Merge pull request #385 from ldecicco-USGS/main

Fix links

Author: ldecicco-USGS

R/readNWISSample.R

@@ -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.
@@ -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

README.Rmd

@@ -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:
 
@@ -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
@@ -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}

README.md

@@ -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:
 
@@ -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 
@@ -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
@@ -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
 

man/readNWISSample.Rd

@@ -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.