diff --git a/.Rbuildignore b/.Rbuildignore
index 3fd2ad97df00f49bc0032ae751afb2f9e3caed28..ed247f4fe2ec00b7e57ee38984181bcfe99297cf 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -19,10 +19,11 @@ pkgdown/favicon/*
.git
vignettes/prediction.Rmd
vignettes/Pinehurst_eListK.rds
-<<<<<<< HEAD
^ci$
deploy_simple.R
cobertura.xml
test-out.xml
^_pkgdown\.yml$
^pkgdown$
+^review$
+README.rmd
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9cdf96d685be854d848f8abd57dfb2a7455edc04..e655ab5fc72c381b2ccb39adc839508b102a490b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -10,6 +10,7 @@ stages:
- check
- test
- end
+ - deploy
variables:
_R_CHECK_CRAN_INCOMING_: "false"
@@ -25,6 +26,7 @@ variables:
NOT_CRAN: "true"
CONNECT_API_KEY: $CONNECT_API_KEY
CONNECT_SERVER: $CONNECT_SERVER
+ PAGES_OUTDIR: "$CI_PROJECT_DIR/public"
cache:
paths:
@@ -86,16 +88,16 @@ covertests:
path: cobertura.xml
coverage: '/Coverage: \d+.\d+\%/'
-deploy:
+pages:
stage: end
only:
- main
script:
- - Rscript -e 'pkgdown::build_site()'
+ - Rscript -e 'pkgdown::build_site(override = list(destination = "public"))'
- Rscript -e 'source("deploy_simple.R")'
artifacts:
paths:
- - $PKG_PATH
+ - $PAGES_OUTDIR
expire_in: 1 week
Validate Inventory:
diff --git a/DESCRIPTION b/DESCRIPTION
index 17853bab8e66d609964a284f61f2fdd7679b2808..76412378a5814e3a507d39fe4e5c03129d5240ac 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,14 +1,19 @@
Package: EGRETci
Type: Package
Title: Exploration and Graphics for RivEr Trends Confidence Intervals
-Version: 2.0.4.0002
+Version: 2.0.5
Authors@R: c(person("Laura", "DeCicco", role = c("aut","cre"),
email = "ldecicco@usgs.gov",
comment=c(ORCID="0000-0002-3915-9487")),
person("Robert", "Hirsch", role = c("aut"),
email = "rhirsch@usgs.gov",
comment=c(ORCID="0000-0002-4534-075X")),
- person("Jennifer","Murphy", role = c("ctb")))
+ person("Stacey","Archfield", role = c("ctb"),
+ email = "sarch@usgs.gov",
+ comment=c(ORCID="0000-0002-9011-3871")),
+ person("Jennifer","Murphy", role = c("ctb"),
+ email = "jmurphy@usgs.gov",
+ comment=c(ORCID="0000-0002-0881-0919")))
Description: Collection of functions to evaluate uncertainty of results from
water quality analysis using the Weighted Regressions on Time Discharge and
Season (WRTDS) method. This package is an add-on to the EGRET package that
@@ -39,11 +44,11 @@ LazyData: yes
VignetteBuilder: knitr
BuildVignettes: true
URL: https://code.usgs.gov/water/EGRETci
-BugReports: https://github.com/USGS-R/EGRETci/issues
+BugReports: https://github.com/DOI-USGS/EGRETci/issues
Copyright: This software is in the public domain because it contains materials
that originally came from the United States Geological Survey, an agency of
the United States Department of Interior. For more information, see the
official USGS copyright policy at
- http://www.usgs.gov/visual-id/credit_usgs.html#copyright
+ hhttps://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits
RoxygenNote: 7.2.3
Roxygen: list(old_usage = TRUE)
diff --git a/LICENSE.md b/LICENSE.md
new file mode 100644
index 0000000000000000000000000000000000000000..7dbcd7cea347980e42dfd4ec5e341e79ce03fc4c
--- /dev/null
+++ b/LICENSE.md
@@ -0,0 +1,46 @@
+License
+=======
+
+Unless otherwise noted, This project is in the public domain in the United
+States because it contains materials that originally came from the United
+States Geological Survey, an agency of the United States Department of
+Interior. For more information, see the official USGS copyright policy at
+https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits
+
+Additionally, we waive copyright and related rights in the work
+worldwide through the CC0 1.0 Universal public domain dedication.
+
+
+CC0 1.0 Universal Summary
+-------------------------
+
+This is a human-readable summary of the
+[Legal Code (read the full text)][1].
+
+
+### No Copyright
+
+The person who associated a work with this deed has dedicated the work to
+the public domain by waiving all of his or her rights to the work worldwide
+under copyright law, including all related and neighboring rights, to the
+extent allowed by law.
+
+You can copy, modify, distribute and perform the work, even for commercial
+purposes, all without asking permission.
+
+
+### Other Information
+
+In no way are the patent or trademark rights of any person affected by CC0,
+nor are the rights that other persons may have in the work or in how the
+work is used, such as publicity or privacy rights.
+
+Unless expressly stated otherwise, the person who associated a work with
+this deed makes no warranties about the work, and disclaims liability for
+all uses of the work, to the fullest extent permitted by applicable law.
+When using or citing the work, you should not imply endorsement by the
+author or the affirmer.
+
+
+
+[1]: https://creativecommons.org/publicdomain/zero/1.0/legalcode
diff --git a/R/plotCIs.R b/R/plotCIs.R
index 7a0e2a098722cf693f29a8eafcaf0d02d013b03d..b17f6164a9d7fa184bff63994218d8da8bd03a6f 100644
--- a/R/plotCIs.R
+++ b/R/plotCIs.R
@@ -632,7 +632,7 @@ plotHistogramTrend <- function (eList, eBoot, caseSetUp,
#'
#' @param eList named list with at least the Daily, Sample, and INFO dataframes. Created from the EGRET package, after running \code{\link[EGRET]{modelEstimation}}.
#' @param startSeed setSeed value. Defaults to 494817. This is used to make repeatable output.
-#' @param verbose logical specifying whether or not to display progress messag, default = TRUE
+#' @param verbose logical specifying whether or not to display progress message, default = TRUE
#' @param jitterOn logical, if TRUE, adds "jitter" to the data in an attempt to avoid some numerical problems. Default = FALSE. See Details below.
#' @param V numeric a multiplier for addition of jitter to the data, default = 0.2. See Details below.
#' @param nBoot number of times the bootstrap resampling and model estimating is done.
@@ -645,13 +645,15 @@ plotHistogramTrend <- function (eList, eBoot, caseSetUp,
#'
#' @export
#'
-#' @return CIAnnualResults a data frame with the following columns
-#' Year, mean decYear value for the year being reported
-#' FNConcLow, the lower confidence limit for flow normalized concentration, in mg/L
-#' FNConcHigh, the upper confidence limit for flow normalized concentration, in mg/L
-#' FNFluxLow, the lower confidence limit for flow normalized flux, in kg
-#' FNFluxLow, the lower confidence limit for flow normalized flux, in kg
-#'
+#' @return CIAnnualResults a data frame with the following columns:
+#' \tabular{ll}{
+#' Year \tab mean decYear value for the year being reported \cr
+#' FNConcLow \tab the lower confidence limit for flow normalized concentration, in mg/L \cr
+#' FNConcHigh \tab the upper confidence limit for flow normalized concentration, in mg/L \cr
+#' FNFluxLow \tab the lower confidence limit for flow normalized flux, in kg/day \cr
+#' FNFluxLow \tab the lower confidence limit for flow normalized flux, in kg/day \cr
+#' }
+#'
#' @details
#' In some situations numerical problems are encountered in the bootstrap process, resulting in highly unreasonable spikes in the confidence intervals.
#' The use of "jitter" can often prevent these problems, but should only be used when it is clearly needed.
diff --git a/R/wBTCode.R b/R/wBTCode.R
index f1670c65a4f0762753cd3abe1ab6b725943bbc88..fe71f1f5392787cc20f66ee82621280bfb7a3b9e 100644
--- a/R/wBTCode.R
+++ b/R/wBTCode.R
@@ -18,7 +18,7 @@ Extended Documentation: https://rconnect.usgs.gov/EGRETci")
#' that originally came from the United States Geological Survey, an agency of
#' the United States Department of Interior. For more information, see the
#' official USGS copyright policy at
-#' http://www.usgs.gov/visual-id/credit_usgs.html#copyright\cr
+#' \url{https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits}\cr
#' LazyLoad: \tab yes\cr
#' }
#' Collection of functions to evaluate uncertainty of results from water quality analysis using
diff --git a/README.Rmd b/README.Rmd
index cb002df72bd73ecc7c72e792e65eaefd61de27ba..f816ce65477c71783c8c9209f0790409402ab06e 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -39,12 +39,12 @@ citation(package = "EGRETci")
### Reporting bugs
Please consider reporting bugs and asking questions on the Issues page:
-[https://github.com/USGS-R/EGRETci/issues](https://github.com/USGS-R/EGRET/issues)
+[https://github.com/DOI-USGS/EGRETci/issues](https://github.com/DOI-USGS/EGRET/issues)
### Code of Conduct
-We want to encourage a warm, welcoming, and safe environment for contributing to this project. See the [code of conduct](https://github.com/USGS-R/EGRETci/blob/master/CONDUCT.md) for more information.
+We want to encourage a warm, welcoming, and safe environment for contributing to this project. See the [code of conduct](https://code.usgs.gov/water/EGRETci/-/blob/main/CONDUCT.md) for more information.
## Model Archive
diff --git a/README.md b/README.md
index f03893bc3fb393be0ab71de324b1606abeb8ddf4..53cce2d74f70964be71d01e2db26f73f8bcf4958 100644
--- a/README.md
+++ b/README.md
@@ -44,31 +44,31 @@ citation(package = "EGRETci")
#>
#> To cite EGRETci in publications, please use:
#>
-#> Hirsch, R.M., Archfield, S.A., De Cicco, L.A., "A bootstrap method
-#> for estimating uncertainty of water quality trends", Environmental
-#> Modelling & Software, Vol 73, Nov 2015, p 148-166. doi:
-#> 10.1016/j.envsoft.2015.07.017
+#> Hirsch, R.M., De Cicco, L.A., Archfield, S.A., Murphy, J.C., 2023,
+#> Exploration and Graphics for RivEr Trends (EGRET) Uncertainty and
+#> Confidence Intervals, version 2.0.5, doi:10.5066/P9CC9JEX
#>
#> A BibTeX entry for LaTeX users is
#>
-#> @Article{,
-#> author = {Robert M. Hirsch and Stacey A. Archfield and Laura A. {De Cicco}},
-#> title = {A bootstrap method for estimating uncertainty of water quality trends},
-#> journal = {Journal of Environmental Modelling and Software},
-#> year = {2015},
+#> @Manual{,
+#> author = {Robert M. Hirsch and Laura A. {De Cicco} and Stacey A. Archfield and Jennifer C. Murphy},
+#> title = {EGRETci},
+#> publisher = {U.S. Geological Survey},
+#> year = {2023},
+#> url = {https://pubs.usgs.gov/tm/04/a10/},
#> }
```
### Reporting bugs
Please consider reporting bugs and asking questions on the Issues page:
-[https://github.com/USGS-R/EGRETci/issues](https://github.com/USGS-R/EGRET/issues)
+[https://github.com/DOI-USGS/EGRETci/issues](https://github.com/DOI-USGS/EGRET/issues)
### Code of Conduct
We want to encourage a warm, welcoming, and safe environment for
contributing to this project. See the [code of
-conduct](https://github.com/USGS-R/EGRETci/blob/master/CONDUCT.md) for
+conduct](https://code.usgs.gov/water/EGRETci/-/blob/main/CONDUCT.md) for
more information.
## Model Archive
@@ -93,29 +93,23 @@ sessioninfo::session_info()
#> collate English_United States.utf8
#> ctype English_United States.utf8
#> tz America/Chicago
-#> date 2022-12-09
-#> pandoc 2.19.2 @ C:/Program Files/RStudio/bin/quarto/bin/tools/ (via rmarkdown)
+#> date 2023-03-06
+#> pandoc 2.19.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
-#> cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.1)
-#> digest 0.6.30 2022-10-18 [1] CRAN (R 4.2.2)
-#> evaluate 0.18 2022-11-07 [1] CRAN (R 4.2.2)
+#> cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.2)
+#> digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.2)
+#> evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.2)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.1)
-#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.3)
#> htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.2)
-#> knitr 1.41 2022-11-18 [1] CRAN (R 4.2.2)
-#> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.1)
-#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.3)
+#> knitr 1.42 2023-01-25 [1] CRAN (R 4.2.2)
#> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
-#> rmarkdown 2.18 2022-11-09 [1] CRAN (R 4.2.2)
+#> rmarkdown 2.20 2023-01-19 [1] CRAN (R 4.2.2)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
-#> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1)
-#> stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.2)
-#> vctrs 0.5.1 2022-11-16 [1] CRAN (R 4.2.2)
-#> xfun 0.35 2022-11-16 [1] CRAN (R 4.2.2)
-#> yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.1)
+#> xfun 0.37 2023-01-31 [1] CRAN (R 4.2.2)
+#> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.2)
#>
#> [1] C:/Users/ldecicco/Documents/R/win-library/4.2
#> [2] C:/Program Files/R/R-4.2.2/library
diff --git a/deploy_simple.R b/deploy_simple.R
index f882c1a7d11485566a1c184472cb31ffa2516699..0657f020c4c85dbc2f5f23d40ce21465771347fb 100644
--- a/deploy_simple.R
+++ b/deploy_simple.R
@@ -2,11 +2,11 @@ library(connectapi)
client <- connect(server = Sys.getenv("CONNECT_SERVER"),
api_key = Sys.getenv("CONNECT_API_KEY"))
-file.copy(from = "./docs/articles/logo.png",
- to = "./docs/reference/logo.png")
+file.copy(from = "./public/articles/logo.png",
+ to = "./public/reference/logo.png")
-rsconnect::writeManifest(appDir = "./docs")
-bundle <- bundle_dir("./docs")
+rsconnect::writeManifest(appDir = "./public")
+bundle <- bundle_dir("./public")
content <- client %>%
deploy(bundle, name = "EGRETci") %>%
diff --git a/inst/CITATION b/inst/CITATION
index dfe3ba122812505fea93471c37588a0b52871513..6d919ccebcc7584ae2f77d955be3f45e2abdbe67 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -1,13 +1,14 @@
citHeader("To cite EGRETci in publications, please use:")
-bibentry(bibtype = "article",
+bibentry(bibtype = "Manual",
author = personList(
as.person("Robert M. Hirsch"),
+ as.person("Laura A. De Cicco"),
as.person("Stacey A. Archfield"),
- as.person("Laura A. De Cicco")),
- title = "A bootstrap method for estimating uncertainty of water quality trends",
- journal = "Journal of Environmental Modelling and Software",
- year = 2015,
- textVersion = 'Hirsch, R.M., Archfield, S.A., De Cicco, L.A., "A bootstrap method for estimating uncertainty of water quality trends", Environmental Modelling & Software, Vol 73, Nov 2015, p 148-166. doi: 10.1016/j.envsoft.2015.07.017'
+ as.person("Jennifer C. Murphy")),
+ title = "EGRETci",
+ publisher = "U.S. Geological Survey",
+ year = 2023,
+ url = "https://pubs.usgs.gov/tm/04/a10/",
+ textVersion = "Hirsch, R.M., De Cicco, L.A., Archfield, S.A., Murphy, J.C., 2023, Exploration and Graphics for RivEr Trends (EGRET) Uncertainty and Confidence Intervals, version 2.0.5, doi:10.5066/P9CC9JEX"
)
-
diff --git a/man/EGRETci-package.Rd b/man/EGRETci-package.Rd
index 7300fa934b4bc2b29edfb94005462eeab7cd9812..af337b5226a3c4bd0098da745b6f51e8da8bc843 100644
--- a/man/EGRETci-package.Rd
+++ b/man/EGRETci-package.Rd
@@ -16,7 +16,7 @@ Copyright: \tab This software is in the public domain because it contains materi
that originally came from the United States Geological Survey, an agency of
the United States Department of Interior. For more information, see the
official USGS copyright policy at
-http://www.usgs.gov/visual-id/credit_usgs.html#copyright\cr
+\url{https://www.usgs.gov/information-policies-and-instructions/copyrights-and-credits}\cr
LazyLoad: \tab yes\cr
}
Collection of functions to evaluate uncertainty of results from water quality analysis using
diff --git a/man/ciCalculations.Rd b/man/ciCalculations.Rd
index bde1c509aa0d3f9ab74e1bfbac606fc6a844d491..ecd5f63127564ff6909d3a3843811c73de10efaa 100644
--- a/man/ciCalculations.Rd
+++ b/man/ciCalculations.Rd
@@ -13,7 +13,7 @@ ciCalculations(eList, startSeed = 494817, verbose = TRUE,
\item{startSeed}{setSeed value. Defaults to 494817. This is used to make repeatable output.}
-\item{verbose}{logical specifying whether or not to display progress messag, default = TRUE}
+\item{verbose}{logical specifying whether or not to display progress message, default = TRUE}
\item{jitterOn}{logical, if TRUE, adds "jitter" to the data in an attempt to avoid some numerical problems. Default = FALSE. See Details below.}
@@ -30,12 +30,14 @@ been found to be a good choice.}
confidence intervals will be calculated with 90\%.}
}
\value{
-CIAnnualResults a data frame with the following columns
- Year, mean decYear value for the year being reported
- FNConcLow, the lower confidence limit for flow normalized concentration, in mg/L
- FNConcHigh, the upper confidence limit for flow normalized concentration, in mg/L
- FNFluxLow, the lower confidence limit for flow normalized flux, in kg
- FNFluxLow, the lower confidence limit for flow normalized flux, in kg
+CIAnnualResults a data frame with the following columns:
+\tabular{ll}{
+Year \tab mean decYear value for the year being reported \cr
+FNConcLow \tab the lower confidence limit for flow normalized concentration, in mg/L \cr
+FNConcHigh \tab the upper confidence limit for flow normalized concentration, in mg/L \cr
+FNFluxLow \tab the lower confidence limit for flow normalized flux, in kg/day \cr
+FNFluxLow \tab the lower confidence limit for flow normalized flux, in kg/day \cr
+}
}
\description{
Function to calculate confidence bands for flow normalized concentration or
diff --git a/tests/testthat/tests_kalman.R b/tests/testthat/tests_kalman.R
index d52aefef9c3372da4f194d5fa3dd72d24830de66..4d73e3f27bd13f45eb5697ee9957b3336b01acdb 100644
--- a/tests/testthat/tests_kalman.R
+++ b/tests/testthat/tests_kalman.R
@@ -10,8 +10,8 @@ test_that("Kalman Bootstrapping", {
expect_equal(nrow(dailyBootOut), nrow(eList$Daily))
expect_equal(ncol(dailyBootOut), 4)
- expect_equal(round(dailyBootOut[1,1], digits = 2), 161.57)
- expect_equal(round(dailyBootOut[2,2], digits = 2), 131.96)
+ expect_equal(round(dailyBootOut[1,1], digits = 2), 197.5)
+ expect_equal(round(dailyBootOut[2,2], digits = 2), 128.74)
})