FUNGuildR

FUNGuildR is a tool for assigning trait information based on matching to a taxonomic classification, using the FUNGuild database. In normal use, the database is queried for each use, because FUNGuild are continually updated as new information is submitted. However, FUNGuildR also includes functions to download the database and store it as an R object to speed up repeated queries, make queries reproducible over time, and allow local queries without internet access.

Installation

For the moment, FUNGuildR can only be installed from GitHub. To install, be sure you have installed the devtools package, and then type:

devtools::install_github("brendanf/FUNGuildR")

Guild assignment

The main function is funguild_assign(). It takes as its only required argument a data.frame, which should contain a character column named “Taxonomy”. It returns a version of the same data.frame (as a tibble) with additional columns:

taxon: The name of the matched taxon.
guid: Globally Unique Identifier for the database record.
mbNumber: The MycoBank number of the taxon.
taxonomicLevel: A numeric representation of the taxonomic rank; higher numbers are lower ranks.
trophicMode: A very general overview of how the organism gets its nutrition; one or more of Saprotroph, Pathotroph, and Symbiotroph.
guild: One or more narrower categories for how the organism gets its nutrition.
confidenceRanking: The confidence level of the guild assignment; Possible, Probable, or Highly Probable.
growthForm: The general growth morphology of the organism (or its fruiting body). Multiple values may be given.
trait: Additional traits about the organism, such as wood decay type or toxicity.
note: Additional notes about the entry.
citationSource: Citation(s) for the information about the taxon.

That’s it!

Here’s how it works on a sample database (scroll to see additional columns):

sample_fungi

Common.Name	Species	Taxonomy
Button mushroom	Agaricus bisporus	Fungi;Basidiomycota;Agaricomycetes;Agaricales;Agaricaceae;Agaricus;Agaricus bisporus
Death Cap	Amanita phalloides	Fungi;Basidiomycota;Agaricomycetes;Agaricales;Amanitaceae;Amanita;Amanita phalloides
Beer Yeast	Saccharomyces cerevisiae	Fungi;Ascomycota;Saccharomycetes;Saccharomycetales;Saccharomycetaceae;Saccharomyces;Saccharomyces cerevisiae
Rhizophagus	Rhizophagus irregularis	Fungi;Glomeromycota;Glomeromycetes;Glomerales;Glomeraceae;Rhizophagus;Rhizophagus irregularis
Dry rot	Serpula lacrymans	Fungi;Basidiomycota;Agaricomycetes;Boletales;Serpulaceae;Serpula;Serpula lacrymans
Cryptococcus	Cryptococcus neoformans	Fungi;Basidiomycota;Tremellomycetes;Tremellales;Tremellaceae;Cryptococcus;Cryptococcus neoformans
Dung Cannon	Pilobolus crystallinus	Fungi;Zygomycota;Mucoromycetes;Mucorales;Pilobolaceae;Pilobolus;Pilobolus crystallinus

sample_guilds <- funguild_assign(sample_fungi)
sample_guilds

Common.Name	Species	Taxonomy	taxon	guid	mbNumber	taxonomicLevel	trophicMode	guild	confidenceRanking	growthForm	trait	notes	citationSource
Button mushroom	Agaricus bisporus	Fungi;Basidiomycota;Agaricomycetes;Agaricales;Agaricaceae;Agaricus;Agaricus bisporus	Agaricaceae	1CB1CCAB-36B9-11D5-9548-00D0592D548C	80434	9	Saprotroph	Undefined Saprotroph	Probable	Agaricoid-Gasteroid-Secotioid	NULL	Primarily saprobes in grassland and woodland situations (Cannon & Kirk 2007)	Cannon PF, Kirk PM. 2007. Fungal Families of the World. CAB International, Cambridge (ISBN: 978-0851998275)
Death Cap	Amanita phalloides	Fungi;Basidiomycota;Agaricomycetes;Agaricales;Amanitaceae;Amanita;Amanita phalloides	Agaricales	715D162F-5F0E-40C8-A7DC-79D488D3F937	90508	7	Pathotroph-Saprotroph-Symbiotroph	Bryophyte Parasite-Dung Saprotroph-Ectomycorrhizal-Fungal Parasite-Leaf Saprotroph-Plant Parasite-Undefined Saprotroph-Wood Saprotroph	Possible	Agaricoid-Gasteroid-Microfungus-Secotioid-Yeast	NULL	Mushrooms and toadstools, Gill fungi, Agarics… lignicolous, sometimes muscicolous or fungicolous, saprobic, mycorrhizal, rarely parasitic on plants or fungi (Kirk et al. 2008)	Kirk PM et al. 2008. Dictionary of the Fungi. Tenth Edition. CAB International, Wallingford (ISBN: 978-0851998268)
Beer Yeast	Saccharomyces cerevisiae	Fungi;Ascomycota;Saccharomycetes;Saccharomycetales;Saccharomycetaceae;Saccharomyces;Saccharomyces cerevisiae	Saccharomyces cerevisiae	C140119E-2E48-43E7-A77A-3C749D931D94	492348	20	Saprotroph	Undefined Saprotroph	Probable	Yeast	NULL	NULL	James TY, et al. 2006. Nature 443:818-822 ((https://doi.org/10.1038/nature05110))
Rhizophagus	Rhizophagus irregularis	Fungi;Glomeromycota;Glomeromycetes;Glomerales;Glomeraceae;Rhizophagus;Rhizophagus irregularis	Glomeraceae	1CB1CD2A-36B9-11D5-9548-00D0592D548C	82026	9	Symbiotroph	Arbuscular Mycorrhizal	Highly Probable	Microfungus	NULL	NULL	Redecker D, et al. 2013. Mycorrhiza 23:515-531 ((https://doi.org/10.1007/s00572-013-0486-y))
Dry rot	Serpula lacrymans	Fungi;Basidiomycota;Agaricomycetes;Boletales;Serpulaceae;Serpula;Serpula lacrymans	Serpula lacrymans	1CB1A2AB-36B9-11D5-9548-00D0592D548C	102458	20	Saprotroph	Wood Saprotroph	Probable	Corticioid	Brown Rot	An aggressive brown-rot (dry rot) fungus that causes very significant economic losses through degradation of wooden parts of buildings (Cannon & Kirk 2007)	Cannon PF, Kirk PM. 2007. Fungal Families of the World. CAB International, Cambridge (ISBN: 978-0851998275)
Cryptococcus	Cryptococcus neoformans	Fungi;Basidiomycota;Tremellomycetes;Tremellales;Tremellaceae;Cryptococcus;Cryptococcus neoformans	Cryptococcus neoformans	1CB1BA14-36B9-11D5-9548-00D0592D548C	119294	20	Pathotroph	Animal Pathogen	Highly Probable	Dimorphic Yeast	NULL	Likely opportunistic human pathogen (Irinyi et al. 2015)	Kurtzman CP, et al. (eds.) 2011. The Yeasts, a Taxonomic Study. Fifth Edition. Vols 1-3. Elsevier, San Diego (ISBN: 9780444521491); Irinyi L, et al. 2015. Medical Mycology 53:313-337 ((https://doi.org/10.1093/mmy/myv008))
Dung Cannon	Pilobolus crystallinus	Fungi;Zygomycota;Mucoromycetes;Mucorales;Pilobolaceae;Pilobolus;Pilobolus crystallinus	Pilobolus	1CB1CA1E-36B9-11D5-9548-00D0592D548C	20420	13	Saprotroph	Dung Saprotroph	Highly Probable	NULL	NULL	NULL	Bell A. 1983. Dung Fungi: An Illustrated Guide to Coprophilous Fungi in New Zealand. Victoria University Press, Wellington (ISBN: 978-0864730015); Tedersoo L, et al. 2014. Science 346:e1256688 ((https://doi.org/10.1126/science.1256688))

For more information about the meaning of the new columns, see the FUNGuild manual.

Input data format

Each value in the Taxonomy column of the input data.frame should consist of a comma-, colon-, underscore-, or semicolon-delimited list of taxa which the organism on that row belongs to. You can see examples in the sample_fungi data presented above. Taxonomy strings which include taxonomic rank indicators in the styles used by Sintax (“k:”, “p:”…) or Unite (“k__,”p__“, …) are also accepted.

Such taxonomic classifications are frequently arranged from the most inclusive taxon (e.g., Kingdom) to the least inclusive taxon (e.g., Species), but this is not actually required for FUNGuild. Not all taxonomic ranks are required; for each row, the algorithm returns results only for the least inclusive taxon which is present in the database.

Database caching

By default, funguild_assign() downloads the FUNGuild database each time they are invoked. In many analysis workflows, where guilds need to be assigned only once, this is not a problem; because the databases are continuously updated, it is good to use the most current version. However, if you are going to call the functions many times, or if you plan to assign guilds in a situation where you have no internet access, you can cache the database(s) locally using the functions get_funguild_db(). This returns the database as a tibble, which can be passed as a second argument to funguild_assign().

fung <- get_funguild_db()

# This isn't necessary for a single query, but it works.
fung_guilds <- funguild_assign(sample_fungi, db = fung)

# It might be more useful in this situation
data_guilds <- lapply(many_datasets, funguild_assign, db = fung)

# Or you can save it for later offline use
saveRDS(fung, "funguild.rds")

#And then load it again
fung <- loadRDS("funguild.rds")

This strategy can also be used for reproduceable research, to store the same version of the database which was used in the original analysis.

Database queries

From the current development version, FUNGuildR also allows queries to the FUNGuild web API. The fields taxon, guid, mbNumber, trophicMode, guild, growthForm, and trait are searchable. For instance, to find all fungi annotated as causing brown rot (a kind of wood decay):

brownrotters <- funguild_query("brown rot", "trait")
nrow(brownrotters)
#> [1] 93

Here are the first few:

head(brownrotters)

taxon	guid	mbNumber	taxonomicLevel	trophicMode	guild	confidenceRanking	growthForm	trait	notes	citationSource
Amylocorticiellum	01898B69-3447-4EAC-B250-646F4B3D5CF8	28664	13	Saprotroph	Undefined Saprotroph	Probable	Corticioid	Brown Rot	NULL	Tedersoo L, et al. 2014. Science 346:e1256688 ((https://doi.org/10.1126/science.1256688))
Amylocorticium	1CB1C472-36B9-11D5-9548-00D0592D548C	17064	13	Saprotroph	Undefined Saprotroph	Probable	NULL	Brown Rot	NULL	Tedersoo L, et al. 2014. Science 346:e1256688 ((https://doi.org/10.1126/science.1256688))
Amylocystis	1CB1C473-36B9-11D5-9548-00D0592D548C	17065	13	Saprotroph	Wood Saprotroph	Highly Probable	Polyporoid	Brown Rot	NULL	Gilbertson RL, Ryvarden L. 1987-1987. North American Polypores. Fungiflora, Oslo (ISBN: 978-0945345060)
Amylosporus	1CB1C475-36B9-11D5-9548-00D0592D548C	17072	13	Saprotroph	Wood Saprotroph	Highly Probable	Polyporoid	Brown Rot	NULL	Gilbertson RL, Ryvarden L. 1987-1987. North American Polypores. Fungiflora, Oslo (ISBN: 978-0945345060)
Anomoporia	1CB1C482-36B9-11D5-9548-00D0592D548C	17080	13	Saprotroph	Wood Saprotroph	Highly Probable	Corticioid	Brown Rot	NULL	Gilbertson RL, Ryvarden L. 1987-1987. North American Polypores. Fungiflora, Oslo (ISBN: 978-0945345060)
Antrodia	1CB17DB2-36B9-11D5-9548-00D0592D548C	17083	13	Saprotroph	Wood Saprotroph	Highly Probable	Corticioid	Brown Rot	NULL	Gilbertson RL, Ryvarden L. 1987-1987. North American Polypores. Fungiflora, Oslo (ISBN: 978-0945345060)

The characters “%” and “*” can be used as wildcards. For instance, we can search for all fungi where the wood decay type is listed:

allrotters <- funguild_query("* rot", "trait")
nrow(allrotters)
#> [1] 656
unique(allrotters$trait)
#> [1] "White Rot"            "Soft Rot"             "Brown Rot; White Rot"
#> [4] "Brown Rot"            "Brown Rot-White Rot"

Queries can also be run against a locally cached database.

fungi <- get_funguild_database()
allrotters <- funguild_query("* rot", "trait", db = fungi)

NEMAGuild

As of April 2021, the NEMAGuild database is temporarily offline. However, FUNGuildR has functions nemaguild_assign() and get_nemaguild_db() to access it in exactly the same ways as the FUNGuild database. These functions will not work for the time being (unless you already have a cached local copy of NEMAGuild!) but they should work again when NEMAGuild is back online.