Retrieve data for taxomomic groups.
Source:vignettes/data_for_taxa_groups.Rmd
data_for_taxa_groups.RmdStep 1: Securing and loading the API key.
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.
Step2: Fetching groups data and visualisation
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 theecoparamsparameter of thefw_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. Fishes
1.1: Single species
migration <- fw_fetchdata(data = "Abramis brama",
organismgroup = 'fi',
ecoparams = 'migration')
#> ========================================================================
#> Congratulations!!! Ready to interact with www.freshwaterecology.info database
#> =========================================================================
head(migration$ecodata)
#> ID_FWE OrganismGroup TaxaGroup Family Genus Species Taxonname
#> 1 210 fi Cypriniformes Cyprinidae Abramis brama Abramis brama
#> Author Parameter CategoryName CategoryAttributes
#> 1 (Linnaeus, 1758) migration potamodromous NA
#> CategoryExplanation DataType
#> 1 migratory fish species; whole life cycle is spent in freshwaters Nominal
#> ClassificationType AssignementInfo
#> 1 single category assignment system <NA>
#species data archived in fwtraits
data("speciesdata")
traitsout <- fw_fetchdata(data = speciesdata,
organismgroup = 'fi',
taxonomic_column = 'scientificName',
ecoparams = c('migration', 'threat austria',
'oxygen tolerence', 'migration fibs'),
taxalevel = 'species')
head(traitsout$ecodata)
#> ID_FWE OrganismGroup TaxaGroup Family Genus Species
#> 1 210 fi Cypriniformes Cyprinidae Abramis brama
#> 2 216 fi Cypriniformes Cyprinidae Alburnus alburnus
#> 3 222 fi Anguilliformes Anguillidae Anguilla anguilla
#> 4 226 fi Cypriniformes Nemacheilidae Barbatula barbatula
#> 5 227 fi Cypriniformes Cyprinidae Barbus barbus
#> 6 239 fi Scorpaeniformes Cottidae Cottus gobio
#> Taxonname Author Parameter CategoryName
#> 1 Abramis brama (Linnaeus, 1758) migration potamodromous
#> 2 Alburnus alburnus (Linnaeus, 1758) migration potamodromous
#> 3 Anguilla anguilla (Linnaeus, 1758) migration diadromous
#> 4 Barbatula barbatula (Linnaeus, 1758) migration potamodromous
#> 5 Barbus barbus (Linnaeus, 1758) migration potamodromous
#> 6 Cottus gobio Linnaeus, 1758 migration no migration
#> CategoryAttributes
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>
#> CategoryExplanation
#> 1 migratory fish species; whole life cycle is spent in freshwaters
#> 2 migratory fish species; whole life cycle is spent in freshwaters
#> 3 migratory fish species; parts of the life cycle are spent in fresh and salt water
#> 4 migratory fish species; whole life cycle is spent in freshwaters
#> 5 migratory fish species; whole life cycle is spent in freshwaters
#> 6 species with no migration movements
#> DataType ClassificationType AssignementInfo
#> 1 Nominal single category assignment system <NA>
#> 2 Nominal single category assignment system <NA>
#> 3 Nominal single category assignment system <NA>
#> 4 Nominal single category assignment system <NA>
#> 5 Nominal single category assignment system <NA>
#> 6 Nominal single category assignment system <NA>1.3 Visualizing fish traits
fw_visualize(output = traitsout)
2. Macroinvertebrates
2.1: Single species
mmdata_traits <- fw_fetchdata(data = "Margaritifera margaritifera",
organismgroup = 'mi',
ecoparams = c('stream zonation preference'),
inform = TRUE)
#> Macroinvertebrates for parameter -1- data is downloading. Be patient..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)
#> Macroinvertebrates data was already downloaded.
head(multspp$ecodata)
#> ID_FWE OrganismGroup TaxaGroup Family Genus Species
#> 1 5943 mi Bivalvia MARGARITIFERIDAE Margaritifera margaritifera
#> 2 5943 mi Bivalvia MARGARITIFERIDAE Margaritifera margaritifera
#> 3 5943 mi Bivalvia MARGARITIFERIDAE Margaritifera margaritifera
#> 4 6653 mi Bivalvia MARGARITIFERIDAE Pseudunio auricularius
#> 5 6653 mi Bivalvia MARGARITIFERIDAE Pseudunio auricularius
#> 6 6653 mi Bivalvia MARGARITIFERIDAE Pseudunio auricularius
#> Taxonname Author Parameter
#> 1 Margaritifera margaritifera (LINNAEUS, 1758) stream zonation preference
#> 2 Margaritifera margaritifera (LINNAEUS, 1758) stream zonation preference
#> 3 Margaritifera margaritifera (LINNAEUS, 1758) stream zonation preference
#> 4 Pseudunio auricularius (SPENGLER, 1793) stream zonation preference
#> 5 Pseudunio auricularius (SPENGLER, 1793) stream zonation preference
#> 6 Pseudunio auricularius (SPENGLER, 1793) stream zonation preference
#> CategoryName CategoryAttributes CategoryExplanation DataType
#> 1 epirhithral 2 upper-trout region Fuzzy
#> 2 metarhithral 5 lower-trout region Fuzzy
#> 3 hyporhithral 3 grayling region Fuzzy
#> 4 <NA> <NA> <NA> Fuzzy
#> 5 <NA> <NA> <NA> Fuzzy
#> 6 <NA> <NA> <NA> Fuzzy
#> ClassificationType AssignementInfo
#> 1 10 point assignment system <NA>
#> 2 10 point assignment system <NA>
#> 3 10 point assignment system <NA>
#> 4 10 point assignment system <NA>
#> 5 10 point assignment system <NA>
#> 6 10 point assignment system <NA>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)
#> Macroinvertebrates for parameter -1- data is downloading. Be patient..
#> Macroinvertebrates for parameter -3- data is downloading. Be patient..
head(multspp_df$ecodata)
#> ID_FWE OrganismGroup TaxaGroup Family Genus Species
#> 1 4999 mi Bivalvia DREISSENIDAE Dreissena polymorpha
#> 2 4999 mi Bivalvia DREISSENIDAE Dreissena polymorpha
#> 3 4999 mi Bivalvia DREISSENIDAE Dreissena polymorpha
#> 4 5943 mi Bivalvia MARGARITIFERIDAE Margaritifera margaritifera
#> 5 5943 mi Bivalvia MARGARITIFERIDAE Margaritifera margaritifera
#> 6 5943 mi Bivalvia MARGARITIFERIDAE Margaritifera margaritifera
#> Taxonname Author Parameter
#> 1 Dreissena polymorpha (PALLAS, 1771) stream zonation preference
#> 2 Dreissena polymorpha (PALLAS, 1771) stream zonation preference
#> 3 Dreissena polymorpha (PALLAS, 1771) stream zonation preference
#> 4 Margaritifera margaritifera (LINNAEUS, 1758) stream zonation preference
#> 5 Margaritifera margaritifera (LINNAEUS, 1758) stream zonation preference
#> 6 Margaritifera margaritifera (LINNAEUS, 1758) stream zonation preference
#> CategoryName CategoryAttributes
#> 1 epipotamal 2
#> 2 metapotamal 4
#> 3 littoral 4
#> 4 epirhithral 2
#> 5 metarhithral 5
#> 6 hyporhithral 3
#> CategoryExplanation DataType
#> 1 barbel region Fuzzy
#> 2 bream region Fuzzy
#> 3 lake and stream shorelines, lentic sites, ponds etc. Fuzzy
#> 4 upper-trout region Fuzzy
#> 5 lower-trout region Fuzzy
#> 6 grayling region Fuzzy
#> ClassificationType AssignementInfo
#> 1 10 point assignment system <NA>
#> 2 10 point assignment system <NA>
#> 3 10 point assignment system <NA>
#> 4 10 point assignment system <NA>
#> 5 10 point assignment system <NA>
#> 6 10 point assignment system <NA>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.
fw_visualize(output = multspp)
fw_visualize(output = multspp_df)
3. Macrophytes
mpp <- fw_fetchdata(data = c("Amblystegium fluviatile",
"Amblystegium humile",
"Amblystegium riparium",
"Amblystegium serpens",
"Amblystegium tenax",
"Amblystegium varium"),
organismgroup = 'mp',
ecoparams = c('zone - systema'))4. Phytobenthos
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)
#> ID_FWE OrganismGroup TaxaGroup Family Genus Species
#> 1 9503 pb Chlorophyceae Chaetophoraceae Gongrosira debaryana
#> 2 9503 pb Chlorophyceae Chaetophoraceae Gongrosira debaryana
#> 3 9504 pb Chlorophyceae Chaetophoraceae Gongrosira fluminensis
#> 4 9576 pb Chlorophyceae Chlorophyceae Sphaerobotrys fluviatilis
#> 5 9584 pb Chlorophyceae Chaetophoraceae Stigeoclonium farctum
#> 6 9584 pb Chlorophyceae Chaetophoraceae Stigeoclonium farctum
#> Taxonname Author Parameter CategoryName
#> 1 Gongrosira debaryana Rabenhorst 0 substrate preference epilithic
#> 2 Gongrosira debaryana Rabenhorst 0 substrate preference epiphytic
#> 3 Gongrosira fluminensis F.E.Fritsch 0 substrate preference epilithic
#> 4 Sphaerobotrys fluviatilis Butcher 0 substrate preference epilithic
#> 5 Stigeoclonium farctum Berthold 0 substrate preference epilithic
#> 6 Stigeoclonium farctum Berthold 0 substrate preference epiphytic
#> CategoryAttributes CategoryExplanation DataType
#> 1 NA on stone Nominal
#> 2 NA on plants Nominal
#> 3 NA on stone Nominal
#> 4 NA on stone Nominal
#> 5 NA on stone Nominal
#> 6 NA on plants Nominal
#> ClassificationType AssignementInfo
#> 1 presence/absence assignment system <NA>
#> 2 presence/absence assignment system <NA>
#> 3 presence/absence assignment system <NA>
#> 4 presence/absence assignment system <NA>
#> 5 presence/absence assignment system <NA>
#> 6 presence/absence assignment system <NA>
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)
#> ======================================
#> DATA OUTPUT SUMMARY
#> ======================================
#> Number of Organism Groups Considered : 2
#> Number of Organism Groups Considered : mi,pb
#> Succesful organism Groups : 2
#> Failed organism Groups : 0
#> Taxa level used : species
#> Failed at taxa level : NA
#> Number of parameters : 2
#> Error rate for wrong names : 20
#> Caching folder : cache
#> ======================================
head(mipbdata$ecodata)
#> ID_FWE OrganismGroup TaxaGroup Family Genus Species
#> 1 4999 mi Bivalvia DREISSENIDAE Dreissena polymorpha
#> 2 4999 mi Bivalvia DREISSENIDAE Dreissena polymorpha
#> 3 4999 mi Bivalvia DREISSENIDAE Dreissena polymorpha
#> 4 11585 mi Bivalvia DREISSENIDAE Congeria leucophaeata
#> 5 11585 mi Bivalvia DREISSENIDAE Congeria leucophaeata
#> 6 21963 mi Bivalvia DREISSENIDAE Congeria kusceri
#> Taxonname Author Parameter CategoryName
#> 1 Dreissena polymorpha (PALLAS, 1771) stream zonation preference epipotamal
#> 2 Dreissena polymorpha (PALLAS, 1771) stream zonation preference metapotamal
#> 3 Dreissena polymorpha (PALLAS, 1771) stream zonation preference littoral
#> 4 Congeria leucophaeata (CONRAD, 1831) stream zonation preference metapotamal
#> 5 Congeria leucophaeata (CONRAD, 1831) stream zonation preference hypopotamal
#> 6 Congeria kusceri BOLE, 1962 stream zonation preference <NA>
#> CategoryAttributes CategoryExplanation
#> 1 2 barbel region
#> 2 4 bream region
#> 3 4 lake and stream shorelines, lentic sites, ponds etc.
#> 4 4 bream region
#> 5 6 brackish water region
#> 6 <NA> <NA>
#> DataType ClassificationType AssignementInfo
#> 1 Fuzzy 10 point assignment system <NA>
#> 2 Fuzzy 10 point assignment system <NA>
#> 3 Fuzzy 10 point assignment system <NA>
#> 4 Fuzzy 10 point assignment system <NA>
#> 5 Fuzzy 10 point assignment system <NA>
#> 6 Fuzzy 10 point assignment system <NA>5. Phytoplankton
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)
#> Phytoplankton data is downloading, be calm and patient on the first run...
#> Phytoplankton data is downloading, be calm and patient on the first run...
head(ppdata$ecodata)
#> ID_FWE OrganismGroup TaxaGroup Family Genus Species
#> 1 221 pp Bacillariophyceae Achnanthidium catenatum
#> 2 221 pp Bacillariophyceae Achnanthidium catenatum
#> 3 221 pp Bacillariophyceae Achnanthidium catenatum
#> 4 779 pp Bacillariophyceae Achnanthidium subatomus
#> 5 6197 pp Bacillariophyceae Navicula radiosa
#> 6 6197 pp Bacillariophyceae Navicula radiosa
#> Taxonname Author Parameter CategoryName
#> 1 Achnanthidium catenatum (Bily & Marvan) Lange-Bertalot life form planktic
#> 2 Achnanthidium catenatum (Bily & Marvan) Lange-Bertalot life form benthic
#> 3 Achnanthidium catenatum (Bily & Marvan) Lange-Bertalot life form pleuston
#> 4 Achnanthidium subatomus (Hustedt) Lange-Bertalot life form B_drifted
#> 5 Navicula radiosa Kützing life form planktic
#> 6 Navicula radiosa Kützing life form benthic
#> CategoryAttributes CategoryExplanation DataType
#> 1 <NA> planktic living species Nominal
#> 2 <NA> benthic living species Nominal
#> 3 <NA> species living on the water surface Nominal
#> 4 <NA> <NA> Nominal
#> 5 <NA> planktic living species Nominal
#> 6 <NA> benthic living species Nominal
#> ClassificationType AssignementInfo
#> 1 presence/absence assignment system <NA>
#> 2 presence/absence assignment system <NA>
#> 3 presence/absence assignment system <NA>
#> 4 presence/absence assignment system <NA>
#> 5 presence/absence assignment system <NA>
#> 6 presence/absence assignment system <NA>Collating by family and genus taxa levels for different species
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)
#> Phytoplankton data was already downloaded.
#> Phytoplankton data was already downloaded.
#Only Navicula genus but but multiple species
print(unique(ppdata_genus$ecodata$Genus))
#> [1] "Navicula"
ppdata_taxagroup <- fw_fetchdata(data = c("Bacillariophyceae"),
organismgroup = 'pp',
ecoparams = c('stenoecy factor', 'life form'),
cachefolder = 'cache',
taxalevel = 'taxagroup',
inform = TRUE)
#> Phytoplankton data was already downloaded.
#> Phytoplankton data was already downloaded.
#More than more 1 genus
print(unique(ppdata_taxagroup$ecodata$Genus)[1:5])
#> [1] "Achnanthidium" "Amphora" "Asterionella" "Aulacoseira"
#> [5] "Caloneis"Step3. References
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