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