Package: PEcAn.benchmark 1.7.5.9000

Mike Dietze

PEcAn.benchmark: PEcAn Functions Used for Benchmarking

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. The PEcAn.benchmark package provides utilities for comparing models and data, including a suite of statistical metrics and plots.

Authors:Michael Dietze, Betsy Cowdery, David LeBauer, Rob Kooper, Toni Viskari

PEcAn.benchmark_1.7.5.9000.tar.gz
PEcAn.benchmark_1.7.5.9000.zip(r-4.7)PEcAn.benchmark_1.7.5.9000.zip(r-4.6)PEcAn.benchmark_1.7.5.9000.zip(r-4.5)
PEcAn.benchmark_1.7.5.9000.tgz(r-4.6-any)PEcAn.benchmark_1.7.5.9000.tgz(r-4.5-any)
PEcAn.benchmark_1.7.5.9000.tar.gz(r-4.7-any)PEcAn.benchmark_1.7.5.9000.tar.gz(r-4.6-any)
PEcAn.benchmark_1.7.5.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PEcAn.benchmark/json (API)

# Install 'PEcAn.benchmark' in R:
install.packages('PEcAn.benchmark', repos = c('https://pecanproject.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pecanproject/pecan/issues

On CRAN:

Conda:

model-evaluationmodel-data-comparisonpecanbayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationplants

10.41 score 238 stars 3 packages 476 scripts 41 exports 74 dependencies

Last updated from:2405ae8905. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE185
source / vignettesOK288
linux-release-x86_64NOTE146
macos-release-arm64NOTE99
macos-oldrel-arm64NOTE150
windows-develNOTE98
windows-releaseNOTE113
windows-oldrelNOTE101
wasm-releaseOK145

Exports:add_workflow_infoalign_by_first_observationalign_dataalign_data_to_data_pftalign_pftbm_settings2pecan_settingscalc_benchmarkcalc_metricscheck_BRRclean_settings_BRRcreate_BRRdefine_benchmarkformat_wide2longload_and_map_dataload_csvload_dataload_rdsload_tab_separated_valuesload_x_netcdfmatch_timestepmean_over_larger_timestepmetric_AMEmetric_cormetric_Coveragemetric_Frechetmetric_lmDiag_plotmetric_MAEmetric_MSEmetric_PMUmetric_PPMCmetric_R2metric_RAEmetric_residual_plotmetric_RMSEmetric_runmetric_scatter_plotmetric_timeseries_plotpecan_metric_registryread_settings_BRRregister_metricrun_benchmark

Dependencies:abindaskpassblobclicodetoolscpp11curlDBIdbplyrdigestdplyrfarverforeachfsfurrrfuturegenericsggplot2globalsgluegridExtragtablehttrisobanditeratorsjsonlitelabelinglatticelifecyclelistenvlubridatemagrittrmimencdf4openssloptparseparallellyPEcAn.DBPEcAn.loggerPEcAn.remotePEcAn.settingsPEcAn.utilspillarpkgconfigplyrpurrrR.methodsS3R.ooR.utilsR6RColorBrewerRcppreshape2rlangS7scalesSimilarityMeasuresstringistringrsystibbletidyrtidyselecttimechangetriebeardunitsurltoolsutf8vctrsviridisLitewithrXMLyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Add workflow specific info to settings list for benchmarkingadd_workflow_info
align_first_observationalign_by_first_observation
Align model and observation data frames by nearest timealign_by_time
Align timeseries dataalign_data
align_data_to_data_pftalign_data_to_data_pft
Align vectors of Plant Functional Type and species.align_pft
Move benchmarking settings back in to original pecan settings objectbm_settings2pecan_settings
Validate benchmark input dataframesbm_validate
Calculate benchmarking statisticscalc_benchmark
calc_metricscalc_metrics
Check whether a run has been registered as a reference run in BETYcheck_BRR
check_if_legal_tablecheck_if_legal_table
check_if_list_of_pftscheck_if_list_of_pfts
check_if_species_listcheck_if_species_list
Cleans PEcAn settings file and prepares the settings to be saved in a reference run record in BETYclean_settings_BRR
Compute benchmark metricscompute_metrics
Create benchmark reference run and ensemblecreate_BRR
Benchmark Definition: Retrieve or Create Bety Benchmarking Recordsdefine_benchmark
Function to convert wide format to long formatformat_wide2long
get_species_list_standardget_species_list_standard
Load and standardize arbitrary tabular data using a YAML mapping configurationload_and_map_data
load_csvload_csv
load dataload_data
load_rdsload_rds
Load files with mime-type 'text/tab-separated-values'load_tab_separated_values
Load from netCDFload_x_netcdf
Match time stepmatch_timestep
Calculate benchmarking statisticsmean_over_larger_timestep
Absolute Maximum Errormetric_AME
Correlation Coefficientmetric_cor
Prediction Interval Coveragemetric_Coverage
Frechet Distancemetric_Frechet
Linear Regression Diagnostic Plotmetric_lmDiag_plot
Mean Absolute Errormetric_MAE
Mean Square Errormetric_MSE
Predictive Model Uncertainty (PMU)metric_PMU
Pearson Product Moment Correlationmetric_PPMC
Coefficient of Determination (R2)metric_R2
Relative Absolute Errormetric_RAE
Residual Plotmetric_residual_plot
Root Mean Square Errormetric_RMSE
Model Run Checkmetric_run
Scatter Plotmetric_scatter_plot
Timeseries Plotmetric_timeseries_plot
Metric Registry for PEcAn.benchmarkpecan_metric_registry
Plot model vs observations time seriesplot_time_series
Read settings from database using reference run idread_settings_BRR
Register a new benchmark metricregister_metric
Run a simple benchmark pipelinerun_benchmark