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datecollected field flagged by ridigbio
maintainers as inappropriate field–should be eventDate. See
scrubr::fix_names() (#263)wellknown about to be archived. Replaced with
s2 and wk.as.bison() is now defunct. BISON API is being
sunsetted, BISON data now available via GBIF (#252)as.ecoengine() is now defunct. ecoengine R
pkg wasn’t used, we used internal code, but since ecoengine
R is archived since Feb 2020, probably best to remove here (#239)wellknown now instead of wicket for
Well-known text manipulation (#235)fixnames() is now defunct. it was deprecated in a
previous version. See scrubr::fix_names() (#231)occ() can now handle sf objects passed to
geometry. spocc itself does not import/suggest
sf, but uses some code donated by Michael Sumner to pull out well known
text (WKT) needed for spatially defined queriesocc(): factor out functions already defined
inside of occ, add assertions for user parameters
(#228)occ(): total records found
count was always 0 because ALA changed the records found field to
totalRecordsocc(): was using an old
parameter query passed to
rvertnet::searchbyterm() - changed to
scientificname insteadif statement was failing
because we were trying to access an element of a list that is not there
sometimes, leading to NULL which caused the if
statement to failsource = "inat" can now return photos. do a query as
normal for inat data, and index to the photos slot in the
data.frame, that will give a nested list of data.frames for each record
with links/metadata for the photos (#214) (#217)iNaturalist notes in the
?occ manual page for help with iNaturalist pagination and
rate limiting (#215)tibble::data_frame/tibble::as_data_frame
replaced by tibble::tibble/tibble::as_tibble
throughout packagefixnames() is now deprecated; still useable here until
the next version released; please move to using
scrubr::fix_names (#196)occ() queries: change from
http to https for the inat base url (#213)?occ for details); as.obis.numeric is gone and
replaced with as.obis.character (#218)fixnames(), coerce taxon name to character in
case the name is factor class (#211)occ() now attempts to collect errors from requests that
fail and puts these error messages (character strings) in the
$meta$errors spot. We can not always collect errors, and
some data providers do not error well: they do not provide a meaningful
error message other than that there was an error. (#189) (#207)occ() gains new parameter throw_warnings
(logical). By default set to TRUE (matches previous
behavior) and throws warnings about errors that occur and when no
results found for a query. We now prefix each warning with the data
provider so you can match up an error or warning with a data provider
and (hopefully) query. If set to FALSE, warnings are
suppressed (#189) (#207)spocc. The AntWeb API has
been down for a while, and no response from maintainers (#202)
(#203)rebird on
CRAN requires a few changes in parameters used. Importantly, ebird now
wants species codes instead of full scientific names, but we internally
attempt to handle this, so users still just pass scientific names
(#205)?spocc_duplicates manual file for duplicate
records, refer to scrubr and CoordinateCleaner
packages (#198)inspect() manual file, clarify what the function
does (#194)occ() gains a return block with detail
about what’s returned from the function (#208)occ() gains new parameter date to do date
range based searches across data sources without having to know the
vagaries of each data source (#181)print.occdatind so that empty data.frame’s don’t
throw tibble warnings (#184)stand_dates() due to ALA giving back a timestamp now (#182)
(#185)wicket C++ based package instead. So you no longer need V8
which should make installation easier on some platforms. (#172)httr replaced with crul for HTTP reqeusts
(#174)curl::curl_options() (#176)as.*() functions can now pass on curl options to
the http client (#177)foo_ala() - the internal plugin for
occ() that handles ALA queries: changed query from full
text query using q=foo bar to
q=taxon_name="foo bar" - in addition, improved error
handling as sometimes occurrences slot is returned in
results but is empty, whereas before it seemd to always be absent if no
results (#178)ala (#98)obis (#155)occ2df() more robust to varied inputs - allowing
for users that may on purpose or not have a subset of the data source
slots normally in the occdat class object (#171)rvertnet, a dependency dealing with data from Vertnet,
was failing on certain searches. rvertnet was fixed and a
new version on CRAN now. No changes here other than requiring the new
version of rvertnet (#168)datetime to observed_on.is() to inherits(), and namespace
all setNames() callsrgbif::occ_data() instead of
rgbif::occ_search()rvertnet::searchbyterm() instead of
rgbif::vertsearch()occ() now allows queries that only pass
from and one of the data source opts params (e.g.,
gbifopts) - allows specifying any options passed down to
the internal functions used to do data queries without having to use the
other params in occ (#163)tibble for representing data.frames
(#164)encoding="UTF-8" in
httr::content() calls to parse raw data from web requests
(#160)ridigbio as its on CRAN - was using internal
fxns prior to this (#154)has_coords
also fixed. (#161)data.table::setDF() instead of
data.frame() to set a data.table style table
to a data.framevertnet as an option to
occ_options() to get the options for passing to
vertopts in occ()print.occdatind() - which in last version
introduced a bug in this print method - wasn’t fatal as only applied to
empty slots in the output of a call to occ(), but
nonetheless, not good (#159)data.table for fast list to data.frameas.vertnet() to coerce various inputs
(e.g., result from occ(), occ2df(), or a key
itself) to occurrence data objects (#142)occ() gains two parameters start and
page to facilitate paging through results across data
sources, instead of having to page individually for each data source.
Some sources use the start parameter, while others use the
page parameter. See Paging section in
?occ for details on Paging (#140)wkt_vis() now works with WKT polygons with multipe
polygons, e.g.,
spocc::wkt_vis("POLYGON((-125 38.4, -121.8 38.4, -121.8 40.9, -125 40.9, -125 38.4), (-115 22.4, -111.8 22.4, -111.8 30.9, -115 30.9, -115 22.4))")
(#147)print.occdatind() to print more helpful info
when a geometry search is used as opposed to a taxonomy based search
(#149)print.occdatind() to not fail when first element
not present; proceeds to next slot with data (#143)occ() failed when multiple
geometry elements passed in along with taxonomic names
(#146)occ2df() for combining outputs to not fail when
AntWeb doesn’t give back dates (#144) (#145) - thanks @timcdlucasocc2df() to not fail when date field missing
(#141)spocc (#136)
(#124)occ() function. Each data source
is taken care of in a separate package or set of wrapper functions, and
the man file now details what API parameters are being queried
(#138)Datetime variable
changed to datetimeoccurrenceID
variable changed to occurrenceidspoccutils (#132)occ() gains new parameter has_coords - a
global parameter (except for ebird and bison) to return only records
with lat/long data. (#128)type (#134) and rank (#133) parameters
dropped from occ()occ() is printed, we now
include a message that total count of records found (not returned) is
not completely known if ebird is included, because
eBird does not include data on records found on their servers with
requests to their API (#111)as.*() (e.g., as.gbif) for
most data sources. These functions take in occurrence keys or sets of
keys, and retrieve detailed occurrence record data for each key
(#112)occ2df() now returns more fields. This function
collapses all essential fields that are easy to get in all data sources:
name, lat, long,
prov, date, key. The
key field is the occurrence key for each record, which you
can use to keep track of individual records, get more data on the
record, etc. (#103) (#108)inspect() - takes output from
occ() or individual occurrence keys and gets detailed
occurrence data.jsonlite, V8,
utils, and methods. No longer importing:
ggmap, maptools, rworldmap,
sp, rgeos, RColorBrewer,
rgdal, and leafletR. Pkgs removed mostly due
to splitting off some functionality into spoccutils.
related issues: (#131) (#132)methods, utils (#120)occ2df() (#106)wkt_vis() now only has an option to view a WKT shape in
the browser.assertthat, plyr, data.table, and
XML (#102)gistr now to post interactive geojson
maps on GitHub gists (#100)rgbif now must be v0.7.7 or greater (the
latest version on CRAN).occ2sp()
removed. The function occ_to_sp() function is the working
version. (#97)\donttest to \dontrun in
examples as requested by CRAN maintainers (#99)occ_names() to search only for
taxonomic names. The goal here is to use ths function if there is some
question about what names you want to use to search for occurrences
with. (#84). Suggested by @jarioksaocc_names_options() to quickly get
parameter options to pass to occ_names().summary() method for the occdat
S3 object that is output from occ() (#83)spocc (README, vignette,
occ() documentation file, at package startup), we make it
clear that there could be duplicate records returned in certain
scenarios. And a new documentation page detailing what to watch out for:
?spocc_duplicates. (#77)latitude,
decimalLatitude, Latitude, lat,
and decimal_latitude. (#91)limit parameter in
occ() (#78)limit to each functions options
parameter, and it will work. Each data source can have a different
parameter internally from limit, but now internally within
spocc, we allow you to use limit so you don’t
have to know what the data source specific parameter is. (#81)occ_options() gains new parameter where to
print either in the console or to open man file in the IDE, or prints to
console in command line R.occ() gains new parameter callopts to pass
on curl debugging options to httr::GET() (#35)wkt_vis() now by default plots a well known text area
(WKT) on an interactive mapbox map in your default browser. New
parameter which allows you to choose the interactive map or
a static ggplot2 map. (#70)occ() gains new class. In the
previous version of this package, a data.frame was printed.
Now the data is assigned the object occdatind (short for
occdat individual).occ() now uses a print method for the
occdatind class, adopted from dplyr that
prints a brief data.frame, with columns wrapped to fit the
width of your console, and additional columns not printed given at
bottom with their class type. Note that the print behavior for the
resulting object of an occ() call remains the same. (#69)
(#74)whisker as a package import to use in the
wkt_vis() function. (#70)mapggplot() accepted the output of occ(), of
class occdat, while the other two functions for mapping,
mapleaflet() and mapgist() accepted a
data.frame. Now all three functions accept the output of
occ(), an object of class occdat. (#75)meta slot in each returned object (indexed by
object$meta) contains spots for returned and
found, to designate number of records returned, and number
of records found. (#64)name. (#71)occ().spocc depends on: rgbif. A number of input and
output parameter names changed. A new version of rgbif was
pushed to CRAN. (#56)clean_spocc() started (not finished yet)
to attempt to clean data. For example, one use case is removing
impossible lat/long values (i.e., longitue values greater than absolute
180). Another, not implemented yet, is to remove points that are not in
the country or habitat your points are supposed to be in. (#44)fixnames() to trim species names with
optional input parameters to make data easier to use for mapping.wkt_vis() to visualize a WKT (well-known
text) area on a map. Uses ggmap to pull down a Google map
so that the visualization has some geographic and natural earth context.
We’ll soon introduce an interactive version of this function that will
bring up a small Shiny app to draw a WKT area, then return those
coordinates to your R session. (#34)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.