Selecting and ordering variables
William K. Morris
Source:vignettes/v03_selecting_variables.Rmd
v03_selecting_variables.RmdWhen requesting data using finbif you can select from
among (or order by) many variables (properties of the occurrence
records). The default set of variables returned is a small subset of
those available. Note that not all variables are available for all
records. See ?variables for details.
Selecting variables
Limiting variables
To retrieve a limited set of variables from FinBIF simply specify the
desired variables in the select argument.
finbif_occurrence(
genus = "Falco",
select = c("scientific_name", "life_stage", "sex")
)Click to show/hide output.
#> Records downloaded: 10
#> Records available: 342668
#> A data.frame [10 x 3]
#> scientific_name life_stage sex
#> 1 Falco columbarius L… NA NA
#> 2 Falco tinnunculus L… NA NA
#> 3 Falco tinnunculus L… NA NA
#> 4 Falco subbuteo Linn… NA NA
#> 5 Falco tinnunculus L… NA NA
#> 6 Falco subbuteo Linn… NA NA
#> 7 Falco tinnunculus L… NA NA
#> 8 Falco tinnunculus L… NA NA
#> 9 Falco tinnunculus L… NA NA
#> 10 Falco subbuteo Linn… NA NAExtra variables
To get extra variables as well as the default set, specify the extra
variables in addition to the keyword "default_vars".
finbif_occurrence(select = c("default_vars", "life_stage"))Click to show/hide output.
#> Records downloaded: 10
#> Records available: 47159747
#> A data.frame [10 x 13]
#> record_id scientific_name abundance lat_wgs84 lon_wgs84
#> 1 …JX.1594385#3 Sciurus vulgaris Li… 1 60.23584 25.05693
#> 2 …KE.176/64895825d5de884fa20e297d#Unit1 Heracleum persicum … NA 61.08302 22.38983
#> 3 …JX.1594382#9 Hirundo rustica Lin… NA 64.12716 23.99111
#> 4 …JX.1594382#37 Pica pica (Linnaeus… NA 64.12716 23.99111
#> 5 …JX.1594382#49 Muscicapa striata (… NA 64.12716 23.99111
#> 6 …JX.1594382#39 Larus canus Linnaeu… NA 64.12716 23.99111
#> 7 …JX.1594382#5 Emberiza citrinella… NA 64.12716 23.99111
#> 8 …JX.1594382#31 Ficedula hypoleuca … NA 64.12716 23.99111
#> 9 …JX.1594382#41 Alauda arvensis Lin… NA 64.12716 23.99111
#> 10 …JX.1594382#21 Numenius arquata (L… NA 64.12716 23.99111
#> ...with 0 more record and 8 more variables:
#> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification,
#> record_reliability, record_quality, life_stageOrdering
You can change the order of occurrence records before they are
fetched from the server by using the order_by argument. The
default ordering is date_start descending, then
load_date descending, then reported_name.
Ascending order
By default occurrence records are ordered by variables in ascending order.
finbif_occurrence("Cygnus cygnus", order_by = "abundance")Click to show/hide output.
#> Records downloaded: 10
#> Records available: 95730
#> A data.frame [10 x 12]
#> record_id scientific_name abundance lat_wgs84 lon_wgs84
#> 1 …KE.67/9403350#Unit Cygnus cygnus (Linn… 1 60.41667 16
#> 2 …HR.3691/OBS810893905_Unit Cygnus cygnus (Linn… NA 61.56563 29.56771
#> 3 …JX.1026351#259 Cygnus cygnus (Linn… 1 65.89416 28.90961
#> 4 …JX.1025175#3 Cygnus cygnus (Linn… 1 61.83248 23.40816
#> 5 …KE.67/9069501#Unit Cygnus cygnus (Linn… 1 52.71667 1.55
#> 6 …JX.1252188#3 Cygnus cygnus (Linn… NA 60.17258 24.27095
#> 7 …KE.67/9465507#Unit Cygnus cygnus (Linn… 1 61.8 22.76667
#> 8 …KE.67/9607357#Unit Cygnus cygnus (Linn… 1 63.13333 22.43333
#> 9 …MHU.10961285 Cygnus cygnus (Linn… NA 64.97813 24.74932
#> 10 …HR.3691/OBS886590077_Unit Cygnus cygnus (Linn… NA 61.27566 22.557
#> date_time
#> 1 1997-04-01 13:00:00
#> 2 2007-05-18 12:00:00
#> 3 2013-06-24 03:12:00
#> 4 2014-06-08 03:45:00
#> 5 1997-01-03 14:00:00
#> 6 2021-05-23 06:15:00
#> 7 2000-03-22 12:00:00
#> 8 2003-06-07 12:00:00
#> 9 2008-07-12 12:00:00
#> 10 2020-03-31 12:00:00
#> ...with 0 more record and 6 more variables:
#> coordinates_uncertainty, any_issues, requires_verification, requires_identification,
#> record_reliability, record_qualityDescending order
You can switch to descending order by prefixing the variable with a dash.
finbif_occurrence("Cygnus cygnus", order_by = "-abundance")Click to show/hide output.
#> Records downloaded: 10
#> Records available: 95730
#> A data.frame [10 x 12]
#> record_id scientific_name abundance lat_wgs84 lon_wgs84
#> 1 …MHU.2981587 Cygnus cygnus (Linn… 6000 64.4 -14.54
#> 2 …HR.3691/OBS1101526155_Unit Cygnus cygnus (Linn… 1760 62.16389 21.45786
#> 3 …HR.3691/OBS604642304_Unit Cygnus cygnus (Linn… 1753 64.50736 24.27894
#> 4 …HR.3691/OBS663568887_Unit Cygnus cygnus (Linn… 1600 65.98787 24.06341
#> 5 …MHU.28815250 Cygnus cygnus (Linn… 1500 NA NA
#> 6 …HR.3691/OBS671353848_Unit Cygnus cygnus (Linn… 1361 64.71656 24.53188
#> 7 …JX.1357345#5 Cygnus cygnus (Linn… 1300 64.8465 25.2883
#> 8 …JX.1398409#3 Cygnus cygnus (Linn… 1280 64.8448 25.2816
#> 9 …MHU.28815110 Cygnus cygnus (Linn… 1200 NA NA
#> 10 …HR.3691/OBS1119137190_Unit Cygnus cygnus (Linn… 1163 64.71656 24.53188
#> ...with 0 more record and 7 more variables:
#> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification,
#> record_reliability, record_qualityMultiple variables
You can specify multiple variables to order by. Sorting primacy is from left to right.
finbif_occurrence("Cygnus olor", order_by = c("municipality_id", "-abundance"))Click to show/hide output.
#> Records downloaded: 10
#> Records available: 42951
#> A data.frame [10 x 12]
#> record_id scientific_name abundance lat_wgs84 lon_wgs84 date_time
#> 1 …12015253 Cygnus olor (J.F. G… 2500 NA NA 2008-08-17 12:00:00
#> 2 …13633876 Cygnus olor (J.F. G… 1500 NA NA 2008-10-03 12:00:00
#> 3 …781416 Cygnus olor (J.F. G… 1300 NA NA 2006-02-14 12:00:00
#> 4 …780984 Cygnus olor (J.F. G… 1300 NA NA 2006-02-14 12:00:00
#> 5 …2062563 Cygnus olor (J.F. G… 1200 NA NA 2006-12-19 12:00:00
#> 6 …10352894 Cygnus olor (J.F. G… 1100 NA NA 2008-06-28 12:00:00
#> 7 …927797 Cygnus olor (J.F. G… 1050 NA NA 2006-04-05 12:00:00
#> 8 …3110953 Cygnus olor (J.F. G… 960 NA NA 2007-10-06 12:00:00
#> 9 …26309317 Cygnus olor (J.F. G… 900 NA NA 2009-07-08 12:00:00
#> 10 …1260385 Cygnus olor (J.F. G… 800 58.66 23.57 2006-04-26 18:00:00
#> ...with 0 more record and 6 more variables:
#> coordinates_uncertainty, any_issues, requires_verification, requires_identification,
#> record_reliability, record_qualityRandom sample
You can also request a random sample (random order) of occurrence
records by setting the sample argument to
TRUE.
finbif_occurrence(sample = TRUE)Click to show/hide output.
#> Records downloaded: 10
#> Records available: 47159747
#> A data.frame [10 x 12]
#> record_id scientific_name abundance lat_wgs84 lon_wgs84
#> 1 …KE.67/5632630#Unit Ficedula hypoleuca … 1 61.74637 22.77479
#> 2 …MHU.40397 Prunus padus L. NA 60.28016 20.25637
#> 3 …JX.775148#3 Yezognophos vittari… 1 60.44245 27.006
#> 4 …KE.67/11580538#Unit Cyanistes caeruleus… 1 60.32754 24.64944
#> 5 …JX.328070#23 Pechipogo strigilat… NA 61.54883 21.64192
#> 6 …HR.3691/OBS889952298_Unit Parus major Linnaeu… 5 66.6165 24.68816
#> 7 …JX.1025818#50 Garrulus glandarius… 1 63.43302 27.74526
#> 8 …HR.3691/OBS1104249688_Unit Alauda arvensis Lin… NA 60.05577 24.06798
#> 9 …KE.67/8616657#Unit Cyanistes caeruleus… 1 61.5 24.83333
#> 10 …JX.101375#9 Poecile montanus (C… 7 63.09517 23.1341
#> ...with 0 more record and 7 more variables:
#> date_time, coordinates_uncertainty, any_issues, requires_verification, requires_identification,
#> record_reliability, record_quality