Title: | R Interface to 'FishBase' |
---|---|
Description: | A programmatic interface to 'FishBase', re-written based on an accompanying 'RESTful' API. Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more. This package also supports experimental access to 'SeaLifeBase' data, which contains nearly 200,000 species records for all types of aquatic life not covered by 'FishBase.' |
Authors: | Carl Boettiger [cre, aut] |
Maintainer: | Carl Boettiger <[email protected]> |
License: | CC0 |
Version: | 5.0.0 |
Built: | 2024-08-31 00:49:20 UTC |
Source: | https://github.com/ropensci/rfishbase |
List available releases
available_releases(server = c("fishbase", "sealifebase"))
available_releases(server = c("fishbase", "sealifebase"))
server |
fishbase or sealifebase |
available_releases()
available_releases()
brains
brains( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
brains( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species brains
## Not run: brains("Oreochromis niloticus") ## End(Not run)
## Not run: brains("Oreochromis niloticus") ## End(Not run)
return a table of country information for the requested c_code, as reported in FishBASE.org
c_code( c_code = NULL, server = getOption("FISHBASE_API", "fishbase"), version = get_latest_release(), db = default_db(), ... )
c_code( c_code = NULL, server = getOption("FISHBASE_API", "fishbase"), version = get_latest_release(), db = default_db(), ... )
c_code |
a C_Code or list of C_Codes (FishBase country code) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
c_code(440)
c_code(440)
Return a table of common names
common_names( species_list = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, Language = "English", fields = NULL )
common_names( species_list = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, Language = "English", fields = NULL )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
Language |
a string specifying the language for the common name, e.g. "English" |
fields |
subset to these columns. (recommend to omit this and handle manually) |
Note that there are many common names for a given sci name
a data.frame of common names by species queried. If multiple species are queried, The resulting data.frames are concatenated.
common_names("Bolbometopon muricatum")
common_names("Bolbometopon muricatum")
Return a list of scientific names corresponding to given the common name(s).
common_to_sci( x, Language = "English", server = c("fishbase", "sealifebase"), version = "latest", db = NULL )
common_to_sci( x, Language = "English", server = c("fishbase", "sealifebase"), version = "latest", db = NULL )
x |
a common name or list of common names |
Language |
a string specifying the language for the common name, e.g. "English" |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
If more than one scientific name matches the common name (e.g. "trout"), the function will simply return a list of all matching scientific names. If given more than one common name, the resulting strings of matching scientific names are simply concatenated.
a character vector of scientific names
common_to_sci(c("Bicolor cleaner wrasse", "humphead parrotfish"), Language="English") common_to_sci(c("Coho Salmon", "trout"))
common_to_sci(c("Bicolor cleaner wrasse", "humphead parrotfish"), Language="English") common_to_sci(c("Coho Salmon", "trout"))
return a table of country for the requested species, as reported in FishBASE.org
country( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
country( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
## Not run: country("Bolbometopon muricatum") ## End(Not run)
## Not run: country("Bolbometopon muricatum") ## End(Not run)
return a table of countrysub for the requested species
countrysub( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
countrysub( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
## Not run: countrysub(species_list(Genus='Labroides')) ## End(Not run)
## Not run: countrysub(species_list(Genus='Labroides')) ## End(Not run)
return a table of countrysubref
countrysubref( server = getOption("FISHBASE_API", "fishbase"), version = get_latest_release(), db = default_db(), ... )
countrysubref( server = getOption("FISHBASE_API", "fishbase"), version = get_latest_release(), db = default_db(), ... )
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
## Not run: countrysubref() ## End(Not run)
## Not run: countrysubref() ## End(Not run)
diet
diet( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
diet( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species diet
http://www.fishbase.org/manual/english/fishbasethe_diet_table.htm
## Not run: diet() ## End(Not run)
## Not run: diet() ## End(Not run)
diet_items
diet_items(...)
diet_items(...)
... |
additional arguments (not used) |
a table of diet_items
## Not run: diet_items() ## End(Not run)
## Not run: diet_items() ## End(Not run)
ecology
ecology( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
ecology( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
By default, will only return one entry (row) per species. Increase limit to get multiple returns for different stocks of the same species, though often data is either identical to the first or simply missing in the additional stocks.
a table of species ecology data
http://www.fishbase.org/manual/english/fishbasethe_ecology_table.htm
## Not run: ecology("Oreochromis niloticus") ## trophic levels and standard errors for a list of species ecology(c("Oreochromis niloticus", "Salmo trutta"), fields=c("SpecCode", "FoodTroph", "FoodSeTroph", "DietTroph", "DietSeTroph")) ## End(Not run)
## Not run: ecology("Oreochromis niloticus") ## trophic levels and standard errors for a list of species ecology(c("Oreochromis niloticus", "Salmo trutta"), fields=c("SpecCode", "FoodTroph", "FoodSeTroph", "DietTroph", "DietSeTroph")) ## End(Not run)
ecosystem
ecosystem( species_list = NULL, fields = NULL, server = getOption("FISHBASE_API", "fishbase"), version = "latest", db = NULL, ... )
ecosystem( species_list = NULL, fields = NULL, server = getOption("FISHBASE_API", "fishbase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species ecosystems data
## Not run: ecosystem("Oreochromis niloticus") ## End(Not run)
## Not run: ecosystem("Oreochromis niloticus") ## End(Not run)
estimate
estimate( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
estimate( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of estimates from some models on trophic levels
http://www.fishbase.us/manual/English/FishbaseThe_FOOD_ITEMS_table.htm
## Not run: estimate("Oreochromis niloticus") ## End(Not run)
## Not run: estimate("Oreochromis niloticus") ## End(Not run)
return a table of species locations as reported in FishBASE.org FAO location data
faoareas( species_list = NULL, fields = NULL, server = getOption("FISHBASE_API", "fishbase"), version = "latest", db = NULL, ... )
faoareas( species_list = NULL, fields = NULL, server = getOption("FISHBASE_API", "fishbase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a tibble, empty tibble if no results found
faoareas()
faoareas()
These table names can be used to access each of the corresponding tables
using [fb_tbl()]
. Please note that following RDB design, it is often
necessary to join multiple tables. Other data cleaning steps are sometimes
necessary as well.
fb_tables(server = c("fishbase", "sealifebase"), version = "latest")
fb_tables(server = c("fishbase", "sealifebase"), version = "latest")
server |
Access data from fishbase or sealifebase? |
version |
Version, see |
fb_tables()
fb_tables()
Please note that rfishbase accesses static snapshots of the raw database tables used by FishBase and Sealifebase websites. Because these are static snapshots, they may lag behind the latest available information on the web interface, but should provide stable results.
fb_tbl( tbl, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, collect = TRUE )
fb_tbl( tbl, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, collect = TRUE )
tbl |
table name, as it appears in the database. See |
server |
Access data from fishbase or sealifebase? |
version |
Version, see |
db |
database connection, deprecated |
collect |
should we return an in-memory table? Generally best to leave as TRUE unless RAM is too limited. A remote table can be used with most dplyr functions (filter, select, joins, etc) to further refine. |
Please also note that the website pages are not organized precisely along the lines of these tables. A given page for a species may draw on data from multiple tables, and sometimes presents the data in a processed or summarized form. Following RDB design, it is often necessary to join multiple tables. Other data cleaning steps are sometimes necessary as well.
fb_tbl("species")
fb_tbl("species")
fecundity
fecundity( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
fecundity( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species fecundity
## Not run: fecundity("Oreochromis niloticus") ## End(Not run)
## Not run: fecundity("Oreochromis niloticus") ## End(Not run)
A table of all the the species found in FishBase, including taxonomic classification and the Species Code (SpecCode) by which the species is identified in FishBase.
Carl Boettiger [email protected]
fooditems
fooditems( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
fooditems( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species fooditems
http://www.fishbase.org/manual/english/fishbasethe_food_items_table.htm
## Not run: fooditems("Oreochromis niloticus") ## End(Not run)
## Not run: fooditems("Oreochromis niloticus") ## End(Not run)
genetics
genetics( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
genetics( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species genetics data
## Not run: genetics("Oreochromis niloticus") genetics("Labroides dimidiatus") ## End(Not run)
## Not run: genetics("Oreochromis niloticus") genetics("Labroides dimidiatus") ## End(Not run)
introductions
introductions( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
introductions( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species introductions data
## Not run: introductions("Oreochromis niloticus") ## End(Not run)
## Not run: introductions("Oreochromis niloticus") ## End(Not run)
larvae
larvae( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
larvae( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of larval data
## Not run: larvae("Oreochromis niloticus") ## End(Not run)
## Not run: larvae("Oreochromis niloticus") ## End(Not run)
return a table of species fooditems
length_freq( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
length_freq( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of length_freq information by species; see details
http://www.fishbase.org/manual/english/lengthfrequency.htm
## Not run: length_freq("Oreochromis niloticus") ## End(Not run)
## Not run: length_freq("Oreochromis niloticus") ## End(Not run)
return a table of lengths
length_length( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
length_length( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
This table contains relationships for the conversion of one length type to another for over 8,000 species of fish, derived from different publications, e.g. Moutopoulos and Stergiou (2002) and Gaygusuz et al (2006), or from fish pictures, e.g. Collette and Nauen (1983), Compagno (1984) and Randall (1997). The relationships, which always refer to centimeters, may consist either of a regression linking two length types, of the form: Length type (2) = a + b x Length type (1) Length type (2) = b' x Length type (1) The available length types are, as elsewhere in FishBase, TL = total length; FL = fork length; SL = standard length; WD = width (in rays); OT = other type (to be specified in the Comment field). When a version of equation (1) is presented, the length range, the number of fish used in the regression, the sex and the correlation coefficient are presented, if available. When a version of equation (2) is presented, the range and the correlation coefficient are omitted, as the ratio in (2) will usually be estimated from a single specimen, or a few fish covering a narrow range of lengths.
a table of lengths
http://www.fishbase.org/manual/english/PDF/FB_Book_CBinohlan_Length-Length_RF_JG.pdf
## Not run: length_length("Oreochromis niloticus") ## End(Not run)
## Not run: length_length("Oreochromis niloticus") ## End(Not run)
The LENGTH-WEIGHT table presents the a and b values of over 5,000 length-weight relationships of the form W = a x Lb, pertaining to about over 2,000 fish species.
length_weight( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
length_weight( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
See references for official documentation. From FishBase.org: Length-weight relationships are important in fisheries science, notably to raise length-frequency samples to total catch, or to estimate biomass from underwater length observations. The units of length and weight in FishBase are centimeter and gram, respectively. Thus when length-weight relationships are not in cm-g, the intercept 'a' is transformed as follows:
a'(cm, g) = a (mm, g)*10^b a'(cm, g) = a (cm, kg)*1000 a'(cm, g) = a (mm, mg)*10^b/1000 a'(cm, g) = a (mm, kg)10^b1000
However, published length-weight relationships are sometimes difficult to use, as they may be based on a length measurement type (e.g., fork length) different from ones length measurements (expressed e.g., as total length). Therefore, to facilitate conversion between length types, an additional LENGTH-LENGTH table, #' presented below, was devised which presents linear regressions or ratios linking length types (e.g., FL vs. TL). We included a calculated field with the weight of a 10 cm fish (which should be in the order of 10 g for normal, fusiform shaped fish), to allow identification of gross errors, given knowledge of the body form of a species.
a table of length_weight information by species; see details
http://www.fishbase.org/manual/english/fishbasethe_length_weight_table.htm
## Not run: length_weight("Oreochromis niloticus") ## End(Not run)
## Not run: length_weight("Oreochromis niloticus") ## End(Not run)
Show scientific classification of taxa Note: species_names() is an alias for load taxa.
load_taxa(server = c("fishbase", "sealifebase"), version = "latest", ...)
load_taxa(server = c("fishbase", "sealifebase"), version = "latest", ...)
server |
Either "fishbase" (the default) or "sealifebase" |
version |
the version of the database you want. Will default to the
latest available; see |
... |
for compatibility with previous versions |
the taxa list
maturity
maturity( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
maturity( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species maturity
## Not run: maturity("Oreochromis niloticus") ## End(Not run)
## Not run: maturity("Oreochromis niloticus") ## End(Not run)
morphology
morphology( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
morphology( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species morphology data
## Not run: morphology("Oreochromis niloticus") ## End(Not run)
## Not run: morphology("Oreochromis niloticus") ## End(Not run)
morphometrics
morphometrics( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
morphometrics( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species morphometrics data
## Not run: morphometrics("Oreochromis niloticus") ## End(Not run)
## Not run: morphometrics("Oreochromis niloticus") ## End(Not run)
oxygen
oxygen( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
oxygen( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species oxygen data
## Not run: oxygen("Oreochromis niloticus") ## End(Not run)
## Not run: oxygen("Oreochromis niloticus") ## End(Not run)
Table of maximum length (Lmax), weight (Wmax) and age (tmax)
popchar( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
popchar( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
See references for official documentation. From FishBase.org: This table presents information on maximum length (Lmax), weight (Wmax) and age (tmax) from various localities where a species occurs. The largest values from this table are also entered in the SPECIES table. The POPCHAR table also indicates whether the Lmax, Wmax and tmax values or various combinations thereof refer to the same individual fish.
http://www.fishbase.org/manual/english/fishbasethe_popchar_table.htm
## Not run: popchar("Oreochromis niloticus") ## End(Not run)
## Not run: popchar("Oreochromis niloticus") ## End(Not run)
This table contains information on growth, natural mortality and length at first maturity, which serve as inputs to many fish stock assessment models. The data can also be used to generate empirical relationships between growth parameters or natural mortality estimates, and their correlates (e.g., body shape, temperature, etc.), a line of research that is useful both for stock assessment and for increasing understanding of the evolution of life-history strategies
popgrowth( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
popgrowth( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of population growth information by species; see details
http://www.fishbase.org/manual/english/fishbasethe_popgrowth_table.htm
## Not run: popgrowth("Oreochromis niloticus") ## End(Not run)
## Not run: popgrowth("Oreochromis niloticus") ## End(Not run)
popqb
popqb( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
popqb( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species popqb
http://www.fishbase.org/manual/english/fishbasethe_popqb_table.htm
## Not run: popqb("Oreochromis niloticus") ## End(Not run)
## Not run: popqb("Oreochromis niloticus") ## End(Not run)
predators
predators( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
predators( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of predators
http://www.fishbase.org/manual/english/fishbasethe_predators_table.htm
## Not run: predators("Oreochromis niloticus") ## End(Not run)
## Not run: predators("Oreochromis niloticus") ## End(Not run)
ration
ration( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
ration( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species ration
http://www.fishbase.org/manual/english/fishbasethe_ration_table.htm
## Not run: ration("Oreochromis niloticus") ## End(Not run)
## Not run: ration("Oreochromis niloticus") ## End(Not run)
references
references( codes = NULL, fields = NULL, server = getOption("FISHBASE_API", "fishbase"), version = get_latest_release(), db = default_db(), ... )
references( codes = NULL, fields = NULL, server = getOption("FISHBASE_API", "fishbase"), version = get_latest_release(), db = default_db(), ... )
codes |
One or more Fishbase reference numbers, matching the RefNo field |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a tibble (data.frame) of reference data
## Not run: references(codes = 1) references(codes = 1:6) references(codes = 1:6, fields = c('Author', 'Year', 'Title')) references() # all references ## End(Not run)
## Not run: references(codes = 1) references(codes = 1:6) references(codes = 1:6, fields = c('Author', 'Year', 'Title')) references() # all references ## End(Not run)
reproduction
reproduction( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
reproduction( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species reproduction
## Not run: reproduction("Oreochromis niloticus") ## End(Not run)
## Not run: reproduction("Oreochromis niloticus") ## End(Not run)
A table of all the the species found in SeaLifeBase, including taxonomic classification and the Species Code (SpecCode) by which the species is identified in SeaLifeBase
Carl Boettiger [email protected]
spawning
spawning( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
spawning( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species spawning
## Not run: spawning("Oreochromis niloticus") ## End(Not run)
## Not run: spawning("Oreochromis niloticus") ## End(Not run)
Provide wrapper to work with species lists.
species( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
The Species table is the heart of FishBase. This function provides a convenient way to query, tidy, and assemble data from that table given an entire list of species. For details, see: http://www.fishbase.org/manual/english/fishbasethe_species_table.htm
Species scientific names are defined according to fishbase taxonomy and nomenclature.
a data.frame with rows for species and columns for the fields returned by the query (FishBase 'species' table)
## Not run: species(c("Labroides bicolor", "Bolbometopon muricatum")) ## End(Not run)
## Not run: species(c("Labroides bicolor", "Bolbometopon muricatum")) ## End(Not run)
Species list by ecosystem
species_by_ecosystem( ecosystem, species_list = NULL, server = getOption("FISHBASE_API", "fishbase"), version = "latest", db = NULL, ... )
species_by_ecosystem( ecosystem, species_list = NULL, server = getOption("FISHBASE_API", "fishbase"), version = "latest", db = NULL, ... )
ecosystem |
(character) an ecosystem name |
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species ecosystems data
## Not run: species_by_ecosystem(ecosystem = "Arctic", server = "sealifebase") ## End(Not run)
## Not run: species_by_ecosystem(ecosystem = "Arctic", server = "sealifebase") ## End(Not run)
Show scientific classification of taxa Note: species_names() is an alias for load_taxa().
species_names(server = c("fishbase", "sealifebase"), version = "latest", ...)
species_names(server = c("fishbase", "sealifebase"), version = "latest", ...)
server |
Either "fishbase" (the default) or "sealifebase" |
version |
the version of the database you want. Will default to the
latest available; see |
... |
for compatibility with previous versions |
the taxa list
speed
speed( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
speed( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species speed data
## Not run: speed("Oreochromis niloticus") ## End(Not run)
## Not run: speed("Oreochromis niloticus") ## End(Not run)
stocks
stocks( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
stocks( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species stocks data
## Not run: stocks("Oreochromis niloticus") ## End(Not run)
## Not run: stocks("Oreochromis niloticus") ## End(Not run)
swimming
swimming( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
swimming( species_list = NULL, fields = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
fields |
subset to these columns. (recommend to omit this and handle manually) |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a table of species swimming data
## Not run: swimming("Oreochromis niloticus") ## End(Not run)
## Not run: swimming("Oreochromis niloticus") ## End(Not run)
Check for alternate versions of a scientific name
synonyms( species_list = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
synonyms( species_list = NULL, server = c("fishbase", "sealifebase"), version = "latest", db = NULL, ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
For further information on fields returned, see: http://www.fishbase.org/manual/english/fishbasethe_synonyms_table.htm
A table with information about the synonym. Will generally be only a single row if a species name is given. If a FishBase SpecCode is given, all synonyms matching that SpecCode are shown, and the table indicates which one is Valid for FishBase. This may or may not match the valid name for Catalog of Life (Col), also shown in the table. See examples for details.
Check for alternate versions of a scientific name and return the scientific names FishBase recognizes as valid
validate_names( species_list, server = getOption("FISHBASE_API", "fishbase"), version = get_latest_release(), db = default_db(), ... )
validate_names( species_list, server = getOption("FISHBASE_API", "fishbase"), version = get_latest_release(), db = default_db(), ... )
species_list |
A vector of scientific names (each element as "genus species"). If empty, a table for all fish will be returned. |
server |
Either "fishbase" or "sealifebase". |
version |
a version string for the database. See |
db |
database connection, now deprecated. |
... |
additional arguments, currently ignored |
a string of the validated names
validate_names("Abramites ternetzi")
validate_names("Abramites ternetzi")