A_03_Taxon_matching_across_datasets.R

Taxonomic matching across datasets

Every dataset uses it’s own taxonomy. In order to assess as many species based on field data as possible, we decided to keep the original taxonomies for all analyses. That means that same species that are now recognized to belong to different clades, will be assessed based on their old taxonomy. Subspecies and hybrids will also be based on the old taxonomy although more updated nomenclature is available.

There are 3 data sources that may lead to information loss if species are not standardized to match the taxonomy in those datasets. Those are:

BirdLife global range maps for the calculation of global climate niche breadth (version: 2024)
BirdTree phylogeny for the calculation of phylogenetic distinctiveness and assessment of phylogenetic autocorrelation in the model residuals. (version: 2012)
AVONET trait database for the extraction of species traits (version 2022)

(4. IUCN but this is part of BirdLife2024 and has the same taxonomy)

Source 00_Configuration.R

Code

source(here::here("Code/00_Configuration.R"))
x <- lapply(package_list, require, character = TRUE)
rm(x)

1. BirdLife 2024 + dataset verbatim names

The data was matched to BirdLife 2024 taxonomy (there was only one change in scientific name)

“scientificName” should match the taxonomy of the BirdLife range maps (2024) and IUCN data

Code

tax_lookup <- 
  readRDS(here::here("Data/output/1_data_filtered.rds")) %>%
  distinct(verbatimIdentification, scientificName) %>% 
  na.omit() # BirdLife 2024 taxonomy

head(tax_lookup)

   verbatimIdentification          scientificName
1 Nucifraga caryocatactes Nucifraga caryocatactes
2      Anas platyrhynchos      Anas platyrhynchos
3         Aythya fuligula         Aythya fuligula
4           Ciconia nigra           Ciconia nigra
5     Carduelis carduelis     Carduelis carduelis
6         Passer montanus         Passer montanus

Code

length(unique(tax_lookup$scientificName)) # 726 standardized species

[1] 726

Code

length(unique(tax_lookup$verbatimIdentification)) # 762 from raw data

[1] 762

2. Crosswalk for BL2010-BL2018

Code

crosswalk <- readxl::read_excel("c:/Users/wolke/OneDrive - CZU v Praze/Frieda_PhD_files/02_StaticPatterns/Git/Data/input/BL_taxonomy_crosswalk.xlsx",
                                sheet = "Crosswalk") %>%
  dplyr::select(1,41) %>% # 2018 & 2010 taxonomy
  setNames(c("ScientificName2018", "ScientificName2010"))

Code

crosswalk %>% 
  filter(ScientificName2018 == "Not Recognised") %>% 
  kable()

ScientificName2018	ScientificName2010
Not Recognised	Larus thayeri
Not Recognised	Corapipo altera
Not Recognised	Serpophaga munda
Not Recognised	Epinecrophylla fjeldsaai
Not Recognised	Myrmotherula fluminensis
Not Recognised	Formicivora littoralis
Not Recognised	Upucerthia jelskii
Not Recognised	Asthenes sclateri
Not Recognised	Hylexetastes uniformis
Not Recognised	Hylexetastes brigidai
Not Recognised	Philemon novaeguineae
Not Recognised	Lichmera limbata
Not Recognised	Sericornis virgatus
Not Recognised	Telophorus quadricolor
Not Recognised	Lanius marwitzi
Not Recognised	Monarcha erythrostictus
Not Recognised	Aphelocoma insularis
Not Recognised	Corvus levaillantii
Not Recognised	Parotia helenae
Not Recognised	Hirundo domicola
Not Recognised	Mirafra cantillans
Not Recognised	Heteromirafra sidamoensis
Not Recognised	Certhilauda barlowi
Not Recognised	Calandrella cheleensis
Not Recognised	Alauda japonica
Not Recognised	Cisticola discolor
Not Recognised	Phyllastrephus leucolepis
Not Recognised	Cettia vulcania
Not Recognised	Bradypterus timorensis
Not Recognised	Nesillas longicaudata
Not Recognised	Phylloscopus makirensis
Not Recognised	Sylvia minula
Not Recognised	Sylvia althaea
Not Recognised	Stachyris ambigua
Not Recognised	Polioptila clementsi
Not Recognised	Lamprotornis elisabeth
Not Recognised	Zoothera imbricata
Not Recognised	Oenanthe lugentoides
Not Recognised	Dicaeum aeruginosum
Not Recognised	Arachnothera everetti
Not Recognised	Lagonosticta landanae
Not Recognised	Erythrura regia
Not Recognised	Lonchura nigriceps
Not Recognised	Lonchura nigerrima
Not Recognised	Prunella fagani
Not Recognised	Anthus longicaudatus
Not Recognised	Sporophila melanops
Not Recognised	Amaurospiza concolor
Not Recognised	Amaurospiza carrizalensis
Not Recognised	Lophura hatinhensis
Not Recognised	Lophura hoogerwerfi
Not Recognised	Butorides virescens
Not Recognised	Falco pelegrinoides
Not Recognised	Fulica caribaea
Not Recognised	Haematopus finschi
Not Recognised	Haematopus bachmani
Not Recognised	Himantopus leucocephalus
Not Recognised	Himantopus mexicanus
Not Recognised	Larus scopulinus
Not Recognised	Catharacta lonnbergi
Not Recognised	Dysmoropelia dekarchiskos
Not Recognised	Gallicolumba norfolciensis
Not Recognised	Cyanoramphus cookii
Not Recognised	Cyanoramphus saisseti
Not Recognised	Ara gossei
Not Recognised	Ara atwoodi
Not Recognised	Ara erythrocephala
Not Recognised	Ara guadeloupensis
Not Recognised	Aratinga brevipes
Not Recognised	Cuculus optatus
Not Recognised	Cacomantis sepulcralis
Not Recognised	Chrysococcyx russatus
Not Recognised	Eudynamys melanorhynchus
Not Recognised	Neomorphus squamiger
Not Recognised	Tyto manusi
Not Recognised	Tyto sororcula
Not Recognised	Bubo vosseleri
Not Recognised	Batrachostomus affinis
Not Recognised	Caprimulgus nigriscapularis
Not Recognised	Caprimulgus ruwenzorii
Not Recognised	Collocalia rogersi
Not Recognised	Collocalia amelis
Not Recognised	Collocalia palawanensis
Not Recognised	Collocalia ocista
Not Recognised	Collocalia germani
Not Recognised	Chaetura viridipennis
Not Recognised	Campylopterus excellens
Not Recognised	Chlorostilbon melanorhynchus
Not Recognised	Chlorostilbon alice
Not Recognised	Thalurania fannyi
Not Recognised	Trogon aurantiiventris
Not Recognised	Not Recognised
Not Recognised	Trogon caligatus
Not Recognised	Ceyx rufidorsa
Not Recognised	Penelopides samarensis
Not Recognised	Ramphastos swainsonii
Not Recognised	Picoides dorsalis
Not Recognised	Hypositta perdita
Not Recognised	Argusianus bipunctatus
Not Recognised	Apus toulsoni
Not Recognised	Zoothera tanganjicae
Not Recognised	Serinus whytii
Not Recognised	Carduelis hornemanni
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised

Code

crosswalk %>% 
  filter(ScientificName2010 == "Not Recognised") %>% 
  kable()

ScientificName2018	ScientificName2010
Ortalis columbiana	Not Recognised
Melanitta stejnegeri	Not Recognised
Melanitta deglandi	Not Recognised
Chenonetta finschi	Not Recognised
Anas zonorhyncha	Not Recognised
Columba thiriouxi	Not Recognised
Nesoenas cicur	Not Recognised
Alectroenas payandeei	Not Recognised
Antrostomus arizonae	Not Recognised
Phaethornis aethopygus	Not Recognised
Mentocrex beankaensis	Not Recognised
Dryolimnas augusti	Not Recognised
Porphyrio paepae	Not Recognised
Tribonyx hodgenorum	Not Recognised
Oceanites pincoyae	Not Recognised
Puffinus bryani	Not Recognised
Nyctanassa carcinocatactes	Not Recognised
Tyto almae	Not Recognised
Aegolius gradyi	Not Recognised
Bermuteo avivorus	Not Recognised
Buteo socotraensis	Not Recognised
Merops mentalis	Not Recognised
Capito fitzpatricki	Not Recognised
Picus sharpei	Not Recognised
Colaptes oceanicus	Not Recognised
Psittacus timneh	Not Recognised
Eclectus infectus	Not Recognised
Hydrornis schwaneri	Not Recognised
Hydrornis irena	Not Recognised
Formicivora grantsaui	Not Recognised
Formicivora paludicola	Not Recognised
Herpsilochmus praedictus	Not Recognised
Herpsilochmus stotzi	Not Recognised
Willisornis vidua	Not Recognised
Sipia palliata	Not Recognised
Grallaria fenwickorum	Not Recognised
Grallaricula cumanensis	Not Recognised
Scytalopus diamantinensis	Not Recognised
Cichlocolaptes mazarbarnetti	Not Recognised
Clibanornis rufipectus	Not Recognised
Automolus lammi	Not Recognised
Thripophaga amacurensis	Not Recognised
Synallaxis beverlyae	Not Recognised
Phibalura boliviana	Not Recognised
Tityra leucura	Not Recognised
Hemitriccus cohnhafti	Not Recognised
Zimmerius chicomendesi	Not Recognised
Pseudocolopteryx citreola	Not Recognised
Batis erlangeri	Not Recognised
Dicrurus menagei	Not Recognised
Chasiempis sclateri	Not Recognised
Chasiempis ibidis	Not Recognised
Cissa jefferyi	Not Recognised
Cyanocorax hafferi	Not Recognised
Orthotomus chaktomuk	Not Recognised
Locustella chengi	Not Recognised
Thryophilus sernai	Not Recognised
Aplonis ulietensis	Not Recognised
Turdus xanthorhynchus	Not Recognised
Alethe castanea	Not Recognised
Oenanthe heuglinii	Not Recognised
Passer zarudnyi	Not Recognised
Rhodopechys alienus	Not Recognised
Crithagra reichenowi	Not Recognised
Pipilo naufragus	Not Recognised
Icterus northropi	Not Recognised
Icterus melanopsis	Not Recognised
Icterus portoricensis	Not Recognised
Icterus pyrrhopterus	Not Recognised
Setophaga flavescens	Not Recognised
Sporophila iberaensis	Not Recognised
Paroaria nigrogenis	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised
Not Recognised	Not Recognised

Code

skim(crosswalk)

Data summary
Name	crosswalk
Number of rows	11241
Number of columns	2
_______________________
Column type frequency:
character	2
________________________
Group variables	None

Variable type: character

skim_variable	n_missing	complete_rate	min	max	empty	n_unique	whitespace
ScientificName2018	0	1	9	36	0	11127	0
ScientificName2010	0	1	9	33	0	10028	0

remove rows where both columns have “Not Recognised” to avoid wrong matches

Code

crosswalk <- 
  crosswalk %>%
  filter(!(ScientificName2018 == "Not Recognised" & 
             ScientificName2010 == "Not Recognised"))

Differences between BL2024 & BL2018

Code

nm <- 
  setdiff(tax_lookup$scientificName, 
          crosswalk$ScientificName2018) # 20 not matched

setdiff(tax_lookup$verbatimIdentification, 
        crosswalk$ScientificName2018) #98 not matched

 [1] "Parus palustris"                  "Carduelis chloris"               
 [3] "Carduelis cannabina"              "Dendrocopos minor"               
 [5] "Parus ater"                       "Parus montanus"                  
 [7] "Carduelis spinus"                 "Corvus corone cornix"            
 [9] "Miliaria calandra"                "Delichon urbica"                 
[11] "Parus cristatus"                  "Parus caeruleus"                 
[13] "Corvus corone corone"             "Saxicola torquata"               
[15] "Regulus ignicapillus"             "Anas querquedula"                
[17] "Carduelis flammea"                "Tetrao tetrix"                   
[19] "Anas strepera"                    "Dendrocopos medius"              
[21] "Carduelis flammea cabaret"        "Anas clypeata"                   
[23] "Luscinia svecica svecica"         "Charadrius morinellus"           
[25] "Aquila pomarina"                  "Porzana parva"                   
[27] "Luscinia svecica cyanecula"       "Dendroica pensylvanica"          
[29] "Carpodacus mexicanus"             "Dryocopus pileatus"              
[31] "Vermivora pinus"                  "Dendroica petechia"              
[33] "Picoides pubescens"               "Dendroica fusca"                 
[35] "Dendroica magnolia"               "Wilsonia citrina"                
[37] "Carpodacus purpureus"             "Seiurus motacilla"               
[39] "Oporornis philadelphia"           "Dendroica caerulescens"          
[41] "Dendroica coronata"               "Dendroica virens"                
[43] "Butorides virescens"              "Picoides villosus"               
[45] "Seiurus noveboracensis"           "Ammodramus henslowii"            
[47] "Coccothraustes vespertinus"       "Wilsonia canadensis"             
[49] "Anas discors"                     "Vermivora ruficapilla"           
[51] "Parula americana"                 "Dendroica pinus"                 
[53] "Dendroica cerulea"                "Hydropogne caspia"               
[55] "Anas americana"                   "Dendroica discolor"              
[57] "Oporornis formosus"               "Phalacrocorax auritus"           
[59] "Caprimulgus vociferus"            "Dendroica dominica"              
[61] "Picoides dorsalis"                "Dendroica castanea"              
[63] "Dendroica striata"                "Vermivora peregrina"             
[65] "Dendroica palmarum"               "Dendroica tigrina"               
[67] "Wilsonia pusilla"                 "Ammodramus caudacutus"           
[69] "Caprimulgus carolinensis"         "Leucophaeus atricilla"           
[71] "Ammodramus maritimus"             "Anas platyrhynchos x A. rubripes"
[73] "Vermivora chrysoptera x V. pinus" "Egretta intermedia"              
[75] "Cettia diphone"                   "Parus minor"                     
[77] "Porzana fusca"                    "Sterna albifrons"                
[79] "Poecile varius"                   "Hirundo daurica"                 
[81] "Luscinia komadori"                "Dendrocopos kizuki"              
[83] "Sapheopipo noguchii"              "Luscinia akahige"                
[85] "Cuculus optatus"                  "Luscinia calliope"               
[87] "Anas falcata"                     "Zoothera sibirica"               
[89] "Passer rutilans"                  "Luscinia cyane"                  
[91] "Uragus sibiricus"                 "Phalacrocorax pelagicus"         
[93] "Oceanodroma monorhis"             "Porzana pusilla"                 
[95] "Oceanodroma leucorhoa"            "Oceanodroma castro"              
[97] "Tetrastes bonasia"                "Phalacrocorax urile"

Code

setdiff(tax_lookup$verbatimIdentification, 
        crosswalk$ScientificName2010) #93 not matched

 [1] "Corvus corone cornix"             "Delichon urbica"                 
 [3] "Corvus corone corone"             "Saxicola torquata"               
 [5] "Regulus ignicapillus"             "Carduelis flammea cabaret"       
 [7] "Luscinia svecica svecica"         "Charadrius morinellus"           
 [9] "Luscinia svecica cyanecula"       "Spinus tristis"                  
[11] "Poecile atricapillus"             "Gallinago delicata"              
[13] "Spinus pinus"                     "Hydropogne caspia"               
[15] "Ardea alba"                       "Poecile hudsonicus"              
[17] "Falcipennis canadensis"           "Leucophaeus atricilla"           
[19] "Tringa semipalmata"               "Anas platyrhynchos x A. rubripes"
[21] "Sternula antillarum"              "Gelochelidon nilotica"           
[23] "Vermivora chrysoptera x V. pinus" "Egretta intermedia"              
[25] "Hypsipetes amaurotis"             "Anas zonorhyncha"                
[27] "Parus minor"                      "Poecile varius"                  
[29] "Luscinia komadori"                "Acrocephalus orientalis"         
[31] "Spodiopsar cineraceus"            "Otus lempiji"                    
[33] "Sapheopipo noguchii"              "Hierococcyx hyperythrus"         
[35] "Periparus ater"                   "Chloris sinica"                  
[37] "Phylloscopus xanthodryas"         "Luscinia akahige"                
[39] "Pernis ptilorhynchus"             "Poecile montanus"                
[41] "Agropsar philippensis"            "Tetrastes bonasia"               
[43] "Poecile palustris"                "Calonectris borealis"            
[45] "Hydrobates castro"                "Mareca penelope"                 
[47] "Acanthis flammea"                 "Gulosus aristotelis"             
[49] "Mareca strepera"                  "Spinus spinus"                   
[51] "Hydrobates leucorhous"            "Spatula clypeata"                
[53] "Hydrocoloeus minutus"             "Emberiza calandra"               
[55] "Cyanopica cooki"                  "Cecropis daurica"                
[57] "Cyanistes caeruleus"              "Picus sharpei"                   
[59] "Lophophanes cristatus"            "Sternula albifrons"              
[61] "Aquila fasciata"                  "Linaria cannabina"               
[63] "Dryobates minor"                  "Lanius meridionalis"             
[65] "Zapornia pusilla"                 "Ptyonoprogne rupestris"          
[67] "Alaudala rufescens"               "Cercotrichas galactotes"         
[69] "Iduna opaca"                      "Spatula querquedula"             
[71] "Zapornia parva"                   "Cyanecula svecica"               
[73] "Leiopicus medius"                 "Thalasseus sandvicensis"         
[75] "Linaria flavirostris"             "Calidris pugnax"                 
[77] "Lyrurus tetrix"                   "Bubo scandiacus"                 
[79] "Hydroprogne caspia"               "Clanga pomarina"                 
[81] "Passer italiae"                   "Calidris falcinellus"            
[83] "Poecile cinctus"                  "Spilopelia senegalensis"         
[85] "Microcarbo pygmaeus"              "Sylvia crassirostris"            
[87] "Iduna pallida"                    "Pastor roseus"                   
[89] "Poecile lugubris"                 "Phylloscopus orientalis"         
[91] "Clanga clanga"                    "Cyanistes cyanus"                
[93] "Anthropoides virgo"

Code

setdiff(
  tax_lookup %>% filter(scientificName %in% nm) %>% pull(verbatimIdentification),
  crosswalk$ScientificName2010)

[1] "Luscinia svecica svecica"         "Luscinia svecica cyanecula"      
[3] "Falcipennis canadensis"           "Anas platyrhynchos x A. rubripes"
[5] "Vermivora chrysoptera x V. pinus" "Tetrastes bonasia"               
[7] "Cyanecula svecica"                "Sylvia crassirostris"

Code

# 8 out of 20 not matched (but 12 more matched)

Merge taxonomies

step 1: merge scientificName & ScientificName2018 step 2: merge verbatimIdentification & ScientificName2010

Code

tax_lookup2 <- tax_lookup %>%
  left_join(
    crosswalk,
    by = join_by(scientificName == ScientificName2018), keep = TRUE) %>%
  left_join(
    crosswalk,
    by = join_by(verbatimIdentification == ScientificName2010),
    keep = TRUE) %>%
  mutate(ScientificName2010 = coalesce(ScientificName2010.x, ScientificName2010.y)) %>%
  select(-ScientificName2010.x, -ScientificName2010.y) %>%
  mutate(ScientificName2018 = coalesce(ScientificName2018.x, ScientificName2018.y)) %>%
  select(-ScientificName2018.x, -ScientificName2018.y) %>%
  mutate(ScientificName2010 = case_when(ScientificName2010 == "Not Recognised" ~ NA,.default = ScientificName2010),
         ScientificName2018 = case_when(ScientificName2018 == "Not Recognised" ~ NA,.default = ScientificName2018))

Code

skim(tax_lookup2)

Data summary
Name	tax_lookup2
Number of rows	863
Number of columns	4
_______________________
Column type frequency:
character	4
________________________
Group variables	None

Variable type: character

skim_variable	n_missing	complete_rate	min	max	n_unique
verbatimIdentification	0	1.00	9	32	762
scientificName	0	1.00	9	39	726
ScientificName2010	10	0.99	9	29	711
ScientificName2018	9	0.99	9	29	723

Code

tax_lookup2 %>% filter(is.na(ScientificName2010)) %>% 
  kable()

verbatimIdentification	scientificName	ScientificName2010	ScientificName2018
Luscinia svecica svecica	Luscinia svecica	NA	NA
Luscinia svecica cyanecula	Luscinia svecica	NA	NA
Falcipennis canadensis	Canachites canadensis	NA	NA
Anas platyrhynchos x A. rubripes	Anas platyrhynchos x Anas rubripes	NA	NA
Vermivora chrysoptera x V. pinus	Vermivora chrysoptera x Vermivora pinus	NA	NA
Anas zonorhyncha	Anas zonorhyncha	NA	Anas zonorhyncha
Tetrastes bonasia	Tetrastes bonasia	NA	NA
Picus sharpei	Picus sharpei	NA	Picus sharpei
Cyanecula svecica	Luscinia svecica	NA	NA
Sylvia crassirostris	Curruca crassirostris	NA	NA

Code

tax_lookup2 %>% filter(is.na(ScientificName2018)) %>% 
  kable()

verbatimIdentification	scientificName	ScientificName2010	ScientificName2018
Luscinia svecica svecica	Luscinia svecica	NA	NA
Luscinia svecica cyanecula	Luscinia svecica	NA	NA
Falcipennis canadensis	Canachites canadensis	NA	NA
Anas platyrhynchos x A. rubripes	Anas platyrhynchos x Anas rubripes	NA	NA
Vermivora chrysoptera x V. pinus	Vermivora chrysoptera x Vermivora pinus	NA	NA
Cuculus optatus	Cuculus optatus	Cuculus optatus	NA
Tetrastes bonasia	Tetrastes bonasia	NA	NA
Cyanecula svecica	Luscinia svecica	NA	NA
Sylvia crassirostris	Curruca crassirostris	NA	NA

Notes: there are NAs in the ScientificName2018, 2010 columns We have to be careful not to match NAs to NAs which would add wrong data.

3. Avonet crosswalk: Birdlife / BirdTree (Species 1 = ScientificName2018)

Code

BL_BT_crosswalk <- 
  read_excel(
    "c:/Users/wolke/OneDrive - CZU v Praze/Frieda_PhD_files/02_StaticPatterns/Git/Data/input/AVONET Supplementary dataset 1.xlsx",
    sheet = "BirdLife–BirdTree crosswalk")

dd_BL_notMatched <- 
  setdiff(tax_lookup2$ScientificName2018 %>% na.omit(),
          BL_BT_crosswalk$Species1 %>% na.omit())

intersect(dd_BL_notMatched, 
          BL_BT_crosswalk$Species3)

character(0)

Code

# missing species found in Species3 ("Psittacula krameri")

Code

tax_lookup3 <- 
  tax_lookup2 %>%
  select(ScientificName2018) %>% unique() %>%
  na.omit() %>%
  left_join(BL_BT_crosswalk %>% filter(!is.na(Species1)) %>%
              select(-Match.type, -Match.notes),
            by = join_by("ScientificName2018" == "Species1"),
                         keep = FALSE) %>%
  setNames(c("ScientificName2018", "BirdTree")) %>%
  left_join(BL_BT_crosswalk %>% 
              filter(Species3 == "Psittacula krameri") %>% 
              select(Species1, Species3), 
            by = join_by("ScientificName2018" == "Species3"), 
            keep = TRUE) %>%
  right_join(tax_lookup2) %>%
  select(verbatimIdentification, scientificName, 
         ScientificName2010, ScientificName2018, BirdTree)

skim(tax_lookup3)

Data summary
Name	tax_lookup3
Number of rows	890
Number of columns	5
_______________________
Column type frequency:
character	5
________________________
Group variables	None

Variable type: character

skim_variable	n_missing	complete_rate	min	max	n_unique
verbatimIdentification	0	1.00	9	32	762
scientificName	0	1.00	9	39	726
ScientificName2010	10	0.99	9	29	711
ScientificName2018	9	0.99	9	29	723
BirdTree	9	0.99	9	29	733

check NAs:

Code

tax_lookup3 %>% 
  filter(if_any(everything(), is.na))

             verbatimIdentification                          scientificName
1                  Anas zonorhyncha                        Anas zonorhyncha
2                     Picus sharpei                           Picus sharpei
3          Luscinia svecica svecica                        Luscinia svecica
4        Luscinia svecica cyanecula                        Luscinia svecica
5            Falcipennis canadensis                   Canachites canadensis
6  Anas platyrhynchos x A. rubripes      Anas platyrhynchos x Anas rubripes
7  Vermivora chrysoptera x V. pinus Vermivora chrysoptera x Vermivora pinus
8                   Cuculus optatus                         Cuculus optatus
9                 Tetrastes bonasia                       Tetrastes bonasia
10                Cyanecula svecica                        Luscinia svecica
11             Sylvia crassirostris                   Curruca crassirostris
   ScientificName2010 ScientificName2018            BirdTree
1                <NA>   Anas zonorhyncha Anas poecilorhyncha
2                <NA>      Picus sharpei       Picus viridis
3                <NA>               <NA>                <NA>
4                <NA>               <NA>                <NA>
5                <NA>               <NA>                <NA>
6                <NA>               <NA>                <NA>
7                <NA>               <NA>                <NA>
8     Cuculus optatus               <NA>                <NA>
9                <NA>               <NA>                <NA>
10               <NA>               <NA>                <NA>
11               <NA>               <NA>                <NA>

10 species missing from phylo 8 species missing from AVONET (9 in ScientificName2018)

BirdTree consensus (based on recommendations from: https://doi.org/10.1093/czoolo/61.6.959) created in python

Code

library(ape)
tips <- ape::read.tree(
  here::here("Data/input/MRC_consensus_BirdTree.tre"))$tip.label
tree_sp <- data.frame(tip.label = tips)
tree_sp$tip_label <- gsub("_", " ", tree_sp$tip.label)

setdiff(unique(tax_lookup3$BirdTree)[-734], tree_sp$tip_label)

character(0)

all matched (we dropped the NA (row 734) from BirdTree column)

Merge with actual bird tree tip labels (not just the ones from Avonet)

Code

tax_lookup4 <- 
  tax_lookup3 %>%
  left_join(tree_sp, 
            by = join_by("BirdTree" == "tip_label"), 
            keep = FALSE)

tax_lookup4 %>% 
  filter(is.na(BirdTree)) %>% 
  kable() #9

verbatimIdentification	scientificName	ScientificName2010	ScientificName2018	BirdTree	tip.label
Luscinia svecica svecica	Luscinia svecica	NA	NA	NA	NA
Luscinia svecica cyanecula	Luscinia svecica	NA	NA	NA	NA
Falcipennis canadensis	Canachites canadensis	NA	NA	NA	NA
Anas platyrhynchos x A. rubripes	Anas platyrhynchos x Anas rubripes	NA	NA	NA	NA
Vermivora chrysoptera x V. pinus	Vermivora chrysoptera x Vermivora pinus	NA	NA	NA	NA
Cuculus optatus	Cuculus optatus	Cuculus optatus	NA	NA	NA
Tetrastes bonasia	Tetrastes bonasia	NA	NA	NA	NA
Cyanecula svecica	Luscinia svecica	NA	NA	NA	NA
Sylvia crassirostris	Curruca crassirostris	NA	NA	NA	NA

Write to file (csv)

Code

write.csv(tax_lookup4, here::here("Data/input/Tax_lookup.csv"))