Title: | Species Trait Data from Around the Web |
---|---|
Description: | Species trait data from many different sources, including sequence data from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>), plant trait data from 'BETYdb', data from 'EOL' 'Traitbank', 'Birdlife' International, and more. |
Authors: | David LeBauer [aut, cre] |
Maintainer: | David LeBauer <[email protected]> |
License: | MIT + file LICENSE |
Version: | 0.5.1 |
Built: | 2024-08-18 05:34:38 UTC |
Source: | https://github.com/ropensci/traits |
Currently included in traits
with the associated function name or
function prefix:
BETYdb http://www.betydb.org - betydb_
National Center for Biotechnology Information - NCBI
http://www.ncbi.nlm.nih.gov/ - ncbi_
Encyclopedia of Life Traitbank - traitbank_
Birdlife International https://www.birdlife.org/ -
birdlife_
LEDA Traitbase http://www.leda-traitbase.org/LEDAportal/index.jsp -
leda_
Zanne et al. plant dataset - tr_zanne()
Amniote life history dataset - tr_ernest()
See also traits-defunct
Scott Chamberlain
Ignasi Bartomeus
Zachary Foster
David LeBauer
David Harris
Rupert Collins
Search for traits from BETYdb
Get details about a single item from a table
betydb_record( id, table, api_version = NULL, betyurl = NULL, fmt = NULL, key = NULL, user = NULL, pwd = NULL, progress = TRUE, ... ) betydb_trait( id, genus = NULL, species = NULL, api_version = NULL, betyurl = NULL, fmt = "json", key = NULL, user = NULL, pwd = NULL, progress = TRUE, ... ) betydb_specie( id, genus = NULL, species = NULL, api_version = NULL, betyurl = NULL, fmt = "json", key = NULL, user = NULL, pwd = NULL, progress = TRUE, ... ) betydb_citation( id, genus = NULL, species = NULL, api_version = NULL, betyurl = NULL, fmt = "json", key = NULL, user = NULL, pwd = NULL, progress = TRUE, ... ) betydb_site( id, api_version = NULL, betyurl = NULL, fmt = "json", key = NULL, user = NULL, pwd = NULL, progress = TRUE, ... ) betydb_experiment( id, api_version = NULL, betyurl = NULL, fmt = "json", key = NULL, user = NULL, pwd = NULL, progress = TRUE, ... )
betydb_record( id, table, api_version = NULL, betyurl = NULL, fmt = NULL, key = NULL, user = NULL, pwd = NULL, progress = TRUE, ... ) betydb_trait( id, genus = NULL, species = NULL, api_version = NULL, betyurl = NULL, fmt = "json", key = NULL, user = NULL, pwd = NULL, progress = TRUE, ... ) betydb_specie( id, genus = NULL, species = NULL, api_version = NULL, betyurl = NULL, fmt = "json", key = NULL, user = NULL, pwd = NULL, progress = TRUE, ... ) betydb_citation( id, genus = NULL, species = NULL, api_version = NULL, betyurl = NULL, fmt = "json", key = NULL, user = NULL, pwd = NULL, progress = TRUE, ... ) betydb_site( id, api_version = NULL, betyurl = NULL, fmt = "json", key = NULL, user = NULL, pwd = NULL, progress = TRUE, ... ) betydb_experiment( id, api_version = NULL, betyurl = NULL, fmt = "json", key = NULL, user = NULL, pwd = NULL, progress = TRUE, ... )
id |
(integer) One or more ids for a species, site, variable, etc. |
table |
(character) Name of the database table with which this ID is associated. |
api_version |
(character) Which version of the BETY API should we query? One of "v0" or "beta". Default is |
betyurl |
(string) url to target instance of betydb. Default is |
fmt |
(character) Format to return data in, one of json, xml, csv. Only json currently supported. |
key |
(character) An API key. Use this or user/pwd combo. Save in your
|
user , pwd
|
(character) A user name and password. Use a user/pwd combo or an API key.
Save in your |
progress |
show progress bar? default: |
... |
Curl options passed on to |
genus |
(character) A genus name. Optional |
species |
(character) A specific epithet. Optional |
BETYdb includes a primary home page (betydb.org) focused on bioenergy crops as well as a network of harmonized databases that support and share data among more focused research programs.
For a list of publicly accessible instances of BETYdb and the urls that can be queried, see https://pecan.gitbooks.io/betydb-documentation/content/distributed_betydb.html
This package queries plant traits, phenotypes, biomass yields, and ecosystem functions. It does not currently interface with the workflow and provenance data that support PEcAn Project (pecanproject.org) and TERRA REF (terraref.org) software.
API documentation: https://pecan.gitbooks.io/betydb-data-access/content/API.html
API endpoints are here: https://www.betydb.org/api/docs
This package currently uses the original 'v0' API by default.
To use a newer version, set api_version
.
Newer versions of the API will support database inserts.
Defers to use API key first since it's simpler, but if you don't have an API key, you can supply a username and password.
Singular functions like betydb_trait
accept an id and additional parameters,
and return a list of variable outputs depending on the inputs.
However, plural functions like betydb_traits
accept query parameters, but not
ids, and always return a single data.frame.
betydb_search("Search terms", ...)
is a convenience wrapper that passes all further arguments to betydb_query(table = "search", search = "Search terms", ...)
. See there for details on possible arguments.
API documentation https://pecan.gitbooks.io/betydb-data-access/content/API.html and https://www.betydb.org/api/docs
## Not run: # General Search out <- betydb_search(query = "Switchgrass Yield") library("dplyr") out %>% group_by(id) %>% summarise(mean_result = mean(as.numeric(mean), na.rm = TRUE)) %>% arrange(desc(mean_result)) # Get by ID ## Traits betydb_trait(id = 10) ## Species betydb_specie(id = 1) ## Citations betydb_citation(id = 1) ## Site information betydb_site(id = 795) ## End(Not run)
## Not run: # General Search out <- betydb_search(query = "Switchgrass Yield") library("dplyr") out %>% group_by(id) %>% summarise(mean_result = mean(as.numeric(mean), na.rm = TRUE)) %>% arrange(desc(mean_result)) # Get by ID ## Traits betydb_trait(id = 10) ## Species betydb_specie(id = 1) ## Citations betydb_citation(id = 1) ## Site information betydb_site(id = 795) ## End(Not run)
Query a BETY table
betydb_query( ..., table = "search", key = NULL, api_version = NULL, betyurl = NULL, user = NULL, pwd = NULL, progress = TRUE ) betydb_search( query = "Maple SLA", ..., include_unchecked = NULL, progress = TRUE )
betydb_query( ..., table = "search", key = NULL, api_version = NULL, betyurl = NULL, user = NULL, pwd = NULL, progress = TRUE ) betydb_search( query = "Maple SLA", ..., include_unchecked = NULL, progress = TRUE )
... |
(named character) Columns to query, as key="value" pairs. Note that betydb_query passes these along to BETY with no check whether the requested keys exist in the specified table. |
table |
(character) The name of the database table to query, or "search" (the default) for the traits and yields view |
key |
(character) An API key. Use this or user/pwd combo.
Save in your |
api_version |
(character) Which version of the BETY API should we query? One of "v0" or "beta".
Default is |
betyurl |
(string) url to target instance of betydb.
Default is |
user , pwd
|
(character) A user name and password. Use a user/pwd combo or an API key.
Save in your |
progress |
show progress bar? default: |
query |
(character) A string containing one or more words to be queried across all columns of the "search" table. |
include_unchecked |
(logical) Include results that have not been quality checked? Applies only to tables with a "checked" column: "search", "traits", "yields". Default is to exclude unchecked values. |
Use betydb_query to retrieve records from a table that match on all the column filters specified in '...'. If no filters are specified, retrieves the whole table. In API versions that support it (i.e. not in v0), filter strings beginning with "~" are treated as regular expressions.
A data.frame with attributes containing request metadata, or NULL if the query produced no results
## Not run: # literal vs regular expression vs anchored regular expression: betydb_query(units = "Mg", table = "variables") # NULL betydb_query(units = "Mg/ha", table = "variables") %>% select(name) %>% c() # $name # [1] "a_biomass" "root_live_biomass" # [3] "leaf_dead_biomass_in_Mg_ha" "SDM" betydb_query(genus = "Miscanthus", table = "species") %>% nrow() # [1] 10 (betydb_query(genus = "~misc", table = "species", api_version = "beta") %>% select(genus) %>% unique() %>% c()) # $genus # [1] "Platymiscium" "Miscanthus" "Dermiscellum" (betydb_query(genus = "~^misc", table = "species", api_version = "beta") %>% select(genus) %>% unique() %>% c()) # $genus # [1] "Miscanthus" ## End(Not run)
## Not run: # literal vs regular expression vs anchored regular expression: betydb_query(units = "Mg", table = "variables") # NULL betydb_query(units = "Mg/ha", table = "variables") %>% select(name) %>% c() # $name # [1] "a_biomass" "root_live_biomass" # [3] "leaf_dead_biomass_in_Mg_ha" "SDM" betydb_query(genus = "Miscanthus", table = "species") %>% nrow() # [1] 10 (betydb_query(genus = "~misc", table = "species", api_version = "beta") %>% select(genus) %>% unique() %>% c()) # $genus # [1] "Platymiscium" "Miscanthus" "Dermiscellum" (betydb_query(genus = "~^misc", table = "species", api_version = "beta") %>% select(genus) %>% unique() %>% c()) # $genus # [1] "Miscanthus" ## End(Not run)
Get bird habitat information from BirdLife/IUCN
birdlife_habitat(id)
birdlife_habitat(id)
id |
A single IUCN species ID |
a data.frame
with level 1 and level 2 habitat classes, as
well as importance ratings and occurrence type (e.g. breeding or
non-breeding). The habitat classification scheme is described
at https://www.iucnredlist.org/resources/classification-schemes
David J. Harris [email protected]
Other birdlife:
birdlife_threats()
## Not run: # Setophaga chrysoparia birdlife_habitat(22721692) # Passer domesticus birdlife_habitat(103818789) ## End(Not run)
## Not run: # Setophaga chrysoparia birdlife_habitat(22721692) # Passer domesticus birdlife_habitat(103818789) ## End(Not run)
Get bird threat information from BirdLife/IUCN
birdlife_threats(id)
birdlife_threats(id)
id |
A single IUCN species ID |
a data.frame
with the species ID and two levels of threat
descriptions, plus stresses, timing, scope, severity, and impact associated
with each stressor.
David J. Harris [email protected]
Other birdlife:
birdlife_habitat()
## Not run: # Setophaga chrysoparia birdlife_threats(22721692) # Aburria aburri birdlife_threats(22678440) ## End(Not run)
## Not run: # Setophaga chrysoparia birdlife_threats(22721692) # Aburria aburri birdlife_threats(22678440) ## End(Not run)
Access LEDA trait data
leda(trait = "age_first_flowering", ...)
leda(trait = "age_first_flowering", ...)
trait |
(character) Trait to get. See Details. |
... |
Curl options passed on to crul::verb-GET |
For parameter trait
, one of age_first_flowering, branching,
buds_seasonality, buds_vertical_dist, canopy_height, dispersal_type,
leaf_distribution, ldmc_geo, leaf_mass, leaf_size, morphology_disperal,
growth_form, life_span, releasing_height, seed_longevity,
seed_mass, seed_number, seed_shape, shoot_growth_form, snp, ssd, tv,
or clonal_growth_organs
The following are not supported as they are too much of a pain to parse: buoyancy, seed_bank, sla_geo
## Not run: # Age of first flowering leda(trait = "age_first_flowering") # Seed number leda("seed_number") # Releasing height leda(trait = "releasing_height") # Clonal growth organs leda(trait = "clonal_growth_organs") all <- c("age_first_flowering", "branching", "buds_seasonality", "buds_vertical_dist", "canopy_height", "dispersal_type", "leaf_distribution", "ldmc_geo", "leaf_mass", "leaf_size", "morphology_disperal", "growth_form", "life_span", "releasing_height", "seed_longevity", "seed_mass", "seed_number", "seed_shape", "shoot_growth_form", "snp", "ssd", "tv", "clonal_growth_organs") out <- list() for (i in seq_along(all)) { cat(all[i], sep="\n") out[[i]] <- leda(all[i]) } sapply(out, NROW) ## End(Not run)
## Not run: # Age of first flowering leda(trait = "age_first_flowering") # Seed number leda("seed_number") # Releasing height leda(trait = "releasing_height") # Clonal growth organs leda(trait = "clonal_growth_organs") all <- c("age_first_flowering", "branching", "buds_seasonality", "buds_vertical_dist", "canopy_height", "dispersal_type", "leaf_distribution", "ldmc_geo", "leaf_mass", "leaf_size", "morphology_disperal", "growth_form", "life_span", "releasing_height", "seed_longevity", "seed_mass", "seed_number", "seed_shape", "shoot_growth_form", "snp", "ssd", "tv", "clonal_growth_organs") out <- list() for (i in seq_along(all)) { cat(all[i], sep="\n") out[[i]] <- leda(all[i]) } sapply(out, NROW) ## End(Not run)
Retrieve gene sequences from NCBI by accession number.
ncbi_byid(ids, format = NULL, verbose = TRUE)
ncbi_byid(ids, format = NULL, verbose = TRUE)
ids |
(character) GenBank ids to search for. One or more. Required. |
format |
(character) Return type, e.g., |
verbose |
(logical) If |
If bad ids are included with good ones, the bad ones are silently dropped. If all ids are bad you'll get a stop with error message.
data.frame of the form:
taxon - taxonomic name (may include some junk, but hard to parse off)
taxonomy - organism lineage
gene_desc - gene description
organelle - if mitochondrial or chloroplast
gi_no - GI number
acc_no - accession number
keyword - if official DNA barcode
specimen_voucher - museum/lab accession number of vouchered material
lat_lon - longitude/latitude of specimen collection event
country - country/location of specimen collection event
paper_title - title of study
journal - journal study published in (if published)
first_author - first author of study
uploaded_date - date sequence was uploaded to GenBank
length - sequence length
sequence - sequence character string
Scott Chamberlain, Rupert Collins
ncbi_searcher()
, ncbi_byname()]
## Not run: # A single gene ncbi_byid(ids="360040093") # Many genes (with different accession numbers) ncbi_byid(ids=c("360040093","347448433")) ## End(Not run)
## Not run: # A single gene ncbi_byid(ids="360040093") # Many genes (with different accession numbers) ncbi_byid(ids=c("360040093","347448433")) ## End(Not run)
Retrieve gene sequences from NCBI by taxon name and gene names.
ncbi_byname( taxa, gene = "COI", seqrange = "1:3000", getrelated = FALSE, verbose = TRUE, ... )
ncbi_byname( taxa, gene = "COI", seqrange = "1:3000", getrelated = FALSE, verbose = TRUE, ... )
taxa |
(character) Scientific name to search for. |
gene |
(character) Gene or genes (in a vector) to search for. See examples. |
seqrange |
(character) Sequence range, as e.g., |
getrelated |
(logical) If |
verbose |
(logical) If |
... |
Curl options passed on to crul::verb-GET |
Removes predicted sequences so you don't have to remove them. Predicted sequences are those with accession numbers that have "XM_" or "XR_" prefixes. This function retrieves one sequences for each species, picking the longest available for the given gene.
data.frame
Scott Chamberlain
## Not run: # A single species ncbi_byname(taxa="Acipenser brevirostrum") # Many species species <- c("Colletes similis","Halictus ligatus","Perdita californica") ncbi_byname(taxa=species, gene = c("coi", "co1"), seqrange = "1:2000") ## End(Not run)
## Not run: # A single species ncbi_byname(taxa="Acipenser brevirostrum") # Many species species <- c("Colletes similis","Halictus ligatus","Perdita californica") ncbi_byname(taxa=species, gene = c("coi", "co1"), seqrange = "1:2000") ## End(Not run)
Search for gene sequences available for taxa from NCBI.
ncbi_searcher( taxa = NULL, id = NULL, seqrange = "1:3000", getrelated = FALSE, fuzzy = FALSE, limit = 500, entrez_query = NULL, hypothetical = FALSE, verbose = TRUE, sleep = 0L )
ncbi_searcher( taxa = NULL, id = NULL, seqrange = "1:3000", getrelated = FALSE, fuzzy = FALSE, limit = 500, entrez_query = NULL, hypothetical = FALSE, verbose = TRUE, sleep = 0L )
taxa |
(character) Scientific name to search for. |
id |
( |
seqrange |
(character) Sequence range, as e.g., |
getrelated |
(logical) If |
fuzzy |
(logical) Whether to do fuzzy taxonomic ID search or exact
search. If |
limit |
( |
entrez_query |
( |
hypothetical |
( |
verbose |
(logical) If |
sleep |
(integer) number of seconds to sleep before each HTTP request. use if running to 429 Too Many Requests errors from NCBI. default: 0 (no sleep) |
data.frame
of results if a single input is given. A list of
data.frame
s if multiple inputs are given.
NCBI rate limits requests. If you set an API key you have a higher rate limit.
Set your API key like Sys.setenv(ENTREZ_KEY="yourkey")
or you can use
?rentrez::set_entrez_key
. set verbose curl output (crul::set_verbose()
) to
make sure your api key is being sent in the requests
Scott Chamberlain, Zachary Foster [email protected]
## Not run: # A single species out <- ncbi_searcher(taxa="Umbra limi", seqrange = "1:2000") # Get the same species information using a taxonomy id out <- ncbi_searcher(id = "75935", seqrange = "1:2000") # If the taxon name is unique, using the taxon name and id are equivalent all(ncbi_searcher(id = "75935") == ncbi_searcher(taxa="Umbra limi")) # If the taxon name is not unique, use taxon id # "266948" is the uid for the butterfly genus, but there is also a genus # of orchids with the # same name nrow(ncbi_searcher(id = "266948")) == nrow(ncbi_searcher(taxa="Satyrium")) # get list of genes available, removing non-unique unique(out$gene_desc) # does the string 'RAG1' exist in any of the gene names out[grep("RAG1", out$gene_desc, ignore.case=TRUE),] # A single species without records in NCBI out <- ncbi_searcher(taxa="Sequoia wellingtonia", seqrange="1:2000", getrelated=TRUE) # Many species, can run in parallel or not using plyr species <- c("Salvelinus alpinus","Ictalurus nebulosus","Carassius auratus") out2 <- ncbi_searcher(taxa=species, seqrange = "1:2000") lapply(out2, head) library("plyr") out2df <- ldply(out2) # make data.frame of all unique(out2df$gene_desc) # get list of genes available, removing non-unique out2df[grep("12S", out2df$gene_desc, ignore.case=TRUE), ] # Using the getrelated and entrez_query options ncbi_searcher(taxa = "Olpidiopsidales", limit = 5, getrelated = TRUE, entrez_query = "18S[title] AND 28S[title]") # get refseqs one <- ncbi_searcher(taxa = "Salmonella enterica", entrez_query="srcdb_refseq[PROP]") two <- ncbi_searcher(taxa = "Salmonella enterica") ## End(Not run)
## Not run: # A single species out <- ncbi_searcher(taxa="Umbra limi", seqrange = "1:2000") # Get the same species information using a taxonomy id out <- ncbi_searcher(id = "75935", seqrange = "1:2000") # If the taxon name is unique, using the taxon name and id are equivalent all(ncbi_searcher(id = "75935") == ncbi_searcher(taxa="Umbra limi")) # If the taxon name is not unique, use taxon id # "266948" is the uid for the butterfly genus, but there is also a genus # of orchids with the # same name nrow(ncbi_searcher(id = "266948")) == nrow(ncbi_searcher(taxa="Satyrium")) # get list of genes available, removing non-unique unique(out$gene_desc) # does the string 'RAG1' exist in any of the gene names out[grep("RAG1", out$gene_desc, ignore.case=TRUE),] # A single species without records in NCBI out <- ncbi_searcher(taxa="Sequoia wellingtonia", seqrange="1:2000", getrelated=TRUE) # Many species, can run in parallel or not using plyr species <- c("Salvelinus alpinus","Ictalurus nebulosus","Carassius auratus") out2 <- ncbi_searcher(taxa=species, seqrange = "1:2000") lapply(out2, head) library("plyr") out2df <- ldply(out2) # make data.frame of all unique(out2df$gene_desc) # get list of genes available, removing non-unique out2df[grep("12S", out2df$gene_desc, ignore.case=TRUE), ] # Using the getrelated and entrez_query options ncbi_searcher(taxa = "Olpidiopsidales", limit = 5, getrelated = TRUE, entrez_query = "18S[title] AND 28S[title]") # get refseqs one <- ncbi_searcher(taxa = "Salmonella enterica", entrez_query="srcdb_refseq[PROP]") two <- ncbi_searcher(taxa = "Salmonella enterica") ## End(Not run)
Search for traits by taxa names
taxa_search(x, db, ...)
taxa_search(x, db, ...)
x |
(character) Taxonomic name(s) to search for |
db |
(character) only 'ncbi' for now - other options maybe in the future |
... |
Curl options passed on to |
A data.frame
Scott Chamberlain
## Not run: taxa_search("Poa annua", db = "ncbi") ## End(Not run)
## Not run: taxa_search("Poa annua", db = "ncbi") ## End(Not run)
Amniote life history dataset
tr_ernest(read = TRUE, ...)
tr_ernest(read = TRUE, ...)
read |
(logical) read in csv files. Default: |
... |
Curl options passed on to |
When using this data, cite the paper:
Myhrvold, N. P., Baldridge, E., Chan, B., Sivam, D., Freeman, D. L. and Ernest, S. K. M. (2015), An amniote life-history database to perform comparative analyses with birds, mammals, and reptiles. Ecology, 96: 3109. https://doi.org/10.1890/15-0846R.1
As well as the Dryad data package:
L. Freeman, Daniel; P. Myhrvold, Nathan; Chan, Benjamin; Sivam, Dhileep; Ernest, S. K. Morgan; Baldridge, Elita (2016): Full Archive. figshare. https://doi.org/10.6084/m9.figshare.3563457.v1
paths to the files (character) if read=FALSE
or
a list of data.frame's if read=TRUE
https://doi.org/10.1890/15-0846R.1 https://doi.org/10.6084/m9.figshare.3563457.v1
## Not run: res <- tr_ernest() res$data res$references res$sparse res$range_count ## End(Not run)
## Not run: res <- tr_ernest() res$data res$references res$sparse res$range_count ## End(Not run)
Zanne et al. plant dataset
tr_zanne(read = TRUE, ...)
tr_zanne(read = TRUE, ...)
read |
(logical) read in csv files. Default: |
... |
Curl options passed on to |
This data is a dataset stored on Dryad (doi: 10.5061/dryad.63q27). When using this data, cite the paper:
Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O'Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, Aarssen L, Bertin RI, Calaminus A, Govaerts R, Hemmings F, Leishman MR, Oleksyn J, Soltis PS, Swenson NG, Warman L, Beaulieu JM, Ordonez A (2014) Three keys to the radiation of angiosperms into freezing environments. Nature 506(7486): 89-92. http://dx.doi.org/10.1038/nature12872
As well as the Dryad data package:
Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O'Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, Aarssen L, Bertin RI, Calaminus A, Govaerts R, Hemmings F, Leishman MR, Oleksyn J, Soltis PS, Swenson NG, Warman L, Beaulieu JM, Ordonez A (2013) Data from: Three keys to the radiation of angiosperms into freezing environments. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.63q27.2
paths to the files (character) if read=FALSE
or
a list of data.frame's if read=TRUE
http://datadryad.org/resource/doi:10.5061/dryad.63q27
## Not run: res <- tr_zanne() res$tax_lookup res$woodiness res$freezing res$leaf_phenology ## End(Not run)
## Not run: res <- tr_zanne() res$tax_lookup res$woodiness res$freezing res$leaf_phenology ## End(Not run)
Search for traits from EOL's Traitbank
traitbank(query, key = NULL, ...)
traitbank(query, key = NULL, ...)
query |
(character) a query to the EOL Cypher service that holds Traitbank data. required. no default query given. see examples |
key |
(character) EOL Cypher query API key. required, either passed in or as an environment variable |
... |
Curl options passed on to |
traitbank
is an interface to the EOL Cypher query.
Note that the previous interface EOL had for Traits has been completely
replaced - thus, this function is completely different. You no longer
query by EOL page id, but using the query language for a database
called Neo4J. See the docs for help. Later we plan to make a more
user friendly interface to get Traitbank data that doesn't
require knowing the Neo4J query syntax
a list
You'll need an EOL cypher key to use this function. Get one by signing in to your EOL account https://eol.org/users/sign_in then head to https://eol.org/services/authenticate to get a key. Store your key in your .Renviron file or similar under the name "EOL_CYPHER_KEY", and we will use that key in this function. Alternatively, you can pass in your key to the key parameter, but we do not recommend doing that as you risk accidentally committing your key to the public web.
https://github.com/EOL/eol_website/blob/master/doc/api.md https://github.com/EOL/eol_website/blob/master/doc/query-examples.md
## Not run: # traitbank_query function traitbank(query = "MATCH (n:Trait) RETURN n LIMIT 1;") # traitbank function res <- traitbank(query = "MATCH (n:Trait) RETURN n LIMIT 2;") res ## End(Not run)
## Not run: # traitbank_query function traitbank(query = "MATCH (n:Trait) RETURN n LIMIT 1;") # traitbank function res <- traitbank(query = "MATCH (n:Trait) RETURN n LIMIT 2;") res ## End(Not run)
Manage cached traits
package files with hoardr
The dafault cache directory is
paste0(rappdirs::user_cache_dir(), "/R/traits")
, but you can set
your own path using cache_path_set()
cache_delete
only accepts 1 file name, while
cache_delete_all
doesn't accept any names, but deletes all files.
For deleting many specific files, use cache_delete
in a lapply()
type call
traits_cache$cache_path_get()
get cache path
traits_cache$cache_path_set()
set cache path
traits_cache$list()
returns a character vector of full
path file names
traits_cache$files()
returns file objects with metadata
traits_cache$details()
returns files with details
traits_cache$delete()
delete specific files
traits_cache$delete_all()
delete all files, returns nothing
## Not run: traits_cache # list files in cache traits_cache$list() # delete certain database files # traits_cache$delete("file path") # traits_cache$list() # delete all files in cache # traits_cache$delete_all() # traits_cache$list() # set a different cache path from the default ## End(Not run)
## Not run: traits_cache # list files in cache traits_cache$list() # delete certain database files # traits_cache$delete("file path") # traits_cache$list() # delete all files in cache # traits_cache$delete_all() # traits_cache$list() # set a different cache path from the default ## End(Not run)
These functions have been removed.
eol_invasive_
: This function has moved to a new package.
See originr::eol
fe_native
: This function has moved to a new package.
See originr::flora_europaea
g_invasive
: This function has moved to a new package.
See originr::gisd
is_native
: This function has moved to a new package. See
originr::is_native
tr_usda
: the API behind this function is down for good
coral_locations
: API down for good, as far as I can tell
coral_methodologies
: API down for good, as far as I can tell
coral_resources
: API down for good, as far as I can tell
coral_species
: API down for good, as far as I can tell
coral_taxa
: API down for good, as far as I can tell
coral_traits
: API down for good, as far as I can tell