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Fix links #385

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Nov 5, 2024
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Fix links #385

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0024506
Cleaning up links
ldecicco-USGS Nov 5, 2024
c0ae617
Better links
ldecicco-USGS Nov 5, 2024
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5 changes: 2 additions & 3 deletions R/readNWISSample.R
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@@ -1,8 +1,7 @@
#' Import NWIS Sample Data for EGRET analysis
#'
#' Imports data from NWIS web service.
#' A list of parameter and statistic codes can be found here: \url{https://help.waterdata.usgs.gov/codes-and-parameters}
#' For raw data, use \code{\link[dataRetrieval]{readNWISqw}} from the dataRetrieval package.
#' For raw data, use \code{\link[dataRetrieval]{readWQPqw}} from the dataRetrieval package.
#' This function will retrieve the raw data, and compress it (summing constituents) if
#' more than 1 parameter code is supplied. See
#' section 3.2.4 of the vignette for more details.
Expand Down Expand Up @@ -33,7 +32,7 @@
#' CosDY \tab numeric \tab Cosine of the DecYear
#' }
#' @seealso \code{\link{compressData}}, \code{\link{populateSampleColumns}},
#' \code{\link[dataRetrieval]{readNWISqw}}
#' \code{\link[dataRetrieval]{readWQPqw}}
#' @examples
#' \donttest{
#' # These examples require an internet connection to run
Expand Down
6 changes: 3 additions & 3 deletions README.Rmd
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Expand Up @@ -26,7 +26,7 @@ Exploration and Graphics for RivEr Trends (`EGRET`):
An R-package for the analysis of long-term changes in water quality and streamflow, including the water-quality method Weighted Regressions on Time, Discharge, and Season (WRTDS).

Look for new and improved documentation here:
<https://doi-usgs.github.io/EGRET/\>
<https://doi-usgs.github.io/EGRET/>

The link for the official USGS publication user guide is here:

Expand Down Expand Up @@ -218,7 +218,7 @@ sessioninfo::session_info()
## Reporting bugs

Please consider reporting bugs and asking questions on the Issues page:
[https://github.com/DOI-USGS/EGRET/issues](https://github.com/DOI-USGS/EGRET/issues)
<https://github.com/DOI-USGS/EGRET/issues>


## Subscribe
Expand Down Expand Up @@ -251,7 +251,7 @@ citation(package = "EGRET")

See this list for WRTDS applications in print:

<https://doi-usgs.github.io/EGRET/articles/References_WRTDS.html\>
<https://doi-usgs.github.io/EGRET/articles/References_WRTDS.html>


```{r disclaimer, child="DISCLAIMER.md", eval=TRUE}
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147 changes: 85 additions & 62 deletions README.md
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Expand Up @@ -11,8 +11,7 @@ including the water-quality method Weighted Regressions on Time,
Discharge, and Season (WRTDS).

Look for new and improved documentation here:
<a href="https://doi-usgs.github.io/EGRET/\"
class="uri">https://doi-usgs.github.io/EGRET/\</a>
<https://doi-usgs.github.io/EGRET/>

The link for the official USGS publication user guide is here:

Expand Down Expand Up @@ -328,13 +327,37 @@ siteID <- "01491000" #Choptank River at Greensboro, MD
startDate <- "" # Get earliest date
endDate <- "" # Get latest date
Daily <- readNWISDaily(siteID, "00060", startDate, endDate)
#> GET: https://waterservices.usgs.gov/nwis/dv/?site=01491000&format=rdb,1.0&ParameterCd=00060&StatCd=00003&startDT=1851-01-01
#> There are 28058 data points, and 28058 days.
#> <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.
# Gather site and parameter information:
# Here user must input some values for
# the default (interactive=TRUE)
INFO <- readNWISInfo(siteID, "00060")
#> GET: https://waterservices.usgs.gov/nwis/site/?siteOutput=Expanded&format=rdb&site=01491000
#> <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
#> Your site for streamflow data is:
#> 01491000 .
#> Your site name is CHOPTANK RIVER NEAR GREENSBORO, MD
Expand Down Expand Up @@ -422,63 +445,65 @@ sessioninfo::session_info()
#> collate English_United States.utf8
#> ctype English_United States.utf8
#> tz America/Chicago
#> date 2024-10-26
#> 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 2024-10-25 [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 2024-10-26 [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)
#> httr 1.4.7 2023-08-15 [1] CRAN (R 4.4.0)
#> 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)
#> 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)
#> 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)
#> 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
Expand Down Expand Up @@ -546,9 +571,7 @@ citation(package = "EGRET")

See this list for WRTDS applications in print:

<a
href="https://doi-usgs.github.io/EGRET/articles/References_WRTDS.html\"
class="uri">https://doi-usgs.github.io/EGRET/articles/References_WRTDS.html\</a>
<https://doi-usgs.github.io/EGRET/articles/References_WRTDS.html>

# Disclaimer

Expand Down
5 changes: 2 additions & 3 deletions man/readNWISSample.Rd
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2 changes: 1 addition & 1 deletion vignettes/EGRET.Rmd
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Expand Up @@ -415,7 +415,7 @@ knitr::kable(DF, caption="Example data",

```

EGRET will "add up" all the values in a given row to form the total for that sample when using the Sample data frame. Thus, you only want to enter data that should be added together. If you want a data frame with multiple constituents that are not summed, do not use `readNWISSample`, `readWQPSample`, or `readUserSample`. The raw data functions: `getWQPdata`, `readNWISqw`, `readWQPqw`, `readWQPdata` from the EGRET package will not sum constituents, but leave them in their individual columns.
EGRET will "add up" all the values in a given row to form the total for that sample when using the Sample data frame. Thus, you only want to enter data that should be added together. If you want a data frame with multiple constituents that are not summed, do not use `readNWISSample`, `readWQPSample`, or `readUserSample`. The raw data functions: `getWQPdata`, `readWQPqw`, `readWQPdata` from the EGRET package will not sum constituents, but leave them in their individual columns.

For example, we might know the value for dp on 5/30/2005, but we don't want to put it in the table because under the rules of this data set, we are not supposed to add it in to the values in 2005.

Expand Down
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