Tue, 30 Jul 2024 11:12:51 -0400 Subject: [PATCH 2/4] package-specific REF for calc_sedc; LICENSE.md file --- LICENSE | 23 ++--------------------- LICENSE.md | 21 +++++++++++++++++++++ R/calculate_covariates.R | 1 + inst/REFERENCES.bib | 4 ++++ man/calc_sedc.Rd | 2 +- 5 files changed, 29 insertions(+), 22 deletions(-) create mode 100644 LICENSE.md diff --git a/LICENSE b/LICENSE index 7cdec7c2..117989f0 100644 --- a/LICENSE +++ b/LICENSE @@ -1,21 +1,2 @@ -MIT License - -Copyright (c) 2024 Spatiotemporal Exposures and Toxicology Group - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. +YEAR: 2024 +COPYRIGHT HOLDER: Spatiotemporal Exposures and Toxicology Group \ No newline at end of file diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 00000000..eb5ff5a6 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,21 @@ +# MIT License + +Copyright (c) 2024 Spatiotemporal Exposures and Toxicology Group + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/R/calculate_covariates.R b/R/calculate_covariates.R index 26627406..b434d497 100644 --- a/R/calculate_covariates.R +++ b/R/calculate_covariates.R @@ -1136,6 +1136,7 @@ calc_temporal_dummies <- #' @author Insang Song #' @references #' \insertRef{messier2012integrating}{amadeus} +#' \insertRef{web_sedctutorial_package}{amadeus} #' @examples #' library(terra) #' library(sf) diff --git a/inst/REFERENCES.bib b/inst/REFERENCES.bib index 729ecfcd..9ac3b9fd 100644 --- a/inst/REFERENCES.bib +++ b/inst/REFERENCES.bib @@ -376,6 +376,10 @@ @misc{web_sedctutorial author = {Corinne Wiesner}, url = {https://mserre.sph.unc.edu/BMElab_web/SEDCtutorial/index.html} } +@misc{web_sedctutorial_package, + title = {Euclidean Sum of Exponentially Decaying Contributions Tutorial}, + author = {Corinne Wiesner} +} @misc{web_ropensci, title = {Packages}, publisher = {rOpenSci}, diff --git a/man/calc_sedc.Rd b/man/calc_sedc.Rd index 7a735972..bfd717bd 100644 --- a/man/calc_sedc.Rd +++ b/man/calc_sedc.Rd @@ -73,7 +73,7 @@ calc_sedc(pnt_locs, pnt_from, "NAME", 1e4, vals) } \references{ \insertRef{messier2012integrating}{amadeus} -\insertRef{web_sedctutorial}{amadeus} +\insertRef{web_sedctutorial_package}{amadeus} } \author{ Insang Song From ed45712a1db4de4c3ef27b52bd33bf03abbe11b0 Mon Sep 17 00:00:00 2001 From: mitchellmanware Date: Tue, 30 Jul 2024 11:13:26 -0400 Subject: [PATCH 3/4] 1.0.2 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5ba99ed0..aed18825 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: amadeus Title: A Machine for Data, Environments, and User Setup for Common Environmental and Climate Health Datasets -Version: 1.0.1 +Version: 1.0.2 Authors@R: c( person(given = "Mitchell", family = "Manware", role = c("aut", "ctb"), comment = c(ORCID = "0009-0003-6440-6106")), person(given = "Insang", family = "Song", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-8732-3256")), From 7d25e44162c3c5b724b1e8fa9f7146438985842f Mon Sep 17 00:00:00 2001 From: mitchellmanware Date: Tue, 30 Jul 2024 11:33:49 -0400 Subject: [PATCH 4/4] LICENSE.md to .Rbuildignore --- .Rbuildignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.Rbuildignore b/.Rbuildignore index 666c0c9f..66fc6947 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -22,4 +22,5 @@ R/olm_functions.R vignettes/download_functions.Rmd vignettes/epa_download.Rmd vignettes/protected_datasets.Rmd -inst/extdata/air.2m \ No newline at end of file +inst/extdata/air.2m +LICENSE.md \ No newline at end of file