The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
Please follow the secure_the_api_key)
steps and secure the API in the R environment before retrieving the
species traits form the database. To check on the available traits in
the database, you can check with the
fw_dbguide() or browse the database
directly in the species
traits.
To ensure the exact trait spellings are used, the user is
strongly advised to run fw_dbguide()
function and filter out the organism groups. The trait names can be
copied and pasted in the ecoparams
parameter of the fw_fetchdata()
function.
Multiple species can be set in a list or dataframe.
Wide data formats can be displayed, but the longer version is the output by default.
Ensure the right species names are indicated to avoid detailed checks that delays data search and might lead to erroneous trait extraction or errors. Checks are conducted on the species names to ensure they are harmonized to trait searches.
Data output columns and meaning
| Function | Explanation |
|---|---|
ID_FWE |
Indicates the record ID number in the www.freshwaterecology.info database. |
OrganismGroup |
The highest taxonomic group nomenclature, which
includes five groups, namely macroinvertebrates, fish, phytoplankton, phtyobenthos (diatoms) and macrophtes. |
TaxaGroup |
The taxonomic classification of a species. Its a class
for phytobenthos but sometimes order, family.Not recommended for querying data. |
Family |
Family of particular species or taxonomic group.
Recommended for data search. search since taxa families are taxonomic classification. |
Genus |
The taxonomic genera for a particular taxon. Recommended for data search. |
Species |
The specific epithet for a particular species.
Combining both the genera forms the taxonomic scientific name. Recommended for data search but the but its disadvantageous if many are required and are from the same genus or family genus or family |
Taxonname |
Complete taxonomic but without the naming authorities.
Not used in data search |
Author |
The taxonomic authority of a particular of taxon. |
Parameter |
The ecological parameter being searched from the
database. The raw and tidyr names can be obtained using the fw_dbguide() function. |
CategoryName |
The particular ecological trait of taxon or species. |
CategoryLevels |
Some ecological parameters such as stream ecological preference for macroinvertebrates, catchment region for fish, provide more information. For example, for catchment region, beside knowing where the basin is located, its indicated whether the . specie is native or invasive in particular basin. |
DataType |
The type, whether fuzzy, factor, categorical or
numerical. However, the author reclassify the data in the subsequent analysis |
ClassificationType |
The data classification criteria based on Schmidt-Kloiber & Herring et al., 2012. |
CategoryExplanaiton |
Describe the different category meaning. |
1.1: Single species
migration <- fw_fetchdata(data = "Abramis brama",
organismgroup = 'fi',
ecoparams = 'migration')
head(migration$ecodata)
#species data archived in fwtraits
data("speciesdata")
traitsout <- fw_fetchdata(data = speciesdata,
organismgroup = 'fi',
taxonomic_column = 'scientificName',
ecoparams = c('migration', 'threat austria',
'oxygen tolerence', 'migration fibs'),
taxalevel = 'species')
head(traitsout$ecodata)1.3 Visualizing fish traits
2.1: Single species
mmdata_traits <- fw_fetchdata(data = "Margaritifera margaritifera",
organismgroup = 'mi',
ecoparams = c('stream zonation preference'),
inform = TRUE)2.2: More than one species in a vector/list
speciesvec <- c("Margaritifera margaritifera",
"Pseudunio auricularius",
"Musculium lacustre",
"Musculium transversum",
"Parastenocaris germanica")
multspp <- fw_fetchdata(data = speciesvec,
organismgroup = 'mi',
ecoparams = c('stream zonation preference'),
inform = TRUE)
head(multspp$ecodata)2.3: More than one species in a dataframe
macrodf <- data.frame(organismgroup = rep('mi', 13),
species = c("Margaritifera margaritifera",
"Pseudunio auricularius",
"Musculium lacustre",
"Musculium transversum",
"Corbicula fluminea",
"Congeria leucophaeata",
"Dreissena polymorpha",
"Dreissena rostriformis bugensis",
"Parastenocaris germaica",
"Branchiobdella balcanica",
"Branchiobdella hexadonta",
"Branchiobdella parasita",
"Branchiobdella pentadonta"))
multspp_df <- fw_fetchdata(data = macrodf,
organismgroup = 'mi',
taxonomic_column = 'species',
ecoparams = c("stream zonation preference", "feeding type"),
inform = TRUE)
head(multspp_df$ecodata)2.4: Data visualization for macroinvertebrates
If the species considered are more than 1, then visualization can be to determine the frequency of each trait. This is an optional function for post data searches.
pbdata <- fw_fetchdata(data = c("Gongrosira debaryana",
"Gongrosira fluminensis",
"Hydrodictyon reticulatum",
"Sphaerobotrys fluviatilis",
"Stigeoclonium farctum",
"Stigeoclonium tenue",
"Tetraspora gelatinosa",
"Thorea hispida"),
organismgroup = 'pb',
ecoparams = c('substrate preference'))
head(pbdata$ecodata)
mipbdata <- fw_fetchdata(data = list(mi=c("Congeria kusceri",
"Congeria leucophaeata",
"Dreissena polymorpha",
"Dreissena rostriformis bugensis"),
pb= c("Gongrosira debaryana",
"Gongrosira fluminensis",
"Hydrodictyon reticulatum",
"Sphaerobotrys fluviatilis",
"Stigeoclonium farctum",
"Stigeoclonium tenue",
"Tetraspora gelatinosa",
"Thorea hispida")),
organismgroup = c('mi','pb'),
ecoparams = list(mi = c('stream zonation preference'),
pb = c('substrate preference')), details = TRUE)
head(mipbdata$ecodata)
ppdata <- fw_fetchdata(data = c("Navicula radiosa", 'Acanthoceras zachariasii',
"Achnanthes brevipes",
"Achnanthidium catenatum",
"Actinocyclus normanii",
"Achnanthidium subatomus"),
organismgroup = 'pp',
ecoparams = c('stenoecy factor', 'life form'),
cachefolder = 'cache',
warn = TRUE,
inform = TRUE)
head(ppdata$ecodata)NOTE: Based the on the FWE database, the phytoplantkon don’t have families but rather taxa groups, genus, and species levels. Therefore, for data extraction the family level for phytoplankton is not possible.Check the table for the definition of a Taxa Group.
ppdata_genus <- fw_fetchdata(data = c("Navicula"),
organismgroup = 'pp',
ecoparams = c('stenoecy factor', 'life form'),
cachefolder = 'cache',
taxalevel = 'genus',
inform = TRUE)
#Only Navicula genus but but multiple species
print(unique(ppdata_genus$ecodata$Genus))
ppdata_taxagroup <- fw_fetchdata(data = c("Bacillariophyceae"),
organismgroup = 'pp',
ecoparams = c('stenoecy factor', 'life form'),
cachefolder = 'cache',
taxalevel = 'taxagroup',
inform = TRUE)
#More than more 1 genus
print(unique(ppdata_taxagroup$ecodata$Genus)[1:5])Schmidt-Kloiber, A., & Hering, D. (2015). www.freshwaterecology.info - An online tool that unifies, standardises and codifies more than 20,000 European freshwater organisms and their ecological preferences. Ecological Indicators, 53, 271-282. https://doi.org/10.1016/j.ecolind.2015.02.007
Wickham H (2024). httr2: Perform HTTP Requests and Process the Responses. R package version 1.0.3,https://CRAN.R-project.org/package=httr2
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.