Overview
agroclimR is an R package developed to facilitate the management and transformation of agroclimatic data into crop model-ready formats. It supports major modeling systems such as DSSAT v 4.8, ORYZA v3.0, and Aquacrop v6.0. This toolkit serves as a resource for researchers and students specializing in agricultural sciences.
Features
- Efficient Data Management: Provides a relational database structure that simplifies data handling and seamlessly integrates with the agroclimR framework. Learn more about the data structure in data-format
- Easy Data Transformation to Crop Model-Ready Formats: Utilizes R to convert various model format files efficiently.
- Tidyverse Integration: Employs tidyverse functions for smooth data manipulation and offers insightful data visualization capabilities using ggplot2.
Installation
You can install the development version of agroclimR from GitHub with:
# install.packages("devtools")
devtools::install_github("jrodriguez88/agroclimR")Example: Creating Weather and Soil Model Format Files
Weather Model Files
Here’s a basic example demonstrating how to create a crop model weather file using agroclimR:
library(agroclimR)
path = "."
wth_data = weather
lat = 3.8
lon = -76.5
elev = 650
## basic example code to create ORYZA weather file
wth_files_oryza <- write_wth_oryza(path, "wth_oryza", wth_data, lat, lon, elev, tag = TRUE)
#> Early morning vapor pressure (VP; kPa) derived from relative humidity data
#> Oryza Weather Files created in . :
#> ./wth_oryza1.013 ,./wth_oryza1.014 ,./wth_oryza1.015 ,./wth_oryza1.016
readLines(wth_files_oryza[1], n = 24) |> writeLines()
#> *-----------------------------------------------------------
#> * Station Name: wth_oryza
#> * ORYZA Weather file - by agroclimR
#> * Longitude: -76.5 -- Latitude: 3.8 -- Elevation: 650m
#> *-----------------------------------------------------------
#> * Date: 2013-01-01 : 2016-12-31
#> *
#> * Column Daily Value
#> * 1 Station number
#> * 2 Year
#> * 3 Day
#> * 4 irradiance KJ m-2 d-1
#> * 5 min temperature oC
#> * 6 max temperature oC
#> * 7 vapor pressure kPa
#> * 8 mean wind speed m s-1
#> * 9 precipitation mm d-1
#> *-----------------------------------------------------------
#> -76.5,3.8,650,0,0
#> 1,2013,1,20889.29,25.73,36.03,3.07,-99,0
#> 1,2013,2,21632.15,25.08,35.68,3.31,-99,0.2
#> 1,2013,3,23106.91,23.99,38.49,3.01,-99,0
#> 1,2013,4,21408.98,22.91,35.71,2.98,-99,0
#> 1,2013,5,22908.94,23.81,38.81,3.43,-99,0
file.remove(wth_files_oryza)
#> [1] TRUE TRUE TRUE TRUE
## basic example code to create DSSAT weather file
wth_files_dssat <- write_wth_dssat(path, "wth_dssat", wth_data, lat, lon, elev)
#> DSSAT Weather Files created in . :
#> ./wth_dssat.WTH
readLines(wth_files_dssat[1], n = 10) |> writeLines()
#> *WEATHER DATA : wth_dssat DSSAT Weather file - by agroclimR
#>
#> @ INSI LAT LONG ELEV TAV AMP REFHT WNDHT
#> ACRP 3.800 -76.500 650 28.7 9.9 2.0 2.0
#> @DATE SRAD TMAX TMIN RAIN DEWP WIND PAR EVAP RHUM
#> 13001 20.9 36.0 25.7 0.0 NA 66.3
#> 13002 21.6 35.7 25.1 0.2 NA 73.3
#> 13003 23.1 38.5 24.0 0.0 NA 61.4
#> 13004 21.4 35.7 22.9 0.0 NA 68.9
#> 13005 22.9 38.8 23.8 0.0 NA 69.5
file.remove(wth_files_dssat)
#> [1] TRUE
## basic example code to create AquaCrop weather file
wth_files_aquacrop <- write_wth_aquacrop(path, "wth_aquacrop", wth_data, lat, lon, elev)
#> Reference evapotranspiration (ETo) Method: FAO Penman-Monteith equation
#> Oryza Weather Files created in . :
#> ./wth_aquacrop.CLI ,./wth_aquacrop.Tnx ,./wth_aquacrop.PLU ,./wth_aquacrop.ETo
readLines(wth_files_aquacrop[1], n = 10) |> writeLines()
#> wth_aquacrop Station, lat: 3.8 long: -76.5 - by agroclimR
#> 6.0 : AquaCrop Version (March 2017)
#> wth_aquacrop.Tnx
#> wth_aquacrop.ETo
#> wth_aquacrop.PLU
#> MaunaLoa.CO2
readLines(wth_files_aquacrop[2], n = 13) |> writeLines()
#> wth_aquacrop : daily temperature data (01 enero 2013 - 31 diciembre 2016)
#> 1 : Daily records (1=daily, 2=10-daily and 3=monthly data)
#> 1 : First day of record (1, 11 or 21 for 10-day or 1 for months)
#> 1 : First month of record
#> 2013 : First year of record (1901 if not linked to a specific year)
#>
#> Tmin (C) TMax (C)
#> =======================
#> 25.7 36.0
#> 25.1 35.7
#> 24.0 38.5
#> 22.9 35.7
#> 23.8 38.8
file.remove(wth_files_aquacrop)
#> [1] TRUE TRUE TRUE TRUESoil Model Files
This is a basic example which shows you how to create a crop model Soil file with agroclimR:
soil_sample = dplyr::group_by(soil, NL) |>
dplyr::sample_n(1) |> dplyr::ungroup()
# basic example code to create ORYZA soil file
soil_files_oryza <- write_soil_oryza(id_name = "soil_oryza", soil_data = soil_sample)
#> Oryza Experimental Files created in . :
#> ./soil_oryza.sol
readLines(soil_files_oryza[1], n = 27) |> writeLines()
#> **********************************************************************
#> * Template soil data file for PADDY soil water balance model. *
#> **********************************************************************
#> * Soil : soil_oryza - texture classes:c("Lo", "Lo", "SaLo")
#> * File name : soil_oryza.sol
#> * Sampling date : 2015-12-23
#> * Additional info : Create with agroclimR
#> *--------------------------------------------------------------------*
#>
#> SCODE = 'PADDY'
#>
#> *---------------------------------------------------------------*
#> * 1. Various soil and management parameters
#> *---------------------------------------------------------------*
#> WL0MX = 100. ! Bund height (mm)
#> NL = 3 ! Number of soil layers (maximum is 10) (-)
#> TKL = 0.20, 0.20, 0.20 ! Thickness of each soil layer (m)
#> ZRTMS = 0.5 ! Maximum rooting depth in the soil (m)
#>
#> *---------------------------------------------------------------*
#> * 2. Puddling switch: 1=PUDDLED or 0=NON PUDDLED
#> *---------------------------------------------------------------*
#> SWITPD = 0 !Non puddled
#> NLPUD = 1
#> WCSTRP = 0.38, 0.38, 0.43
#> PFCR = 6.0
#> DPLOWPAN = 0.6
file.remove(soil_files_oryza)
#> [1] TRUE
# basic example code to create DSSAT soil file
soil_files_dssat <- write_soil_dssat(path = ".", "soil_dssat", soil_sample)
#> Minimun data are available
#> DSSAT soil Files created in . :
#> .soil_dssat.SOL
readLines(soil_files_dssat[1], n = 15) |> writeLines()
#> *SOILS: AgroclimR DSSAT Soil Input File - by agroclimR
#>
#> *soil_dssat000001 AgroclimRV1 LO 60 AgroClimR soil_dssat
#> @SITE COUNTRY LAT LONG SCS FAMILY
#> soil_dssat AgroclimR -99 -99 USDA Texture: Lo
#> @ SCOM SALB SLU1 SLDR SLRO SLNF SLPF SMHB SMPX SMKE
#> -99 0.13 6 0.6 75 1.00 1.00 IB001 IB001 IB001
#> @ SLB SLMH SLLL SDUL SSAT SRGF SSKS SBDM SLOC SLCL SLSI SLCF SLNI SLHW SLHB SCEC SADC
#> 20 -99 0.318 0.365 0.379 0.810 21.86 1.56 1.32 18.3 39.1 1.5 0.6 6.3 -99 9.6 -99
#> 40 -99 0.177 0.276 0.377 0.640 30.67 1.76 0.24 13.4 39.0 1.5 0.3 6.4 -99 6.7 -99
#> 60 -99 0.051 0.126 0.429 0.490 77.61 1.46 0.14 14.4 7.8 1.5 0.3 6.5 -99 7.9 -99
file.remove(soil_files_dssat)
#> [1] TRUE
# basic example code to create Aquacrop soil file
soil_files_aquacrop <- write_soil_aquacrop(path = ".", "soil_dssat", soil_sample)
#> AquaCrop soil Files created in . :
#> ./soil_dssat.SOL
readLines(soil_files_aquacrop[1], n = 15) |> writeLines()
#> soil_dssat AquaCrop soil file - by agroclimR
#> 6.1 : AquaCrop Version (May 2018)
#> 65 : CN (Curve Number)
#> 8 : Readily evaporable water from top layer (mm)
#> 3 : number of soil horizons
#> -9 : variable no longer applicable
#> Thickness Sat FC WP Ksat Penetrability Gravel CRa CRb description
#> ---(m)- ----(vol %)----- (mm/day) (%) (%) -----------------------------------------
#> 0.20 37.9 36.5 31.8 524.7 100 0 -0.451380 0.860353 Lo
#> 0.20 37.7 27.6 17.7 736.2 100 0 -0.432343 1.022189 Lo
#> 0.20 42.9 12.6 5.1 1862.6 100 0 -0.329826 0.325586 SaLo
file.remove(soil_files_aquacrop)
#> [1] TRUEConnect
For inquiries or feedback, contact Jeferson Rodriguez-Espinoza at jrodriguezespinoza@outlook.com.