Merge pull request #386 from ldecicco-USGS/main

fix some links

Author: ldecicco-USGS

README.Rmd

@@ -65,9 +65,8 @@ The second is an application to nitrate data for 8 monitoring sites on the Missi
 
 [https://pubs.acs.org/doi/abs/10.1021/es201221s](https://pubs.acs.org/doi/abs/10.1021/es201221s)
 
-For a thorough discussion of the generalized flow normalization method implemented in the EGRET enhancements, see the paper: "Tracking changes in nutrient delivery to western Lake Erie: Approaches to compensate for variability and trends in streamflow":
+For a thorough discussion of the generalized flow normalization method implemented in the EGRET enhancements, see the paper: "Tracking changes in nutrient delivery to western Lake Erie: Approaches to compensate for variability and trends in streamflow" (doi:10.1016/j.jglr.2018.11.012).
 
-<https://www.sciencedirect.com/science/article/pii/S0380133018302235/>.
 
 ## Sample Workflow
 
@@ -206,15 +205,6 @@ plotFourStats(eList, qUnit=3)
 
 ```
 
-
-## Model Archive
-
-When using the `WRTDS` model, it is important to be able to reproduce the results in the future. The following version of R and package dependencies were used most recently to pass the embedded tests within this package. There is no guarantee of reproducible results using future versions of R or updated versions of package dependencies; however, we will make diligent efforts to test and update future modeling environments.
-
-```{r eval=TRUE}
-sessioninfo::session_info()
-```
-
 ## Reporting bugs
 
 Please consider reporting bugs and asking questions on the Issues page:
@@ -228,10 +218,6 @@ egret_comments@usgs.gov
 
 Additionally, to subscribe to an email list concerning updates to these R packages, please send a request to egret_comments@usgs.gov.
 
-## Code of Conduct
-
-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/EGRET/-/blob/main/CONDUCT.md) for more information.
-
 ## Package Support
 
 The Water Mission Area of the USGS has supported the development and maintenance of the `EGRET` R-package. Further maintenance is expected to be stable through October 2024. Resources are available primarily for maintenance and responding to user questions. Priorities on the development of new features are determined by the `EGRET` development team.

README.md

@@ -91,9 +91,8 @@ the Mississippi River or its major tributaries. The URL is:
 For a thorough discussion of the generalized flow normalization method
 implemented in the EGRET enhancements, see the paper: “Tracking changes
 in nutrient delivery to western Lake Erie: Approaches to compensate for
-variability and trends in streamflow”:
-
-<https://www.sciencedirect.com/science/article/pii/S0380133018302235/>.
+variability and trends in streamflow”
+(<doi:10.1016/j.jglr.2018.11.012>).
 
 ## Sample Workflow
 
@@ -327,37 +326,13 @@ siteID <- "01491000" #Choptank River at Greensboro, MD
 startDate <- "" # Get earliest date
 endDate <- "" # Get latest date
 Daily <- readNWISDaily(siteID, "00060", startDate, endDate)
-#> <httr2_request>
-#> GET
-#> https://waterservices.usgs.gov/nwis/dv/?site=01491000&format=rdb%2C1.0&ParameterCd=00060&StatCd=00003&startDT=1851-01-01
-#> Headers:
-#> • Accept-Encoding: 'compress'
-#> • Accept-Encoding: 'gzip'
-#> • Accept-Encoding: 'deflate'
-#> Body: empty
-#> Options:
-#> • useragent: 'libcurl/8.3.0 httr2/1.0.5 dataRetrieval/2.7.17.1'
-#> Policies:
-#> • throttle_delay: a function
-#> • retry_max_tries: 3
-#> • retry_on_failure: FALSE
-#> • retry_backoff: a <rlang_lambda_function> object
-#> There are 28068 data points, and 28068 days.
+#> GET: https://waterservices.usgs.gov/nwis/dv/?site=01491000&format=rdb,1.0&ParameterCd=00060&StatCd=00003&startDT=1851-01-01
+#> There are 28082 data points, and 28082 days.
 # Gather site and parameter information:
 # Here user must input some values for
 # the default (interactive=TRUE)
 INFO <- readNWISInfo(siteID, "00060")
-#> <httr2_request>
-#> GET
-#> https://waterservices.usgs.gov/nwis/site/?siteOutput=Expanded&format=rdb&site=01491000
-#> Body: empty
-#> Options:
-#> • useragent: 'libcurl/8.3.0 httr2/1.0.5 dataRetrieval/2.7.17.1'
-#> Policies:
-#> • throttle_delay: a function
-#> • retry_max_tries: 3
-#> • retry_on_failure: FALSE
-#> • retry_backoff: a <rlang_lambda_function> object
+#> GET: https://waterservices.usgs.gov/nwis/site/?siteOutput=Expanded&format=rdb&site=01491000
 #> Your site for streamflow data is:
 #>  01491000 .
 #> Your site name is CHOPTANK RIVER NEAR GREENSBORO, MD 
@@ -423,94 +398,6 @@ plotFourStats(eList, qUnit=3)
 
 ![](man/figures/README-plotFours-2.png)
 
-## Model Archive
-
-When using the `WRTDS` model, it is important to be able to reproduce
-the results in the future. The following version of R and package
-dependencies were used most recently to pass the embedded tests within
-this package. There is no guarantee of reproducible results using future
-versions of R or updated versions of package dependencies; however, we
-will make diligent efforts to test and update future modeling
-environments.
-
-``` r
-sessioninfo::session_info()
-#> ─ Session info ───────────────────────────────────────────────────────────────
-#>  setting  value
-#>  version  R version 4.4.1 (2024-06-14 ucrt)
-#>  os       Windows 11 x64 (build 22631)
-#>  system   x86_64, mingw32
-#>  ui       RTerm
-#>  language (EN)
-#>  collate  English_United States.utf8
-#>  ctype    English_United States.utf8
-#>  tz       America/Chicago
-#>  date     2024-11-05
-#>  pandoc   3.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
-#> 
-#> ─ Packages ───────────────────────────────────────────────────────────────────
-#>  package       * version  date (UTC) lib source
-#>  bit             4.5.0    2024-09-20 [1] CRAN (R 4.4.1)
-#>  bit64           4.5.2    2024-09-22 [1] CRAN (R 4.4.1)
-#>  class           7.3-22   2023-05-03 [2] CRAN (R 4.4.1)
-#>  classInt        0.4-10   2023-09-05 [1] CRAN (R 4.4.0)
-#>  cli             3.6.3    2024-06-21 [1] CRAN (R 4.4.1)
-#>  crayon          1.5.3    2024-06-20 [1] CRAN (R 4.4.1)
-#>  curl            5.2.3    2024-09-20 [1] CRAN (R 4.4.1)
-#>  dataRetrieval   2.7.17.1 2024-11-05 [1] local
-#>  DBI             1.2.3    2024-06-02 [1] CRAN (R 4.4.0)
-#>  digest          0.6.37   2024-08-19 [1] CRAN (R 4.4.1)
-#>  dotCall64       1.2      2024-10-04 [1] CRAN (R 4.4.1)
-#>  e1071           1.7-16   2024-09-16 [1] CRAN (R 4.4.1)
-#>  EGRET         * 3.0.10   2024-11-05 [1] local
-#>  evaluate        1.0.1    2024-10-10 [1] CRAN (R 4.4.1)
-#>  fansi           1.0.6    2023-12-08 [1] CRAN (R 4.4.0)
-#>  fastmap         1.2.0    2024-05-15 [1] CRAN (R 4.4.0)
-#>  fields          16.3     2024-09-30 [1] CRAN (R 4.4.1)
-#>  glue            1.8.0    2024-09-30 [1] CRAN (R 4.4.1)
-#>  highr           0.11     2024-05-26 [1] CRAN (R 4.4.0)
-#>  hms             1.1.3    2023-03-21 [1] CRAN (R 4.4.0)
-#>  htmltools       0.5.8.1  2024-04-04 [1] CRAN (R 4.4.0)
-#>  httr2           1.0.5    2024-09-26 [1] CRAN (R 4.4.1)
-#>  KernSmooth      2.23-24  2024-05-17 [2] CRAN (R 4.4.1)
-#>  knitr           1.48     2024-07-07 [1] CRAN (R 4.4.1)
-#>  lattice         0.22-6   2024-03-20 [1] CRAN (R 4.4.0)
-#>  lifecycle       1.0.4    2023-11-07 [1] CRAN (R 4.4.0)
-#>  magrittr        2.0.3    2022-03-30 [1] CRAN (R 4.4.0)
-#>  maps            3.4.2    2023-12-15 [1] CRAN (R 4.4.0)
-#>  Matrix          1.7-0    2024-04-26 [2] CRAN (R 4.4.1)
-#>  pillar          1.9.0    2023-03-22 [1] CRAN (R 4.4.0)
-#>  pkgconfig       2.0.3    2019-09-22 [1] CRAN (R 4.4.0)
-#>  proxy           0.4-27   2022-06-09 [1] CRAN (R 4.4.0)
-#>  R6              2.5.1    2021-08-19 [1] CRAN (R 4.4.0)
-#>  rappdirs        0.3.3    2021-01-31 [1] CRAN (R 4.4.0)
-#>  Rcpp            1.0.13   2024-07-17 [1] CRAN (R 4.4.1)
-#>  readr           2.1.5    2024-01-10 [1] CRAN (R 4.4.0)
-#>  rlang           1.1.4    2024-06-04 [1] CRAN (R 4.4.1)
-#>  rmarkdown       2.28     2024-08-17 [1] CRAN (R 4.4.1)
-#>  rstudioapi      0.17.1   2024-10-22 [1] CRAN (R 4.4.1)
-#>  sessioninfo     1.2.2    2021-12-06 [1] CRAN (R 4.4.0)
-#>  sf              1.0-18   2024-10-11 [1] CRAN (R 4.4.1)
-#>  spam            2.11-0   2024-10-03 [1] CRAN (R 4.4.1)
-#>  survival        3.6-4    2024-04-24 [2] CRAN (R 4.4.1)
-#>  tibble          3.2.1    2023-03-20 [1] CRAN (R 4.4.0)
-#>  tidyselect      1.2.1    2024-03-11 [1] CRAN (R 4.4.0)
-#>  tzdb            0.4.0    2023-05-12 [1] CRAN (R 4.4.0)
-#>  units           0.8-5    2023-11-28 [1] CRAN (R 4.4.0)
-#>  utf8            1.2.4    2023-10-22 [1] CRAN (R 4.4.0)
-#>  vctrs           0.6.5    2023-12-01 [1] CRAN (R 4.4.0)
-#>  viridisLite     0.4.2    2023-05-02 [1] CRAN (R 4.4.0)
-#>  vroom           1.6.5    2023-12-05 [1] CRAN (R 4.4.0)
-#>  withr           3.0.1    2024-07-31 [1] CRAN (R 4.4.1)
-#>  xfun            0.48     2024-10-03 [1] CRAN (R 4.4.1)
-#>  yaml            2.3.10   2024-07-26 [1] CRAN (R 4.4.1)
-#> 
-#>  [1] C:/Users/ldecicco/AppData/Local/R/win-library/4.4
-#>  [2] C:/Program Files/R/R-4.4.1/library
-#> 
-#> ──────────────────────────────────────────────────────────────────────────────
-```
-
 ## Reporting bugs
 
 Please consider reporting bugs and asking questions on the Issues page:
@@ -524,13 +411,6 @@ Please email questions, comments, and feedback to:
 Additionally, to subscribe to an email list concerning updates to these
 R packages, please send a request to <egret_comments@usgs.gov>.
 
-## Code of Conduct
-
-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/EGRET/-/blob/main/CONDUCT.md) for
-more information.
-
 ## Package Support
 
 The Water Mission Area of the USGS has supported the development and