tests/testthat/test_rarify.R
In leppott/BioMonTools: Tools for Biomonitoring and Bioassessment
# rarify ####
test_that("rarify", {
# load bio data
df_biodata <- BioMonTools::data_bio2rarify
# subsample
mySize <- 500
Seed_US <- 17760704
df_calc <- BioMonTools::rarify(inbug=df_biodata
, sample.ID = "SampleID"
, abund = "N_Taxa"
, subsiz = mySize
, mySeed = Seed_US)
# QC data
SampleID <- c("01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
)
TaxaID <- c("Ephemerellidae"
, "Mystacides"
, "Zaitzevia"
, "Ceratopogoninae"
, "Chironomini"
, "Elmidae"
, "Hyalella"
, "Hydropsyche"
, "Hydrozoa"
, "Libellulidae"
, "Limonia"
, "Oligochaeta"
, "Optioservus"
, "Orthocladiinae"
, "Ostracoda"
, "Tanypodinae"
, "Tanytarsini"
, "Trepaxonemata"
, "Tricorythodes"
, "Trombidiformes"
, "Cheumatopsyche"
, "Coenagrionidae"
, "Dubiraphia"
, "Ephydridae"
, "Physella"
, "Planorbidae"
, "Prostoma"
, "Corbicula"
, "Cladocera"
, "Calineuria californica"
, "Drunella doddsii"
, "Neophylax splendens"
, "Octogomphus specularis"
, "Cinygmula"
, "Diphetor hageni"
, "Dixa"
, "Glossosoma"
, "Hesperoperla pacifica"
, "Heterlimnius corpulentus"
, "Maruina"
, "Rhithrogena"
, "Rhyacophila brunnea/vemna group"
, "Sweltsa"
, "Wormaldia"
, "Zaitzevia"
, "Zapada oregonensis group"
, "Baetis tricaudatus complex"
, "Ceratopogoninae"
, "Chelifera/Metachela"
, "Cinygma"
, "Dicranota"
, "Hydropsyche"
, "Juga"
, "Lara"
, "Malenka"
, "Narpus concolor"
, "Oligochaeta"
, "Optioservus"
, "Orthocladiinae"
, "Paraleptophlebia"
, "Pericoma/Telmatoscopus"
, "Simulium"
, "Sphaeriidae"
, "Tanypodinae"
, "Tanytarsini"
, "Trombidiformes"
, "Zapada cinctipes"
, "Chloroperlidae"
, "Baetidae"
, "Baetis tricaudatus complex"
, "Chelifera/Metachela"
, "Chironomini"
, "Ferrissia"
, "Hydroptila"
, "Juga"
, "Oligochaeta"
, "Orthocladiinae"
, "Paraleptophlebia"
, "Simulium"
, "Sphaeriidae"
, "Tanypodinae"
, "Tanytarsini"
, "Trombidiformes"
, "Cheumatopsyche"
, "Copepoda"
, "Cinygmula"
, "Despaxia augusta"
, "Diphetor hageni"
, "Epeorus"
, "Epeorus albertae group"
, "Glossosoma"
, "Glossosomatidae"
, "Heptageniidae"
, "Hesperoperla pacifica"
, "Ironodes"
, "Micrasema"
, "Perlidae"
, "Perlodidae"
, "Rhyacophila betteni group"
, "Rhyacophila blarina"
, "Sweltsa"
, "Wormaldia"
, "Zaitzevia"
, "Zapada"
, "Zapada oregonensis group"
, "Baetidae"
, "Baetis tricaudatus complex"
, "Ceratopogoninae"
, "Chelifera/Metachela"
, "Chironomini"
, "Dicranota"
, "Ferrissia"
, "Hydropsyche"
, "Juga"
, "Lara"
, "Malenka"
, "Nemata"
, "Oligochaeta"
, "Optioservus"
, "Orthocladiinae"
, "Paraleptophlebia"
, "Simulium"
, "Tanypodinae"
, "Tanytarsini"
, "Trombidiformes"
, "Zapada cinctipes"
, "Limnephilidae"
, "Yoraperla"
, "Diphetor hageni"
, "Isoperla"
, "Baetidae"
, "Baetis tricaudatus complex"
, "Hydropsychidae"
, "Juga"
, "Oligochaeta"
, "Paraleptophlebia"
, "Simulium"
, "Sphaeriidae"
, "Tanypodinae"
, "Tanytarsini"
, "Cheumatopsyche"
, "Gammarus"
, "Ampumixis dispar"
, "Blephariceridae"
, "Calineuria californica"
, "Drunella doddsii"
, "Acentrella turbida"
, "Clinocera"
, "Dicosmoecus gilvipes"
, "Diphetor hageni"
, "Epeorus albertae group"
, "Hesperoperla pacifica"
, "Neophylax rickeri"
, "Ordobrevia nubifera"
, "Perlidae"
, "Perlodidae"
, "Rhithrogena"
, "Rhyacophila brunnea/vemna group"
, "Stempellinella"
, "Wormaldia"
, "Zaitzevia"
, "Baetis flavistriga complex"
, "Baetis tricaudatus complex"
, "Cricotopus bicinctus group"
, "Cricotopus/Orthocladius"
, "Eukiefferiella"
, "Fluminicola"
, "Hydropsyche"
, "Juga"
, "Lepidostoma"
, "Leucotrichia"
, "Malenka"
, "Micropsectra"
, "Optioservus"
, "Pagastia"
, "Paraleptophlebia"
, "Polypedilum"
, "Rheocricotopus"
, "Rheotanytarsus"
, "Simulium"
, "Trombidiformes"
, "Zapada cinctipes"
, "Cheumatopsyche"
, "Goera archaon"
, "Centroptilum/Procloeon"
, "Isoperla"
, "Paraleptophlebia bicornuta group"
, "Zaitzevia"
, "Caenis"
, "Chironomidae"
, "Ferrissia"
, "Fluminicola"
, "Juga"
, "Oligochaeta"
, "Optioservus"
, "Paralauterborniella"
, "Paraleptophlebia"
, "Stictochironomus"
, "Tricorythodes"
, "Trombidiformes"
, "Copepoda"
, "Calineuria californica"
, "Doroneuria"
, "Octogomphus specularis"
, "Chloroperlidae"
, "Cinygmula"
, "Diphetor hageni"
, "Dixa"
, "Glossosoma"
, "Hesperoperla pacifica"
, "Isoperla"
, "Sweltsa"
, "Zaitzevia"
, "Baetidae"
, "Ceratopogoninae"
, "Chelifera/Metachela"
, "Dicranota"
, "Hydropsyche"
, "Juga"
, "Lepidostoma-panel case larvae"
, "Malenka"
, "Micropsectra"
, "Narpus concolor"
, "Nemata"
, "Oligochaeta"
, "Optioservus"
, "Paraleptophlebia"
, "Parametriocnemus"
, "Polypedilum"
, "Simulium"
, "Sphaeriidae"
, "Trombidiformes"
, "Zapada cinctipes"
, "Stempellinella/Zavrelia (Bad ID)"
, "Ablabesmyia"
, "Ceratopogoninae"
, "Chironomidae"
, "Cladotanytarsus"
, "Corynoneura"
, "Dicrotendipes"
, "Hyalella"
, "Labrundinia"
, "Micropsectra"
, "Oecetis"
, "Oligochaeta"
, "Ostracoda"
, "Paracricotopus"
, "Polypedilum"
, "Pseudochironomus"
, "Tanytarsus"
, "Trepaxonemata"
, "Trombidiformes"
, "Coenagrionidae"
, "Cryptochironomus"
, "Dubiraphia"
, "Endochironomus"
, "Gammarus"
, "Helobdella"
, "Oxyethira"
, "Physella"
, "Planorbidae"
, "Procladius"
, "Tanypus"
, "Cladocera"
, "Copepoda"
, "Corixidae"
, "Alotanypus"
, "Baetidae"
, "Chironomini"
, "Cricotopus/Orthocladius"
, "Oligochaeta"
, "Orthocladiinae"
, "Paratendipes"
, "Phaenopsectra"
, "Sialis"
, "Sphaeriidae"
, "Tanytarsini"
, "Thienemannimyia group"
, "Chironomus"
, "Cryptochironomus"
, "Ephydridae"
, "Gammarus"
, "Lymnaeidae"
, "Physella"
, "Planorbidae"
, "Copepoda"
, "Clinocera"
, "Argia"
, "Baetidae"
, "Baetis tricaudatus complex"
, "Brillia"
, "Chelifera/Metachela"
, "Dytiscidae"
, "Eukiefferiella claripennis group"
, "Ferrissia"
, "Micropsectra"
, "Oligochaeta"
, "Polypedilum"
, "Rheotanytarsus"
, "Simulium"
, "Sphaeriidae"
, "Tanypodinae"
, "Thienemannimyia group"
, "Tipula"
, "Menetus"
, "Physella"
, "Copepoda"
, "Calineuria californica"
, "Cleptelmis addenda"
, "Diphetor hageni"
, "Heptageniidae"
, "Hesperoperla pacifica"
, "Ironodes"
, "Isoperla"
, "Rhyacophila betteni group"
, "Rhyacophila brunnea/vemna group"
, "Skwala"
, "Sweltsa"
, "Wormaldia"
, "Zaitzevia"
, "Baetidae"
, "Baetis tricaudatus complex"
, "Brillia"
, "Chelifera/Metachela"
, "Chironomini"
, "Cricotopus"
, "Dicranota"
, "Eukiefferiella claripennis group"
, "Eukiefferiella gracei group"
, "Ferrissia"
, "Hydropsychidae"
, "Hydroptila"
, "Juga"
, "Micropsectra"
, "Nilotanypus"
, "Optioservus"
, "Paraleptophlebia"
, "Parametriocnemus"
, "Polypedilum"
, "Rheotanytarsus"
, "Simulium"
, "Sphaeriidae"
, "Tanytarsus"
, "Thienemannimyia group"
, "Trombidiformes"
, "Truncatelloidea"
, "Zapada cinctipes"
, "Cheumatopsyche"
, "Gammarus"
, "Isopoda"
)
N_Taxa <- c(56
, 2
, 24
, 142
, 4
, 16
, 4
, 5
, 34
, 13
, 11
, 1
, 28
, 37
, 2
, 1
, 1
, 14
, 9
, 11
, 0
, 1
, 9
, 18
, 25
, 9
, 21
, 1
, 1
, 1
, 3
, 1
, 1
, 14
, 6
, 1
, 14
, 6
, 5
, 1
, 9
, 2
, 8
, 2
, 4
, 1
, 10
, 1
, 1
, 1
, 1
, 6
, 319
, 1
, 4
, 1
, 1
, 2
, 23
, 10
, 1
, 1
, 2
, 1
, 25
, 7
, 3
, 1
, 44
, 50
, 7
, 160
, 1
, 1
, 130
, 29
, 40
, 4
, 4
, 1
, 2
, 13
, 3
, 9
, 1
, 18
, 3
, 8
, 4
, 2
, 25
, 23
, 8
, 1
, 1
, 1
, 5
, 1
, 11
, 47
, 27
, 6
, 5
, 2
, 3
, 4
, 13
, 3
, 6
, 7
, 4
, 0
, 36
, 34
, 1
, 2
, 1
, 18
, 21
, 2
, 30
, 11
, 2
, 72
, 4
, 27
, 1
, 2
, 1
, 6
, 3
, 29
, 48
, 6
, 1
, 23
, 8
, 3
, 1
, 5
, 345
, 19
, 1
, 13
, 5
, 6
, 38
, 1
, 1
, 4
, 4
, 2
, 1
, 2
, 1
, 1
, 42
, 1
, 1
, 40
, 3
, 2
, 44
, 1
, 1
, 13
, 1
, 80
, 2
, 2
, 1
, 2
, 16
, 12
, 1
, 2
, 26
, 1
, 1
, 28
, 1
, 11
, 85
, 1
, 2
, 8
, 6
, 10
, 313
, 3
, 9
, 33
, 36
, 16
, 13
, 1
, 6
, 4
, 21
, 10
, 8
, 3
, 1
, 6
, 10
, 14
, 21
, 2
, 1
, 11
, 6
, 8
, 2
, 8
, 6
, 3
, 1
, 19
, 262
, 1
, 2
, 1
, 1
, 3
, 6
, 7
, 19
, 7
, 2
, 0
, 8
, 7
, 37
, 15
, 3
, 5
, 3
, 1
, 1
, 5
, 125
, 16
, 1
, 14
, 65
, 1
, 3
, 1
, 2
, 2
, 53
, 31
, 12
, 1
, 4
, 3
, 3
, 2
, 2
, 17
, 4
, 1
, 4
, 45
, 69
, 1
, 1
, 0
, 1
, 3
, 45
, 1
, 2
, 1
, 9
, 205
, 1
, 1
, 1
, 1
, 1
, 135
, 3
, 86
, 2
, 1
, 1
, 1
, 18
, 59
, 97
, 3
, 1
, 26
, 1
, 124
, 1
, 2
, 1
, 132
, 5
, 5
, 1
, 6
, 9
, 7
, 0
, 1
, 2
, 6
, 1
, 2
, 1
, 2
, 1
, 5
, 4
, 1
, 4
, 33
, 22
, 65
, 4
, 5
, 5
, 1
, 11
, 2
, 16
, 1
, 5
, 1
, 5
, 2
, 1
, 20
, 8
, 90
, 10
, 13
, 83
, 1
, 3
, 6
, 1
, 1
, 11
, 36
, 5
, 3
)
df_QC <- data.frame(SampleID, TaxaID, N_Taxa, stringsAsFactors = TRUE)
# test
testthat::expect_equivalent(df_calc, df_QC, tolerance = 0.01)
})## Test ~ rarify ~ END
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
leppott/BioMonTools documentation built on March 1, 2025, 7:18 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# rarify ####
test_that("rarify", {
# load bio data
df_biodata <- BioMonTools::data_bio2rarify
# subsample
mySize <- 500
Seed_US <- 17760704
df_calc <- BioMonTools::rarify(inbug=df_biodata
, sample.ID = "SampleID"
, abund = "N_Taxa"
, subsiz = mySize
, mySeed = Seed_US)
# QC data
SampleID <- c("01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "01103CSR_Bug_2001-08-27_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "02087REF_Bug_2002-08-22_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03013CSR_Bug_2003-07-01_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03053CSR_Bug_2003-08-14_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "03054CSR_Bug_2003-08-18_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06012CSR_Bug_2006-09-05_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06019CSRw_Bug_2006-09-14_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06021CSR_Bug_2006-08-01_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06022CSR_Bug_2006-08-17_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06024CSR_Bug_2006-07-27_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06025CSR_Bug_2006-08-03_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
, "06027CSR_Bug_2006-07-17_0"
)
TaxaID <- c("Ephemerellidae"
, "Mystacides"
, "Zaitzevia"
, "Ceratopogoninae"
, "Chironomini"
, "Elmidae"
, "Hyalella"
, "Hydropsyche"
, "Hydrozoa"
, "Libellulidae"
, "Limonia"
, "Oligochaeta"
, "Optioservus"
, "Orthocladiinae"
, "Ostracoda"
, "Tanypodinae"
, "Tanytarsini"
, "Trepaxonemata"
, "Tricorythodes"
, "Trombidiformes"
, "Cheumatopsyche"
, "Coenagrionidae"
, "Dubiraphia"
, "Ephydridae"
, "Physella"
, "Planorbidae"
, "Prostoma"
, "Corbicula"
, "Cladocera"
, "Calineuria californica"
, "Drunella doddsii"
, "Neophylax splendens"
, "Octogomphus specularis"
, "Cinygmula"
, "Diphetor hageni"
, "Dixa"
, "Glossosoma"
, "Hesperoperla pacifica"
, "Heterlimnius corpulentus"
, "Maruina"
, "Rhithrogena"
, "Rhyacophila brunnea/vemna group"
, "Sweltsa"
, "Wormaldia"
, "Zaitzevia"
, "Zapada oregonensis group"
, "Baetis tricaudatus complex"
, "Ceratopogoninae"
, "Chelifera/Metachela"
, "Cinygma"
, "Dicranota"
, "Hydropsyche"
, "Juga"
, "Lara"
, "Malenka"
, "Narpus concolor"
, "Oligochaeta"
, "Optioservus"
, "Orthocladiinae"
, "Paraleptophlebia"
, "Pericoma/Telmatoscopus"
, "Simulium"
, "Sphaeriidae"
, "Tanypodinae"
, "Tanytarsini"
, "Trombidiformes"
, "Zapada cinctipes"
, "Chloroperlidae"
, "Baetidae"
, "Baetis tricaudatus complex"
, "Chelifera/Metachela"
, "Chironomini"
, "Ferrissia"
, "Hydroptila"
, "Juga"
, "Oligochaeta"
, "Orthocladiinae"
, "Paraleptophlebia"
, "Simulium"
, "Sphaeriidae"
, "Tanypodinae"
, "Tanytarsini"
, "Trombidiformes"
, "Cheumatopsyche"
, "Copepoda"
, "Cinygmula"
, "Despaxia augusta"
, "Diphetor hageni"
, "Epeorus"
, "Epeorus albertae group"
, "Glossosoma"
, "Glossosomatidae"
, "Heptageniidae"
, "Hesperoperla pacifica"
, "Ironodes"
, "Micrasema"
, "Perlidae"
, "Perlodidae"
, "Rhyacophila betteni group"
, "Rhyacophila blarina"
, "Sweltsa"
, "Wormaldia"
, "Zaitzevia"
, "Zapada"
, "Zapada oregonensis group"
, "Baetidae"
, "Baetis tricaudatus complex"
, "Ceratopogoninae"
, "Chelifera/Metachela"
, "Chironomini"
, "Dicranota"
, "Ferrissia"
, "Hydropsyche"
, "Juga"
, "Lara"
, "Malenka"
, "Nemata"
, "Oligochaeta"
, "Optioservus"
, "Orthocladiinae"
, "Paraleptophlebia"
, "Simulium"
, "Tanypodinae"
, "Tanytarsini"
, "Trombidiformes"
, "Zapada cinctipes"
, "Limnephilidae"
, "Yoraperla"
, "Diphetor hageni"
, "Isoperla"
, "Baetidae"
, "Baetis tricaudatus complex"
, "Hydropsychidae"
, "Juga"
, "Oligochaeta"
, "Paraleptophlebia"
, "Simulium"
, "Sphaeriidae"
, "Tanypodinae"
, "Tanytarsini"
, "Cheumatopsyche"
, "Gammarus"
, "Ampumixis dispar"
, "Blephariceridae"
, "Calineuria californica"
, "Drunella doddsii"
, "Acentrella turbida"
, "Clinocera"
, "Dicosmoecus gilvipes"
, "Diphetor hageni"
, "Epeorus albertae group"
, "Hesperoperla pacifica"
, "Neophylax rickeri"
, "Ordobrevia nubifera"
, "Perlidae"
, "Perlodidae"
, "Rhithrogena"
, "Rhyacophila brunnea/vemna group"
, "Stempellinella"
, "Wormaldia"
, "Zaitzevia"
, "Baetis flavistriga complex"
, "Baetis tricaudatus complex"
, "Cricotopus bicinctus group"
, "Cricotopus/Orthocladius"
, "Eukiefferiella"
, "Fluminicola"
, "Hydropsyche"
, "Juga"
, "Lepidostoma"
, "Leucotrichia"
, "Malenka"
, "Micropsectra"
, "Optioservus"
, "Pagastia"
, "Paraleptophlebia"
, "Polypedilum"
, "Rheocricotopus"
, "Rheotanytarsus"
, "Simulium"
, "Trombidiformes"
, "Zapada cinctipes"
, "Cheumatopsyche"
, "Goera archaon"
, "Centroptilum/Procloeon"
, "Isoperla"
, "Paraleptophlebia bicornuta group"
, "Zaitzevia"
, "Caenis"
, "Chironomidae"
, "Ferrissia"
, "Fluminicola"
, "Juga"
, "Oligochaeta"
, "Optioservus"
, "Paralauterborniella"
, "Paraleptophlebia"
, "Stictochironomus"
, "Tricorythodes"
, "Trombidiformes"
, "Copepoda"
, "Calineuria californica"
, "Doroneuria"
, "Octogomphus specularis"
, "Chloroperlidae"
, "Cinygmula"
, "Diphetor hageni"
, "Dixa"
, "Glossosoma"
, "Hesperoperla pacifica"
, "Isoperla"
, "Sweltsa"
, "Zaitzevia"
, "Baetidae"
, "Ceratopogoninae"
, "Chelifera/Metachela"
, "Dicranota"
, "Hydropsyche"
, "Juga"
, "Lepidostoma-panel case larvae"
, "Malenka"
, "Micropsectra"
, "Narpus concolor"
, "Nemata"
, "Oligochaeta"
, "Optioservus"
, "Paraleptophlebia"
, "Parametriocnemus"
, "Polypedilum"
, "Simulium"
, "Sphaeriidae"
, "Trombidiformes"
, "Zapada cinctipes"
, "Stempellinella/Zavrelia (Bad ID)"
, "Ablabesmyia"
, "Ceratopogoninae"
, "Chironomidae"
, "Cladotanytarsus"
, "Corynoneura"
, "Dicrotendipes"
, "Hyalella"
, "Labrundinia"
, "Micropsectra"
, "Oecetis"
, "Oligochaeta"
, "Ostracoda"
, "Paracricotopus"
, "Polypedilum"
, "Pseudochironomus"
, "Tanytarsus"
, "Trepaxonemata"
, "Trombidiformes"
, "Coenagrionidae"
, "Cryptochironomus"
, "Dubiraphia"
, "Endochironomus"
, "Gammarus"
, "Helobdella"
, "Oxyethira"
, "Physella"
, "Planorbidae"
, "Procladius"
, "Tanypus"
, "Cladocera"
, "Copepoda"
, "Corixidae"
, "Alotanypus"
, "Baetidae"
, "Chironomini"
, "Cricotopus/Orthocladius"
, "Oligochaeta"
, "Orthocladiinae"
, "Paratendipes"
, "Phaenopsectra"
, "Sialis"
, "Sphaeriidae"
, "Tanytarsini"
, "Thienemannimyia group"
, "Chironomus"
, "Cryptochironomus"
, "Ephydridae"
, "Gammarus"
, "Lymnaeidae"
, "Physella"
, "Planorbidae"
, "Copepoda"
, "Clinocera"
, "Argia"
, "Baetidae"
, "Baetis tricaudatus complex"
, "Brillia"
, "Chelifera/Metachela"
, "Dytiscidae"
, "Eukiefferiella claripennis group"
, "Ferrissia"
, "Micropsectra"
, "Oligochaeta"
, "Polypedilum"
, "Rheotanytarsus"
, "Simulium"
, "Sphaeriidae"
, "Tanypodinae"
, "Thienemannimyia group"
, "Tipula"
, "Menetus"
, "Physella"
, "Copepoda"
, "Calineuria californica"
, "Cleptelmis addenda"
, "Diphetor hageni"
, "Heptageniidae"
, "Hesperoperla pacifica"
, "Ironodes"
, "Isoperla"
, "Rhyacophila betteni group"
, "Rhyacophila brunnea/vemna group"
, "Skwala"
, "Sweltsa"
, "Wormaldia"
, "Zaitzevia"
, "Baetidae"
, "Baetis tricaudatus complex"
, "Brillia"
, "Chelifera/Metachela"
, "Chironomini"
, "Cricotopus"
, "Dicranota"
, "Eukiefferiella claripennis group"
, "Eukiefferiella gracei group"
, "Ferrissia"
, "Hydropsychidae"
, "Hydroptila"
, "Juga"
, "Micropsectra"
, "Nilotanypus"
, "Optioservus"
, "Paraleptophlebia"
, "Parametriocnemus"
, "Polypedilum"
, "Rheotanytarsus"
, "Simulium"
, "Sphaeriidae"
, "Tanytarsus"
, "Thienemannimyia group"
, "Trombidiformes"
, "Truncatelloidea"
, "Zapada cinctipes"
, "Cheumatopsyche"
, "Gammarus"
, "Isopoda"
)
N_Taxa <- c(56
, 2
, 24
, 142
, 4
, 16
, 4
, 5
, 34
, 13
, 11
, 1
, 28
, 37
, 2
, 1
, 1
, 14
, 9
, 11
, 0
, 1
, 9
, 18
, 25
, 9
, 21
, 1
, 1
, 1
, 3
, 1
, 1
, 14
, 6
, 1
, 14
, 6
, 5
, 1
, 9
, 2
, 8
, 2
, 4
, 1
, 10
, 1
, 1
, 1
, 1
, 6
, 319
, 1
, 4
, 1
, 1
, 2
, 23
, 10
, 1
, 1
, 2
, 1
, 25
, 7
, 3
, 1
, 44
, 50
, 7
, 160
, 1
, 1
, 130
, 29
, 40
, 4
, 4
, 1
, 2
, 13
, 3
, 9
, 1
, 18
, 3
, 8
, 4
, 2
, 25
, 23
, 8
, 1
, 1
, 1
, 5
, 1
, 11
, 47
, 27
, 6
, 5
, 2
, 3
, 4
, 13
, 3
, 6
, 7
, 4
, 0
, 36
, 34
, 1
, 2
, 1
, 18
, 21
, 2
, 30
, 11
, 2
, 72
, 4
, 27
, 1
, 2
, 1
, 6
, 3
, 29
, 48
, 6
, 1
, 23
, 8
, 3
, 1
, 5
, 345
, 19
, 1
, 13
, 5
, 6
, 38
, 1
, 1
, 4
, 4
, 2
, 1
, 2
, 1
, 1
, 42
, 1
, 1
, 40
, 3
, 2
, 44
, 1
, 1
, 13
, 1
, 80
, 2
, 2
, 1
, 2
, 16
, 12
, 1
, 2
, 26
, 1
, 1
, 28
, 1
, 11
, 85
, 1
, 2
, 8
, 6
, 10
, 313
, 3
, 9
, 33
, 36
, 16
, 13
, 1
, 6
, 4
, 21
, 10
, 8
, 3
, 1
, 6
, 10
, 14
, 21
, 2
, 1
, 11
, 6
, 8
, 2
, 8
, 6
, 3
, 1
, 19
, 262
, 1
, 2
, 1
, 1
, 3
, 6
, 7
, 19
, 7
, 2
, 0
, 8
, 7
, 37
, 15
, 3
, 5
, 3
, 1
, 1
, 5
, 125
, 16
, 1
, 14
, 65
, 1
, 3
, 1
, 2
, 2
, 53
, 31
, 12
, 1
, 4
, 3
, 3
, 2
, 2
, 17
, 4
, 1
, 4
, 45
, 69
, 1
, 1
, 0
, 1
, 3
, 45
, 1
, 2
, 1
, 9
, 205
, 1
, 1
, 1
, 1
, 1
, 135
, 3
, 86
, 2
, 1
, 1
, 1
, 18
, 59
, 97
, 3
, 1
, 26
, 1
, 124
, 1
, 2
, 1
, 132
, 5
, 5
, 1
, 6
, 9
, 7
, 0
, 1
, 2
, 6
, 1
, 2
, 1
, 2
, 1
, 5
, 4
, 1
, 4
, 33
, 22
, 65
, 4
, 5
, 5
, 1
, 11
, 2
, 16
, 1
, 5
, 1
, 5
, 2
, 1
, 20
, 8
, 90
, 10
, 13
, 83
, 1
, 3
, 6
, 1
, 1
, 11
, 36
, 5
, 3
)
df_QC <- data.frame(SampleID, TaxaID, N_Taxa, stringsAsFactors = TRUE)
# test
testthat::expect_equivalent(df_calc, df_QC, tolerance = 0.01)
})## Test ~ rarify ~ END
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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