---
title: "PEcAn: Generating met drivers for the MAAT model using AmerifluxLBL tower observations"
author: "Shawn Serbin"
date: "2018-08-28"
output: rmarkdown::html_vignette
vignette: |
  %\VignetteIndexEntry{PEcAn: Generating met drivers for the MAAT model using AmerifluxLBL tower observations}
  %\VignetteEngine{knitr::rmarkdown}
---

# Overview
This is a demonstration of the PEcAn utilities for downloading met data, converting it to the PEcAn-CF format (which is based on the Climate Forecasting conventions and similar to MsTMIP), gapfilling the CF driver data, and converting to model-specific drivers for the MAAT model. These variables are defined in the [PEcAn documentation](https://pecanproject.github.io/pecan-documentation/available-meteorological-drivers.html).

In this example we will download 6 years of met data from the [Willow Creek Eddy Covariance tower site (US-WCr)](http://ameriflux.lbl.gov/sites/siteinfo/US-WCr). It has an Ameriflux `SITE_ID` of `US-WCr`

The PEcAn.data.atmosphere source code is in [`modules/data.atmosphere`](https://github.com/PecanProject/pecan/tree/develop/modules/data.atmosphere) and the documentation can be found with either `package?PEcAn.data.atmosphere` or in the [data.atmosphere package documentation](https://pecanproject.github.io/pecan//modules/data.atmosphere/inst/web/index.html).

First make sure you have the nescessary PEcAn package for processing met data
```{r install, eval=FALSE}
options(repos = c(getOption("repos"), PEcAn = "pecanproject.r-universe.dev"))
install.packages("PEcAn.data.atmosphere")
```

```{r}
library(PEcAn.data.atmosphere)

```

```{r echo=FALSE}

knitr::opts_chunk$set(message = FALSE, warnings = FALSE,  cache = FALSE,
                      fig.height= 3, fig.width = 8)

```

## Connect to BETY database and retrieve appropriate format for AmerifluxLBL datasets [TODO: Update to work with R-OpenSci traits BETY]
```{r bety, eval = FALSE}

con <- PEcAn.DB::db.open(
   list(user='bety', password='bety', host='localhost',
        dbname='bety', driver='PostgreSQL',write=TRUE))
format.id <- 5000000002
format <- PEcAn.DB::query.format.vars(format.id=format.id,bety = con)
format$time_zone <- "America/Chicago"
```
(Note: To avoid needing a database connection at vignette build time, we use code that does not display in the compiled vignette to construct a static version of the `format` object. When running this document interactively, with a live database connention, you can use the result from `query.format.vars` directly.)

```{r dummy-format, show = FALSE}
# copy-pasted from `dput(format)` after evaluating the `bety` chunk above
# using Chris Black's development version of BeTY on 2024-09-16
format <- list(
   file_name = "AMERIFLUX_BASE_HH",
   mimetype = "csv",
   vars = structure(
      list(
         bety_name = c("air_pressure", "airT", "co2atm", "datetime", "FC", "H",
            "LE", "NEE", "PAR", "precipitation_flux", "relative_humidity",
            "soilM", "soilT", "solar_radiation", "specific_humidity",
            "surface_downwelling_longwave_flux_in_air", "TotalResp", "UST",
            "VPD", "wind_direction", "Wspd"),
         variable_id = c(554, 86, 135, 5000000001, 1000000042, 299, 298, 297,
            136, 555, 556, 391, 379, 547, 557, 561, 1000000206, 1000000041, 387,
            560, 390),
         input_name = c("PA", "TA", "CO2_1", "TIMESTAMP_START", "FC", "H", "LE",
            "NEE_PI", "PPFD_IN", "P", "RH", "SWC_1", "TS_1", "SW_IN", "H2O",
            "LW_IN", "RECO_PI", "USTAR", "VPD", "WD", "WS"),
         input_units = c("kPa", "celsius", "umol mol-1", "ymd_hms",
            "umol C m-2 s-1", "W m-2","W m-2", "umol C m-2 s-1", "umol m-2 s-1",
            "kg m-2 (30 minute)-1", "percent", "%", "celsius", "W m-2",
            "g kg-1", "W m-2", "umol C m-2 s-1", "m s-1", "hPa", "degrees",
            "m s-1"),
         storage_type = c("", "", "", "%Y%m%d%H%M", "", "", "", "", "", "", "",
            "", "", "", "", "", "", "", "", "", ""),
         column_number = c(19L, 4L, 20L, 1L, 8L, 10L, 12L, 7L, 26L, 17L, 18L,
            23L, 15L, 27L, 33L, 31L, NA, 3L, NA, 5L, 6L),
         bety_units = c("Pa", "degrees C", "ppm (= umol mol-1)", "ymd_hms",
            "umol C m-2 s-1", "W m-2", "W m-2", "umol C m-2 s-1",
            "umol m-2 s-1", "Kg/m2/s", "%", "%", "degrees C", "W/m^2", "g g-1",
            "W m-2", "kg C m-2 s-1", "m s-1", "Pa", "degrees", "m s-1"),
         mstmip_name = c("Psurf", "Tair", "CO2air", NA, "FC", "Qh", "Qle",
            "NEE", NA, "Rainf", NA, "SoilMoistFrac", "SoilTemp", "SWdown",
            "Qair", "LWdown", "TotalResp", NA, NA, NA, NA),
         mstmip_units = c("Pa", "K", "micromol mol-1", NA, "kg C m-2 s-1",
            "W m-2", "W m-2", "kg C m-2 s-1", NA, "kg m-2 s-1", NA, "1", "K",
            "W/m^2", "kg kg-1", "W/m2", "kg C m-2 s-1", NA, NA, NA, NA),
         pecan_name = c("Psurf", "Tair", "CO2air", "datetime", "FC", "Qh",
            "Qle", "NEE", "PAR", "Rainf", "relative_humidity", "SoilMoistFrac",
            "SoilTemp", "SWdown", "Qair", "LWdown", "TotalResp", "UST", "VPD",
            "wind_direction", "Wspd"),
         pecan_units = c("Pa", "K", "micromol mol-1", "ymd_hms", "kg C m-2 s-1",
            "W m-2", "W m-2", "kg C m-2 s-1", "umol m-2 s-1", "kg m-2 s-1", "%",
            "1", "K", "W/m^2", "kg kg-1", "W/m2", "kg C m-2 s-1", "m s-1", "Pa",
            "degrees", "m s-1")),
      row.names = c(NA, -21L),
      class = "data.frame"),
   skip = 2,
   header = 1,
   na.strings = c("-9999", "-6999", "9999", "NA"),
   time.row = 4L,
   site = NULL,
   lat = NULL,
   lon = NULL,
   time_zone = "America/Chicago")
```


## Download AmerifluxLBL data for selected site and dates (US-WCr, 2000 to 2005)
```{r download}
m2mdir <- tempfile("met2model_testing")
dir.create(m2mdir)
download.AmerifluxLBL(sitename = "US-WCr", outfolder = m2mdir,
                   start_date = "2000-01-01", end_date = "2005-12-31", overwrite = TRUE, verbose = TRUE)
```

## Convert downloaded AmerifluxLBL data to CF format
```{r met2cf}
cfdir <- file.path(m2mdir, "CF")
met2CF.AmerifluxLBL(in.path = m2mdir, in.prefix = "AMF_US-WCr", outfolder = cfdir,
                 start_date = "2000-01-01", end_date = "2005-12-31",format=format)
```

## Gapfill CF met drivers
```{r metgapfill}
gapfilldir <- file.path(cfdir, "gapfill")
metgapfill(in.path = cfdir, in.prefix = "AMF_US-WCr_BASE_HH_14-5",
           outfolder = gapfilldir, start_date = "2000-01-01", end_date = "2005-12-31")
```

## Create MAAT model-specific met drivers
```{r met2model}
in.path <- gapfilldir
in.prefix <- "AMF_US-WCr_BASE_HH_14-5"
outfolder <- file.path(gapfilldir, "maat_drivers")
start_date <- "2000-01-01"
end_date <- "2005-12-31"
overwrite <- TRUE
verbose <- TRUE
leap_year = TRUE
PEcAn.MAAT::met2model.MAAT(in.path, in.prefix, outfolder, start_date, end_date,
                           overwrite = overwrite, verbose = verbose)
```