Merge pull request #4 from mps9506/load-report

Load report

R/metadata.R

@@ -0,0 +1,26 @@
+## document metadata
+
+## note: this is run outside of the targets workflow
+library(dataspice)
+create_spice(dir = "data/Output/")
+
+prep_access(data_path = "data/Output",
+            access_path = "data/Output/metadata/access.csv",
+            recursive = TRUE)
+
+edit_access(metadata_dir = "data/Output/metadata")
+
+prep_attributes(data_path = "data/Output",
+                attributes_path = "data/Output/metadata/attributes.csv",
+                recursive = TRUE)
+
+edit_attributes(metadata_dir = "data/Output/metadata")
+
+edit_creators(metadata_dir = "data/Output/metadata")
+
+edit_biblio(metadata_dir = "data/Output/metadata")
+
+write_spice(path = "data/Output/metadata")
+
+
+build_site("data/Output/metadata/dataspice.json")

README.Rmd

@@ -8,7 +8,14 @@ output: github_document
 knitr::opts_chunk$set(echo = TRUE)
 ```
 
-This is a placeholder.
+This is the analysis code and data for the Texas Coastal Nutrient Input Repository project. This project develops estimates of actual and flow-normalized daily nitrate (NO^3^-N) and total phosphorus (TP) watershed loads. Reports and publications are forthcoming.
+
+Data analysis and models were developed in R using the [renv](https://rstudio.github.io/renv/) and [targets](https://docs.ropensci.org/targets/) R packages to facilitate reproducibility. To reproduce this analysis clone the repository to your local machine, ensure both renv and targets are installed and open the project. The analysis can be reproduced using:
+
+```r
+renv::restore()
+targets::tar_make()
+```
 
 ## Funding
 

README.md

@@ -2,7 +2,22 @@ Texas Coastal Nutrient Input Repository (Phase 1 - Lavaca Bay)
 ================
 Michael Schramm - Texas Water Resources Institute, Research Specialist
 
-This is a placeholder.
+This is the analysis code and data for the Texas Coastal Nutrient Input
+Repository project. This project develops estimates of actual and
+flow-normalized daily nitrate (NO<sup>3</sup>-N) and total phosphorus
+(TP) watershed loads. Reports and publications are forthcoming.
+
+Data analysis and models were developed in R using the
+[renv](https://rstudio.github.io/renv/) and
+[targets](https://docs.ropensci.org/targets/) R packages to facilitate
+reproducibility. To reproduce this analysis clone the repository to your
+local machine, ensure both renv and targets are installed and open the
+project. The analysis can be reproduced using:
+
+``` r
+renv::restore()
+targets::tar_make()
+```
 
 ## Funding
 

_targets.R

@@ -647,14 +647,313 @@ list(
              ))
   ,
 
+  ### NO3 navidad
+  tar_target(daily_no3_08164390,
+             predict_daily(
+               model = no3_08164390, # target
+               data = model_data, # target
+               site_no = "usgs08164390", # quoted string
+               date = "2005-01-01", # quoted string
+               output_name = NO3_Estimate, #unquoted
+               output_upper = NO3_Upper, #unquoted
+               output_lower = NO3_Lower #unquoted
+             )),
+  ## flow-normalized NO3
+  tar_target(daily_no3_08164390_fn,
+             predict_daily(
+               model = no3_08164390, # target
+               data = flow_normalized_data, # target
+               site_no = "usgs08164390", # quoted string
+               date = "2005-01-01", # quoted string
+               output_name = NO3_Estimate, #unquoted
+               output_upper = NO3_Upper, #unquoted
+               output_lower = NO3_Lower, #unquoted
+               fn_data = TRUE
+             )),
+  ### TP navidad
+  tar_target(daily_tp_08164390,
+             predict_daily(
+               model = tp_08164390, # target
+               data = model_data, # target
+               site_no = "usgs08164390", # quoted string
+               date = "2000-01-01", # quoted string
+               output_name = TP_Estimate, #unquoted
+               output_upper = TP_Upper, #unquoted
+               output_lower = TP_Lower #unquoted
+             )),
+  ### flow-normalized TP
+  tar_target(daily_tp_08164390_fn,
+             predict_daily(
+               model = tp_08164390, # target
+               data = flow_normalized_data, # target
+               site_no = "usgs08164390", # quoted string
+               date = "2000-01-01", # quoted string
+               output_name = TP_Estimate, #unquoted
+               output_upper = TP_Upper, #unquoted
+               output_lower = TP_Lower, #unquoted
+               fn_data = TRUE
+             )),
 
-  # create loading output file (csv)
-  tar_target(write_daily, 
-             loads_to_csv(list("lav" = tar_read(daily_tp_08164000), 
-                               "tex" = tar_read(daily_tp_texana)),
+  ### NO3 sandy
+  tar_target(daily_no3_08164450,
+             predict_daily(
+               model = no3_08164450, # target
+               data = model_data, # target
+               site_no = "usgs08164450", # quoted string
+               date = "2005-01-01", # quoted string
+               output_name = NO3_Estimate, #unquoted
+               output_upper = NO3_Upper, #unquoted
+               output_lower = NO3_Lower #unquoted
+             )),
+  ## flow-normalized NO3
+  tar_target(daily_no3_08164450_fn,
+             predict_daily(
+               model = no3_08164450, # target
+               data = flow_normalized_data, # target
+               site_no = "usgs08164450", # quoted string
+               date = "2005-01-01", # quoted string
+               output_name = NO3_Estimate, #unquoted
+               output_upper = NO3_Upper, #unquoted
+               output_lower = NO3_Lower, #unquoted
+               fn_data = TRUE
+             )),
+  ### TP sandy
+  tar_target(daily_tp_08164450,
+             predict_daily(
+               model = tp_08164450, # target
+               data = model_data, # target
+               site_no = "usgs08164450", # quoted string
+               date = "2000-01-01", # quoted string
+               output_name = TP_Estimate, #unquoted
+               output_upper = TP_Upper, #unquoted
+               output_lower = TP_Lower #unquoted
+             )),
+  ### flow-normalized TP
+  tar_target(daily_tp_08164450_fn,
+             predict_daily(
+               model = tp_08164450, # target
+               data = flow_normalized_data, # target
+               site_no = "usgs08164450", # quoted string
+               date = "2000-01-01", # quoted string
+               output_name = TP_Estimate, #unquoted
+               output_upper = TP_Upper, #unquoted
+               output_lower = TP_Lower, #unquoted
+               fn_data = TRUE
+             )),
+  ### NO3 W Mustang
+  tar_target(daily_no3_08164503,
+             predict_daily(
+               model = no3_08164503, # target
+               data = model_data, # target
+               site_no = "usgs08164503", # quoted string
+               date = "2005-01-01", # quoted string
+               output_name = NO3_Estimate, #unquoted
+               output_upper = NO3_Upper, #unquoted
+               output_lower = NO3_Lower #unquoted
+             )),
+  ## flow-normalized NO3
+  tar_target(daily_no3_08164503_fn,
+             predict_daily(
+               model = no3_08164503, # target
+               data = flow_normalized_data, # target
+               site_no = "usgs08164503", # quoted string
+               date = "2005-01-01", # quoted string
+               output_name = NO3_Estimate, #unquoted
+               output_upper = NO3_Upper, #unquoted
+               output_lower = NO3_Lower, #unquoted
+               fn_data = TRUE
+             )),
+  ### TP W Mustang
+  tar_target(daily_tp_08164503,
+             predict_daily(
+               model = no3_08164503, # target
+               data = model_data, # target
+               site_no = "usgs08164503", # quoted string
+               date = "2000-01-01", # quoted string
+               output_name = TP_Estimate, #unquoted
+               output_upper = TP_Upper, #unquoted
+               output_lower = TP_Lower #unquoted
+             )),
+  ### flow-normalized TP
+  tar_target(daily_tp_08164503_fn,
+             predict_daily(
+               model = tp_08164503, # target
+               data = flow_normalized_data, # target
+               site_no = "usgs08164503", # quoted string
+               date = "2000-01-01", # quoted string
+               output_name = TP_Estimate, #unquoted
+               output_upper = TP_Upper, #unquoted
+               output_lower = TP_Lower, #unquoted
+               fn_data = TRUE
+             )),
+  ### NO3 E Mustang
+  tar_target(daily_no3_08164504,
+             predict_daily(
+               model = no3_08164504, # target
+               data = model_data, # target
+               site_no = "usgs08164504", # quoted string
+               date = "2005-01-01", # quoted string
+               output_name = NO3_Estimate, #unquoted
+               output_upper = NO3_Upper, #unquoted
+               output_lower = NO3_Lower #unquoted
+             )),
+  ## flow-normalized NO3
+  tar_target(daily_no3_08164504_fn,
+             predict_daily(
+               model = no3_08164504, # target
+               data = flow_normalized_data, # target
+               site_no = "usgs08164504", # quoted string
+               date = "2005-01-01", # quoted string
+               output_name = NO3_Estimate, #unquoted
+               output_upper = NO3_Upper, #unquoted
+               output_lower = NO3_Lower, #unquoted
+               fn_data = TRUE
+             )),
+  ### TP E Mustang
+  tar_target(daily_tp_08164504,
+             predict_daily(
+               model = tp_08164504, # target
+               data = model_data, # target
+               site_no = "usgs08164504", # quoted string
+               date = "2000-01-01", # quoted string
+               output_name = TP_Estimate, #unquoted
+               output_upper = TP_Upper, #unquoted
+               output_lower = TP_Lower #unquoted
+             )),
+  ### flow-normalized TP
+  tar_target(daily_tp_08164504_fn,
+             predict_daily(
+               model = tp_08164504, # target
+               data = flow_normalized_data, # target
+               site_no = "usgs08164504", # quoted string
+               date = "2000-01-01", # quoted string
+               output_name = TP_Estimate, #unquoted
+               output_upper = TP_Upper, #unquoted
+               output_lower = TP_Lower, #unquoted
+               fn_data = TRUE
+             )),
+  # create loading output files (csv)
+  tar_target(write_daily_tp, 
+             loads_to_csv(list("lavaca" = tar_read(daily_tp_08164000), 
+                               "texana" = tar_read(daily_tp_texana),
+                               "navidad" = tar_read(daily_tp_08164390),
+                               "sandy" = tar_read(daily_tp_08164450),
+                               "w_mustang" = tar_read(daily_tp_08164503),
+                               "e_mustang" = tar_read(daily_tp_08164504)),
                           df = "daily",
                           output = "data/Output/daily_loads/tp_daily_loads.csv"),
              format = "file"),
+  tar_target(write_daily_tp_fn, 
+             loads_to_csv(list("lavaca" = tar_read(daily_tp_08164000_fn), 
+                               "texana" = tar_read(daily_tp_texana_fn),
+                               "navidad" = tar_read(daily_tp_08164390_fn),
+                               "sandy" = tar_read(daily_tp_08164450_fn),
+                               "w_mustang" = tar_read(daily_tp_08164503_fn),
+                               "e_mustang" = tar_read(daily_tp_08164504_fn)),
+                          df = "daily",
+                          output = "data/Output/daily_loads/tp_daily_loads_flow_normalized.csv"),
+             format = "file"),
+  tar_target(write_monthly_tp, 
+             loads_to_csv(list("lavaca" = tar_read(daily_tp_08164000), 
+                               "texana" = tar_read(daily_tp_texana),
+                               "navidad" = tar_read(daily_tp_08164390),
+                               "sandy" = tar_read(daily_tp_08164450),
+                               "w_mustang" = tar_read(daily_tp_08164503),
+                               "e_mustang" = tar_read(daily_tp_08164504)),
+                          df = "monthly",
+                          output = "data/Output/monthly_loads/tp_monthly_loads.csv"),
+             format = "file"),
+  tar_target(write_monthly_tp_fn, 
+             loads_to_csv(list("lavaca" = tar_read(daily_tp_08164000_fn), 
+                               "texana" = tar_read(daily_tp_texana_fn),
+                               "navidad" = tar_read(daily_tp_08164390_fn),
+                               "sandy" = tar_read(daily_tp_08164450_fn),
+                               "w_mustang" = tar_read(daily_tp_08164503_fn),
+                               "e_mustang" = tar_read(daily_tp_08164504_fn)),
+                          df = "monthly",
+                          output = "data/Output/monthly_loads/tp_monthly_loads_flow_normalized.csv"),
+             format = "file"),
+  tar_target(write_annual_tp, 
+             loads_to_csv(list("lavaca" = tar_read(daily_tp_08164000), 
+                               "texana" = tar_read(daily_tp_texana),
+                               "navidad" = tar_read(daily_tp_08164390),
+                               "sandy" = tar_read(daily_tp_08164450),
+                               "w_mustang" = tar_read(daily_tp_08164503),
+                               "e_mustang" = tar_read(daily_tp_08164504)),
+                          df = "annually",
+                          output = "data/Output/annual_loads/tp_annual_loads.csv"),
+             format = "file"),
+  tar_target(write_annual_tp_fn, 
+             loads_to_csv(list("lavaca" = tar_read(daily_tp_08164000_fn), 
+                               "texana" = tar_read(daily_tp_texana_fn),
+                               "navidad" = tar_read(daily_tp_08164390_fn),
+                               "sandy" = tar_read(daily_tp_08164450_fn),
+                               "w_mustang" = tar_read(daily_tp_08164503_fn),
+                               "e_mustang" = tar_read(daily_tp_08164504_fn)),
+                          df = "annually",
+                          output = "data/Output/annual_loads/tp_annual_loads_flow_normalized.csv"),
+             format = "file"),
+
+  tar_target(write_daily_no3, 
+             loads_to_csv(list("lavaca" = tar_read(daily_no3_08164000), 
+                               "texana" = tar_read(daily_no3_texana),
+                               "navidad" = tar_read(daily_no3_08164390),
+                               "sandy" = tar_read(daily_no3_08164450),
+                               "w_mustang" = tar_read(daily_no3_08164503),
+                               "e_mustang" = tar_read(daily_no3_08164504)),
+                          df = "daily",
+                          output = "data/Output/daily_loads/no3_daily_loads.csv"),
+             format = "file"),
+  tar_target(write_daily_no3_fn, 
+             loads_to_csv(list("lavaca" = tar_read(daily_no3_08164000_fn), 
+                               "texana" = tar_read(daily_no3_texana_fn),
+                               "navidad" = tar_read(daily_no3_08164390_fn),
+                               "sandy" = tar_read(daily_no3_08164450_fn),
+                               "w_mustang" = tar_read(daily_no3_08164503_fn),
+                               "e_mustang" = tar_read(daily_no3_08164504_fn)),
+                          df = "daily",
+                          output = "data/Output/daily_loads/no3_daily_loads_flow_normalized.csv"),
+             format = "file"),
+  tar_target(write_monthly_no3, 
+             loads_to_csv(list("lavaca" = tar_read(daily_no3_08164000), 
+                               "texana" = tar_read(daily_no3_texana),
+                               "navidad" = tar_read(daily_no3_08164390),
+                               "sandy" = tar_read(daily_no3_08164450),
+                               "w_mustang" = tar_read(daily_no3_08164503),
+                               "e_mustang" = tar_read(daily_no3_08164504)),
+                          df = "monthly",
+                          output = "data/Output/monthly_loads/no3_monthly_loads.csv"),
+             format = "file"),
+  tar_target(write_monthly_no3_fn, 
+             loads_to_csv(list("lavaca" = tar_read(daily_no3_08164000_fn), 
+                               "texana" = tar_read(daily_no3_texana_fn),
+                               "navidad" = tar_read(daily_no3_08164390_fn),
+                               "sandy" = tar_read(daily_no3_08164450_fn),
+                               "w_mustang" = tar_read(daily_no3_08164503_fn),
+                               "e_mustang" = tar_read(daily_no3_08164504_fn)),
+                          df = "monthly",
+                          output = "data/Output/monthly_loads/no3_monthly_loads_flow_normalized.csv"),
+             format = "file"),
+  tar_target(write_annual_no3, 
+             loads_to_csv(list("lavaca" = tar_read(daily_no3_08164000), 
+                               "texana" = tar_read(daily_no3_texana),
+                               "navidad" = tar_read(daily_no3_08164390),
+                               "sandy" = tar_read(daily_no3_08164450),
+                               "w_mustang" = tar_read(daily_no3_08164503),
+                               "e_mustang" = tar_read(daily_no3_08164504)),
+                          df = "annually",
+                          output = "data/Output/annual_loads/no3_annual_loads.csv"),
+             format = "file"),
+  tar_target(write_annual_no3_flow_normalized, 
+             loads_to_csv(list("lavaca" = tar_read(daily_no3_08164000_fn), 
+                               "texana" = tar_read(daily_no3_texana_fn),
+                               "navidad" = tar_read(daily_no3_08164390_fn),
+                               "sandy" = tar_read(daily_no3_08164450_fn),
+                               "w_mustang" = tar_read(daily_no3_08164503_fn),
+                               "e_mustang" = tar_read(daily_no3_08164504_fn)),
+                          df = "annually",
+                          output = "data/Output/annual_loads/no3_annual_loads_flow_normalized.csv"),
+             format = "file"),
 
   # loading estimates pdf
   tar_quarto(loading_estimates, "reports/load_estimates/load_estimates.qmd"),