new code for data download and filtering, updated folder structure

.Rbuildignore

@@ -1,2 +1,4 @@
 ^\.github$
-tools/
+tools/
+^.*\.Rproj$
+^\.Rproj\.user$

NRTAPmodel.Rproj

@@ -11,3 +11,7 @@ Encoding: UTF-8
 
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

R/data_download_preprocess/aqs_download_filter.R

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+# Download EPA AQS data and filter to a single POC per site#
+# Author: Mariana Alifa Kassien
+# September 2023
+
+# Source functions
+source("R/data_download_preprocess/download_aqs_data.R")
+source("R/data_download_preprocess/filter_minimum_poc.R")
+
+# Define parameters of interest for download
+parameter_code = 88101
+year_start = 2018
+year_end = 2022
+resolution_temporal = "daily"
+directory_to_download = "./input/aqs/"
+directory_to_save = "./input/aqs/"
+url_aqs_download = "https://aqs.epa.gov/aqsweb/airdata/"
+
+# Run data download function
+download_aqs_data(parameter_code, year_start,year_end,resolution_temporal,
+                  directory_to_download, directory_to_save,
+                  url_aqs_download, remove_zips = FALSE)
+
+# Read in sites dataframe for filtering
+input_df= read.csv(paste(directory_to_save, resolution_temporal, "_", parameter_code, "_", year_start, "-", year_end, ".csv", sep=""), 
+                   stringsAsFactors = F)
+
+# Optional: view column names to determine right inputs for filtering
+#colnames(input_df)
+
+# Create a site ID column that does not include the POC number
+input_df = input_df |>
+  mutate(ID.Site = substr(ID.Monitor, 1, 17))
+
+site_id="ID.Site"
+poc_name="POC"
+
+# Filter sites with multiple POCs (select lowest-numbered POC per site)
+data_filtered =filter_minimum_poc(input_df, site_id, poc_name)
+
+# Save new filtered data - wasn't sure what to name it so I added "filtered_" to the beginning. We can change that too if there's a better idea.
+output_name=paste(directory_to_save, "filtered_",resolution_temporal, "_", parameter_code, "_", year_start, "-", year_end, ".csv", sep="") 
+  # output_name
+  # [1] "./input/aqs/filtered_daily_88101_2018-2022.csv"
+write.csv(data_filtered, output_name)