create_report accepts character parameter names, and isn't limited to those in the params object.

Author: Hill

R/create_report.R

@@ -5,7 +5,7 @@
 #' @param org organization (short name in WQP) whose data should be used to build the report. Multiple organization names can be input as a character vector; names will be homogenized and data will be pooled for analysis purposes. A list of acceptable organization names is available in this csv: https://cdx.epa.gov/wqx/download/DomainValues/Organization.CSV.
 #' @param startDate start date for data used in the report, in format `\%m-\%d-\%Y`
 #' @param endDate final date for data used in the report, in format `\%m-\%d-\%Y`
-#' @param parameters parameters to use in report. Must be entered as an index of acceptable parameters listed in params$params (e.g., `parameters = c(1:4,7)`)
+#' @param parameters parameters to use in report. Can be entered as exact characteristic names (for a complete list, see: https://cdx.epa.gov/wqx/download/DomainValues/Characteristic.CSV). Alternatively, this argument can be a numeric index of parameters listed in params$params (e.g., `parameters = c(1:4,7)`)
 #' @param extFile name of report-generating script, located in the inst/extdata folder of the R8WD R package
 #' @param prompt_user if TRUE, user is prompted to use one of the organization short names in the `tribes` object provided with `R8WD`. .
 #' @param output either 'docx' or 'html'
@@ -21,7 +21,7 @@
 create_report <- function(org = 'TURTLEMT',
                           startDate = '01-01-2015',
                           endDate   = '12-31-2022',
-                          parameters = 1:11,
+                          parameters = c('Total Phosphorus, mixed forms', 'Total Nitrogen, mixed forms', 'Escherichia coli', 'Dissolved oxygen (DO)', 'Temperature', 'Temperature, water', 'pH', 'Turbidity', 'Conductivity', 'Total suspended solids'),
                           extFile = 'script_generateReport.qmd',
                           prompt_user = TRUE,
                           output = 'html',
@@ -70,7 +70,13 @@ create_report <- function(org = 'TURTLEMT',
   ### add params
   # parameters
   # REPLACE_PARAMS
-  newParams  <- paste0(paste0(gsub(x = as.character(parameters), pattern = "\'|\"", replacement = ''), collapse = ','))
+  if (all(is.numeric(parameters))) {
+    newParams  <- paste0(paste0(gsub(x = as.character(parameters), pattern = "\'|\"", replacement = ''), collapse = ','))
+  } else if (all(is.character(parameters))) {
+    # newParams  <- dput(parameters)
+    newParams  <- paste0('"', x = paste0(gsub(x = as.character(parameters), pattern = "\'|\"", replacement = "'"), collapse='","'), '"')
+  }
+
   # tst <- gsub(x = readLines(targetFile), pattern = token, replacement = newParams)
   newText    <- gsub(x = newText, pattern = '\'REPLACE_PARAMS\'', replacement = newParams)
 

README.md

@@ -38,7 +38,7 @@ remotes::install_github("USEPA/R8WD")
 ```
 
 
-## Example
+## A brief example
 
 After installing `R8WD`, it can be loaded and a quarto report generated. A list of organization names available in the Water Quality Portal is available in this csv: https://cdx.epa.gov/wqx/download/DomainValues/Organization.CSV. Note that a given organization may not have data available for the time period or parameters selected.
 
@@ -47,7 +47,10 @@ After installing `R8WD`, it can be loaded and a quarto report generated. A list
 library(R8WD)
 
 # generate a report
-create_report('BLCKFEET')
+org_name <- 'BLCKFEET'
+params   <- c("Total Phosphorus, mixed forms","Total Nitrogen, mixed forms","Escherichia coli","Dissolved oxygen (DO)")
+
+create_report(org = org_name, parameters = params)
 ```
 
 This will create and open a quarto document in RStudio. Render the quarto document to html output by pressing `Ctrl+Shift+K`.

inst/extdata/script_generateReport.qmd

@@ -32,6 +32,15 @@ replicate_variation_tolerance <- 30
 #| echo: false
 #| output: false
 #| include: false
+if (all(is.numeric(params_to_use))) {
+  ### accommodate character parameters or numeric index of params object
+  params_used   <- params$params[params_to_use]
+  unique_params <- unique(params$new_param[params_to_use])
+} else {
+  params_used   <- params_to_use
+  ### unique parameters are only defined for those in params$params
+  unique_params <- unique(c(params_to_use[which(!(params_to_use) %in% params$params)], params$new_param[na.omit(match(params_to_use, params$params))]))
+}
 
 plot_summary_period <- 'month'
 if (draft_report) {
@@ -42,7 +51,7 @@ if (draft_report) {
 
 tribeData2 <- getWQP(
        organization       = Tribal_org,
-       characteristicName = params$params[params_to_use],
+       characteristicName = params_used, # params$params[params_to_use],
        startDate          = start_date,
        endDate            = end_date,
        multiplier         = 0.5)
@@ -79,7 +88,8 @@ if (any(unique(allSummary$data[allSummary$data$CharacteristicName == 'TN', 'Resu
 
 included_params <- sentencify(unique(tribeData2$CharacteristicName))
 
-params_not_found <- unique(params$new_param[params_to_use])[!(unique(params$new_param[params_to_use]) %in% unique(tribeData2$CharacteristicName))]
+# params_not_found <- unique(params$new_param[params_to_use])[!(unique(params$new_param[params_to_use]) %in% unique(tribeData2$CharacteristicName))]
+params_not_found <- unique_params[!(unique_params %in% unique(tribeData2$CharacteristicName))]
 if (length(params_not_found) == 0) {
   params_not_found_message <- "All core parameters sought for this report were available in the organization's WQP data." 
 } else if (length(params_not_found) == 1) {