GIFT —An R package to access the Global Inventory of Floras and Traits

Abstract

Advancing knowledge of biodiversity requires global open‐access databases. Having large‐scale information on plant distributions, functional traits and evolutionary history will enable the scientific community to improve its understanding of the patterns and drivers of plant diversity on a global scale.
The Global Inventory of Floras and Traits (GIFT) is a global database of regional plant checklists that has proven successful in documenting biogeographical patterns of plants. Since the release of the first version of GIFT, the database kept on expanding. We introduce GIFT version 3.0, which contains 5169 plant checklists referring to 3400 regions worldwide. These checklists include a total of 371,148 land plant species, mostly vascular plants, of which 354,848 have accepted species names, and species‐level data for 109 functional traits. This new version of GIFT relies on new resources for taxonomic name standardization, is matched to a new plant phylogeny, comes with a new trait aggregation workflow and includes additional environmental variables.
We also present the GIFT R ‐package, which contains all necessary functions to retrieve distributional, functional, phylogenetic, and environmental data from the GIFT database. The package comes with a dedicated website, https://biogeomacro.github.io/GIFT/ , which includes three vignettes to guide users in retrieving data from GIFT.
The recent development of GIFT and its associated R ‐package provide ecologists with access to one of the largest plant databases. This will foster research into regional to global patterns of plant diversity and their underlying mechanisms. The ability to retrieve and cite data from any previous and current instance of the GIFT database will ensure the reproducibility of studies that utilise it.

Full text

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Methods Ecol Evol. 2023;14:2738–2748.wileyonlinelibrary.com/journal/mee3
Received: 7 June 2023
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Accepted: 29 Augus t 2023
DOI : 10.1111/20 41-210X .14213
APPLICATION
GIFT— An R package to access the Global Inventory of Floras
an d Trait s
Pierre Denelle1 | Patrick Weigelt1,2,3 | Holger Kreft1,2,3
This is an op en access arti cle under the ter ms of the Creative Commons Attribution L icense, which pe rmits use, dis tribu tion and reprod uction in any med ium,
provide d the original wor k is properly cited.
© 2023 The Authors . Methods in Ecolog y and Evolution published by John Wiley & S ons Ltd on behalf of British Ecologic al Society.
1Biodive rsity, Macroeco logy &
Biogeography, Universit y of Gött ingen,
Göttingen, Germany
2Centre of B iodiversity and Sustainable
Land Use, Univer sity of G öttingen,
Göttingen, Germany
3Campus Institute Data Science,
Göttingen, Germany
Correspondence
Patrick Weigelt
Email: pweigel@uni-goettingen.de
Handling Editor: Si- Chong Ch en
Abstract
1. Advancing knowledge of biodiversity requires global open- access databases.
Having large- scale information on plant distributions, functional traits and evolu-
tionary history will enable the scientific community to improve its understanding
of the patterns and drivers of plant diversity on a global scale.
2. The Global Inventory of Floras and Traits (GIFT) is a global database of regional
plant checklists that has proven successful in documenting biogeographical pat-
terns of plants. Since the release of the first version of GIFT, the database kept on
expanding. We introduce GIFT version 3.0, which contains 5169 plant checklists
referring to 340 0 regions worldwide. These checklists include a total of 371,148
land plant species, mostly vascular plants, of which 354,848 have accepted spe-
cies names, and species- level data for 109 functional traits. This new version of
GIFT relies on new resources for taxonomic name standardization, is matched to
a new plant phylogeny, comes with a new trait aggregation workflow and includes
additional environmental variables.
3. We also present the GIFT R- package, which contains all necessary functions to
retrieve distributional, functional, phylogenetic, and environmental data from
the GIFT database. The package comes with a dedicated website, https://bioge
omacro.github.io/GIFT/, which includes three vignettes to guide users in retriev-
ing data from GIFT.
4. The recent development of GIFT and its associated R- package provide ecologists
with access to one of the largest plant databases. This will foster research into
regional to global patterns of plant diversity and their underlying mechanisms.
The ability to retrieve and cite data from any previous and current instance of the
GIFT database will ensure the reproducibility of studies that utilise it.
KEYWORDS
biodiversity, functional traits, global plant database, phylogeny, plant distributions, regional
checklists, R- package, vascular plants

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1 | INTRODUC TION
Documenting and understanding species distributions and other
dimensions of biodiversity requires global open- access data. While
global databases with species ranges and trait information are avail-
able for some taxa, such as birds, mammals, amphibians and reptiles
(BirdLife International, 2013; Myhrvold et al., 2015), equivalent data
for plants still lag behind, although recent efforts have improved
their spatial and taxonomic coverage. Together with the Botanical
Information and Ecolog y Network (Enquist et al., 2016), the World
Checklist of Vascular Plants (WCVP; Brown et al., 2023; Govaerts
et al., 2021), the Global Naturalized Flora (van Kleunen et al., 2 019)
and the Global Biodiversit y Information Facility (GBIF, www.
gbif.or g), the Global Inventory of Floras and Traits (GIFT; Weigelt
et al., 2020) has contributed to improving our knowledge of plant
distributions and multiple aspect s of plant diversity. However, until
now, the GIFT database of regional plant checklists and species- level
traits has not been publicly available. Here, we present the latest
update of the GIFT database, with the release of version 3.0, and the
GIFT R- package, which grants open access for users to retrieve data.
1.1 | A short history of GIFT
GIFT is a global database of regional plant checklists, species- level
functional traits and environmental region characteristics (Weigelt
et al., 2020). Prior to GIFT and similar initiatives, plant diversit y re-
search using regional floras only considered the number of species
per region and ignored species identities. However, a wide range of
environmental predictors were already considered (e.g. in Kreft &
Jetz, 2007). These earlier studies resulted in exper t- drawn diversity
maps (Barthlott et al., 1996; Mutke & Barthlott, 2005), estimated
plant richness per ecoregion (Kier et al., 20 05) and modelled global
species richness pat terns (Kreft & Jet z, 20 07), the latter being re-
cently updated (Cai, Kreft, Taylor, Denelle, et al., 2023). These ef-
forts highlighted an under- representation of islands. To address this
shortcoming, there has been a strong push for data collection for
islands. With checklists now available for 1057 islands larger than
1 km2, representing 80.7% of the world's total island area (Weigelt
et al., 2013), GIFT is the most comprehensive plant database for
studying patterns of island biogeography. This high coverage has led
to global assessments of vascular plants (Kreft et al., 2008; Weigelt
& Kreft, 2013) and pteridophyte (Kreft et al., 2010) richness on is-
lands, characterization of island environmental features (Weigelt
et al., 2013; Weigelt & Kreft, 2013), and of the past and present
drivers of plant diversity on islands (Cabral et al., 2014; Schrader
et al., 2020; Weigelt et al., 2016).
Making use of the species composition per region and the floris-
tic status of occurrences, studies using the GIFT database provided
global assessments for specific plant groups such as epiphy tes (Tay-
lor et al., 2022), phylogenetic diversity (Cai, Kreft, Taylor, Denelle,
et al., 2023; Weigelt et al., 2015) and endemism (Cai, Kref t, Taylor,
Schrader, et al., 2023), and β- diversity (König et al., 2017). Unlike
other databases where species composition is available at the plot
level (e.g. sPlot; Bruelheide et al., 2019) or comes from an aggre-
gation of georeferenced occurrences (e.g. GBIF, www.gbif.org),
regional- level species composition data in GIF T has high geographic
coverage and is spatially less biased although being coarser in res-
olution/grain (König et al., 2019). There are also functional trait
data in GIFT, which mainly come from species descriptions in floras,
checklists and online databases, and are mainly available at the spe-
cies level, whereas trait data in other databases like TRY (Kattge
et al., 2011) are usually individual measurements making GIFT data
a complementary addition. Functional traits in GIFT have been used
to map the distribution of growth and life forms on a global scale
(Taylor et al., 2023) and to address taxonomic and functional dishar-
monies between island and mainland floras (König et al., 2021; Raza-
najatovo et al., 2019; Taylor et al., 2 019, 2021; Zizka et al., 2022).
Finally, GIFT has also been used to advance our understanding of the
distribution of alien plant species compared to native species (e.g.
Bach et al., 2022; Omer et al., 2022; van Kleunen et al., 2015; Yang
et al., 2021) as well as species interactions (Delavaux et al., 2019;
Luo et al., 2023).
1.2 | From GIFT 1.0 to GIFT 3.0
Since the release of version 1.0 in 2018 (https://gift.uni- goett ingen.
de/about), the number of plant checklists and geographical regions in
GI F T has st ead i ly in c rea sed (Figure 1). GI F T 3.0 cont ains 5169 ch eck-
lists, which is 50% more checklists than version 1.0. These checklists
refer to 3400 georeferenced regions, of which 2899 regions have
at least one checklist for all native vascular plants (Figure 1a). Dif-
ferent combinations of taxonomic group and floristic status can be
queried, leading to different region numbers (Figure S1). Altogether,
these regions cover the entire terrestrial surface of the Earth, as
shown on the GIF T website: https://gift.uni- goett ingen.de/map
(Figure 2a). Unless other wise noted, numbers in this manuscript
refer to the data including restricted resources. Across all checklists,
GIFT 3.0 includes a total of 1,161,174 original names (orig_ID in the
database, Figure S2) corresponding to a tot al of 371,148 standard-
ized plant species (work_ID in the database). GIFT 3.0 comes with
more trait records than previous versions (Figure 1b, Figure S3), re-
sulting in very high coverage of whole plant traits, such as growth
form (246,901 species with growth form) and plant height (81,248
species) which are frequently mentioned in floras and checklists
(Figure 1b). 281,836 species have at least one trait available.
To facilitate studies of diversity- environment relationships, GIFT
regions are linked to 213 environmental variables, including miscel-
laneous variables and variables derived from raster layers (Table S1).
In GIFT 3.0, we added some recently published datasets including
paleoclimatic variables (Brown et al., 2018; Karger et al., 2021), new
bioclimatic variables (Brun et al., 2022), global soil temperature vari-
ables (Lembrechts et al., 2022), indices of climate stability (Owens &
Guralnick, 2 019) or aridity (Zomer et al., 2022) that were not avail-
able in previous versions. We also added the prediction of plant
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richness per region extracted from the recent work of Cai, Kreft,
Taylor, Denelle, et al. (2023). Extraction of raster values for GIFT
regions now uses the exactextractr R- package (Baston et al., 2022).
1.3 | Workflow updates
In addition to increasing the number of checklists, species, trait re-
cords and environmental variables, we have updated the taxonomic
standardization of the original species names, since the superseded
Plant List (thepl antli st.org/) was used in previous versions of GIF T.
To standardize the original species names, GIFT now uses the World
Checklist of Vascular Plants (Govaerts et al., 2021), the TNRS R-
package (Maitner et al., 2023) and the additional resources used
therein, namely The World Flora Online (world flora online.org/),
Tropicos (tropi cos.org), and the USDA plant database (plants.usda.
gov). 99.1% of all original names could be matched and standardized
to an existing species name using these resources. Of these stand-
ardized names, 95.6% are accepted species names in the above-
mentioned resources (Figure S2). If a species name does not match,
we keep the original species name. With this new taxonomic work-
flow, standardized species names also come with author names.
In GIFT 3.0, all standardized species names are linked to a phy-
logeny built using the U.PhyloMaker R- package (Jin & Qian, 2022)
which is stored in the database and accessible via the GIFT R- package.
For seed plants, it is based on the GBOTB megatree from Smith and
Brown (2018) and for pteridophytes, on Zanne et al. (2014), both
standardized according to WCVP. Missing species and genera were
bound to their respective genera and families using ‘Scenario 3’ from
the U.PhyloMaker R- package.
The aggregation of a trait value at the species level is different
depending on whether a trait is categorical or continuous. When
querying a categorical trait for a given species, the most frequent
category is returned as the trait value, alternative trait values are
indicated and the proportion of references that agree on a given trait
value is given. For continuous traits, the aggregated trait value can
be the minimum, mean (e.g. for average plant height) or maximum
(e.g. for maximum plant height) of all trait values from the different
references included in GIFT. To acknowledge the variation across
references, the coefficient of variation is returned.
1.4 | Package functionality
The GIFT R- package cont ains 27 functions (Table 1) that allow
users to retrieve plant checklists matching specific criteria, spe-
cies distribution information, functional traits, environmental vari-
ables, spatial information and a phylogeny. Most of these functions
allow retrieving tables at the global scale or only for a subset of re-
gions or plant species. The GIFT R- package comes with a website
(https://bioge omacro.github.io/GIFT/), with vignettes, tutorials and
detailed documentation for each func tion. The R- package calls an
FIGURE 1 Amount of information in different versions of GIFT. (a) Number of regions available for different filters applied. Black lines
represent the total number of regions per version, while green lines represent the number of regions with species lists of native vascular
plants. Continuous lines represent the information directly available with the GIFT R- package and default Application Programming Interface
settings, dashed lines represent numbers including restricted data which require contacting data owners before using them. (b) Number
of species with certain trait or distribution information available in the different versions of GIFT. Black colour corresponds to the total
number of species, red colour corresponds to species with distribution information, the three blue colours represent species with at least
one available trait, growth form (e.g. tree, shrub, herb) or plant height values. The number of species with growth form available decreases
slightly between version 2.2 and version 3.0 due to the change of the taxonomic backbone used to harmonize the species names.
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Application Programming Interface (API), and the API then accesses
the database to retrieve the desired data. If necessary, the API can
also be called programmatically or through the browser indepen-
dently of the R- package (https://bioge omacro.github.io/GIFT/artic
les/GIFT_API.html).
Most of the functions are interconnected and interdependent
(Figure S4). Some arguments are shared with other functions, such
as the identification numbers for references (ref_ID), checklists (list_
ID), unstandardized species names (name_ID), standardized species
names (work_ID), traits (trait_ID) and regions (entity_ID). We provide
the possibility to extract and work with any existing version of the
database. Each of the functions presented below has an argument
called GIFT_version that allows retrieving data from a specific in-
stance of the database (Table 1). Because all versions are available
through the R- package, analyses can be reproduced even af ter the
database has been updated.
A small number of data providers have asked to restrict access to
their data at this time. This implies that among all the data that can be
retrieved with the R- package, a small propor tion of references (6.7%,
Figure 1a) are restricted. These data have mostly been contributed
by data owners who plan to publish their data independently before
making them publicly available via GIFT or come from large online
databases that are better accessed directly (e.g. WC VP; Govaerts
et al., 2021). A password- protec ted API, that can be made available
upon request, is needed to retrieve these restricted data. On top
of the password- restricted API, approval from the data providers is
needed. The GIFT_coverage() func tion gives an over view of the po-
tential information available in the restricted references and can be
run before considering its use. Regardless, all data sources, open ac-
cess and restricted, used in studies using GIFT data should be cited.
2 | REGIONAL PLANT CHECKLISTS
The main function of the package, GIFT_checklists(), allows one to
retrieve plant checklists for regions that meet certain criteria. A
complete tutorial on how to use this function is available in the main
vignette of the package, https://bioge omacro.github.io/GIFT/artic
les/GIFT.html, and, in the following, the main options are presented.
GIFT_checklists() returns a list with two objects: the metadata of the
regions matching the input criteria, together with the identification
numbers of the corresponding references and checklists, and a table
FIGURE 2 Different facets of GIFT by geographic region. (a) Richness of native vascular plants, with a log- transformed colour scale,
based on GIFT_richness(). (b) Distribution of Impatiens glandulifera with it s floristic status in each region as indicated in the primary
references used in GIFT, based on GIFT_species_distribution(). (c) Coverage for the growth form of vascular plants based on GIFT_coverage().
(d) Mean annual temperature (°C) per region based on GIFT_env(). The projection used for all panels is Ecker t IV (EPSG: 54012). R- code to
generate such figures based on functions from the GIFT R- package is accessible in the main vignette of the R- package https://bioge omacro.
github.io/GIFT/artic les/GIFT.html. The GIFT_shapes() function was used to retrieve the spatial polygons associated with each region.
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with the species composition per checklist and region. By default,
the standardized species names and their floristic status are re-
turned in this table but the original non- standardized species names
can also be returned on request.
GIFT_checklists() allows one to define a taxonomic and a flo-
ristic group of interest. The taxonomic group can take several val-
ues, for example all vascular plants (taxon_name = “Tracheophyta”)
or other taxonomic groups within land plants (e.g. a plant family,
taxon_name = “Orchidaceae”). All available options can be viewed
by running the GIFT_taxonomy() func tion. The floristic_group indi-
cates whether the species retrieved should be native, naturalized,
endemic or if all species should be retrieved. Both arguments have
a companion argument, complete_taxon and complete_floristic re-
spectively, which can be set to TRUE or FALSE. These arguments
define whether only regions that are covered by checklists of the
entire taxonomic group or floristic status should be retrieved or if
regions covered for only a subset can be returned. For example, with
taxon_name = “Tracheophyta”, a region covered only by an orchid
checklist will only be retrieved if complete_taxon = FALSE. Equiva-
lently, with floristic_group = “native”, a region covered only by lists of
endemic species or only trees will only be retrieved if complete_flo-
ristic = FALSE. More detailed explanations can be found in the main
vignette of the package.
Second, GIFT_checklists() works with or without spatial restric-
tion. By default, there is no restriction, meaning that regions covered
by checklists meeting the other criteria will be retrieved all over the
world. It is also possible to provide a shapefile or a set of coordi-
nates to spatially constrain the query. As an example, we provide a
shape of the western Mediterranean basin, which can be retrieved
using the western_mediterranean dat a function. Regions that corre-
spond to, fall inside or intersect the spatial input can then be re-
trieved. Another important consideration is whether users want to
retrieve several checklists for nested and overlapping regions or if
only non- overlapping regions should be considered. This can be eas-
ily set with the remove_overlap argument. Overlapping regions can
be removed in favour of smaller or larger regions (above or below a
user- defined area threshold) in case of overlap (see Figures S5 and
S6 and the main tutorial on the website https://bioge omacro.github.
io/GIFT/artic le s/GIFT.html). We also provide the option to remove
overlapping regions only if they belong to the same reference (see
TAB LE 1 Overview of the 27 functions available in the GIFT R- package.
Category Functions Description
Regional checklists and specie s
distributions
GIFT_checklists() Checklists for regions matching certain criteria
GIFT_checklists_conditional() Metadata of checklist s for regions matching certain criteria
GIFT_checklists_raw() Checklists by reference (ref_ID)
GIFT_lists() Metadata of checklist s and regions per reference
GIFT_species_distribution() Distributions of individual plant species
Species names, taxonomy and
phylogeny
GIFT_phylogeny() Phylogeny linked to st andardized species names
GIFT_species_lookup() Taxonomic information per species name
GIFT_species() All standardized species available
GIFT_taxonomy() Taxonomy lookup
GIFT_taxgroup() Assigns taxonomic groups to species
Traits GIFT_traits() Aggregated tr ait values per sp ecies
GIFT_traits_meta() Metadata for tr aits
GIFT_traits_raw() Non- aggreg ated reference- level trait values
GIFT_traits_tax() Trait values at t axonomic group level
Spatial and environmental data GIFT_env() Environmental data per region
GIFT_env_meta_misc() Metadata for miscellaneous environmental variables
GIFT_env_meta_raster() Metadata for environmental raster layers
GIFT_spatial() Regions matching spatial input
GIFT_regions() Miscellaneous information per region
GIFT_shapes() Spatial polygons of selected or all regions
GIFT_overlap() Spatial overlap between GIFT regions and external polygon resources
GIFT_no_overlap() Pairwise overlap between GIFT regions
Utils GIFT_coverage() Taxonomic and trait coverage per region
GIFT_references() Metadata per reference
GIFT_richness() Species richness per region and taxonomic group
GIFT_versions() Versions of GIFT available
western_mediterranean Spatial polygon of the western Mediterranean basin (example data)
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the advanced vignette for more details https://bioge omacro.github.
io/GIFT/artic les/GIFT_advan ced_users.html#by- ref_id). If one is in-
terested in retrieving the species richness of a particular taxonomic
and floristic group per region, one can use the alternative function
GIFT_richness().
3 | DISTRIBUTION OF INDIVIDUAL
PLANT SPECIES
To look up if a plant species is included in GIFT, users can call the
GIFT_species_lookup() function. This function can search for both
original or standardized species names and returns all references
in which the focal species name occurs as well as the original spe-
cies name as found in these references. The complete list of stand-
ardized plant species names available in the GIFT database can be
retrieved with the function GIFT_species(). Second, the function
GIFT_species_distribution() returns a list of regions where the focal
plant species occurs. The floristic status of the species is provided,
allowing for quick identification of regions where the focal plant is
native, naturalised or endemic. The argument aggregation allows to
aggregate this information at the region level, with a note indicating
whether the original references disagree on the st atus. An example
using Impatiens glandulifera, an annual plant native to the Himala-
yas that is now considered naturalized in many areas, is shown in
Figure 2b. This example illustrates that the floristic status must be
treated with caution. While Impatiens glandulifera is considered na-
tive to the Himalayas, some references also classify it as native to
Southeast Asia. This type of conflict, which occurs for many species,
may be due to conflicting references, the fact that the floristic status
refers to the original species names before taxonomic standardiza-
tion, or errors in the references. Alternatively, GIFT data can be used
via the bRacatus R package to estimate a georeferenced occurrence
record's probability of being true or false and its biogeographic sta-
tus based on a probabilistic framework (Arle et al., 2021).
4 | TAXONOMY
The GIFT database includes original species names as taken from
the original references as well as standardized species names and
statistics about the standardization process. Several functions in
the package, such as GIFT_checklists() or GIFT_species_lookup(),
can return the original species names before standardization and
information about the standardization process. It is important to
provide this information because the floristic status of species re-
fers to the original species names, not the standardized names. For
example, a subspecies may be described as endemic in a reference
and standardized to its parent species which is actually considered
non- endemic native, resulting in a misleading floristic status for that
standardized species. Species names derived from infraspecific taxa
or synonyms are therefore highlighted. We also provide match-
ing scores in percent age for genera, epithets and overall species
names between the original species name and the accepted spe-
cies names. These harmonization statistics can hence be used to
filter for only accepted species (Figure S2), or species that were not
subspecies before standardization, and so forth. Therefore, func-
tions that allow to retrieve plant checklists, species distributions or
raw functional traits, namely GIFT_checklists(), GIFT_species_distri-
bution() and GIFT_traits_raw(), allow the inclusion in their output of
both the original and harmonized species names, as well as details
about the standardization and the service used. The original and
taxonomically harmonized names come with an identification num-
ber (name_ID and work_ID, respectively) and allow tracing back the
taxonomic standardization or to run a preferred alternative taxo-
nomic standardization (Grenié et al., 2023). There are 1,161,174
original species names for 371,148 standardized species names in
GIFT 3.0 (Figure S2).
The taxonomy of GIFT assigns species to their respective genera,
families and orders up to higher group levels such as Angiosperms,
Spermatophytes and so for th. It is stored in a table that can be ac-
cessed with GIFT_taxonomy(). This function returns a table which
can be translated into the Newick tree format (Archie et al., 198 6)
in which each taxon, down to the genus level, is placed bet ween a
left and right border. The GIFT_taxgroup() function can be used to
place any of the accepted plant species names within this taxonomy
and to retrieve their higher taxonomic groups (e.g. family, order or
higher group).
5 | PHYLOGENY
The phylogeny in GIFT is based on existing megatrees (Jin &
Qian, 2022; Smith & Brown, 2018; Zanne et al., 2014), includes all
vascular plants from the GIFT database and can be accessed with
the func tion GIFT_phylogeny() from version 3.0 onward. Higher tax-
onomic groups from the taxonomy of GIF T that form monophyletic
groups in the phylogeny can be used to retrieve a phylogeny for a
taxonomic subset of the entire phylogeny. The phylogeny can be re-
trieved as a tree object, which can then be used directly with other R-
packages such as phytools (Revell, 2023) or ape (Paradis et al., 2023),
or as a table mimicking the Newick format (Archie et al., 1986). The
phylogeny, in combination with data from the previously described
functions, allows the calculation of phylogenetic diversity metric s at
the checklist or region level or the estimation of trait coverage along
the phylogeny of vascular plants (Figure 3).
6 | FUNCTIONAL TRAITS
GIFT 3.0 includes data for 109 different functional traits and a
to t a l of 5,679,014 trai t re c ord s agg reg a ted at th e spec i e s leve l (Fig-
ure S3). The different trait s are distributed across six categories:
morphological, ecological, physiological, reproductive, genetic or
life history (Weigelt et al., 2020). Coverage varies considerably
among traits with, for example, the growth form being available
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METHO DS IN ECOLOGY A ND EVOLUTION
for 246,901 plant species while dispersal syndrome is available for
only about 9600 species. Metadata for each of these traits can be
viewed by calling the GIFT_traits_meta() function. When having a
list of trait s of interest, users may start by calling this metadata
function to retrieve their identification number (trait_ID). Once
this number is known, users can call the functions GIFT_traits_
raw() or GIFT_traits() to receive one or several traits at a time. The
functions return the raw traits or the aggregated trait data at the
species level, respectively. In GIFT, there is also trait information
collected at the higher taxonomic level. For example, all species
belonging to the genus Abies are woo dy. Th is da ta can be ret rie ve d
using GIFT_traits_tax(). Querying the raw traits acknowledges the
variati on of tra it val ues across refere nces and is t he re fo re of in te r-
est to ecologists working at the species level. The primary refer-
ences for these trait values are also returned. GIFT_traits() returns
trait values aggregated at the species level. For categorical traits
(such as e.g. growth form), the func tion returns the most frequent
tr ait valu e, al ong with an agre eme nt sc ore . Thi s s co re in dic ate s t he
percentage of references that leads to this most frequent value
out of all references that provide information about this trait. For
example, if a plant is described as tree in t wo sources and as shrub
in a third one, then the value tree is returned with an agreement
score of 66%. Users can decide on a threshold at which they trust
the trait values, or they can include the agreement score and the
associated uncertainty in their statistical analysis. For continuous
traits, the number of references used to aggregate the trait value
is given, together with the coefficient of variation of the continu-
ous value listed in the different references.
Trait records in GIFT can be actual values taken from the ref-
erences but they can also be logically derived from available in-
formation (König et al., 2017). For example, a species can have
its growth form described as tree, and since all trees are pha-
nerophytes, the life form value of this plant species is set to
phanerophyte. Whether a trait is derived or not is indicated in the
raw trait table returned by GIFT_traits_raw(). Trait derivation can
introduce biases in the proportional representation of trait cate-
gories in assemblages. For example, since all trees are phanero-
phytes, but not all herbs are therophytes, this derivation leads to
an overrepresentation of phanerophytes. Similarly, references of
only trees (Beech et al., 2017) or only epiphytes (Zot z et al., 2021)
introduce biases at the assemblage level. Trait values only based
on a ref erenc e or a de riv at io n t ha t intro du ce s a bia s c an be filter ed
out by setting the bias_deriv or bias_ref arguments to FALSE. More
details about the arguments of these two functions can be found
in the main vignette of the package (https://bioge omacro.github.
io/GIFT/artic le s/GIFT.html).
Finally, the GIFT_coverage() function can be used to map the cov-
erage of a particular trait for a given taxonomic and floristic group. In
this case, the argument what of the function has to be set to “trait_
coverage”. Figure 2c maps the coverage of the maximal vegetative
height per plant using this function. This function is complementary
to the GIFT website https://gift.uni- goett ingen.de/map, where trait
coverage can be mapped, and can be used to compare data including
or excluding restricted references. In addition, this function can be
used to indicate whether a combination of region, taxonomic group
and floristic status is covered by at least one checklist for public and
restricted data in comparison.
7 | ENVIRONMENTAL VARIABLES PER
REGION
A major line of research in macroecology and biogeography is to
identify the environmental drivers underpinning species distribu-
tions and diversity gradients (McGill, 2019). To facilitate such re-
search, GIFT 3.0. contains 213 variables, distributed across 34
FIGURE 3 Phylogenetic coverage
of the plant trait ‘growth form’. The
phylogeny is based on Jin and Qian (2022)
and was extracted from Global Inventory
of Floras and Traits using the GIFT_
phylogeny() function and pruned to genus
level (one tip per genus). The two outer
rings illustrate the growth form coverage
either at the genus level (inner ring) or at
the family level (outer ring). Growth form
coverage was calculated as the proportion
of species covered per genus and family
respectively. The R- code to generate this
figure is accessible in the main vignette
of the R- package https://bioge omacro.
github.io/GIFT/artic les/GIFT.html.
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Methods in Ecology and Evoluon
DENELLE et al .
miscellaneous variables and 179 raster layers (Table S1). Raster
layers mostly contain continuous metrics that provide insights
into macroclimatic, topographic, edaphic or paleoclimatic variables
or sometimes categorical information like the distribution of soil
classes (Hengl et al., 2017). Miscellaneous variables provide infor-
mation on the geography, geometry, floristic regions, isolation and
other characteristics of the GIFT regions based on the region's spa-
tial shapes and additional feature layers. The two metadata func-
tions GIFT_env_meta_misc() and GIFT_env_meta_raster() provide an
overview of all environmental variables and the underlying data lay-
ers. Each of these functions returns the list of available raster layers
or miscellaneous variables along with their names and references.
Once the names of the variables of interest have been identified,
users can call the GIFT_env() function for a list of GIFT regions, using
their identification number (entity_ID).
When calling a miscellaneous variable, such as the area or the
biome that encapsulates the region of interest , a single value is re-
turned. For raster layers, however, users need to provide a set of
summary statistics. Indeed, as the raster layers have a finer resolu-
tion than most of the GIFT regions, the environmental information
needs to be aggregated. For example, one can ask for the average
temperature of the raster cells falling into a GIFT region (GIFT_en-
v(rasterlayer = "wc2.0_bio_30s_01", sumstat = "mean"), Figure 2d) or
for the standard deviation of the precipitation values (GIFT_env(ras-
terlayer = "wc2.0_bio_30s_12", sumstat = "sd")). The desired summary
statistics must be passed to the GIFT_env() function using the sum-
stat argument.
8 | OU TLOOK
The GIFT R- package provides easy- to- use functions for accessing the
GIFT database. This tool will support a range of new studies on plant
biogeography while allowing for their reproducibility. In parallel, we
continue integrating new plant checklists into the GIFT database to
increase the coverage of underrepresented regions or environments
of the world, to bridge the gap between local and regional studies of
plant diversity (Puglielli & Pärtel, 2023) and to increase the coverage
of func tional traits. Additions will be made to the beta version of
GIFT, which will be turned into a new stable version once enough
additions have been made and checked for consistency. Updates to
the package are submitted to the CRAN repository and archived on
the Zenodo repository, with each new release having its own DOI
(version 1.2.0 of the package is archived at https://zenodo.org/recor
d/8256 512 ).
AUTHOR CONTRIBUTIONS
Pierre Denelle and Patrick Weigelt developed the GIFT R- package
and the associated GitHub website. Patrick Weigelt led the de-
velopment of the database infrastructure and API. All authors
worked on the advancement of the GIFT database. Pierre Denelle
led the writing of the manuscript to which all authors contributed
critically.
ACKNO WLE DGE MENTS
We thank Mar tin Turjak, Matthias Grenié and other beta- testers
of the R- package for providing useful insights. HK acknowledges
funding from the DFG as part of the research unit FOR 2716 Dy-
naCom and research training group RTG 1644 Scaling Problems
in Statistics.
CONFLICT OF INTEREST STATEMENT
All authors have no conflict of interest to declare.
PEER REVIEW
The peer review history for this article is available at h t t p s ://
www.webof scien ce.com/api/gatew ay/wos/peer- revie
w/10.1111/20 41- 210X .14213.
DATA AVA ILAB ILITY STATE MEN T
The GIFT R- package is available for download from CR AN at
https://CRAN.R- proje ct.org/packa ge=GIFT. The development
version of the package is available at https://github.com/BioGe
o M a c r o / G I F T . An associated website with tutorials is available
at https://bioge omacro.github.io/GIFT/ and an interactive over-
view of the data available can be found at https://gift.uni- goett
ingen.de. A permanent archive of the version 1.2.0 of the pack-
age is available on Zenodo at https://zenodo.org/recor d/8256512
(Denelle et al., 2023).
AUTHORSHIP GUIDELINES
Publications using the GIFT database should cite all primary sources
(Table S2) that were used as well as the version of GIFT and the origi-
nal publication of the GIFT database (Weigelt et al., 2020). All primary
references in GIFT are available with the GIFT_references() function.
If GIFT data are retrieved through the R- package, this paper should
also be cited. We also encourage authors to provide the R- script s
used to retrieve the data as supplementary files to their study to pro-
mote traceability and reproducibility. A few data contributors of GIFT
asked to restric t access to their data for now. These data can be ac-
cessed through the R- package specif ying a password- protected API
(provided by the authors of this article upon request) and their use
requires conta cting the aut ho rs of th e pr im ary res trict ed dat a and as k-
ing for permission to use them. We encourage researchers using GIFT
to contact us if any help is needed regarding the use of GIFT data.
ORCID
Pierre Denelle https://orcid.org/0000-0002-4729-3774
Patrick Weigelt https://orcid.org/0000-0002-2485-3708
Holger Kref t https://orcid.org/0000-0003-4471-8236
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SUPPORTING INFORMATION
Additional supporting information can be found online in the
Suppor ting Information section at the end of this article.
Figure S1: Number of regions retrieved with GIFT_checklists() using
different criteria for GIFT 3.0. The first red lollipop corresponds
to the black dashed line in Figure 1a. For the yellow and green
lollipops, the taxonomic group is set to Tracheophyta, i.e. vascular
plants and complete_taxon is set to TRUE. With complete_floristic =
TRUE, the number of regions with the floristic status set to native
is higher than with the floristic status set to all because it is easier
to get a complete knowledge of only native species in a region
than for all species. For the blue and purple lollipops, the floristic
status is set to native and complete_floristic is set to TRUE. With
complete_taxon = TRUE, the number of regions with angiosperms
is higher than with vascular plants because it is easier to get a
complete knowledge of only angiosperms in a region than for all
vascular plants.
Figure S2: Number of original unstandardized (green) and
standardized (purple) species names compared across versions of
2041210x, 2023, 11, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14213, Wiley Online Library on [02/11/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License

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Methods in Ecology and Evoluon
METHO DS IN ECOLOGY A ND EVOLUTION
GIFT. In GIFT 3.0, the new taxonomic workflow using the World
Checklist of Vascular Plants (Govaerts et al., 2021) allows to classify
species as accepted or not. The majority (95.6%) of standardized
names are considered as accepted.
Figure S3: Number of trait records, and number of traits available
in the different versions of GIFT. Panel (a) indicates how many trait
values are available (a record is a value of a particular trait at the
species level) and panel (b) shows the total number of traits.
Figure S4: Dependency graph of the 27 functions in the GIFT R
package. Each circle represent s one function. If one function uses
another one, then it is connected to it with a grey arrow. Functions
are colored according to their categor y (Table 1). The metadata
function GIFT_versions() is removed from this graph because it is a
metadata function that connected to all other functions.
Figure S5: Principle of the argument remove_overlap and area_
th_mainland in GIFT_spatial(). If remove_overlap is set to TRUE,
overlapping regions are removed. Depending on the value of
area_th_mainland in km2, the smaller or larger regions are kept.
Figure S6: Principle of the argument overlap_th in GIFT_spatial().
overlap_th expresses in percentage and defines above which
threshold regions are considered as overlapping.
Table S1: Number of miscellaneous variables and raster layers
available in all versions of the GIFT database. Numbers in italics
indicate variables that are only accessible through the password-
protected restricted API.
Table S2: Lis t of ref ere n ces us e d to pro duc e the fig u r es of th i s ar tic le.
How to cite this article: Denelle, P., Weigelt, P., & Kreft, H.
(2023). GIFT— An R package to access the Global Inventory
of Floras and Traits. Methods in Ecology and Evolution, 14,
2738–2748. https://doi.o rg /10.1111/2041-210X.14213
2041210x, 2023, 11, Downloaded from https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14213, Wiley Online Library on [02/11/2023]. See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License