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Dataset Open 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

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  <identifier identifierType="DOI">10.5281/zenodo.2530798</identifier>
      <creatorName>Rafael Poyatos</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0003-0521-2523</nameIdentifier>
      <creatorName>Víctor Granda</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0002-0469-1991</nameIdentifier>
      <creatorName>Víctor Flo</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0003-1908-4577</nameIdentifier>
      <creatorName>Roberto Molowny-Horas</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0003-2626-6379</nameIdentifier>
      <creatorName>Kathy Steppe</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0001-6252-0704</nameIdentifier>
      <affiliation>Ghent University</affiliation>
      <creatorName>Maurizio Mencuccini</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0003-0840-1477</nameIdentifier>
      <creatorName>Jordi Martínez-Vilalta</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0002-2332-7298</nameIdentifier>
      <affiliation>CREAF/Universitat Autònoma de Barcelona</affiliation>
    <title>SAPFLUXNET: A global database of sap flow measurements</title>
    <subject>plant hydraulics</subject>
    <subject>sap flux</subject>
    <date dateType="Issued">2019-03-05</date>
  <resourceType resourceTypeGeneral="Dataset"/>
    <alternateIdentifier alternateIdentifierType="url"></alternateIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.2530797</relatedIdentifier>
    <rights rightsURI="">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;General description&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;SAPFLUXNET contains a global database of sap flow and environmental data,&amp;nbsp;together with metadata at different levels.&lt;br&gt;
SAPFLUXNET is a harmonised database, compiled from contributions from&amp;nbsp;researchers worldwide. This first version contains more than 200 datasets,&amp;nbsp;from all over the World, covering a broad range of bioclimatic conditions.&lt;br&gt;
More information on the coverage can be found here: Please note that, according to the data policy (&lt;a href=""&gt;;/a&gt;), the SAPFLUXNET database&amp;nbsp;will remain under restricted access during one year after its initial publication, and will only be available for data contributors.&lt;br&gt;
The SAPFLUXNET project has been developed by researchers at CREAF&amp;nbsp; and other institutions (&lt;a href=""&gt;;/a&gt;), coordinated by Rafael Poyatos (CREAF, &lt;a href=""&gt;;/a&gt;), and initially&amp;nbsp;funded by a Spanish Young Researcher&amp;#39;s Grant &amp;nbsp;(MINECO-MICINN, CGL2014-55883-JIN).&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Variables and units&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;SAPFLUXNET contains whole-plant sap flow and environmental variables&amp;nbsp;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&lt;br&gt;
variables. These flags store quality issues detected during the quality control&amp;nbsp;process and can be used to add further quality flags.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;Metadata contain relevant variables informing about site conditions, stand characteristics,&amp;nbsp;tree and species attributes, sap flow methodology and details on environmental measurements. To learn&amp;nbsp;more about variables, units and data flags please use the functionalities implemented in the sapfluxnetr package&amp;nbsp;(&lt;a href=""&gt;;/a&gt;). In particular, have a look at the package vignettes using R:&lt;/p&gt;

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

&lt;p&gt;&lt;strong&gt;Data formats&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;SAPFLUXNET data can be found in two formats: 1) RData files belonging to the custom-built &amp;#39;sfn_data&amp;#39; class and 2) Text files in .csv format. We recommend using the sfn_data objects together with the sapfluxnetr package, although we also provide&amp;nbsp; 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 &amp;#39;sfn_data&amp;#39; objects in the&amp;nbsp;&lt;a href=""&gt;corresponding vignette&lt;/a&gt;.&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Working with sfn_data files&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;To work with SAPFLUXNET data, first they have to be downloaded from Zenodo, maintaining&amp;nbsp;the folder structure. A first level in the folder hierarchy corresponds to file format, either RData files or csv&amp;#39;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 &amp;#39;sfn-data-classes&amp;#39;). 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).&lt;/p&gt;

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

&lt;p&gt;Please check the following package vignettes to learn more about how to work with sfn_data files:&lt;/p&gt;

&lt;p&gt;&lt;a href=""&gt;Quick guide&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;&lt;a href=""&gt;Metadata and data units&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;&lt;a href=""&gt;sfn_data classes&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;&lt;a href=""&gt;Custom aggregation&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;&lt;a href=""&gt;Memory and parallelization&lt;/a&gt;&lt;/p&gt;


&lt;p&gt;&lt;strong&gt;Working with text files&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;We recommend to work with sfn_data objects using R and the sapfluxnetr package and&amp;nbsp;we do not currently provide code to work with text files.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;Restricted access to data contributors&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;According to the SAPFLUXNET data policy (&lt;a href=""&gt;;/a&gt;), the database will remain under restricted access during one year after its initial release. If you are a SAPFLUXNET data contributor, please see the &amp;#39;Conditions&amp;#39; section below to request access to the database.&lt;/p&gt;</description>
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