The ProfoundData R-package

Ramiro Silveyra Gonzalez, Christopher Reyer, Mats Mahnken, Florian Hartig

2020-03-29

Abstract

This vignette provides an overview of the Profound data R package. For an overview about the database, see the separate vignette PROFOUNDdatabase.

ProfoundData R-package: using the PROFOUND database from R

The ProfoundData package serves as interface to access the PROFOUND database. Three main functions are included to achieve this goal: a browseData function for exploring the database, a getData function for downloading data fromm the database and a plotData function to quickly inspect any variable of the datasets.

The functions allow to retrieve only data from one site and one dataset at a time. For downloading data of more than one dataset or of more than one site, the function should be called as many times as the number of desired sites or datasets. Additionally, flags and other parameters can be passed to the functions. The package also includes utilities functions to do tasks such as inspecting the data or writing NetCDF files.

To see the suggested ciation for the package, run

library(ProfoundData)
citation("ProfoundData")
## 
## To cite the 'ProfoundData' package in publications use:
## 
##   Reyer, C. (2019). The PROFOUND Database for evaluating
##   vegetation models and simulating climate impacts on forest
##   stands. Submitted to Earth System Science Data.
## 
##   Reyer, C., Silveyra Gonzalez, R., Dolos, K., Hartig, F., Hauf,
##   Y., Noack, M., … Frieler, K. (2019). The PROFOUND database for
##   evaluating vegetation models and simulating climate impacts on
##   forests [Data set]. https://doi.org/10.5880/pik.2019.008
## 
## To see these entries in BibTeX format, use 'print(<citation>,
## bibtex=TRUE)', 'toBibtex(.)', or set
## 'options(citation.bibtex.max=999)'.

First Steps

Database download

Profound database is provided in SQLite and can be downloaded either by hand at http://doi.org/10.5880/PIK.2019.008 or via the

Per default, the database is downloaded into the currrent working directory, but you can specify another location in the function. The function returns the current databse location, which can be passed on the the setDB function (see below).

Database connection

For using a locally stored database with the ProfoundData package, the first step is to call the setDB. The function requires a valid absolute path to the PROFOUND database.

To check the database connection you can use the use getDB, which returns the database path and also informs about the database version.

## Database version is 0.2.0
## [1] "/Users/florian/temp/ProfoundData.sqlite"

Exploring the database

The browseData function

The browseData function allows to see what data is included in the database and for what sites the data is available.

site_id site SITES TREE STAND SOIL CLIMATE_LOCAL CLIMATE_ISIMIP2B CLIMATE_ISIMIP2BLBC CLIMATE_ISIMIP2A CLIMATE_ISIMIPFT METEOROLOGICAL FLUX ATMOSPHERICHEATCONDUCTION SOILTS NDEPOSITION_EMEP NDEPOSITION_ISIMIP2B CO2_ISIMIP MODIS_MOD09A1 MODIS_MOD15A2 MODIS_MOD11A2 MODIS_MOD13Q1 MODIS_MOD17A2 MODIS
3 bily_kriz 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
5 collelongo 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
12 hyytiala 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
13 kroof 1 1 1 1 1 1 1 1 1 0 0 0 0 1 1 1 1 1 1 1 1 1
14 le_bray 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
16 peitz 1 1 1 1 1 1 1 1 1 0 0 0 0 1 1 1 1 1 1 1 1 1
20 solling_beech 1 1 1 1 1 1 1 1 1 0 0 0 0 1 1 1 1 1 1 1 1 1
21 soro 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
25 solling_spruce 1 1 1 1 1 1 1 1 1 0 0 0 0 1 1 1 1 1 1 1 1 1

Hint: If you set collapse to FALSE, you will get the full version of the overview table.

Besides returning the overview, browseData allows to check:

Hint: You can also pass a site to check the metadata of a specific site.

Hint: You can also pass a site to check the source of a specific site.

Hint: You can also pass a site to check the policy of a specific site.

The summarizeData function

Data overviews of the available data

The summarizeData function allows to obtain data summaries and overviews of the data depending on mode. If you choose the mode overview, summarizeData will return a data frame with the years and number of observations, the first and last value, and the min and max value, as in the example below.

site site_id variable first last min max mean year_first year_last obs
bily_kriz 3 tmax_degC 1.353014e+01 1.053710e+01 9.310364e+00 1.353014e+01 1.150140e+01 2000 2008 9
bily_kriz 3 tmean_degC 8.536865e+00 7.484678e+00 5.930202e+00 8.536865e+00 7.356880e+00 2000 2008 9
bily_kriz 3 tmin_degC 4.102271e+00 4.652052e+00 2.349707e+00 4.652052e+00 3.801032e+00 2000 2008 9
bily_kriz 3 p_mm 1.490324e+03 1.167563e+03 1.004007e+03 1.750245e+03 1.434560e+03 2000 2008 9
bily_kriz 3 relhum_percent 7.993809e+01 8.380125e+01 7.276064e+01 8.884459e+01 8.198789e+01 2000 2008 9
bily_kriz 3 airpress_hPa 9.127901e+02 9.131897e+02 9.117648e+02 9.144979e+02 9.131942e+02 2000 2008 9
bily_kriz 3 rad_Jcm2day 3.706045e+05 3.871684e+05 3.418508e+05 4.053810e+05 3.787749e+05 2000 2008 9
bily_kriz 3 wind_ms 2.350770e+00 2.404200e+00 1.945468e+00 2.474911e+00 2.188664e+00 2000 2008 9

The overview tables for ISIMIP datasets contain more fields, namely forcing datasets and/or forcing conditions.

site site_id forcingDataset forcingCondition variable first last min max mean year_first year_last obs
bily_kriz 3 GFDLESM2M historical tmax_degC 1.006887e+01 1.147109e+01 8.685277e+00 1.525831e+01 1.154169e+01 1861 2005 145
bily_kriz 3 GFDLESM2M historical tmean_degC 5.878167e+00 6.749036e+00 4.454744e+00 9.924510e+00 6.930977e+00 1861 2005 145
bily_kriz 3 GFDLESM2M historical tmin_degC 1.692771e+00 1.964804e+00 1.069216e-01 4.430233e+00 2.223197e+00 1861 2005 145
bily_kriz 3 GFDLESM2M historical p_mm 9.766867e+02 1.125590e+03 6.073860e+02 1.311257e+03 9.683358e+02 1861 2005 145
bily_kriz 3 GFDLESM2M historical relhum_percent 7.694075e+01 7.747906e+01 6.644276e+01 7.905318e+01 7.428709e+01 1861 2005 145
bily_kriz 3 GFDLESM2M historical airpress_hPa 9.490722e+02 9.495864e+02 9.468872e+02 9.533306e+02 9.498743e+02 1861 2005 145
bily_kriz 3 GFDLESM2M historical rad_Jcm2day 3.780155e+05 3.823430e+05 3.557333e+05 4.346502e+05 3.911453e+05 1861 2005 145
bily_kriz 3 GFDLESM2M historical wind_ms 2.800383e+00 3.286238e+00 2.800383e+00 3.490822e+00 3.217614e+00 1861 2005 145
bily_kriz 3 GFDLESM2M piControl tmax_degC 1.155938e+01 1.118532e+01 8.056727e+00 1.441375e+01 1.153763e+01 1661 2099 439
bily_kriz 3 GFDLESM2M piControl tmean_degC 6.591962e+00 6.797587e+00 3.551189e+00 9.195662e+00 6.811351e+00 1661 2099 439
bily_kriz 3 GFDLESM2M piControl tmin_degC 1.662844e+00 2.404546e+00 -9.935545e-01 4.178733e+00 2.079977e+00 1661 2099 439
bily_kriz 3 GFDLESM2M piControl p_mm 9.001616e+02 1.160674e+03 7.274699e+02 1.399731e+03 1.040637e+03 1661 2099 439
bily_kriz 3 GFDLESM2M piControl relhum_percent 7.657000e+01 7.932156e+01 6.822058e+01 8.215661e+01 7.708760e+01 1661 2099 439
bily_kriz 3 GFDLESM2M piControl airpress_hPa 9.504819e+02 9.497652e+02 9.468040e+02 9.525582e+02 9.497105e+02 1661 2099 439
bily_kriz 3 GFDLESM2M piControl rad_Jcm2day 4.141776e+05 3.772647e+05 3.423868e+05 4.528545e+05 3.912886e+05 1661 2099 439
bily_kriz 3 GFDLESM2M piControl wind_ms 2.586498e+00 2.612632e+00 2.331867e+00 2.819268e+00 2.560670e+00 1661 2099 439
bily_kriz 3 GFDLESM2M rcp2p6 tmax_degC 1.215476e+01 1.316143e+01 1.068443e+01 1.554527e+01 1.289789e+01 2006 2099 94
bily_kriz 3 GFDLESM2M rcp2p6 tmean_degC 7.546677e+00 8.467387e+00 6.442471e+00 1.045057e+01 8.310183e+00 2006 2099 94
bily_kriz 3 GFDLESM2M rcp2p6 tmin_degC 2.838122e+00 3.674079e+00 1.616721e+00 5.559387e+00 3.577403e+00 2006 2099 94
bily_kriz 3 GFDLESM2M rcp2p6 p_mm 1.273594e+03 1.008292e+03 6.054646e+02 1.273594e+03 1.016470e+03 2006 2099 94
bily_kriz 3 GFDLESM2M rcp2p6 relhum_percent 7.915016e+01 7.360668e+01 6.662971e+01 7.915016e+01 7.381166e+01 2006 2099 94
bily_kriz 3 GFDLESM2M rcp2p6 airpress_hPa 9.490538e+02 9.516424e+02 9.471578e+02 9.538344e+02 9.507912e+02 2006 2099 94
bily_kriz 3 GFDLESM2M rcp2p6 rad_Jcm2day 3.780991e+05 3.964951e+05 3.529131e+05 4.402460e+05 3.976782e+05 2006 2099 94
bily_kriz 3 GFDLESM2M rcp2p6 wind_ms 3.209430e+00 3.354782e+00 3.160059e+00 3.826681e+00 3.444829e+00 2006 2099 94
bily_kriz 3 GFDLESM2M rcp4p5 tmax_degC 1.288055e+01 1.406410e+01 1.086514e+01 1.547209e+01 1.341545e+01 2006 2099 94
bily_kriz 3 GFDLESM2M rcp4p5 tmean_degC 8.189510e+00 9.282370e+00 6.527514e+00 1.018920e+01 8.748496e+00 2006 2099 94
bily_kriz 3 GFDLESM2M rcp4p5 tmin_degC 3.500966e+00 4.324320e+00 1.943218e+00 5.135467e+00 3.953199e+00 2006 2099 94
bily_kriz 3 GFDLESM2M rcp4p5 p_mm 1.125624e+03 9.592606e+02 6.383654e+02 1.255992e+03 9.899021e+02 2006 2099 94
bily_kriz 3 GFDLESM2M rcp4p5 relhum_percent 7.530757e+01 7.354885e+01 6.562762e+01 7.757270e+01 7.318045e+01 2006 2099 94
bily_kriz 3 GFDLESM2M rcp4p5 airpress_hPa 9.498213e+02 9.522953e+02 9.481768e+02 9.535832e+02 9.511007e+02 2006 2099 94
bily_kriz 3 GFDLESM2M rcp4p5 rad_Jcm2day 4.187450e+05 3.932176e+05 3.658412e+05 4.397868e+05 4.012383e+05 2006 2099 94
bily_kriz 3 GFDLESM2M rcp4p5 wind_ms 3.400762e+00 3.346777e+00 3.056685e+00 3.704483e+00 3.384756e+00 2006 2099 94
bily_kriz 3 GFDLESM2M rcp6p0 tmax_degC 1.208168e+01 1.311559e+01 9.968399e+00 1.602148e+01 1.326510e+01 2006 2099 94
bily_kriz 3 GFDLESM2M rcp6p0 tmean_degC 7.570482e+00 8.811900e+00 6.057520e+00 1.112778e+01 8.651463e+00 2006 2099 94
bily_kriz 3 GFDLESM2M rcp6p0 tmin_degC 2.989240e+00 4.376124e+00 1.833080e+00 6.031763e+00 3.902593e+00 2006 2099 94
bily_kriz 3 GFDLESM2M rcp6p0 p_mm 1.231269e+03 1.124040e+03 6.924375e+02 1.323759e+03 9.899244e+02 2006 2099 94
bily_kriz 3 GFDLESM2M rcp6p0 relhum_percent 7.804449e+01 7.551482e+01 6.533163e+01 7.829034e+01 7.330648e+01 2006 2099 94
bily_kriz 3 GFDLESM2M rcp6p0 airpress_hPa 9.485220e+02 9.479184e+02 9.479184e+02 9.543837e+02 9.510994e+02 2006 2099 94
bily_kriz 3 GFDLESM2M rcp6p0 rad_Jcm2day 3.782895e+05 3.776877e+05 3.467031e+05 4.440431e+05 3.975791e+05 2006 2099 94
bily_kriz 3 GFDLESM2M rcp6p0 wind_ms 3.288611e+00 3.464434e+00 3.221312e+00 3.704554e+00 3.415027e+00 2006 2099 94
bily_kriz 3 GFDLESM2M rcp8p5 tmax_degC 1.196326e+01 1.518987e+01 1.130086e+01 1.837590e+01 1.410468e+01 2006 2099 94
bily_kriz 3 GFDLESM2M rcp8p5 tmean_degC 7.587771e+00 1.013861e+01 6.961074e+00 1.266328e+01 9.202764e+00 2006 2099 94
bily_kriz 3 GFDLESM2M rcp8p5 tmin_degC 3.015651e+00 4.842265e+00 1.922271e+00 6.747208e+00 4.231603e+00 2006 2099 94
bily_kriz 3 GFDLESM2M rcp8p5 p_mm 1.073079e+03 1.066355e+03 6.471813e+02 1.342434e+03 1.000770e+03 2006 2099 94
bily_kriz 3 GFDLESM2M rcp8p5 relhum_percent 7.824174e+01 7.510250e+01 6.322957e+01 7.912488e+01 7.327579e+01 2006 2099 94
bily_kriz 3 GFDLESM2M rcp8p5 airpress_hPa 9.515534e+02 9.518250e+02 9.482375e+02 9.547403e+02 9.513680e+02 2006 2099 94
bily_kriz 3 GFDLESM2M rcp8p5 rad_Jcm2day 3.672316e+05 3.959328e+05 3.550359e+05 4.419723e+05 3.973588e+05 2006 2099 94
bily_kriz 3 GFDLESM2M rcp8p5 wind_ms 3.231205e+00 3.267776e+00 2.994912e+00 3.386237e+00 3.196491e+00 2006 2099 94
bily_kriz 3 HadGEM2ES historical tmax_degC 1.240796e+01 1.298377e+01 8.781035e+00 1.430560e+01 1.153644e+01 1861 2005 145
bily_kriz 3 HadGEM2ES historical tmean_degC 7.456127e+00 8.608379e+00 4.407828e+00 9.180084e+00 6.750251e+00 1861 2005 145
bily_kriz 3 HadGEM2ES historical tmin_degC 2.329002e+00 4.058239e+00 -6.764856e-01 4.058239e+00 1.824607e+00 1861 2005 145
bily_kriz 3 HadGEM2ES historical p_mm 9.149067e+02 1.003253e+03 5.692869e+02 1.389685e+03 9.490047e+02 1861 2005 145
bily_kriz 3 HadGEM2ES historical relhum_percent 7.123042e+01 7.439501e+01 6.299857e+01 8.089450e+01 7.346432e+01 1861 2005 145
bily_kriz 3 HadGEM2ES historical airpress_hPa 9.486078e+02 9.494245e+02 9.473832e+02 9.533742e+02 9.502473e+02 1861 2005 145
bily_kriz 3 HadGEM2ES historical rad_Jcm2day 4.270536e+05 3.921624e+05 3.381196e+05 4.537614e+05 4.014820e+05 1861 2005 145
bily_kriz 3 HadGEM2ES historical wind_ms 3.270745e+00 3.378617e+00 2.898211e+00 3.746602e+00 3.246359e+00 1861 2005 145
bily_kriz 3 HadGEM2ES piControl tmax_degC 1.239539e+01 1.216643e+01 9.627133e+00 1.542569e+01 1.234029e+01 1661 2299 639
bily_kriz 3 HadGEM2ES piControl tmean_degC 7.430585e+00 7.716153e+00 4.674864e+00 1.035509e+01 7.400779e+00 1661 2299 639
bily_kriz 3 HadGEM2ES piControl tmin_degC 2.339270e+00 3.021990e+00 -2.853242e-01 5.138582e+00 2.314961e+00 1661 2299 639
bily_kriz 3 HadGEM2ES piControl p_mm 8.711580e+02 1.588627e+03 5.898036e+02 1.599551e+03 9.695199e+02 1661 2299 639
bily_kriz 3 HadGEM2ES piControl relhum_percent 7.169393e+01 7.592076e+01 6.377954e+01 8.019184e+01 7.205009e+01 1661 2299 639
bily_kriz 3 HadGEM2ES piControl airpress_hPa 9.509282e+02 9.491502e+02 9.467626e+02 9.529376e+02 9.500176e+02 1661 2299 639
bily_kriz 3 HadGEM2ES piControl rad_Jcm2day 4.408675e+05 3.919564e+05 3.673516e+05 4.890285e+05 4.280856e+05 1661 2299 639
bily_kriz 3 HadGEM2ES piControl wind_ms 3.201148e+00 3.271918e+00 2.818410e+00 3.792542e+00 3.231371e+00 1661 2299 639
bily_kriz 3 HadGEM2ES rcp2p6 tmax_degC 1.336879e+01 1.433306e+01 1.066634e+01 1.725215e+01 1.417385e+01 2006 2299 294
bily_kriz 3 HadGEM2ES rcp2p6 tmean_degC 8.954505e+00 9.362698e+00 6.536817e+00 1.173888e+01 9.440236e+00 2006 2299 294
bily_kriz 3 HadGEM2ES rcp2p6 tmin_degC 4.427333e+00 4.298052e+00 1.926148e+00 6.702829e+00 4.635533e+00 2006 2299 294
bily_kriz 3 HadGEM2ES rcp2p6 p_mm 1.040633e+03 1.060025e+03 5.331777e+02 1.705248e+03 1.086752e+03 2006 2299 294
bily_kriz 3 HadGEM2ES rcp2p6 relhum_percent 7.220592e+01 6.955574e+01 6.225784e+01 8.013845e+01 7.240671e+01 2006 2299 294
bily_kriz 3 HadGEM2ES rcp2p6 airpress_hPa 9.488484e+02 9.493447e+02 9.467316e+02 9.529557e+02 9.500760e+02 2006 2299 294
bily_kriz 3 HadGEM2ES rcp2p6 rad_Jcm2day 3.877499e+05 4.497789e+05 3.776577e+05 4.886075e+05 4.264955e+05 2006 2299 294
bily_kriz 3 HadGEM2ES rcp2p6 wind_ms 3.643074e+00 3.444059e+00 2.758286e+00 3.873323e+00 3.226201e+00 2006 2299 294
bily_kriz 3 HadGEM2ES rcp4p5 tmax_degC 1.407407e+01 1.486035e+01 1.233871e+01 1.893476e+01 1.518882e+01 2006 2099 94
bily_kriz 3 HadGEM2ES rcp4p5 tmean_degC 9.252982e+00 1.023809e+01 7.807531e+00 1.343729e+01 1.035594e+01 2006 2099 94
bily_kriz 3 HadGEM2ES rcp4p5 tmin_degC 4.306459e+00 5.660579e+00 2.954550e+00 7.816934e+00 5.447787e+00 2006 2099 94
bily_kriz 3 HadGEM2ES rcp4p5 p_mm 8.424510e+02 1.241633e+03 5.241117e+02 1.705915e+03 1.013117e+03 2006 2099 94
bily_kriz 3 HadGEM2ES rcp4p5 relhum_percent 6.952648e+01 7.277929e+01 6.028664e+01 7.748811e+01 6.991351e+01 2006 2099 94
bily_kriz 3 HadGEM2ES rcp4p5 airpress_hPa 9.498508e+02 9.501007e+02 9.474724e+02 9.530760e+02 9.504404e+02 2006 2099 94
bily_kriz 3 HadGEM2ES rcp4p5 rad_Jcm2day 4.036507e+05 4.304601e+05 3.571120e+05 4.840511e+05 4.283607e+05 2006 2099 94
bily_kriz 3 HadGEM2ES rcp4p5 wind_ms 3.346421e+00 3.008326e+00 2.778189e+00 3.610636e+00 3.228131e+00 2006 2099 94
bily_kriz 3 HadGEM2ES rcp6p0 tmax_degC 1.377976e+01 1.689714e+01 1.133283e+01 1.833320e+01 1.514908e+01 2006 2099 94
bily_kriz 3 HadGEM2ES rcp6p0 tmean_degC 8.184624e+00 1.220952e+01 6.780259e+00 1.316056e+01 1.034288e+01 2006 2099 94
bily_kriz 3 HadGEM2ES rcp6p0 tmin_degC 2.653739e+00 7.376551e+00 2.069489e+00 7.961926e+00 5.469182e+00 2006 2099 94
bily_kriz 3 HadGEM2ES rcp6p0 p_mm 7.380091e+02 1.006461e+03 5.830797e+02 1.562262e+03 1.020103e+03 2006 2099 94
bily_kriz 3 HadGEM2ES rcp6p0 relhum_percent 6.758564e+01 6.895909e+01 6.078655e+01 7.712791e+01 7.003207e+01 2006 2099 94
bily_kriz 3 HadGEM2ES rcp6p0 airpress_hPa 9.503455e+02 9.500506e+02 9.483097e+02 9.532589e+02 9.504964e+02 2006 2099 94
bily_kriz 3 HadGEM2ES rcp6p0 rad_Jcm2day 4.420520e+05 4.397051e+05 3.743635e+05 4.841025e+05 4.277062e+05 2006 2099 94
bily_kriz 3 HadGEM2ES rcp6p0 wind_ms 3.075746e+00 3.038154e+00 2.956440e+00 3.636227e+00 3.250932e+00 2006 2099 94
bily_kriz 3 HadGEM2ES rcp8p5 tmax_degC 1.344648e+01 1.972161e+01 1.228382e+01 2.119298e+01 1.651697e+01 2006 2099 94
bily_kriz 3 HadGEM2ES rcp8p5 tmean_degC 8.656728e+00 1.482784e+01 7.683308e+00 1.584537e+01 1.159772e+01 2006 2099 94
bily_kriz 3 HadGEM2ES rcp8p5 tmin_degC 3.836115e+00 9.819416e+00 2.772772e+00 1.050681e+01 6.635632e+00 2006 2099 94
bily_kriz 3 HadGEM2ES rcp8p5 p_mm 1.044783e+03 1.013541e+03 5.578729e+02 1.504246e+03 9.901365e+02 2006 2099 94
bily_kriz 3 HadGEM2ES rcp8p5 relhum_percent 7.262943e+01 6.610779e+01 5.935513e+01 7.549967e+01 6.808624e+01 2006 2099 94
bily_kriz 3 HadGEM2ES rcp8p5 airpress_hPa 9.504481e+02 9.501788e+02 9.482010e+02 9.530406e+02 9.507368e+02 2006 2099 94
bily_kriz 3 HadGEM2ES rcp8p5 rad_Jcm2day 4.058588e+05 4.509622e+05 3.958738e+05 4.980015e+05 4.389597e+05 2006 2099 94
bily_kriz 3 HadGEM2ES rcp8p5 wind_ms 3.036766e+00 3.152602e+00 2.935808e+00 3.650375e+00 3.271677e+00 2006 2099 94
bily_kriz 3 IPSLCM5ALR historical tmax_degC 1.199800e+01 1.233205e+01 7.929561e+00 1.326267e+01 1.098010e+01 1861 2005 145
bily_kriz 3 IPSLCM5ALR historical tmean_degC 7.181227e+00 7.945040e+00 3.505916e+00 8.572173e+00 6.358021e+00 1861 2005 145
bily_kriz 3 IPSLCM5ALR historical tmin_degC 2.151261e+00 3.452792e+00 -1.236086e+00 3.784220e+00 1.601908e+00 1861 2005 145
bily_kriz 3 IPSLCM5ALR historical p_mm 1.042106e+03 1.267612e+03 7.187445e+02 1.356358e+03 1.026966e+03 1861 2005 145
bily_kriz 3 IPSLCM5ALR historical relhum_percent 7.513935e+01 7.493006e+01 7.023702e+01 8.112070e+01 7.585932e+01 1861 2005 145
bily_kriz 3 IPSLCM5ALR historical airpress_hPa 9.497655e+02 9.472133e+02 9.462076e+02 9.523612e+02 9.495280e+02 1861 2005 145
bily_kriz 3 IPSLCM5ALR historical rad_Jcm2day 4.301708e+05 3.964781e+05 3.530505e+05 4.510969e+05 3.977368e+05 1861 2005 145
bily_kriz 3 IPSLCM5ALR historical wind_ms 2.915605e+00 3.217643e+00 2.915605e+00 3.593020e+00 3.260216e+00 1861 2005 145
bily_kriz 3 IPSLCM5ALR piControl tmax_degC 9.414541e+00 9.659026e+00 7.981816e+00 1.283197e+01 1.043142e+01 1661 2299 639
bily_kriz 3 IPSLCM5ALR piControl tmean_degC 4.799536e+00 4.813293e+00 3.086220e+00 8.020728e+00 5.751357e+00 1661 2299 639
bily_kriz 3 IPSLCM5ALR piControl tmin_degC -2.675180e-02 -3.598362e-01 -2.418813e+00 3.198123e+00 8.944435e-01 1661 2299 639
bily_kriz 3 IPSLCM5ALR piControl p_mm 1.060398e+03 1.002191e+03 7.333915e+02 1.467790e+03 1.055779e+03 1661 2299 639
bily_kriz 3 IPSLCM5ALR piControl relhum_percent 7.907758e+01 7.742399e+01 7.172206e+01 8.153754e+01 7.661966e+01 1661 2299 639
bily_kriz 3 IPSLCM5ALR piControl airpress_hPa 9.499279e+02 9.508284e+02 9.462248e+02 9.531473e+02 9.493137e+02 1661 2299 639
bily_kriz 3 IPSLCM5ALR piControl rad_Jcm2day 4.056774e+05 4.117241e+05 3.646121e+05 4.807791e+05 4.146426e+05 1661 2299 639
bily_kriz 3 IPSLCM5ALR piControl wind_ms 2.958875e+00 3.131536e+00 2.779596e+00 3.537544e+00 3.111507e+00 1661 2299 639
bily_kriz 3 IPSLCM5ALR rcp2p6 tmax_degC 1.271243e+01 1.206834e+01 1.111059e+01 1.606638e+01 1.335131e+01 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp2p6 tmean_degC 8.245935e+00 7.651714e+00 6.436547e+00 1.085479e+01 8.822487e+00 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp2p6 tmin_degC 3.622934e+00 3.006334e+00 1.604008e+00 6.001023e+00 4.221685e+00 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp2p6 p_mm 1.059338e+03 1.157982e+03 7.838197e+02 1.579415e+03 1.097729e+03 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp2p6 relhum_percent 7.348688e+01 7.610261e+01 6.965373e+01 7.806824e+01 7.385492e+01 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp2p6 airpress_hPa 9.502836e+02 9.483053e+02 9.467434e+02 9.540936e+02 9.497823e+02 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp2p6 rad_Jcm2day 4.192525e+05 4.093297e+05 3.755701e+05 4.724685e+05 4.214701e+05 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp2p6 wind_ms 3.107687e+00 3.209825e+00 2.860877e+00 3.502095e+00 3.215132e+00 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp4p5 tmax_degC 1.191375e+01 1.669228e+01 1.113558e+01 1.761033e+01 1.495644e+01 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp4p5 tmean_degC 7.378555e+00 1.222542e+01 6.156196e+00 1.248705e+01 1.031143e+01 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp4p5 tmin_degC 2.894090e+00 7.676787e+00 1.049118e+00 7.676787e+00 5.649276e+00 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp4p5 p_mm 1.010627e+03 1.117893e+03 7.525715e+02 1.454753e+03 1.047160e+03 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp4p5 relhum_percent 7.352016e+01 7.069703e+01 6.809642e+01 7.708260e+01 7.204049e+01 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp4p5 airpress_hPa 9.497573e+02 9.513709e+02 9.475247e+02 9.545087e+02 9.505808e+02 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp4p5 rad_Jcm2day 4.138551e+05 4.213282e+05 3.825715e+05 4.689618e+05 4.269643e+05 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp4p5 wind_ms 3.210255e+00 3.095609e+00 2.753695e+00 3.495707e+00 3.062641e+00 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp6p0 tmax_degC 1.331781e+01 1.619413e+01 1.164372e+01 1.730295e+01 1.396568e+01 2006 2099 94
bily_kriz 3 IPSLCM5ALR rcp6p0 tmean_degC 8.302739e+00 1.159692e+01 7.272854e+00 1.223028e+01 9.406104e+00 2006 2099 94
bily_kriz 3 IPSLCM5ALR rcp6p0 tmin_degC 3.396871e+00 6.990521e+00 2.516000e+00 7.173803e+00 4.783379e+00 2006 2099 94
bily_kriz 3 IPSLCM5ALR rcp6p0 p_mm 9.563375e+02 9.788523e+02 6.843208e+02 1.350419e+03 1.044151e+03 2006 2099 94
bily_kriz 3 IPSLCM5ALR rcp6p0 relhum_percent 7.157938e+01 6.888948e+01 6.765031e+01 7.785576e+01 7.255214e+01 2006 2099 94
bily_kriz 3 IPSLCM5ALR rcp6p0 airpress_hPa 9.524426e+02 9.497988e+02 9.476348e+02 9.537398e+02 9.501633e+02 2006 2099 94
bily_kriz 3 IPSLCM5ALR rcp6p0 rad_Jcm2day 4.427263e+05 4.408261e+05 3.666051e+05 4.862628e+05 4.200933e+05 2006 2099 94
bily_kriz 3 IPSLCM5ALR rcp6p0 wind_ms 2.966485e+00 3.388938e+00 2.836045e+00 3.419347e+00 3.147624e+00 2006 2099 94
bily_kriz 3 IPSLCM5ALR rcp8p5 tmax_degC 1.129110e+01 2.661842e+01 1.129110e+01 2.872586e+01 2.089522e+01 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp8p5 tmean_degC 6.929035e+00 2.188515e+01 6.838658e+00 2.355456e+01 1.609645e+01 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp8p5 tmin_degC 2.401975e+00 1.716133e+01 1.754659e+00 1.870146e+01 1.129307e+01 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp8p5 p_mm 1.192158e+03 9.140424e+02 5.043313e+02 1.394962e+03 9.394859e+02 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp8p5 relhum_percent 7.559265e+01 6.053796e+01 5.734636e+01 7.780171e+01 6.613040e+01 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp8p5 airpress_hPa 9.491727e+02 9.506043e+02 9.480315e+02 9.545785e+02 9.510250e+02 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp8p5 rad_Jcm2day 3.585790e+05 4.184550e+05 3.585790e+05 4.754847e+05 4.354537e+05 2006 2299 294
bily_kriz 3 IPSLCM5ALR rcp8p5 wind_ms 3.369205e+00 3.138238e+00 2.565214e+00 3.382828e+00 3.019524e+00 2006 2299 294
bily_kriz 3 MIROC5 historical tmax_degC 1.209526e+01 1.288251e+01 8.793722e+00 1.418052e+01 1.153099e+01 1861 2005 145
bily_kriz 3 MIROC5 historical tmean_degC 7.028521e+00 7.674554e+00 4.236689e+00 9.000305e+00 6.838927e+00 1861 2005 145
bily_kriz 3 MIROC5 historical tmin_degC 1.912003e+00 2.383862e+00 -7.711300e-01 3.886889e+00 1.974051e+00 1861 2005 145
bily_kriz 3 MIROC5 historical p_mm 9.499720e+02 9.374091e+02 6.634450e+02 1.334588e+03 9.666290e+02 1861 2005 145
bily_kriz 3 MIROC5 historical relhum_percent 7.073858e+01 7.427323e+01 6.771783e+01 7.820979e+01 7.372307e+01 1861 2005 145
bily_kriz 3 MIROC5 historical airpress_hPa 9.501901e+02 9.498800e+02 9.481898e+02 9.520636e+02 9.501136e+02 1861 2005 145
bily_kriz 3 MIROC5 historical rad_Jcm2day 4.319353e+05 4.356081e+05 3.327256e+05 4.578575e+05 3.980370e+05 1861 2005 145
bily_kriz 3 MIROC5 historical wind_ms 3.247369e+00 2.892433e+00 2.892433e+00 3.593764e+00 3.298318e+00 1861 2005 145
bily_kriz 3 MIROC5 piControl tmax_degC 1.224752e+01 1.394277e+01 1.055379e+01 1.565283e+01 1.297621e+01 1661 2299 639
bily_kriz 3 MIROC5 piControl tmean_degC 7.581752e+00 8.707366e+00 5.260067e+00 1.002929e+01 7.789709e+00 1661 2299 639
bily_kriz 3 MIROC5 piControl tmin_degC 2.671488e+00 3.474802e+00 -1.236649e-01 4.573351e+00 2.546084e+00 1661 2299 639
bily_kriz 3 MIROC5 piControl p_mm 1.100524e+03 9.223519e+02 5.981956e+02 1.450320e+03 1.000430e+03 1661 2299 639
bily_kriz 3 MIROC5 piControl relhum_percent 7.169501e+01 7.160043e+01 6.573467e+01 7.643777e+01 7.112007e+01 1661 2299 639
bily_kriz 3 MIROC5 piControl airpress_hPa 9.490148e+02 9.503783e+02 9.477455e+02 9.520115e+02 9.497192e+02 1661 2299 639
bily_kriz 3 MIROC5 piControl rad_Jcm2day 4.340896e+05 4.622626e+05 4.122271e+05 4.968523e+05 4.536182e+05 1661 2299 639
bily_kriz 3 MIROC5 piControl wind_ms 3.165871e+00 3.088682e+00 2.779904e+00 3.421336e+00 3.090434e+00 1661 2299 639
bily_kriz 3 MIROC5 rcp2p6 tmax_degC 1.267762e+01 1.464753e+01 1.130763e+01 1.766991e+01 1.438910e+01 2006 2299 294
bily_kriz 3 MIROC5 rcp2p6 tmean_degC 7.869374e+00 9.637533e+00 6.665525e+00 1.172847e+01 9.211597e+00 2006 2299 294
bily_kriz 3 MIROC5 rcp2p6 tmin_degC 3.107871e+00 4.501144e+00 1.495701e+00 5.931406e+00 3.954928e+00 2006 2299 294
bily_kriz 3 MIROC5 rcp2p6 p_mm 9.649997e+02 1.232772e+03 6.138350e+02 1.505568e+03 1.032402e+03 2006 2299 294
bily_kriz 3 MIROC5 rcp2p6 relhum_percent 7.326803e+01 6.998136e+01 6.496672e+01 7.411541e+01 6.966650e+01 2006 2299 294
bily_kriz 3 MIROC5 rcp2p6 airpress_hPa 9.506265e+02 9.496163e+02 9.486850e+02 9.527078e+02 9.506783e+02 2006 2299 294
bily_kriz 3 MIROC5 rcp2p6 rad_Jcm2day 4.015045e+05 4.496680e+05 3.932749e+05 4.920393e+05 4.595528e+05 2006 2299 294
bily_kriz 3 MIROC5 rcp2p6 wind_ms 3.050639e+00 3.514055e+00 2.933608e+00 3.758578e+00 3.365197e+00 2006 2299 294
bily_kriz 3 MIROC5 rcp4p5 tmax_degC 1.300568e+01 1.510026e+01 1.151963e+01 1.755379e+01 1.475842e+01 2006 2099 94
bily_kriz 3 MIROC5 rcp4p5 tmean_degC 8.434508e+00 9.775845e+00 6.952403e+00 1.184436e+01 9.597190e+00 2006 2099 94
bily_kriz 3 MIROC5 rcp4p5 tmin_degC 3.869308e+00 4.562683e+00 2.184686e+00 6.364980e+00 4.439743e+00 2006 2099 94
bily_kriz 3 MIROC5 rcp4p5 p_mm 1.249482e+03 9.238703e+02 6.806175e+02 1.525409e+03 1.072190e+03 2006 2099 94
bily_kriz 3 MIROC5 rcp4p5 relhum_percent 7.511250e+01 6.839224e+01 6.537780e+01 7.608938e+01 7.074752e+01 2006 2099 94
bily_kriz 3 MIROC5 rcp4p5 airpress_hPa 9.495245e+02 9.520004e+02 9.486400e+02 9.531066e+02 9.507222e+02 2006 2099 94
bily_kriz 3 MIROC5 rcp4p5 rad_Jcm2day 3.864426e+05 4.578805e+05 3.864426e+05 4.767179e+05 4.429179e+05 2006 2099 94
bily_kriz 3 MIROC5 rcp4p5 wind_ms 3.206825e+00 3.053288e+00 2.738664e+00 3.424915e+00 3.084660e+00 2006 2099 94
bily_kriz 3 MIROC5 rcp6p0 tmax_degC 1.284927e+01 1.712913e+01 1.117872e+01 1.765651e+01 1.454981e+01 2006 2099 94
bily_kriz 3 MIROC5 rcp6p0 tmean_degC 8.199558e+00 1.155381e+01 6.376874e+00 1.202585e+01 9.412531e+00 2006 2099 94
bily_kriz 3 MIROC5 rcp6p0 tmin_degC 3.445637e+00 5.986129e+00 1.129950e+00 6.514371e+00 4.238116e+00 2006 2099 94
bily_kriz 3 MIROC5 rcp6p0 p_mm 1.062149e+03 9.548170e+02 6.743912e+02 1.767767e+03 1.069415e+03 2006 2099 94
bily_kriz 3 MIROC5 rcp6p0 relhum_percent 7.314449e+01 6.843324e+01 6.497104e+01 7.580435e+01 7.059043e+01 2006 2099 94
bily_kriz 3 MIROC5 rcp6p0 airpress_hPa 9.500106e+02 9.510659e+02 9.484295e+02 9.536767e+02 9.505556e+02 2006 2099 94
bily_kriz 3 MIROC5 rcp6p0 rad_Jcm2day 4.104626e+05 4.678674e+05 4.053620e+05 4.883105e+05 4.456123e+05 2006 2099 94
bily_kriz 3 MIROC5 rcp6p0 wind_ms 3.203270e+00 3.285214e+00 2.915114e+00 3.476665e+00 3.168073e+00 2006 2099 94
bily_kriz 3 MIROC5 rcp8p5 tmax_degC 1.370752e+01 2.039066e+01 1.143856e+01 2.039066e+01 1.582312e+01 2006 2099 94
bily_kriz 3 MIROC5 rcp8p5 tmean_degC 8.660868e+00 1.438092e+01 6.973280e+00 1.438092e+01 1.056073e+01 2006 2099 94
bily_kriz 3 MIROC5 rcp8p5 tmin_degC 3.541571e+00 8.389683e+00 2.456856e+00 8.751239e+00 5.286968e+00 2006 2099 94
bily_kriz 3 MIROC5 rcp8p5 p_mm 1.066102e+03 7.791861e+02 7.472848e+02 1.588807e+03 1.067657e+03 2006 2099 94
bily_kriz 3 MIROC5 rcp8p5 relhum_percent 7.126742e+01 6.665186e+01 6.485983e+01 7.568164e+01 6.955227e+01 2006 2099 94
bily_kriz 3 MIROC5 rcp8p5 airpress_hPa 9.500284e+02 9.527342e+02 9.484535e+02 9.530866e+02 9.510911e+02 2006 2099 94
bily_kriz 3 MIROC5 rcp8p5 rad_Jcm2day 4.216762e+05 4.793708e+05 3.965346e+05 4.900858e+05 4.542928e+05 2006 2099 94
bily_kriz 3 MIROC5 rcp8p5 wind_ms 3.052468e+00 3.074464e+00 2.911949e+00 3.389135e+00 3.135116e+00 2006 2099 94

This option is also availabe for TREE and STAND datasets.

site site_id species species_id variable first last min max mean year_first year_last obs
solling_beech 20 Fagus sylvatica fasy size_m2 10000.00000 10000.00000 10000.00000 10000.00000 10000.00000 1967 2014 16
solling_beech 20 Fagus sylvatica fasy density_treeha 245.00000 130.00000 130.00000 245.00000 214.18750 1967 2014 16
solling_beech 20 Fagus sylvatica fasy dbhDQ_cm 37.44884 49.99646 37.44884 49.99646 42.59802 1967 2014 16
solling_beech 20 Fagus sylvatica fasy dbhArith_cm 36.48286 48.84923 36.48286 48.84923 41.52105 1967 2014 16
solling_beech 20 Fagus sylvatica fasy dbhBA_cm 40.19266 53.39641 40.19266 53.39641 45.67458 1967 2014 16
solling_beech 20 Fagus sylvatica fasy heightArith_m 24.63196 30.22754 24.63196 30.22754 27.48854 1967 2014 16
solling_beech 20 Fagus sylvatica fasy heightBA_m 25.44974 30.77684 25.44974 30.77684 28.17222 1967 2014 16
solling_beech 20 Fagus sylvatica fasy ba_m2ha 26.98564 25.52182 25.52182 35.40038 29.88959 1967 2014 16

Please note that the TREE overview table is first summarized by years, pulling all trees together as a stand. Thus, you might find coincidences between the STAND and the TREE overviews.

site site_id species species_id variable first last min max mean year_first year_last obs
solling_beech 20 Fagus sylvatica fasy age 120.00000 168.00000 120.00000 168.00000 137.37500 1967 2014 16
solling_beech 20 Fagus sylvatica fasy dbhArith_cm 36.48286 48.84923 36.48286 48.84923 41.52105 1967 2014 16
solling_beech 20 Fagus sylvatica fasy dbhBA_cm 40.19266 53.39641 40.19266 53.39641 45.67458 1967 2014 16
solling_beech 20 Fagus sylvatica fasy dbhDQ_cm 37.44884 49.99646 37.44884 49.99646 42.59802 1967 2014 16
solling_beech 20 Fagus sylvatica fasy heightArith_m 24.63196 30.22754 24.63196 30.22754 27.48854 1967 2014 16
solling_beech 20 Fagus sylvatica fasy heightBA_m 25.44974 30.77684 25.44974 30.77684 28.17222 1967 2014 16
solling_beech 20 Fagus sylvatica fasy ba_m2ha 26.98564 25.52182 25.52182 35.40038 29.88959 1967 2014 16
solling_beech 20 Fagus sylvatica fasy density_treeha 245.00000 130.00000 130.00000 245.00000 214.18750 1967 2014 16
solling_beech 20 Fagus sylvatica fasy foliageBiomass_kgha 2631.00000 2509.00000 2509.00000 3035.00000 2734.60000 1996 2014 5

Data summaries of the available data

The other value of mode is data. It sets the behaviour of summarizeData to produce result summaries.

TREE

site site_id year species species_id size_m2 density_treeha dbhDQ_cm dbhArith_cm dbhBA_cm heightArith_m heightBA_m ba_m2ha
bily_kriz 3 1997 Picea abies piab 2500 2408 7.391285 7.112625 8.160837 5.631395 6.263354 10.33204
bily_kriz 3 1998 Picea abies piab 2500 2396 8.106565 7.834391 8.863961 6.339399 6.957685 12.36660
bily_kriz 3 1999 Picea abies piab 2500 2392 8.786736 8.504013 9.574108 6.880936 7.499656 14.50461
bily_kriz 3 2000 Picea abies piab 2500 2388 9.415671 9.115075 10.253861 7.497990 8.129110 16.62749
bily_kriz 3 2001 Picea abies piab 2500 1848 10.506718 10.232468 11.265544 8.426840 8.988191 16.02234
bily_kriz 3 2002 Picea abies piab 2500 1836 11.264091 10.981264 12.048025 9.134423 9.692305 18.29594
bily_kriz 3 2003 Picea abies piab 2500 1836 11.955024 11.661656 12.766838 9.801089 10.367013 20.60931
bily_kriz 3 2004 Picea abies piab 2500 1668 12.869809 12.603837 13.621369 10.495923 10.976840 21.69852
bily_kriz 3 2005 Picea abies piab 2500 1664 13.581622 13.299760 14.377679 11.198077 11.690715 24.10718
bily_kriz 3 2006 Picea abies piab 2500 1580 14.278164 13.988861 15.087051 11.515190 12.049585 25.29832
bily_kriz 3 2007 Picea abies piab 2500 1508 14.851371 14.574801 15.631127 11.997878 12.487173 26.12307
bily_kriz 3 2008 Picea abies piab 2500 1500 15.585562 15.301067 16.384768 12.359733 12.868074 28.61713
bily_kriz 3 2009 Picea abies piab 2500 1492 16.186739 15.885791 17.033125 12.892992 13.426940 30.70276
bily_kriz 3 2010 Picea abies piab 2500 1488 16.688517 16.372850 17.570925 13.436828 13.994286 32.54830
bily_kriz 3 2011 Picea abies piab 2500 1488 17.270525 16.935753 18.203030 14.131183 14.721789 34.85812
bily_kriz 3 2012 Picea abies piab 2500 1268 18.269222 17.926183 19.217967 13.517350 14.435891 33.23910
bily_kriz 3 2013 Picea abies piab 2500 1256 18.601908 18.249363 19.574279 13.769745 14.699054 34.13458
bily_kriz 3 2014 Picea abies piab 2500 1256 19.090841 18.723248 20.104355 14.059873 15.011682 35.95255
bily_kriz 3 2015 Picea abies piab 2500 1252 19.387417 18.991693 20.465280 14.233227 15.263984 36.96018

CLIMATE

CLIMATE_LOCAL
site site_id year tmax_degC tmean_degC tmin_degC p_mm relhum_percent airpress_hPa rad_Jcm2day wind_ms
bily_kriz 3 2000 13.530145 8.536865 4.102271 1490.324 79.93809 912.7901 370604.5 2.350770
bily_kriz 3 2001 12.416737 7.674437 3.716715 1567.342 82.74661 912.3483 341850.8 2.474911
bily_kriz 3 2002 12.978551 8.296474 4.418110 1378.978 86.42986 913.0215 375278.4 2.198978
bily_kriz 3 2003 11.091126 6.161538 2.349707 1004.007 72.76064 914.4979 405381.0 1.980277
bily_kriz 3 2004 12.281959 7.683303 3.645454 1651.989 88.84459 912.8626 367439.9 2.254436
bily_kriz 3 2005 9.310364 5.930202 3.031704 1505.717 80.06642 913.9712 387422.4 1.945468
bily_kriz 3 2006 10.399436 6.877683 3.871940 1394.874 81.55814 914.3021 394615.9 2.022121
bily_kriz 3 2007 10.967189 7.566738 4.421340 1750.245 81.74537 911.7648 379212.4 2.066813
bily_kriz 3 2008 10.537101 7.484678 4.652052 1167.563 83.80125 913.1897 387168.4 2.404200
CLIMATE_ISIMIP

For several forcing datasets and/or forcing conditions

forcingDataset forcingCondition year tmax_degC tmean_degC tmin_degC p_mm relhum_percent airpress_hPa rad_Jcm2day wind_ms
GFDLESM2M historical 1861-2005 11.54169 6.930977 2.2231966 968.3358 74.28709 949.8743 391145.3 3.217614
GFDLESM2M piControl 1661-2099 11.53763 6.811351 2.0799773 1040.6370 77.08760 949.7105 391288.6 2.560670
GFDLESM2M rcp2p6 2006-2099 12.89789 8.310183 3.5774033 1016.4696 73.81166 950.7912 397678.2 3.444829
GFDLESM2M rcp4p5 2006-2099 13.41545 8.748496 3.9531990 989.9021 73.18045 951.1007 401238.3 3.384756
GFDLESM2M rcp6p0 2006-2099 13.26510 8.651463 3.9025928 989.9244 73.30648 951.0994 397579.1 3.415027
GFDLESM2M rcp8p5 2006-2099 14.10468 9.202764 4.2316025 1000.7700 73.27579 951.3680 397358.8 3.196491
HadGEM2ES historical 1861-2005 11.53644 6.750251 1.8246069 949.0047 73.46432 950.2473 401482.0 3.246359
HadGEM2ES piControl 1661-2299 12.34029 7.400779 2.3149606 969.5199 72.05009 950.0176 428085.6 3.231371
HadGEM2ES rcp2p6 2006-2299 14.17385 9.440236 4.6355333 1086.7517 72.40671 950.0760 426495.5 3.226201
HadGEM2ES rcp4p5 2006-2099 15.18882 10.355945 5.4477872 1013.1172 69.91351 950.4404 428360.7 3.228131
HadGEM2ES rcp6p0 2006-2099 15.14908 10.342883 5.4691821 1020.1033 70.03207 950.4964 427706.2 3.250932
HadGEM2ES rcp8p5 2006-2099 16.51697 11.597719 6.6356322 990.1365 68.08624 950.7368 438959.7 3.271677
IPSLCM5ALR historical 1861-2005 10.98010 6.358021 1.6019083 1026.9663 75.85932 949.5280 397736.8 3.260216
IPSLCM5ALR piControl 1661-2299 10.43142 5.751357 0.8944435 1055.7788 76.61966 949.3137 414642.6 3.111507
IPSLCM5ALR rcp2p6 2006-2299 13.35131 8.822487 4.2216854 1097.7286 73.85492 949.7823 421470.1 3.215132
IPSLCM5ALR rcp4p5 2006-2299 14.95644 10.311434 5.6492760 1047.1603 72.04049 950.5808 426964.3 3.062641
IPSLCM5ALR rcp6p0 2006-2099 13.96568 9.406104 4.7833788 1044.1505 72.55214 950.1633 420093.3 3.147624
IPSLCM5ALR rcp8p5 2006-2299 20.89522 16.096453 11.2930703 939.4859 66.13040 951.0250 435453.7 3.019524
MIROC5 historical 1861-2005 11.53099 6.838927 1.9740510 966.6290 73.72307 950.1136 398037.0 3.298318
MIROC5 piControl 1661-2299 12.97621 7.789709 2.5460838 1000.4297 71.12007 949.7192 453618.2 3.090434
MIROC5 rcp2p6 2006-2299 14.38910 9.211597 3.9549275 1032.4024 69.66650 950.6783 459552.8 3.365197
MIROC5 rcp4p5 2006-2099 14.75842 9.597190 4.4397434 1072.1900 70.74752 950.7222 442917.9 3.084660
MIROC5 rcp6p0 2006-2099 14.54981 9.412531 4.2381155 1069.4153 70.59043 950.5556 445612.3 3.168073
MIROC5 rcp8p5 2006-2099 15.82312 10.560728 5.2869677 1067.6575 69.55227 951.0911 454292.8 3.135116

For only one forcing dataset and forcing conditions

site site_id year tmax_degC tmean_degC tmin_degC p_mm relhum_percent airpress_hPa rad_Jcm2day wind_ms
bily_kriz 3 1861 11.998002 7.181227 2.1512612 1042.1062 75.13935 949.7655 430170.8 2.915605
bily_kriz 3 1862 8.601109 4.253349 -0.2935495 992.2576 77.44364 948.6095 380275.5 3.273053
bily_kriz 3 1863 10.811001 6.334792 1.6841171 1075.9658 77.80697 948.7587 396601.6 3.161322
bily_kriz 3 1864 9.958074 4.968835 -0.2399347 969.7612 76.24269 949.5919 438632.8 3.278511
bily_kriz 3 1865 11.024017 6.382603 1.6215635 1017.4756 75.40079 948.5346 422913.8 2.987183
bily_kriz 3 1866 12.541975 7.771579 2.9999504 1015.3766 73.85415 950.6490 421603.8 3.134281

FLUX

site site_id year neeCutRef_tCha1 neeVutRef_tCha1 neeCutRefJointunc_tCha1 neeVutRefJointunc_tCha1 recoNtVutRef_tCha1 recoNtVutSe_tCha1 recoNtCutRef_tCha1 recoNtCutSe_tCha1 gppNtVutRef_tCha1 gppNtVutSe_tCha1 gppNtCutRef_tCha1 gppNtCutSe_tCha1 recoDtVutRef_tCha1 recoDtVutSe_tCha1 recoDtCutRef_tCha1 recoDtCutSe_tCha1 gppDtVutRef_tCha1 gppDtVutSe_tCha1 gppDtCutRef_tCha1 gppDtCutSe_tCha1
bily_kriz 3 2000 -38.78573 -39.59809 15.209695 15.86517 97.83216 2.408624 102.09309 2.440183 138.66666 3.967526 145.19560 4.126893 58.23775 7.234624 67.81385 7.632900 107.9271 4.083021 110.7110 4.281572
bily_kriz 3 2001 -32.77164 -36.29736 11.523480 11.77295 51.97413 2.064628 54.90414 2.072944 86.48057 3.049352 99.01904 3.346192 77.40778 3.178191 78.30948 4.676769 116.1664 2.044694 112.0838 2.611838
bily_kriz 3 2002 -36.58319 -37.97092 9.151159 11.09704 63.96572 1.678422 59.06654 2.507639 103.28778 2.665789 98.69803 3.657584 73.20840 3.276043 54.78220 3.948784 114.9007 2.011733 121.0953 2.635683
bily_kriz 3 2003 -91.17122 -90.71734 11.427876 12.15067 113.99077 2.434624 113.01510 2.925302 205.16419 4.039363 203.70148 5.157969 85.56300 3.735950 93.86853 5.552283 177.0804 2.699202 186.4835 4.224106
bily_kriz 3 2004 -84.57856 -83.56907 27.092536 39.38024 63.33830 1.440231 63.31870 1.718276 146.77583 3.967510 150.77614 5.129495 103.02871 4.847279 93.67065 5.601932 174.2867 4.021578 182.9802 4.963656
bily_kriz 3 2005 -79.08237 -82.49708 8.661794 12.04517 52.72831 2.710158 59.54222 2.576154 134.15438 5.274783 142.76343 5.185471 60.53836 6.489167 68.58801 8.837533 182.7498 5.116223 198.8996 5.399609
bily_kriz 3 2006 -64.37540 -65.07293 24.926481 27.89668 78.65130 2.017064 79.05678 1.689278 144.79195 4.331742 146.42456 3.842385 80.37568 5.130079 83.52022 4.773277 191.4361 3.560452 187.8914 3.345761
bily_kriz 3 2007 -75.93613 -74.22389 31.515550 27.52587 110.94775 3.409521 95.03352 3.798527 184.80026 4.826859 181.54589 5.190658 94.69553 7.085845 69.07559 7.696311 193.1778 3.219596 186.9977 4.493286
bily_kriz 3 2008 -83.49085 -82.75882 36.022763 29.02647 100.60264 1.775322 93.38333 1.995026 181.80827 3.722435 181.59439 3.912224 104.22396 8.265871 102.95398 6.246577 202.5231 4.299510 204.7656 3.643597

The getData function

The getData allows to download data from the PROFOUND database. The returned object will be a data frame or a list of data frames, depending on the data that has been requested.

SITES

To obtain the site information use getData and download the table SITES.

##  [1] "site_id"                   "site"                     
##  [3] "lat"                       "lon"                      
##  [5] "epsg"                      "country"                  
##  [7] "aspect_deg"                "elevation_masl"           
##  [9] "slope_percent"             "natVegetation_code1"      
## [11] "natVegetation_code2"       "natVegetation_description"

Optionally, you can specify a site.

site_id site lat lon epsg country aspect_deg elevation_masl slope_percent natVegetation_code1 natVegetation_code2 natVegetation_description
21 soro 55.48584 11.64462 4326 Denmark NA 40 0 F.5.2.1 F108 South Scandinavian-north Central European Galium odoratum- and Milium effusum-beech forests (Fagus sylvatica), partly with Fraxinus excelsior, partly with Stellaria nemorum subsp. Montana, Luzula sylvatica, Polygonatum verticillatum, Ranunculus lanuginosus, Cardamine bulbifera

A text description can be obtained from SITEDESCRIPTION

## [1] "The ICOS site Sorø (DK-Sor in the FLUXNET and ICOS data bases) is located in Denmark at an elevation of 40 m.a.s.l.. The climate is warm temperate and fully humid with a mean annual temperature of 9°C and annual precipitation sum of 774 mm during the period 1996-2010. The soil has been classified as an Alfisols/Molisols. Potential natural vegetation is deciduous broad-leaved forest dominated by Fagus sylvatica. Other species occurring in the area are Fraxinus excelsior, Larix decidua, Picea abies, Quercus spp., Acer spp. However, the region is mostly used as cropland. Data on tree DBH are reconstructed from tree ring measurement (Babst et al. 2014) and historical management information for the time period from 1944 to 2010. The mean DBH of this Fagus sylvatica stand was 29 cm in the year 2010. More information about the site can be found in Ladekarl (2001), Pilegaard et al. (2003, 2011), and Wu et al. (2013)."

DATASETS

To download any dataset, you have to provide a dataset name and a site

collapse

This option specifies whether the returned data should be a data frame or a list of data frames. This argument is relevant when downloading data from SOIL or ISIMIP datasets.

For ISIMIP datasets, by setting collapse to FALSE you will obtain a list with data frames named after the forcing datasets and conditions. Otherwise, the data will return in a unique data frame.

## [1] "GSWP3"     "PRINCETON" "WATCH"     "WFDEI"
##  [1] "record_id"      "site"           "site_id"        "date"          
##  [5] "forcingDataset" "day"            "mo"             "year"          
##  [9] "tmax_degC"      "tmean_degC"     "tmin_degC"      "p_mm"          
## [13] "relhum_percent" "airpress_hPa"   "rad_Jcm2day"    "wind_ms"

We recommend to unset collapse when downloading SOIL data because in many cases SOIL is a collection of tables.

## List of 5
##  $ :'data.frame':    1 obs. of  8 variables:
##  $ :'data.frame':    5 obs. of  16 variables:
##  $ :'data.frame':    3 obs. of  12 variables:
##  $ :'data.frame':    1 obs. of  14 variables:
##  $ :'data.frame':    5 obs. of  12 variables:
## [1] "record_id"     "site"          "site_id"       "table_id"     
## [5] "layer_id"      "upperDepth_cm" "lowerDepth_cm" "type_fao"

forcingDataset, forcingCondition

With the function arguments forcingDataset and forcingCondition it is possible to select specific forcing datasets and conditions, respectively. These arguments are relevant for ISIMIP datasets.

record_id site site_id date forcingDataset forcingCondition day mo year tmax_degC tmean_degC tmin_degC p_mm relhum_percent airpress_hPa rad_Jcm2day wind_ms
2194374 soro 21 2006-01-01 GFDLESM2M rcp2p6 1 1 2006 4.795770 3.271880 -0.661963 3.5799900 83.6211 984.678 213.688 8.91397
2194375 soro 21 2006-01-02 GFDLESM2M rcp2p6 2 1 2006 2.531210 -1.260170 -3.237280 0.0000000 80.6147 1000.790 170.412 6.49315
2194376 soro 21 2006-01-03 GFDLESM2M rcp2p6 3 1 2006 -1.635780 -2.116130 -2.662660 0.0000000 71.5942 1001.730 253.197 2.98789
2194377 soro 21 2006-01-04 GFDLESM2M rcp2p6 4 1 2006 0.781488 -0.917487 -2.497320 0.0000000 73.3637 1001.090 239.468 4.16723
2194378 soro 21 2006-01-05 GFDLESM2M rcp2p6 5 1 2006 0.856897 0.441339 -0.221411 0.0725665 83.6679 998.288 169.763 6.15931
2194379 soro 21 2006-01-06 GFDLESM2M rcp2p6 6 1 2006 2.576410 0.935022 0.253656 0.5808390 86.0278 1006.040 148.146 6.08605

The previous getData call is actually equivalent to

record_id site site_id date forcingDataset forcingCondition day mo year tmax_degC tmean_degC tmin_degC p_mm relhum_percent airpress_hPa rad_Jcm2day wind_ms
2194374 soro 21 2006-01-01 GFDLESM2M rcp2p6 1 1 2006 4.795770 3.271880 -0.661963 3.5799900 83.6211 984.678 213.688 8.91397
2194375 soro 21 2006-01-02 GFDLESM2M rcp2p6 2 1 2006 2.531210 -1.260170 -3.237280 0.0000000 80.6147 1000.790 170.412 6.49315
2194376 soro 21 2006-01-03 GFDLESM2M rcp2p6 3 1 2006 -1.635780 -2.116130 -2.662660 0.0000000 71.5942 1001.730 253.197 2.98789
2194377 soro 21 2006-01-04 GFDLESM2M rcp2p6 4 1 2006 0.781488 -0.917487 -2.497320 0.0000000 73.3637 1001.090 239.468 4.16723
2194378 soro 21 2006-01-05 GFDLESM2M rcp2p6 5 1 2006 0.856897 0.441339 -0.221411 0.0725665 83.6679 998.288 169.763 6.15931
2194379 soro 21 2006-01-06 GFDLESM2M rcp2p6 6 1 2006 2.576410 0.935022 0.253656 0.5808390 86.0278 1006.040 148.146 6.08605

variables

For any dataset it is possible to define the variable or variables to be downloaded

record_id site site_id date year day mo forcingDataset forcingCondition p_mm
2194374 soro 21 2006-01-01 2006 1 1 GFDLESM2M rcp2p6 3.5799900
2194375 soro 21 2006-01-02 2006 2 1 GFDLESM2M rcp2p6 0.0000000
2194376 soro 21 2006-01-03 2006 3 1 GFDLESM2M rcp2p6 0.0000000
2194377 soro 21 2006-01-04 2006 4 1 GFDLESM2M rcp2p6 0.0000000
2194378 soro 21 2006-01-05 2006 5 1 GFDLESM2M rcp2p6 0.0725665
2194379 soro 21 2006-01-06 2006 6 1 GFDLESM2M rcp2p6 0.5808390

species

When downloading TREE or STAND data, you can select species with the argument species. It takes both full species name or the species id.

period

For time series data it is possible to subset the data to a specific period.

## [1] "2006-01-01" "2006-12-31"

quality

Some datasets, such as CLIMATE_LOCAL or FLUX, have quality flags to indicate how the data was obtained. Please be aware of the values of quality flags before using this option. The definition of the flags is available in the metadata.

When passing a quality flag value, you should also define how the threshold should be applied. Values out of the selected range will be dropped from the data based on your query.

The plotData function

The plotData function performs a query to the database, downloads the data, applies the desired options (time period, quality flag, etc.) and shapes the final data into a time series for plotting. It requires a dataset name and a site. Check the help files to see what datasets are supported.

Normal plotting

A simple plot call looks like

Or for TREE data

Note that the argument automaticPanels defines whether the plot in a panel.

Additional options

Besides, plotData supports the same options as getData.

aggregate

You can also aggregate data by defining aggregate and FUN. The data can be aggregated by day, month, year or date, and any statistic is supported, e.g. median.

The queryDB function: parsing your own queries

The package functions are designed to ease the access to the PROFOUND database by providing an R interface. However, if you feel confident with SQL syntax’s, you could perform more advanced queries. The function queryDB allows to perform self-defined queries.

A basic query is SELECT FROM TABLE*, which will return all variables in the table.

overview <- queryDB("SELECT * FROM OVERVIEW")
tree <- queryDB("SELECT * FROM TREE")

More advanced queries include defining variables and conditions as the example below

myQuery <- queryDB("SELECT date, tmax_degC FROM CLIMATE_LOCAL 
                   WHERE tmax_degC > 20 AND site == 'hyytiala' AND year == 2010")

Besides, the database contains several views with ready-made queries (check browseData(“DATASETS”)), so that the two statements below are equivalent

myQuery <- queryDB("SELECT date, tmax_degC FROM CLIMATE_LOCAL 
                   WHERE site == 'hyytiala'")
myQuery <- queryDB("SELECT date, tmax_degC FROM CLIMATE_LOCAL_12")

This also works with tree species

myQuery <- queryDB("SELECT * FROM TREE 
                   WHERE species == 'Picea abies'")
myQuery <- queryDB("SELECT * FROM TREE_piab")

Hint: Check the last section for further information about SQL syntax’s.

The reportDB function

This function makes possible to create reates a site-by-site report of all avalaible data in the PROFOUND database. The summary is created with a rmarkdown document, which is rendered and saved as a html document. The report provdes an exhaustive description and visualization of the PROFOUND database.

The function requires a path where to save the html document. If no path is specified, the working directory will be used as output directory.

reportDB(outDir = tempdir())

Please note that creating the report it might take several minutes.

Using the databse via sql

To access the database you can use an SQLite database explorer such as SQLiteStudio. Such software allows to visualize and download data through an interface, as well as writing SQL statements. Further information on SQLite characteristics can be found on the SQLite website. Besides, there are plenty of resources about using SQL like this one