Package: OptirrigCORE 0.8.0
UMR G-Eau Aqua Department INRAE Montpellier Team Optimiste
OptirrigCORE: Optirrig Core: Simulate and Optimize Irrigation Scenarios
The OptirrigCORE package in R is based on the Optirrig model. It facilitates the extraction and formatting of observation data used by the model, as well as the integration of plant, soil and yield descriptions. It supports various analytical methods, such as Ex-Post and Ex-Ante analyses, with a view to drawing up an optimised irrigation schedule based on the criteria. The package includes all the calculation tools needed to describe biophysical processes with a generalist approach. It can be used as a dependency or complement to modify and reinterpret biophysical descriptions. What's more, it automates the modeling process, the description of biophysical processes and the analysis of results and performance, guaranteeing a reproducible approach. It also makes it easy to compile results in automated reports.
Authors:
OptirrigCORE_0.8.0.tar.gz
OptirrigCORE_0.8.0.zip(r-4.7)OptirrigCORE_0.8.0.zip(r-4.6)OptirrigCORE_0.8.0.zip(r-4.5)
OptirrigCORE_0.8.0.tgz(r-4.6-any)OptirrigCORE_0.8.0.tgz(r-4.5-any)
OptirrigCORE_0.8.0.tar.gz(r-4.6-any)OptirrigCORE_0.8.0.tar.gz(r-4.5-any)
OptirrigCORE_0.8.0.tgz(r-4.5-emscripten)
OptirrigCORE.pdf |OptirrigCORE.html✨
OptirrigCORE/json (API)
NEWS
| # Install 'OptirrigCORE' in R: |
| install.packages('OptirrigCORE', repos = c('https://inrae.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/inrae/optirrigcore/issues
Pkgdown/docs site:https://optirrighive.pages-forge.inrae.fr
- MAIZE_21LAVALETTE_B - Observed biomass for maize trial
- MAIZE_21LAVALETTE_clim - Climate data for maize trial
- MAIZE_21LAVALETTE_irrig - Irrigation schedule for maize trial
- MAIZE_21LAVALETTE_LAI - Observed leaf area index for maize trial
- MAIZE_21LAVALETTE_RES - Observed water reservoir for maize trial
Last updated from:3583825d4f (on main). Checks:7 WARNING, 1 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | WARNING | 617 | ||
| source / vignettes | ERROR | 810 | ||
| linux-release-x86_64 | WARNING | 737 | ||
| macos-release-arm64 | WARNING | 182 | ||
| macos-oldrel-arm64 | WARNING | 117 | ||
| windows-devel | WARNING | 187 | ||
| windows-release | WARNING | 158 | ||
| windows-oldrel | WARNING | 127 | ||
| wasm-release | OK | 649 |
Exports:add_missing_paramscalc_alphacalc_Bcalc_B_rootcalc_Bpcalc_Bp_rootcalc_casecalc_Cpcalc_craccalc_dcalc_d_from_Rgravitycalc_degredcalc_dosecalc_dtheta_RUcalc_dzrootcalc_dzrootpcalc_EScalc_ES0calc_ET0calc_ET0_mulch_effectcalc_ETMcalc_ETRcalc_HIcalc_IRcalc_Kccalc_Kdcalc_Kd_from_saxtoncalc_KEScalc_Kscalc_Ks_from_cosbycalc_Ks_from_ottonicalc_Ks_from_saxtoncalc_ks_rootcalc_KTPcalc_LAIcalc_LAIpcalc_LTcalc_PARcalc_quotacalc_Rcalc_R_from_thetacalc_Rgravitycalc_Rgravity_from_Rcalc_Rgravity_from_thetacalc_RUcalc_RU_from_thetacalc_RUmaxcalc_stresscalc_stress_noci_Bcalc_stress_noci_LAIcalc_stress_Tcalc_stress_watercalc_sugar_accumulationcalc_taucalc_taumcalc_Tcritcalc_thetacalc_theta_fccalc_theta_fc_from_texturecalc_theta_from_Rcalc_theta_rcalc_theta_r_from_texturecalc_theta_relcalc_theta_satcalc_theta_sat_from_texturecalc_theta_wpcalc_theta_wp_from_texturecalc_thresholdcalc_TPcalc_TP0calc_TTcalc_TT_normcalc_TT_relcalc_TT_sowingcalc_Ycalc_Y_sugarcalc_zrootcalc_zrootpcreate_model_inputscreate_model_inputs_climatecreate_model_inputs_cropcreate_model_inputs_irrigationcreate_model_inputs_runcreate_model_inputs_soilget_data_pathget_idayget_model_output_pathget_vars_datainit_modelinit_model_climateinit_model_crop_devinit_model_irrigationinit_model_varsinputs_metaload_configparse_date_timereadrun_modelrun_model_crop_devrun_model_crop_dev_Brun_model_crop_dev_B_rootrun_model_crop_dev_LAIrun_model_crop_dev_stress_waterrun_model_crop_dev_Yrun_model_crop_dev_Y_sugarrun_model_crop_dev_zrootrun_model_financerun_model_irrig_stratrun_model_irrig_strat_doserun_model_water_balancerun_model_water_balance_drainagerun_model_water_balance_ESrun_model_water_balance_ETMrun_model_water_balance_init_statesrun_model_water_balance_othersrun_model_water_balance_routing_waterrun_model_water_balance_TPrun_model_water_balance_update_Rsave_model_outputsselect_output_vars
Dependencies:bitbit64cellrangerclicliprcodetoolscpp11crayondigestdplyrfuturefuture.applygenericsglobalsgluehmsinilifecyclelistenvloggerlubridatemagrittrmintyparallellypillarpkgconfigprettyunitsprogressR6readODSreadrreadxlrematchrlangstringitibbletidyselecttimechangetzdbutf8vctrsvroomwithrzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add Missing Parameters from Reference INI Files | add_missing_params |
| Calculate temperature response alpha parameter | calc_alpha calc_alpha.data.frame calc_alpha.matrix calc_alpha.numeric |
| Calculate Biomass Accumulation (B) | calc_B calc_B.data.frame calc_B.matrix calc_B.NULL calc_B.numeric |
| Calculate biomass root accumulation (B_root) | calc_B_root calc_B_root.data.frame calc_B_root.matrix calc_B_root.numeric |
| Calculate potential biomass production (Bp) | calc_Bp calc_Bp.matrix calc_Bp.model_init |
| Calculate potential biomass root accumulation (Bp_root) | calc_Bp_root calc_Bp_root.matrix |
| Calculate model water balance case | calc_case calc_case.matrix calc_case.numeric |
| Calculate canopy partition coefficient (Cp) | calc_Cp calc_Cp.numeric |
| Calculate root growth parameter (crac) | calc_crac calc_crac.matrix calc_crac.model_output calc_crac.numeric |
| Calculate drainage (d) | calc_d calc_d_from_Rgravity calc_d_from_Rgravity.matrix calc_d_from_Rgravity.numeric |
| Calculate "degred" root growth calculation input | calc_degred calc_degred.Date calc_degred.matrix calc_degred.model_init |
| Generic function to calculate irrigation (dose) | calc_dose calc_dose.NULL calc_dose.numeric |
| Calculate relative soil moisture above field capacity (dtheta_RU) | calc_dtheta_RU calc_dtheta_RU.matrix calc_dtheta_RU.numeric |
| Calculate root depth increment (dzroot) | calc_dzroot calc_dzroot.matrix calc_dzroot.model_output calc_dzroot.numeric |
| Calculate the change in root depth (dzrootp) | calc_dzrootp calc_dzrootp.matrix calc_dzrootp.numeric |
| Calculate soil evaporation (ES) | calc_ES calc_ES.matrix calc_ES.numeric |
| Calculate potential soil evaporation (ES0) | calc_ES0 calc_ES0.matrix calc_ES0.numeric |
| Calculate reference evapotranspiration (ET0) | calc_ET0 calc_ET0.matrix calc_ET0.numeric |
| Calculate mulch effect on reference evapotranspiration (ET0) | calc_ET0_mulch_effect calc_ET0_mulch_effect.NULL calc_ET0_mulch_effect.numeric |
| Calculate maximum crop evapotranspiration (ETM) | calc_ETM calc_ETM.matrix calc_ETM.NULL calc_ETM.numeric |
| Calculate actual evapotranspiration (ETR) | calc_ETR calc_ETR.matrix calc_ETR.numeric |
| Calculate harvest index (HI) | calc_HI calc_HI.matrix calc_HI.numeric |
| Calculate intercepted radiation fraction (IR) | calc_IR calc_IR.matrix calc_IR.NULL calc_IR.numeric |
| Calculate crop coefficient (Kc) from leaf area index (LAI) | calc_Kc calc_Kc.matrix calc_Kc.numeric |
| Calculate hydraulic conductivity (Kd) using various methods | calc_Kd calc_Kd_from_saxton calc_Kd_from_saxton.matrix calc_Kd_from_saxton.numeric |
| Calculate soil evaporation coefficient (KES) | calc_KES calc_KES.matrix calc_KES.numeric |
| Calculate saturated hydraulic conductivity (Ks) from soil texture | calc_Ks calc_Ks_from_cosby calc_Ks_from_cosby.numeric calc_Ks_from_ottoni calc_Ks_from_ottoni.numeric calc_Ks_from_saxton calc_Ks_from_saxton.numeric |
| Calculate root growth ks_root parameter | calc_ks_root calc_ks_root.matrix calc_ks_root.numeric |
| Calculate transpiration reduction coefficient (KTP) | calc_KTP calc_KTP.matrix calc_KTP.numeric |
| Calculate leaf area index (LAI) | calc_LAI calc_LAI.data.frame calc_LAI.matrix calc_LAI.NULL calc_LAI.numeric |
| Calculate potential leaf area index (LAIp) | calc_LAIp calc_LAIp.data.frame calc_LAIp.matrix calc_LAIp.model_init calc_LAIp.NULL calc_LAIp.numeric |
| Calculate logistic temperature index (LT) | calc_LT calc_LT.data.frame calc_LT.matrix calc_LT.numeric |
| Calculate photosynthetically active radiation (PAR) | calc_PAR calc_PAR.data.frame calc_PAR.matrix calc_PAR.numeric |
| Calculate Applied Irrigation Dose with Quota Management | calc_quota |
| Calculate soil water reserve (R) | calc_R calc_R.default calc_R.model_output calc_R_from_theta calc_R_from_theta.data.frame calc_R_from_theta.matrix calc_R_from_theta.numeric |
| Calculate gravitational soil water (Rgravity) | calc_Rgravity calc_Rgravity_from_R calc_Rgravity_from_theta calc_Rgravity_from_theta.matrix calc_Rgravity_from_theta.numeric |
| Calculate soil available water content (RU) | calc_RU calc_RU_from_theta calc_RU_from_theta.data.frame calc_RU_from_theta.matrix calc_RU_from_theta.numeric |
| Calculate maximum soil available water content (RUmax) | calc_RUmax calc_RUmax.data.frame calc_RUmax.matrix calc_RUmax.numeric |
| Calculate LAI stress value | calc_stress calc_stress.matrix calc_stress.model_output calc_stress.numeric |
| Calculate biomass stress nocivity (stress_noci_B) | calc_stress_noci_B calc_stress_noci_B.data.frame calc_stress_noci_B.matrix calc_stress_noci_B.numeric |
| Calculate leaf area index stress nocivity | calc_stress_noci_LAI calc_stress_noci_LAI.matrix calc_stress_noci_LAI.numeric |
| Calculate temperature stress value | calc_stress_T calc_stress_T.matrix calc_stress_T.model_output calc_stress_T.numeric |
| Calculate the stress water ratio | calc_stress_water calc_stress_water.matrix calc_stress_water.model_output calc_stress_water.numeric |
| Calculate sugar accumulation in roots | calc_sugar_accumulation calc_sugar_accumulation.matrix |
| Calculate the tau parameter | calc_tau calc_tau.matrix calc_tau.numeric |
| Calculate root growth taum parameter | calc_taum calc_taum.matrix calc_taum.model_output calc_taum.numeric |
| Calculate Critical Temperature (Tcrit) | calc_Tcrit calc_Tcrit.matrix calc_Tcrit.numeric |
| Calculate soil water content | calc_theta calc_theta_from_R calc_theta_from_R.matrix calc_theta_from_R.numeric |
| Calculate available water capacity at field capacity | calc_theta_fc calc_theta_fc_from_texture calc_theta_fc_from_texture.numeric |
| Calculate Residual Soil Water Content (Theta_r) | calc_theta_r calc_theta_r_from_texture calc_theta_r_from_texture.numeric |
| Calculate Relative Soil Water Content (Theta_rel) | calc_theta_rel calc_theta_rel.matrix calc_theta_rel.numeric |
| Calculate Saturated Water Content (Theta_sat) | calc_theta_sat calc_theta_sat_from_texture calc_theta_sat_from_texture.numeric |
| Calculate available water capacity at wilting point | calc_theta_wp calc_theta_wp_from_texture calc_theta_wp_from_texture.numeric |
| Calculate Irrigation Trigger Conditions | calc_threshold |
| Calculate crop transpiration | calc_TP calc_TP.model_output calc_TP.numeric |
| Calculate potential transpiration (TP0) | calc_TP0 calc_TP0.matrix calc_TP0.numeric |
| Calculate Cumulative Thermal Time (TT) | calc_TT calc_TT.data.frame calc_TT.matrix calc_TT.model_init calc_TT.numeric |
| Calculate normalized thermal time | calc_TT_norm calc_TT_norm.data.frame calc_TT_norm.default calc_TT_norm.matrix |
| Calculate Relative Thermal Time (TT_rel) | calc_TT_rel calc_TT_rel.data.frame calc_TT_rel.matrix calc_TT_rel.numeric |
| Calculate relative thermal time since sowing | calc_TT_sowing calc_TT_sowing.data.frame calc_TT_sowing.matrix calc_TT_sowing.numeric |
| Calculate yield | calc_Y calc_Y.matrix calc_Y.NULL calc_Y.numeric |
| Calculate sugar yield (Y_sugar) | calc_Y_sugar calc_Y_sugar.matrix calc_Y_sugar.numeric |
| Calculate root depth | calc_zroot calc_zroot.matrix calc_zroot.numeric |
| Calculate potential root depth | calc_zrootp calc_zrootp.matrix calc_zrootp.model_init calc_zrootp.numeric |
| Create Model Inputs (docs from createInputsModel) | create_model_inputs create_model_inputs.character create_model_inputs.data.frame create_model_inputs.list |
| Create climate model inputs | create_model_inputs_climate create_model_inputs_climate.character create_model_inputs_climate.data.frame create_model_inputs_climate.list |
| Create crop model inputs | create_model_inputs_crop create_model_inputs_crop.list |
| Create Irrigation Model Inputs | create_model_inputs_irrigation create_model_inputs_irrigation.character create_model_inputs_irrigation.data.frame create_model_inputs_irrigation.list |
| Create run model inputs | create_model_inputs_run create_model_inputs_run.list |
| Create soil model inputs | create_model_inputs_soil create_model_inputs_soil.list |
| Give the complete path of the data and cache data on local disk | get_data_path |
| Get model time indices | get_iday get_iday.matrix get_iday.model_init |
| Generate Output File Path for Model Results | get_model_output_path |
| Retrieve Metadata for Parameters and Variables | get_vars_data |
| Initialize the model simulation | init_model init_model.matrix init_model.model_input init_model.model_inputs |
| Initialize the model simulation - climate | init_model_climate init_model_climate.data.frame init_model_climate.list init_model_climate.matrix init_model_climate.model_input |
| Initialize the model simulation - crop development | init_model_crop_dev init_model_crop_dev.model_init |
| Initialize the model simulation - climate | init_model_irrigation init_model_irrigation.matrix init_model_irrigation.model_input |
| Initialize variables for the model simulation | init_model_vars init_model_vars.matrix init_model_vars.model_init |
| Retrieve inputs metadata (categories, types, subcategories) | inputs_meta |
| Load Package Configuration File | load_config |
| Observed biomass for maize trial (2021, Lavalette) | MAIZE_21LAVALETTE_B |
| Climate data for maize trial (2021, Lavalette) | MAIZE_21LAVALETTE_clim |
| Irrigation schedule for maize trial (2021, Lavalette) | MAIZE_21LAVALETTE_irrig |
| Observed leaf area index for maize trial (2021, Lavalette) | MAIZE_21LAVALETTE_LAI |
| Observed water reservoir for maize trial (2021, Lavalette) | MAIZE_21LAVALETTE_RES |
| Parse date strings into Date objects | parse_date_time |
| Read a file by inferring the reader from the file extension | read |
| Run Optirrig model | run_model run_model.character run_model.data.frame run_model.list run_model.model_init run_model.model_inits run_model.model_input run_model.model_inputs run_model.NULL |
| Crop development module | run_model_crop_dev run_model_crop_dev.model_output |
| Biomass part of model crop development module | run_model_crop_dev_B run_model_crop_dev_B.matrix run_model_crop_dev_B.model_output |
| Run/update crop root biomass (B_root) for a single day | run_model_crop_dev_B_root run_model_crop_dev_B_root.matrix run_model_crop_dev_B_root.model_output |
| LAI part of the crop development module | run_model_crop_dev_LAI run_model_crop_dev_LAI.matrix run_model_crop_dev_LAI.model_output |
| Water stress part of the crop development module | run_model_crop_dev_stress_water run_model_crop_dev_stress_water.matrix |
| Yield part of the crop development module | run_model_crop_dev_Y run_model_crop_dev_Y.matrix run_model_crop_dev_Y.model_output |
| Run model for crop development stage Y (sugar) | run_model_crop_dev_Y_sugar run_model_crop_dev_Y_sugar.matrix run_model_crop_dev_Y_sugar.model_output |
| Root development part of the crop development module | run_model_crop_dev_zroot run_model_crop_dev_zroot.matrix run_model_crop_dev_zroot.model_output |
| Run Financial Model | run_model_finance run_model_finance.model |
| Run Model for Irrigation Strategy | run_model_irrig_strat run_model_irrig_strat.model_output |
| Run Irrigation Strategy Dose Model | run_model_irrig_strat_dose run_model_irrig_strat_dose.matrix run_model_irrig_strat_dose.model_output |
| Water balance module | run_model_water_balance run_model_water_balance.model_output run_model_water_balance_others.matrix run_model_water_balance_others.model_output |
| Drainage part of the water balance module | run_model_water_balance_drainage run_model_water_balance_drainage.matrix run_model_water_balance_drainage.model_output |
| Evaporation part of the water balance module | run_model_water_balance_ES run_model_water_balance_ES.matrix run_model_water_balance_ES.model_output |
| Potential evapotranspiration (ETM) part of the water balance module | run_model_water_balance_ETM run_model_water_balance_ETM.matrix run_model_water_balance_ETM.model_output |
| Initialize soil hydric states for the water balance module | run_model_water_balance_init_states run_model_water_balance_init_states.matrix run_model_water_balance_init_states.model_output |
| Others part of the water balance module | run_model_water_balance_others |
| Route water through the soil layers | run_model_water_balance_routing_water run_model_water_balance_routing_water.matrix run_model_water_balance_routing_water.model_output |
| Transpiration part of the water balance module | run_model_water_balance_TP run_model_water_balance_TP.matrix run_model_water_balance_TP.model_output |
| Update soil hydric states for the water balance module | run_model_water_balance_update_R run_model_water_balance_update_R.matrix run_model_water_balance_update_R.model_output |
| Save Model Outputs | save_model_outputs save_model_outputs.data.frame save_model_outputs.matrix save_model_outputs.model_output save_model_outputs.model_outputs |
| Select variables to return from model outputs | select_output_vars select_output_vars.matrix |
