Dataset Restricted Access

SAPFLUXNET: A global database of sap flow measurements

Rafael Poyatos; Víctor Granda; Víctor Flo; Roberto Molowny-Horas; Kathy Steppe; Maurizio Mencuccini; Jordi Martínez-Vilalta

Data collector(s)
Adams, Mark; Adorján, Balázs; Aguadé, David; Aidar, Marcos P.M.; Allen, Scott; Alvarado, Susana; Anderson-Teixeira, Kristina; Aparecido, Luiza Maria; Arain, Altaf; Aranda, Ismael; Asbjornsen, Heidi; Baxter, Robert; Beamesderfer, Eric; Berry, Carter; Berveiller, Daniel; Blakely, Bethany; Boegelein, Rebekka; Boggs, Johnny; Bohrer, Gil; Bolstad, Paul; Bonal, Damien; Bracho, Rosvel; Brito, Patricia; Brodeur, Jason; Casanoves, Fernando; Chave, Jérôme; Cisneros, Cesar; Clark, Kenneth; Cremonese, Edoardo; Dang, Hongzhong; David, Jorge; David, Teresa; Delpierre, Nicolas; Desai, Ankur; Do, Frederic C.; Dohnal, Michal; Domec , Jean-Christophe; Dzikiti, Sebinasi; Edgar, Colin; Elbers, Jan; Eller, Cleiton; Ellsworth, David; El-Madany, Tarek S.; Euskirchen, Eugénie; Ewers, Brent; Fonti, Patrick; Forner, Alicia; Forrester, David; Freitas, Helber; Galvagno, Marta; Garcia-Tejera, Omar; Ghimire, Chandra Prasad; Gimeno, Teresa; Grace, John; Granier, André; Griebel, Anne; Guangyu, Yan; Gush, Mark; Hanson, Paul; Hasselquist, Niles; Heinrich, Ingo; Hernandez-Santana, Virginia; Herrmann, Valentine; Hölttä, Teemu; Holwerda, Friso; hui, Chen; Irvine, James; Isarangkool na Ayutthaya, Supat; Jarvis, Paul; Jochheim, Hubert; Joly, Carlos A.; Kaplick, Julia; Kim, Hyun Seok; Klemedtsson, Leif; Kropp, Heather; Lagergren, Fredrik; Lane, Patrick; Lang, Petra; Lapenas, Andrei; Lechuga, Víctor; Lee, Minsu; Leuschner, Christoph; Limousin, Jean-Marc; Linares, Juan Carlos; Linderson, Maj-Lena; Lindroth, Anders; Llorens, Pilar; Lopez-Bernal, Alvaro; Loranty, Michael; Lüttschwager, Dietmar; Macinnis-Ng, Cate; Maréchaux, Isabelle; Martin, Timothy; Martínez-Vilalta, Jordi; Matheny, Ashley; McDowell, Nate; McMahon, Sean; Meir, Patrick; Mencuccini, Maurizio; Mészáros, Ilona; Migliavacca, Mirco; Mitchell, Patrick; Mölder, Meelis; Montagnani, Leonardo; Moore, Georgianne; Nakada, Ryogo; Niu, Furong; Nolan, Rachael; Norby, Rich; Novick, Kimberly; Oberhuber, Walter; Obojes, Nikolaus; Oishi, A. Christopher; Oliveira, Rafael; Oren, Ram; Ourcival, Jean-Marc; Paljakka, Teemu; Perez-Priego, Oscar; Peri, Pablo; Peters, Richard L.; Pfautsch, Seabstian; Pockman, William; Poyatos, Rafael; Preisler, Yakir; Rascher, Katherine; Robinson, George; Rocha, Humberto; Rocheteau, Alain; Röll, Alexander; Rosado, Bruno; Rowland, Lucy; Rubtsov, Alexey; Sabaté, Santiago; Salmon, Yann; Salomón, Roberto Luis; Sánchez-Costa, Elisenda; Schäfer, Karina; Schuldt, Bernhard; Shashkin, Alexandr; Stahl, Clément; Stojanović, Marko; Suárez Salazar, Juan Carlos; Sun, Ge; Szatniewska, Justyna; Tatarinov, Fyodor; Tesař, Miroslav; Thomas, Frank M.; Tor-ngern, Pantana; Urban, Josef; Valladares, Fernando; van der Tol, Christiaan; van Meerveld, H.J. (Ilja); Varlagin, Andrej; Voigt, Holm; Warren, Jeffrey; Werner, Willy; Werner, Christiane; Wieser, Gerhard; Wingate, Lisa; Wullschleger, Stan; Yi, Koong; Zweifel, Roman

General description

SAPFLUXNET contains a global database of sap flow and environmental data, together with metadata at different levels.
SAPFLUXNET is a harmonised database, compiled from contributions from researchers worldwide. This first version contains more than 200 datasets, from all over the World, covering a broad range of bioclimatic conditions.
More information on the coverage can be found here: http://sapfluxnet.creaf.cat/shiny/sfn_progress_dashboard/. Please note that, according to the data policy (http://sapfluxnet.creaf.cat/data_policy/), the SAPFLUXNET database will remain under restricted access during one year after its initial publication, and will only be available for data contributors.
The SAPFLUXNET project has been developed by researchers at CREAF  and other institutions (http://sapfluxnet.creaf.cat/#team), coordinated by Rafael Poyatos (CREAF, http://www.creaf.cat/staff/rafael-poyatos-lopez), and initially funded by a Spanish Young Researcher's Grant  (MINECO-MICINN, CGL2014-55883-JIN).

Variables and units

SAPFLUXNET contains whole-plant sap flow and environmental variables at sub-daily temporal resolution. Both sap flow and environmental time series have accompanying flags in a data frame, one for sap flow and another for environmental
variables. These flags store quality issues detected during the quality control process and can be used to add further quality flags. 

Metadata contain relevant variables informing about site conditions, stand characteristics, tree and species attributes, sap flow methodology and details on environmental measurements. To learn more about variables, units and data flags please use the functionalities implemented in the sapfluxnetr package (https://github.com/sapfluxnet/sapfluxnetr). In particular, have a look at the package vignettes using R:

# remotes::install_github(
#   'sapfluxnet/sapfluxnetr',
#   build_opts = c("--no-resave-data", "--no-manual", "--build-vignettes")
# )
library(sapfluxnetr)
# to list all vignettes
vignette(package='sapfluxnetr')
# variables and units
vignette('metadata-and-data-units', package='sapfluxnetr')
# data flags
vignette('data-flags', package='sapfluxnetr')

Data formats

SAPFLUXNET data can be found in two formats: 1) RData files belonging to the custom-built 'sfn_data' class and 2) Text files in .csv format. We recommend using the sfn_data objects together with the sapfluxnetr package, although we also provide  the text files for convenience. For each dataset, text files are structured in the same way as the slots of sfn_data objects; if working with text files, we recommend that you check the data structure of 'sfn_data' objects in the corresponding vignette.

Working with sfn_data files

To work with SAPFLUXNET data, first they have to be downloaded from Zenodo, maintaining the folder structure. A first level in the folder hierarchy corresponds to file format, either RData files or csv's. A second level corresponds to how sap flow is expressed: per plant, per sapwood area or per leaf area. Please note that interconversions among the magnitudes have been performed whenever possible. Below this level, data have been organised per dataset. In the case of RData files, each dataset is contained in a sfn_data object, which stores all data and metadata in different slots (see the vignette 'sfn-data-classes'). In the case of csv files, each dataset has 9 individual files, corresponding to metadata (5), sap flow and environmental data (2) and their corresponding data flags (2).

After downloading the entire database, the sapfluxnetr package can be used to:
- Work with data from a single site: data access, plotting and time aggregation.
- Select the subset datasets to work with.
- Work with data from multiple sites: data access, plotting and time aggregation.

Please check the following package vignettes to learn more about how to work with sfn_data files:

Quick guide

Metadata and data units

sfn_data classes

Custom aggregation

Memory and parallelization

 

Working with text files

We recommend to work with sfn_data objects using R and the sapfluxnetr package and we do not currently provide code to work with text files. 

Restricted access to data contributors

According to the SAPFLUXNET data policy (http://sapfluxnet.creaf.cat/data_policy/), the database will remain under restricted access during one year after its initial release. If you are a SAPFLUXNET data contributor, please see the 'Conditions' section below to request access to the database.

Restricted Access

You may request access to the files in this upload, provided that you fulfil the conditions below. The decision whether to grant/deny access is solely under the responsibility of the record owner.


  • During the first year after publication, only data contributors will have access to the SAPFLUXNET database. 
  • The database will be made public in early 2020.
  • Data contributors, please request access to the database using the Zenodo requests system. We will check whether you are in the data contributors list and will grant you access to download the database.
  • We suggest that data contributors conducting research activities using SAPFLUXNET data inform the SAPFLUXNET core team (sapfluxnet@creaf.uab.cat) about the topic, timeline and responsible researcher of the study. This is to minimise the overlap between similar data syntheses activities carried out by different groups.
  • We also ask that data contributors communicate (sapfluxnet@creaf.uab.cat) any issue detected with the datasets, so that we can fix any problem in subsequent updated versions of the database.

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