Calculate Taxonomic Distinctness Over Time

This function calculates the taxonomic distinctness index as a time series.

Usage

tax_distinct_ts(data, rows = 1, ...)

Arguments

data

A data cube object (class 'processed_cube').

rows

Choose which row to select if there are multiple matches when retrieving taxonomic information from GBIF. (Default is 1. Use NA for interactive mode.)

...

Arguments passed on to compute_indicator_workflow

cell_size: Length of grid cell sides, in km. (Default: 10 for country, 100 for continent or world)
level: Spatial level: 'continent', 'country', or 'world'. (Default: 'continent')
region: The region of interest (e.g., "Europe"). (Default: "Europe")
output_crs: The CRS you want for your calculated indicator. (Leave blank to let the function choose a default based on grid reference system)
first_year: Exclude data before this year. (Uses all data in the cube by default.)
last_year: Exclude data after this year. (Uses all data in the cube by default.)
spherical_geometry: If set to FALSE, will temporarily disable spherical geometry while the function runs. Should only be used to solve specific issues. (Default is TRUE)
make_valid: Calls st_make_valid() from the sf package. Increases processing time but may help if you are getting polygon errors. (Default is FALSE).

Value

An S3 object with the classes 'indicator_ts' and 'tax_distinct' containing the calculated indicator values and metadata.

Examples

td_ts <- tax_distinct_ts(example_cube_1, level = "country", region = "Denmark")
#> ══  106 queries  ═════════════
#> 
#> Retrieving data for taxon 'Phocoena phocoena'
#> ✔  Found:  Phocoena phocoena
#> 
#> Retrieving data for taxon 'Vulpes vulpes'
#> ✔  Found:  Vulpes vulpes
#> 
#> Retrieving data for taxon 'Capreolus capreolus'
#> ✔  Found:  Capreolus capreolus
#> 
#> Retrieving data for taxon 'Meles meles'
#> ✔  Found:  Meles meles
#> 
#> Retrieving data for taxon 'Lepus europaeus'
#> ✔  Found:  Lepus europaeus
#> 
#> Retrieving data for taxon 'Phoca vitulina'
#> ✔  Found:  Phoca vitulina
#> 
#> Retrieving data for taxon 'Mustela nivalis'
#> ✔  Found:  Mustela nivalis
#> 
#> Retrieving data for taxon 'Dama dama'
#> ✔  Found:  Dama dama
#> 
#> Retrieving data for taxon 'Nyctereutes procyonoides'
#> ✔  Found:  Nyctereutes procyonoides
#> 
#> Retrieving data for taxon 'Martes foina'
#> ✔  Found:  Martes foina
#> 
#> Retrieving data for taxon 'Equus caballus'
#> ✔  Found:  Equus caballus
#> 
#> Retrieving data for taxon 'Erinaceus europaeus'
#> ✔  Found:  Erinaceus europaeus
#> 
#> Retrieving data for taxon 'Talpa europaea'
#> ✔  Found:  Talpa europaea
#> 
#> Retrieving data for taxon 'Halichoerus grypus'
#> ✔  Found:  Halichoerus grypus
#> 
#> Retrieving data for taxon 'Neomys fodiens'
#> ✔  Found:  Neomys fodiens
#> 
#> Retrieving data for taxon 'Sorex minutus'
#> ✔  Found:  Sorex minutus
#> 
#> Retrieving data for taxon 'Sorex araneus'
#> ✔  Found:  Sorex araneus
#> 
#> Retrieving data for taxon 'Pipistrellus pygmaeus'
#> ✔  Found:  Pipistrellus pygmaeus
#> 
#> Retrieving data for taxon 'Lutra lutra'
#> ✔  Found:  Lutra lutra
#> 
#> Retrieving data for taxon 'Cervus elaphus'
#> ✔  Found:  Cervus elaphus
#> 
#> Retrieving data for taxon 'Mustela vison'
#> ✔  Found:  Mustela vison
#> 
#> Retrieving data for taxon 'Sciurus vulgaris'
#> ✔  Found:  Sciurus vulgaris
#> 
#> Retrieving data for taxon 'Apodemus agrarius'
#> ✔  Found:  Apodemus agrarius
#> 
#> Retrieving data for taxon 'Mus musculus'
#> ✔  Found:  Mus musculus
#> 
#> Retrieving data for taxon 'Plecotus auritus'
#> ✔  Found:  Plecotus auritus
#> 
#> Retrieving data for taxon 'Microtus agrestis'
#> ✔  Found:  Microtus agrestis
#> 
#> Retrieving data for taxon 'Myotis daubentonii'
#> ✔  Found:  Myotis daubentonii
#> 
#> Retrieving data for taxon 'Rattus norvegicus'
#> ✔  Found:  Rattus norvegicus
#> 
#> Retrieving data for taxon 'Pipistrellus nathusii'
#> ✔  Found:  Pipistrellus nathusii
#> 
#> Retrieving data for taxon 'Nyctalus noctula'
#> ✔  Found:  Nyctalus noctula
#> 
#> Retrieving data for taxon 'Eptesicus serotinus'
#> ✔  Found:  Eptesicus serotinus
#> 
#> Retrieving data for taxon 'Mustela erminea'
#> ✔  Found:  Mustela erminea
#> 
#> Retrieving data for taxon 'Sus scrofa'
#> ✔  Found:  Sus scrofa
#> 
#> Retrieving data for taxon 'Felis catus'
#> ✔  Found:  Felis catus
#> 
#> Retrieving data for taxon 'Barbastella barbastellus'
#> ✔  Found:  Barbastella barbastellus
#> 
#> Retrieving data for taxon 'Myotis brandtii'
#> ✔  Found:  Myotis brandtii
#> 
#> Retrieving data for taxon 'Apodemus flavicollis'
#> ✔  Found:  Apodemus flavicollis
#> 
#> Retrieving data for taxon 'Myotis dasycneme'
#> ✔  Found:  Myotis dasycneme
#> 
#> Retrieving data for taxon 'Pipistrellus pipistrellus'
#> ✔  Found:  Pipistrellus pipistrellus
#> 
#> Retrieving data for taxon 'Apodemus sylvaticus'
#> ✔  Found:  Apodemus sylvaticus
#> 
#> Retrieving data for taxon 'Myodes glareolus'
#> ✔  Found:  Myodes glareolus
#> 
#> Retrieving data for taxon 'Vespertilio murinus'
#> ✔  Found:  Vespertilio murinus
#> 
#> Retrieving data for taxon 'Nyctalus leisleri'
#> ✔  Found:  Nyctalus leisleri
#> 
#> Retrieving data for taxon 'Myotis nattereri'
#> ✔  Found:  Myotis nattereri
#> 
#> Retrieving data for taxon 'Myotis myotis'
#> ✔  Found:  Myotis myotis
#> 
#> Retrieving data for taxon 'Micromys minutus'
#> ✔  Found:  Micromys minutus
#> 
#> Retrieving data for taxon 'Bos taurus'
#> ✔  Found:  Bos taurus
#> 
#> Retrieving data for taxon 'Arvicola amphibius'
#> ✔  Found:  Arvicola amphibius
#> 
#> Retrieving data for taxon 'Oryctolagus cuniculus'
#> ✔  Found:  Oryctolagus cuniculus
#> 
#> Retrieving data for taxon 'Mustela putorius'
#> ✔  Found:  Mustela putorius
#> 
#> Retrieving data for taxon 'Ondatra zibethicus'
#> ✔  Found:  Ondatra zibethicus
#> 
#> Retrieving data for taxon 'Martes martes'
#> ✔  Found:  Martes martes
#> 
#> Retrieving data for taxon 'Myocastor coypus'
#> ✔  Found:  Myocastor coypus
#> 
#> Retrieving data for taxon 'Cervus nippon'
#> ✔  Found:  Cervus nippon
#> 
#> Retrieving data for taxon 'Procyon lotor'
#> ✔  Found:  Procyon lotor
#> 
#> Retrieving data for taxon 'Muscardinus avellanarius'
#> ✔  Found:  Muscardinus avellanarius
#> 
#> Retrieving data for taxon 'Tursiops truncatus'
#> ✔  Found:  Tursiops truncatus
#> 
#> Retrieving data for taxon 'Megaptera novaeangliae'
#> ✔  Found:  Megaptera novaeangliae
#> 
#> Retrieving data for taxon 'Myotis mystacinus'
#> ✔  Found:  Myotis mystacinus
#> 
#> Retrieving data for taxon 'Bubalus bubalis'
#> ✔  Found:  Bubalus bubalis
#> 
#> Retrieving data for taxon 'Pagophilus groenlandicus'
#> ✔  Found:  Pagophilus groenlandicus
#> 
#> Retrieving data for taxon 'Homo sapiens'
#> ✔  Found:  Homo sapiens
#> 
#> Retrieving data for taxon 'Alces alces'
#> ✔  Found:  Alces alces
#> 
#> Retrieving data for taxon 'Ovis aries'
#> ✔  Found:  Ovis aries
#> 
#> Retrieving data for taxon 'Castor fiber'
#> ✔  Found:  Castor fiber
#> 
#> Retrieving data for taxon 'Canis lupus'
#> ✔  Found:  Canis lupus
#> 
#> Retrieving data for taxon 'Pusa hispida'
#> ✔  Found:  Pusa hispida
#> 
#> Retrieving data for taxon 'Microtus arvalis'
#> ✔  Found:  Microtus arvalis
#> 
#> Retrieving data for taxon 'Ovis gmelini'
#> ✔  Found:  Ovis gmelini
#> 
#> Retrieving data for taxon 'Sicista betulina'
#> ✔  Found:  Sicista betulina
#> 
#> Retrieving data for taxon 'Equus ferus'
#> ✔  Found:  Equus ferus
#> 
#> Retrieving data for taxon 'Mammuthus primigenius'
#> ✔  Found:  Mammuthus primigenius
#> 
#> Retrieving data for taxon 'Balaenoptera physalus'
#> ✔  Found:  Balaenoptera physalus
#> 
#> Retrieving data for taxon 'Megaloceros giganteus'
#> ✔  Found:  Megaloceros giganteus
#> 
#> Retrieving data for taxon 'Delphinus delphis'
#> ✔  Found:  Delphinus delphis
#> 
#> Retrieving data for taxon 'Capra hircus'
#> ✔  Found:  Capra hircus
#> 
#> Retrieving data for taxon 'Physeter macrocephalus'
#> ✔  Found:  Physeter macrocephalus
#> 
#> Retrieving data for taxon 'Myotis bechsteinii'
#> ✔  Found:  Myotis bechsteinii
#> 
#> Retrieving data for taxon 'Eptesicus nilssonii'
#> ✔  Found:  Eptesicus nilssonii
#> 
#> Retrieving data for taxon 'Bison bonasus'
#> ✔  Found:  Bison bonasus
#> 
#> Retrieving data for taxon 'Vulpes lagopus'
#> ✔  Found:  Vulpes lagopus
#> 
#> Retrieving data for taxon 'Lagenorhynchus albirostris'
#> ✔  Found:  Lagenorhynchus albirostris
#> 
#> Retrieving data for taxon 'Balaenoptera acutorostrata'
#> ✔  Found:  Balaenoptera acutorostrata
#> 
#> Retrieving data for taxon 'Globicephala melas'
#> ✔  Found:  Globicephala melas
#> 
#> Retrieving data for taxon 'Canis aureus'
#> ✔  Found:  Canis aureus
#> 
#> Retrieving data for taxon 'Muntiacus reevesi'
#> ✔  Found:  Muntiacus reevesi
#> 
#> Retrieving data for taxon 'Eliomys quercinus'
#> ✔  Found:  Eliomys quercinus
#> 
#> Retrieving data for taxon 'Hyperoodon ampullatus'
#> ✔  Found:  Hyperoodon ampullatus
#> 
#> Retrieving data for taxon 'Orcinus orca'
#> ✔  Found:  Orcinus orca
#> 
#> Retrieving data for taxon 'Stenella clymene'
#> ✔  Found:  Stenella clymene
#> 
#> Retrieving data for taxon 'Felis silvestris'
#> ✔  Found:  Felis silvestris
#> 
#> Retrieving data for taxon 'Rangifer tarandus'
#> ✔  Found:  Rangifer tarandus
#> 
#> Retrieving data for taxon 'Odobenus rosmarus'
#> ✔  Found:  Odobenus rosmarus
#> 
#> Retrieving data for taxon 'Ovis ammon'
#> ✔  Found:  Ovis ammon
#> 
#> Retrieving data for taxon 'Lagenorhynchus acutus'
#> ✔  Found:  Lagenorhynchus acutus
#> 
#> Retrieving data for taxon 'Pusa sibirica'
#> ✔  Found:  Pusa sibirica
#> 
#> Retrieving data for taxon 'Panthera tigris'
#> ✔  Found:  Panthera tigris
#> 
#> Retrieving data for taxon 'Lemur catta'
#> ✔  Found:  Lemur catta
#> 
#> Retrieving data for taxon 'Equus asinus'
#> ✔  Found:  Equus asinus
#> 
#> Retrieving data for taxon 'Eschrichtius robustus'
#> ✔  Found:  Eschrichtius robustus
#> 
#> Retrieving data for taxon 'Tamias sibiricus'
#> ✔  Found:  Tamias sibiricus
#> 
#> Retrieving data for taxon 'Erignathus barbatus'
#> ✔  Found:  Erignathus barbatus
#> 
#> Retrieving data for taxon 'Mesocricetus auratus'
#> ✔  Found:  Mesocricetus auratus
#> 
#> Retrieving data for taxon 'Balaenoptera borealis'
#> ✔  Found:  Balaenoptera borealis
#> 
#> Retrieving data for taxon 'Nasua nasua'
#> ✔  Found:  Nasua nasua
#> 
#> Retrieving data for taxon 'Stenella coeruleoalba'
#> ✔  Found:  Stenella coeruleoalba
#> ══  Results  ═════════════════
#> 
#> • Total: 106 
#> • Found: 106 
#> • Not Found: 0
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 2
#> [1] 3
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 2
#> [1] 1
#> [1] 2
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 2
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 1
#> [1] 2
#> [1] 4
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 2
#> [1] 2
#> [1] 2
#> [1] 1
#> [1] 2
#> [1] 1
#> [1] 3
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 2
#> [1] 4
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 3
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 4
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 9
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 6
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 7
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 7
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 6
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 6
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 6
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 4
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 2
#> [1] 5
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 8
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 5
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 1
#> [1] 2
#> [1] 6
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 1
#> [1] 4
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 8
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 2
#> [1] 1
#> [1] 5
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 6
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 11
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 4
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 6
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 3
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 4
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 3
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 12
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 16
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 24
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 7
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 19
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 12
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 11
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 11
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 12
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 12
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 26
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 15
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 20
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 17
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 20
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 19
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 16
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 14
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 22
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 26
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 27
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 20
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 27
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 18
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 23
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 27
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 28
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 26
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 36
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 32
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 32
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 39
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 45
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 45
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 50
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 44
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 48
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 54
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 48
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 51
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 52
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 53
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 58
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 49
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 59
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 53
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 52
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 58
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 59
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 60
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 66
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 68
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 70
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 69
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 67
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
#> [1] 68
#> Get all ranks and their taxIDs
#> Align taxonomy hierarchies...
#> Taxonomy alignment done!
#> Calculate distance matrix
#> Add node labels
#> Warning: There was 1 warning in `dplyr::mutate()`.
#> ℹ In argument: `diversity_val = compute_tax_distinct_formula(., tax_hier)`.
#> Caused by warning in `taxa2dist()`:
#> ! you used 'check=FALSE' and some distances are zero -- was this intended?
plot(td_ts)
#> Warning: Removed 41 rows containing non-finite outside the scale range
#> (`stat_smooth()`).
#> Warning: Removed 41 rows containing non-finite outside the scale range
#> (`stat_smooth()`).
#> Warning: Removed 6 rows containing missing values or values outside the scale range
#> (`geom_line()`).

Usage

Arguments

Value

See also

Examples