Following a significant update to the NZFFD, the nzffdr package has been completely overhauled. The NZFFD update resulted in nzffdr v 1.0.0 functions either i) not working or, ii) being redundant. Therefore I have completely rewritten nzffdr. This does mean there is NO backwards compatibility. I am sorry for this, but it was out of my control given the changes to NZFFD.
On the up side, the NZFFD now contains lots of useful additional information by default, and the new and improved nzffdr has added functionality.
The purpose of this package is to allow for direct access to the NZ Freshwater Fish Database (NZFFD) from R and additional functions for cleaning imported data and adding missing data.
For a detailed guide to using the package see the help page.
A preprint describing the package is now available (if you wish to cite the package please use this):
Lee, F., & Young, N. (2021). nzffdr: an R package to import, clean and update data from the New Zealand Freshwater Fish Database. bioRxiv. https://doi.org/10.1101/2021.06.22.449519
For now, the only functioning version of nzffdr is here on GitHub, I aim to get nzffdr v 2.0.0 on CRAN in early 2022.
To install the latest development version install from GitHub.
This function requires an internet connection to query the NZFFD database.
# import all records between 2010 and 2015
library(nzffdr)
dat <- nzffdr_import(institution = "", catchment_num = "", catchment_name = "",
water_body = "", fish_method = "", taxon = "",
starts = 2010, ends = 2015, download_format = "all")
head(dat)
#> nzffdRecordNumber institutionRecordNumber eventDate eventTime
#> 1 12132 2011-01-18 day
#> 2 12132 2011-01-18 day
#> 3 12132 2011-01-18 day
#> 4 12132 2011-01-18 day
#> 5 12132 2011-01-18 day
#> 6 12132 2011-01-18 day
#> institution samplingPurpose
#> 1 Department of Conservation Canterbury
#> 2 Department of Conservation Canterbury
#> 3 Department of Conservation Canterbury
#> 4 Department of Conservation Canterbury
#> 5 Department of Conservation Canterbury
#> 6 Department of Conservation Canterbury
#> waterBody waterBodyType waterPermanence site
#> 1 Otukaikino Stream tributary Not Entered Perennial NA
#> 2 Otukaikino Stream tributary Not Entered Perennial NA
#> 3 Otukaikino Stream tributary Not Entered Perennial NA
#> 4 Otukaikino Stream tributary Not Entered Perennial NA
#> 5 Otukaikino Stream tributary Not Entered Perennial NA
#> 6 Otukaikino Stream tributary Not Entered Perennial NA
#> catchmentNumber catchmentName eastingNZTM northingNZTM decimalLongitude
#> 1 664 Waimakariri R 1569366 5189668 -43.44526
#> 2 664 Waimakariri R 1569366 5189668 -43.44526
#> 3 664 Waimakariri R 1569366 5189668 -43.44526
#> 4 664 Waimakariri R 1569366 5189668 -43.44526
#> 5 664 Waimakariri R 1569366 5189668 -43.44526
#> 6 664 Waimakariri R 1569366 5189668 -43.44526
#> decimalLatitude recSegment minimumElevation distanceOcean siteTidal
#> 1 172.6214 13121594 10 10.9 n
#> 2 172.6214 13121594 10 10.9 n
#> 3 172.6214 13121594 10 10.9 n
#> 4 172.6214 13121594 10 10.9 n
#> 5 172.6214 13121594 10 10.9 n
#> 6 172.6214 13121594 10 10.9 n
#> siteLandlocked downstreamBarrier eventLocationRemarks siteReachLength
#> 1 u n NA
#> 2 u n NA
#> 3 u n NA
#> 4 u n NA
#> 5 u n NA
#> 6 u n NA
#> siteAverageWidth minimumSampledDepth maximumSampledDepth waterLevel
#> 1 1 NA 0.6 Unknown
#> 2 1 NA 0.6 Unknown
#> 3 1 NA 0.6 Unknown
#> 4 1 NA 0.6 Unknown
#> 5 1 NA 0.6 Unknown
#> 6 1 NA 0.6 Unknown
#> waterColour waterClarity clarityMethod waterTemperature waterConductivity
#> 1 Colourless NA NA 16 NA
#> 2 Colourless NA NA 16 NA
#> 3 Colourless NA NA 16 NA
#> 4 Colourless NA NA 16 NA
#> 5 Colourless NA NA 16 NA
#> 6 Colourless NA NA 16 NA
#> waterDissolvedOxygenPercent waterDissolvedOxygenPPM waterPH waterSalinity
#> 1 NA NA NA NA
#> 2 NA NA NA NA
#> 3 NA NA NA NA
#> 4 NA NA NA NA
#> 5 NA NA NA NA
#> 6 NA NA NA NA
#> habitatFlowPercent
#> 1 Mud:50, Cobbles (64-257 mm):5, Fine gravel:10, Sand (1-2 mm):25, Coarse gravel:10
#> 2 Mud:50, Cobbles (64-257 mm):5, Fine gravel:10, Sand (1-2 mm):25, Coarse gravel:10
#> 3 Mud:50, Cobbles (64-257 mm):5, Fine gravel:10, Sand (1-2 mm):25, Coarse gravel:10
#> 4 Mud:50, Cobbles (64-257 mm):5, Fine gravel:10, Sand (1-2 mm):25, Coarse gravel:10
#> 5 Mud:50, Cobbles (64-257 mm):5, Fine gravel:10, Sand (1-2 mm):25, Coarse gravel:10
#> 6 Mud:50, Cobbles (64-257 mm):5, Fine gravel:10, Sand (1-2 mm):25, Coarse gravel:10
#> habitatSubstratePercent
#> 1 Wood/instream debris:y, Macrophytes-algae:y, Undercut banks:y, Bank vegetation:y
#> 2 Wood/instream debris:y, Macrophytes-algae:y, Undercut banks:y, Bank vegetation:y
#> 3 Wood/instream debris:y, Macrophytes-algae:y, Undercut banks:y, Bank vegetation:y
#> 4 Wood/instream debris:y, Macrophytes-algae:y, Undercut banks:y, Bank vegetation:y
#> 5 Wood/instream debris:y, Macrophytes-algae:y, Undercut banks:y, Bank vegetation:y
#> 6 Wood/instream debris:y, Macrophytes-algae:y, Undercut banks:y, Bank vegetation:y
#> habitatInstreamCoverPresent habitatRiparianVegPercent
#> 1 Pool:5, Run:95 Scrub:10, Grass/tussock:60, Raupo/flax:30
#> 2 Pool:5, Run:95 Scrub:10, Grass/tussock:60, Raupo/flax:30
#> 3 Pool:5, Run:95 Scrub:10, Grass/tussock:60, Raupo/flax:30
#> 4 Pool:5, Run:95 Scrub:10, Grass/tussock:60, Raupo/flax:30
#> 5 Pool:5, Run:95 Scrub:10, Grass/tussock:60, Raupo/flax:30
#> 6 Pool:5, Run:95 Scrub:10, Grass/tussock:60, Raupo/flax:30
#> samplingMethod samplingProtocol EfmNumberOfPasses
#> 1 Other net - combination of nets and traps Unknown NA
#> 2 Other net - combination of nets and traps Unknown NA
#> 3 Other net - combination of nets and traps Unknown NA
#> 4 Other net - combination of nets and traps Unknown NA
#> 5 Other net - combination of nets and traps Unknown NA
#> 6 Other net - combination of nets and traps Unknown NA
#> EfmVoltage EfmPulseRate EfmPulseRateWidth EfmAnodeSize EfmMinutes EfmArea
#> 1 NA NA NA NA NA
#> 2 NA NA NA NA NA
#> 3 NA NA NA NA NA
#> 4 NA NA NA NA NA
#> 5 NA NA NA NA NA
#> 6 NA NA NA NA NA
#> NetsTrapsTotalNumber NetsTrapsBaited NetsTrapsMeshSize NetsTrapsDayNight
#> 1 17 NA NA NA
#> 2 17 NA NA NA
#> 3 17 NA NA NA
#> 4 17 NA NA NA
#> 5 17 NA NA NA
#> 6 17 NA NA NA
#> NetsTrapsAverageSetTime ObservationArea taxonName
#> 1 NA NA Gobiomorphus gobioides
#> 2 NA NA Gobiomorphus breviceps
#> 3 NA NA Galaxias maculatus
#> 4 NA NA Anguilla australis
#> 5 NA NA Gobiomorphus cotidianus
#> 6 NA NA Anguilla dieffenbachii
#> taxonCommonName taxonRemarks totalCount present soughtNotDetected
#> 1 Giant bully 1 false false
#> 2 Upland bully 1 false false
#> 3 Inanga 1 false false
#> 4 Shortfin eel 50 false false
#> 5 Common bully 20 false false
#> 6 Longfin eel 18 false false
#> occurrenceRemarks minLength maxLength indLengths dataVersion
#> 1 NA 125 NA V1
#> 2 NA 56 NA V1
#> 3 NA 150 NA V1
#> 4 NA 250 900 V1
#> 5 NA 40 110 V1
#> 6 NA 400 1100 V1
# To import the entire NZFF Database:
# dat <- nzffd_import()