migrate nhdplusTools to hydrogeofetch

DESCRIPTION

@@ -45,7 +45,7 @@ Description: Tools for using the 'StreamCat' and 'LakeCat' API and
 Depends: R (>= 4.1.0)
 Imports: 
     sf,
-    nhdplusTools,
+    hydrogeofetch,
     jsonlite,
     httr2,
     curl (>= 6.0.0),

R/lc_get_comid.R

@@ -22,7 +22,7 @@
 #' @param crsys The epsg code if using a raw data frame
 #' 
 #' @param buffer The amount of buffer to use to extend search for a waterbody 
-#' (simply passed to nhdplusTools::get_waterbodies)
+#' (simply passed to hydrogeofetch::get_waterbodies)
 #' 
 #' @return A new sf data frame with a populated 'COMID' column
 #'
@@ -56,9 +56,9 @@ lc_get_comid <- function(dd = NULL, xcoord = NULL,
 
   output <- do.call(rbind, lapply(1:nrow(dd), function(i){
     if (is.null(buffer)){
-      wb <- nhdplusTools::get_waterbodies(dd[i,])
+      wb <- hydrogeofetch::get_waterbodies(dd[i,])
     } else {
-      wb <- nhdplusTools::get_waterbodies(dd[i,], buffer=buffer)
+      wb <- hydrogeofetch::get_waterbodies(dd[i,], buffer=buffer)
     }
     if (!is.null(wb)){
       comid <- wb |>

R/sc_get_comid.R

@@ -57,7 +57,7 @@ sc_get_comid <- function(dd = NULL, xcoord = NULL,
   geom_col <- attr(dd, "sf_column")
   run_for <- 1:nrow(dd)
   output <- do.call(rbind, lapply(1:nrow(dd), function(i){
-    comid <- nhdplusTools::discover_nhdplus_id(dd[i,c(geom_col)])
+    comid <- hydrogeofetch::discover_nhdplus_id(dd[i,c(geom_col)])
     if (length(comid)==0L) comid <- NA else comid <- comid
     return(comid)
   }))

R/sc_plot.R

@@ -205,7 +205,7 @@ sc_plotnni <- function(comid, include.nue = FALSE, include.inset = TRUE){
 
   #comid
   comidint <- as.integer(comid)
-  flowline <- nhdplusTools::get_nhdplus(comid = comidint, realization = "flowline")
+  flowline <- hydrogeofetch::get_nhdplus(comid = comidint, realization = "flowline")
   point <- flowline |>
     sf::st_geometry() |>
     sf::st_centroid() |>

vignettes/Articles/Applications.Rmd

@@ -27,13 +27,13 @@ knitr::opts_chunk$set(
 ```
 
 ### Plotting watershed data
-In this example we access a single variable for the Calapooia River using `sc_get_data` function. We then use the `nhdplusTools` library to grab flowlines and watershed for the Calapooia, plot the selected StreamCat metric for the Calapooia River and show the watershed.
+In this example we access a single variable for the Calapooia River using `sc_get_data` function. We then use the `hydrogeofetch` library to grab flowlines and watershed for the Calapooia, plot the selected StreamCat metric for the Calapooia River and show the watershed.
 ```{r wshd, results='hide'}
 library(StreamCatTools)
 start_comid = 23763517
 nldi_feature <- list(featureSource = "comid", featureID = start_comid)
 
-flowline_nldi <- nhdplusTools::navigate_nldi(nldi_feature, mode = "UT", data_source = "flowlines", distance=5000)
+flowline_nldi <- hydrogeofetch::navigate_nldi(nldi_feature, mode = "UT", data_source = "flowlines", distance=5000)
 
 # get StreamCat metrics
 df <- sc_get_data(metric='pctimp2011', aoi='cat', comid=flowline_nldi$UT_flowlines$nhdplus_comid)
@@ -45,7 +45,7 @@ df <- sc_get_data(metric='pctimp2011', aoi='cat', comid=flowline_nldi$UT_flowlin
 flowline_nldi <- flowline_nldi$UT_flowlines
 flowline_nldi$PCTIMP2011CAT <- df$pctimp2011cat[match(flowline_nldi$nhdplus_comid, df$comid)]
 
-basin <- nhdplusTools::get_nldi_basin(nldi_feature = nldi_feature)   
+basin <- hydrogeofetch::get_nldi_basin(nldi_feature = nldi_feature)   
 ```
 
 ```{r wshd pt2}
@@ -64,7 +64,7 @@ dplyr::glimpse(nrsa)
 # Promote data frame to sf spatial points data frame
 nrsa_sf <- sf::st_as_sf(nrsa, coords = c("LON_DD83", "LAT_DD83"), crs = 4269)
 
-# Get COMIDs using nhdplusTools package
+# Get COMIDs using hydrogeofetch package
 # nrsa$COMID<- NA
 # for (i in 1:nrow(nrsa_sf)){
 #   print (i)

vignettes/Articles/LakeCat.Rmd

@@ -76,7 +76,7 @@ head(metrics)
 ```
 
 ## Get Waterbody COMIDs
-In this example we use the `lc_get_comid` function to find COMIDs for a set of example lake locations we load into R.`lc_get_comid` is just a simple wrapper for `get_waterbodies` in the [nhdplusTools](https://doi-usgs.github.io/nhdplusTools/) R package. We can then use the COMIDs we derive for our lake locations to get LakeCat metrics for these lakes as we show in after this.
+In this example we use the `lc_get_comid` function to find COMIDs for a set of example lake locations we load into R.`lc_get_comid` is just a simple wrapper for `get_waterbodies` in the [hydrogeofetch](https://doi-usgs.github.io/hydrogeofetch/) R package. We can then use the COMIDs we derive for our lake locations to get LakeCat metrics for these lakes as we show in after this.
 ```{r comids, warning=FALSE, message=FALSE}
 dd <- data.frame(x = c(-89.198,-114.125,-122.044),
                  y = c(45.502,47.877,43.730)) |> 
@@ -117,10 +117,10 @@ knitr::kable(df)
 
 ## Get lake and lake watersheds as `sf` objects
 
-`StreamCatTools` includes a function `lc_get_watershed` that will return the watershed of any lake by COMID from an AWS S3 bucket of partitioned geoparquet files for all LakeCat lake watersheds (both on-network and off-network lakes).  The watershed requested is returned as an `sf` object and uses `duckDB` as well as optional parallelization for faster data returns and specification of a specific HUC2 if known to reduce search time. **NOTE** `lc_get_watershed` currently only returns one watershed per request. This can be used in conjunction with `nhdplusTools` function `get_waterbodies` to map lake features for which `LakeCat` metrics are requested as shown below.
+`StreamCatTools` includes a function `lc_get_watershed` that will return the watershed of any lake by COMID from an AWS S3 bucket of partitioned geoparquet files for all LakeCat lake watersheds (both on-network and off-network lakes).  The watershed requested is returned as an `sf` object and uses `duckDB` as well as optional parallelization for faster data returns and specification of a specific HUC2 if known to reduce search time. **NOTE** `lc_get_watershed` currently only returns one watershed per request. This can be used in conjunction with `hydrogeofetch` function `get_waterbodies` to map lake features for which `LakeCat` metrics are requested as shown below.
 
 ```{r get_lake}
-lake <- nhdplusTools::get_waterbodies(id = 19334077)
+lake <- hydrogeofetch::get_waterbodies(id = 19334077)
 ```
 
 ```{r get_watershed}

vignettes/Articles/NNI.Rmd

@@ -188,12 +188,12 @@ tibble::tibble(sc_get_nni(year='2017', comid=com, aoi='cat,ws'))
 
 
 ## Plot a single NNI metric for a given watershed
-In this example we access a single National Nutrient Inventory (NNI) metric for the Calapooia River basin using the `sc_get_data` function. We use the `nhdplusTools` library to pull in flowlines and the watershed boundary for the Calapooia River basin, plot the selected NNI metric for the Calapooia River and show the watershed.
+In this example we access a single National Nutrient Inventory (NNI) metric for the Calapooia River basin using the `sc_get_data` function. We use the `hydrogeofetch` library to pull in flowlines and the watershed boundary for the Calapooia River basin, plot the selected NNI metric for the Calapooia River and show the watershed.
 ```{r farmn, results='hide'}
 start_comid = 23763517
 nldi_feature <- list(featureSource = "comid", featureID = start_comid)
 
-flowline_nldi <- nhdplusTools::navigate_nldi(nldi_feature, mode = "UT", data_source = "flowlines", distance=5000)
+flowline_nldi <- hydrogeofetch::navigate_nldi(nldi_feature, mode = "UT", data_source = "flowlines", distance=5000)
 
 # get StreamCat metrics
 comids <- paste(as.integer(flowline_nldi$UT_flowlines$nhdplus_comid), collapse=",",sep="")
@@ -203,7 +203,7 @@ df <- sc_get_data(metric='n_ff_2016', aoi='cat', comid=comids, showAreaSqKm=TRUE
 flowline_nldi <- flowline_nldi$UT_flowlines
 flowline_nldi$Farm_Nitrogon_2016 <- df$n_ff_2016cat[match(flowline_nldi$nhdplus_comid, df$comid)]
 
-basin <- nhdplusTools::get_nldi_basin(nldi_feature = nldi_feature)
+basin <- hydrogeofetch::get_nldi_basin(nldi_feature = nldi_feature)
 ```
 
 ## Map the Results