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fix some links
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ldecicco-USGS authored Nov 20, 2024
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16 changes: 1 addition & 15 deletions README.Rmd
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Expand Up @@ -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

Expand Down Expand Up @@ -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:
Expand All @@ -228,10 +218,6 @@ [email protected]

Additionally, to subscribe to an email list concerning updates to these R packages, please send a request to [email protected].

## 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.
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130 changes: 5 additions & 125 deletions README.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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:
Expand All @@ -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 <[email protected]>.

## 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
Expand Down

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