Checking Taxa Presence in Samples
Source:vignettes/checking-taxa-presence.Rmd
checking-taxa-presence.RmdOverview
One of the key challenges in environmental sequencing studies is
determining whether detected taxa are likely to be actually present at
your sampling sites. This vignette demonstrates how to use
taxinfo’s occurrence checking functions to validate the
likelihood of taxa presence based on known geographic distributions.
As most of taxinfo’s utilities, these functions can
accept either a phyloseq object with cleaned taxonomic names or a vector
of taxonomic names (taxnames parameter). The algorithm used
to assign the taxonomic names must be stringent enough to avoid false
positives. Moreover, we recommend using gna_verifier_pq()
to clean taxonomic names by disambiguating synonyms and correcting
misspellings.
Core Functions
The main functions for checking taxa presence are:
-
tax_occur_check(): Core occurrence checking function for individual taxa -
tax_occur_check_pq(): Check occurrence likelihood within a radius around samples -
tax_occur_multi_check_pq(): Check multiple locations simultaneously
Basic Occurrence Checking for individual taxa
How many Quercus robur occurrences have been reported within 100km of Paris, France?
Q_rob_in_Paris <- tax_occur_check("Quercus robur", 2.3522, 48.8566, 100)
Q_rob_in_Paris$count_in_radius#> [1] 755
# Visualize occurrences around Paris for Fagus sylvatica
res_occ <- tax_occur_check("Fagus sylvatica", 2.3522, 48.8566, 200,
return_all_occ = TRUE
)
occ_data_sf <- sf::st_as_sf(res_occ$occ_data,
coords = c("decimalLongitude", "decimalLatitude"),
crs = 4326
)
if (requireNamespace("leaflet")) {
library(leaflet)
}
if (requireNamespace("leafpop")) {
library(leafpop)
}
leaflet() |>
addTiles() |>
setView(2.3522, 48.8566, zoom = 12) |>
fitBounds(
lat1 = as.vector(sf::st_bbox(occ_data_sf))[2],
lng1 = as.vector(sf::st_bbox(occ_data_sf))[1],
lat2 = as.vector(sf::st_bbox(occ_data_sf))[4],
lng2 = as.vector(sf::st_bbox(occ_data_sf))[3]
) |>
leaflet::addCircles(data = occ_data_sf, color = "blue", stroke = 1, opacity = 0.8) |>
leaflet::addCircleMarkers(2.3522, 48.8566, color = "orange", radius = 2, opacity = 1)#> Error in `loadNamespace()`:
#> ! there is no package called 'webshot'Basic Occurrence Checking fo phyloseq object
Setting Up the Data
# Load example data
data("data_fungi_mini", package = "MiscMetabar")
# Keep only first 20 taxa for speed
data_clean <- prune_taxa(taxa = taxa_names(data_fungi_mini)[1:20], data_fungi_mini) |>
gna_verifier_pq(data_sources = 210)
summary_plot_pq(data_clean)
plot of chunk unnamed-chunk-4
#> Taxonomy Table: [6 taxa by 3 taxonomic ranks]:
#> Genus Species currentCanonicalSimple
#> ASV7 NA NA NA
#> ASV8 "Stereum" "ostrea" "Stereum ostrea"
#> ASV12 "Xylodon" "raduloides" "Xylodon"
#> ASV18 "Stereum" "ostrea" "Stereum ostrea"
#> ASV25 "Ossicaulis" "lachnopus" "Ossicaulis lachnopus"
#> ASV26 "Stereum" "hirsutum" "Stereum hirsutum"Single Location Occurrence Check
Check if taxa in your phyloseq object have been reported within a specific radius of your sampling location:
# Define sampling coordinates (example: Paris, France)
longitude <- 2.3488
latitude <- 48.8534
# Check occurrence within 100km radius
occurrence_check <- tax_occur_check_pq(
data_clean,
longitude = longitude,
latitude = latitude,
radius_km = 100,
n_occur = 1000,
add_to_phyloseq = FALSE
)
# View results
head(occurrence_check)#> # A tibble: 6 × 10
#> taxa_name count_in_radius closest_distance_km mean_distance_km
#> <chr> <dbl> <dbl> <dbl>
#> 1 Stereum ostrea 1 47.1 47.1
#> 2 Ossicaulis lachnopus 0 NA NA
#> 3 Stereum hirsutum 439 8.3 57.2
#> 4 Basidiodendron eyrei 3 55.4 58.9
#> 5 Sistotrema oblongisporum 1 53 53
#> 6 Fomes fomentarius 606 8.17 54.0
#> # ℹ 6 more variables: total_count_in_world <dbl>, search_radius <dbl>,
#> # closest_point_lat <dbl>, closest_point_lon <dbl>, sample_point_lat <dbl>,
#> # sample_point_lon <dbl>Example Visualization
Here’s what occurrence checking results might look like:
plot of chunk unnamed-chunk-7
We can also explore the minimum and mean distance to sampling location.
occurrence_check |>
mutate(Genus = stringr::word(taxa_name, 1)) |>
filter(!is.na(mean_distance_km)) |>
mutate(taxa_name = forcats::fct_reorder(taxa_name, mean_distance_km)) |>
ggplot(aes(x = mean_distance_km, y = taxa_name)) +
geom_col(aes(fill = Genus)) +
scale_fill_idest_d(name = "Genus") +
geom_text(aes(label = paste0("Closest: ", closest_distance_km, " km"), x = 10), size = 3) +
geom_text(aes(label = paste0("n=", count_in_radius)), nudge_x = -2, size = 3)
plot of chunk unnamed-chunk-8
The results include:
-
taxa_name: Taxonomic name checked -
count_in_radius: Number of occurrences within the specified radius -
total_count_in_world: Total global occurrences for this taxon -
radius_km: Search radius used -
longitude/latitude: Center coordinates -
closest_distance_km: The distance to the closest occurrence point -
closest_distance_km: The mean distance to occurrence point
Advanced Occurrence Checking
Multiple Radius Analysis
Compare occurrence patterns at different spatial scales:
# Check multiple radii
radii <- c(50, 100, 200, 500)
occurrence_multi_radius <- purrr::map_dfr(radii, function(r) {
tax_occur_check_pq(data_clean,
longitude = longitude,
latitude = latitude,
radius_km = r,
n_occur = 1000,
add_to_phyloseq = FALSE
) |>
mutate(radius_category = paste(r, "km"))
})
# Visualize scaling patterns
occurrence_multi_radius |>
ggplot(aes(x = radius_category, y = count_in_radius, group = taxa_name)) +
geom_line(alpha = 0.6) +
geom_point(alpha = 0.8) +
facet_wrap(~taxa_name, scales = "free_y") +
labs(
title = "Occurrence Scaling by Radius",
x = "Search Radius",
y = "Count in Radius"
) +
theme_idest(base_size = 8, strip_text_size = 7, strip_text_face = "italic")
plot of chunk unnamed-chunk-10
Filtering Unlikely Taxa
Use occurrence data to filter taxa that are unlikely to be present:
# Set threshold for likely presence (e.g., at least 5 occurrences within 100km)
min_occurrences <- 5
likely_present <- occurrence_check |>
filter(count_in_radius >= min_occurrences) |>
pull(taxa_name)
# Filter phyloseq object to keep only likely present taxa
# Note that all samples are kept, use clean_pq if you want to remove empty samples
data_filtered <- select_taxa_pq(data_clean, taxnames = likely_present)
compar <- MiscMetabar::track_wkflow(
list(
"initial" = data_clean,
"filtered" = clean_pq(data_filtered)
),
verbose = FALSE
)
knitr::kable(compar)<!-- KNITR_ASIS_OUTPUT_TOKEN -->
| | nb_sequences| nb_clusters| nb_samples|
|:--------|------------:|-----------:|----------:|
|initial | 388567| 20| 137|
|filtered | 77836| 6| 27|
<!-- KNITR_ASIS_OUTPUT_TOKEN -->```
</div>
## Multi-Location Checking
For studies with multiple sampling sites:
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<div id='msg-popup-unnamed-chunk-12' class='popup' role='dialog' aria-hidden='true' onclick='event.stopPropagation();'><button class='popup-close' aria-label='Close'>×</button><div class='popup-header'><strong>Messages</strong></div><pre class='popup-pre'>#> ℹ Processing GPS point: "1.4861010918996_47.8236795176018"
#> Cleaning suppress 15 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#> ✔ Found 1 occurrences for species Stereum ostrea:
#> • Closest occurrence: 89.7 km
#> Reading 'ne_50m_land.zip' from naturalearth...
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 281 occurrences remain(s)
#> - Total original: 281
#> - Retention rate: 100%
#> ✔ Found 116 occurrences for species Stereum hirsutum:
#> • Closest occurrence: 8.29 km
#>
■ 1% | ETA: 6m
[K
[Kℹ Processing GPS point: "2.2993352883976_48.2367350320308"
#> ■ 1% | ETA: 6m
Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■ 1% | ETA: 6m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■ 1% | ETA: 6m
#>
[K
#> • Closest occurrence: 21.83 km
#>
#> ■ 1% | ETA: 6m
#>
■■ 2% | ETA: 5m
[K
#>
[K
#> ℹ Processing GPS point: "1.75391880935241_47.8166291060034"
#>
#> ■■ 2% | ETA: 5m
#> Cleaning suppress 15 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■ 2% | ETA: 5m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■ 2% | ETA: 5m
#>
[K
#> • Closest occurrence: 78.8 km
#>
#> ■■ 2% | ETA: 5m
#>
■■ 3% | ETA: 4m
[K
#>
[K
#> ℹ Processing GPS point: "1.75792730852202_48.5406438706496"
#>
#> ■■ 3% | ETA: 4m
#> Cleaning suppress 14 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■ 3% | ETA: 4m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■ 3% | ETA: 4m
#>
[K
#> • Closest occurrence: 40.23 km
#>
#> ■■ 3% | ETA: 4m
#>
■■ 4% | ETA: 4m
[K
#>
[K
#> ℹ Processing GPS point: "2.11533779950779_47.9584116800543"
#>
#> ■■ 4% | ETA: 4m
#> Cleaning suppress 18 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■ 4% | ETA: 4m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■ 4% | ETA: 4m
#>
[K
#> • Closest occurrence: 54.1 km
#>
#> ■■ 4% | ETA: 4m
#>
■■ 4% | ETA: 4m
[K
#>
[K
#> ℹ Processing GPS point: "1.98968665610563_47.7518540364153"
#>
#> ■■ 4% | ETA: 4m
#> Cleaning suppress 18 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■ 4% | ETA: 4m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■ 4% | ETA: 4m
#>
[K
#> • Closest occurrence: 78.69 km
#>
#> ■■ 4% | ETA: 4m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■ 4% | ETA: 4m
#>
■■■ 5% | ETA: 4m
[K
#>
[K
#> ℹ Processing GPS point: "1.99594050913231_47.9730602147973"
#>
#> ■■■ 5% | ETA: 4m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■ 5% | ETA: 4m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■ 5% | ETA: 4m
#>
[K
#> • Closest occurrence: 55.23 km
#>
#> ■■■ 5% | ETA: 4m
#>
■■■ 6% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.68379530350899_47.9636910609151"
#>
#> ■■■ 6% | ETA: 3m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■ 6% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■ 6% | ETA: 3m
#>
[K
#> • Closest occurrence: 68.29 km
#>
#> ■■■ 6% | ETA: 3m
#>
■■■ 7% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.55556511489069_47.9021549864714"
#>
#> ■■■ 7% | ETA: 3m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■ 7% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■ 7% | ETA: 3m
#>
[K
#> • Closest occurrence: 79.73 km
#>
#> ■■■ 7% | ETA: 3m
#>
■■■ 7% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.76283250266615_47.9245699828038"
#>
#> ■■■ 7% | ETA: 3m
#> Cleaning suppress 18 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■ 7% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■ 7% | ETA: 3m
#>
[K
#> • Closest occurrence: 68.23 km
#>
#> ■■■ 7% | ETA: 3m
#>
■■■ 8% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.24408058438146_47.8155687267114"
#>
#> ■■■ 8% | ETA: 3m
#> Cleaning suppress 18 taxa and 0 samples.
#>
#>
[K
#> ! No taxonomic names found at the specified taxonomic rank.Please check the `taxonomic_rank` parameter and your phyloseq object.
#>
#> ■■■ 8% | ETA: 3m
#>
■■■■ 9% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.18060256056189_47.7163803338367"
#>
#> ■■■■ 9% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> • Closest occurrence: 79.98 km
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■ 9% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 211 occurrences remain(s)
#> - Total original: 211
#> - Retention rate: 100%
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> ✔ Found 195 occurrences for species Stereum hirsutum:
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> • Closest occurrence: 15.59 km
#>
#> ■■■■ 9% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 3 occurrences remain(s)
#> - Total original: 3
#> - Retention rate: 100%
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> ✔ Found 3 occurrences for species Basidiodendron eyrei:
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> • Closest occurrence: 81.97 km
#>
#> ■■■■ 9% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Sistotrema oblongisporum:
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> • Closest occurrence: 86.43 km
#>
#> ■■■■ 9% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 495 occurrences remain(s)
#> - Total original: 495
#> - Retention rate: 100%
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> ✔ Found 465 occurrences for species Fomes fomentarius:
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> • Closest occurrence: 12.78 km
#>
#> ■■■■ 9% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 17 occurrences remain(s)
#> - Total original: 17
#> - Retention rate: 100%
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> ✔ Found 17 occurrences for species Cerocorticium molare:
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> • Closest occurrence: 23 km
#>
#> ■■■■ 9% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 5 occurrences remain(s)
#> - Total original: 5
#> - Retention rate: 100%
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> ✔ Found 5 occurrences for species Aporpium canescens:
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> • Closest occurrence: 84.44 km
#>
#> ■■■■ 9% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 22 occurrences remain(s)
#> - Total original: 22
#> - Retention rate: 100%
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> ✔ Found 22 occurrences for species Hypochnicium analogum:
#>
#> ■■■■ 9% | ETA: 3m
#>
[K
#> • Closest occurrence: 81.97 km
#>
#> ■■■■ 9% | ETA: 3m
#>
■■■■ 9% | ETA: 5m
[K
#>
[K
#> ℹ Processing GPS point: "2.194041359546_48.3226996810885"
#>
#> ■■■■ 9% | ETA: 5m
#> Cleaning suppress 17 taxa and 0 samples.
#>
#>
[K
#> ! No taxonomic names found at the specified taxonomic rank.Please check the `taxonomic_rank` parameter and your phyloseq object.
#>
#> ■■■■ 9% | ETA: 5m
#>
[K
#> ℹ Processing GPS point: "1.55570790684956_48.2329909701314"
#>
#> ■■■■ 9% | ETA: 5m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■ 9% | ETA: 5m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■ 9% | ETA: 5m
#>
[K
#> • Closest occurrence: 57.88 km
#>
#> ■■■■ 9% | ETA: 5m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 4 occurrences remain(s)
#> - Total original: 4
#> - Retention rate: 100%
#>
#> ■■■■ 9% | ETA: 5m
#>
[K
#> ✔ Found 4 occurrences for species Basidiodendron eyrei:
#>
#> ■■■■ 9% | ETA: 5m
#>
[K
#> • Closest occurrence: 75.04 km
#>
#> ■■■■ 9% | ETA: 5m
#>
■■■■ 11% | ETA: 4m
[K
#>
[K
#> ℹ Processing GPS point: "1.94402037644304_47.8232108413603"
#>
#> ■■■■ 11% | ETA: 4m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■ 11% | ETA: 4m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■ 11% | ETA: 4m
#>
[K
#> • Closest occurrence: 72.18 km
#>
#> ■■■■ 11% | ETA: 4m
#>
■■■■■ 12% | ETA: 4m
[K
#>
[K
#> ℹ Processing GPS point: "2.15212296392716_48.1076730627936"
#>
#> ■■■■■ 12% | ETA: 4m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■ 12% | ETA: 4m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■ 12% | ETA: 4m
#>
[K
#> • Closest occurrence: 37.33 km
#>
#> ■■■■■ 12% | ETA: 4m
#>
■■■■■ 12% | ETA: 4m
[K
#>
[K
#> ℹ Processing GPS point: "2.17866024451568_47.9784287809566"
#>
#> ■■■■■ 12% | ETA: 4m
#> Cleaning suppress 14 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■ 12% | ETA: 4m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■ 12% | ETA: 4m
#>
[K
#> • Closest occurrence: 51.05 km
#>
#> ■■■■■ 12% | ETA: 4m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■ 12% | ETA: 4m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 3 occurrences remain(s)
#> - Total original: 3
#> - Retention rate: 100%
#>
#> ■■■■■ 12% | ETA: 4m
#>
[K
#> ✔ Found 3 occurrences for species Basidiodendron eyrei:
#>
#> ■■■■■ 12% | ETA: 4m
#>
[K
#> • Closest occurrence: 58.15 km
#>
#> ■■■■■ 12% | ETA: 4m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 5 occurrences remain(s)
#> - Total original: 5
#> - Retention rate: 100%
#>
#> ■■■■■ 12% | ETA: 4m
#>
[K
#> ✔ Found 5 occurrences for species Aporpium canescens:
#>
#> ■■■■■ 12% | ETA: 4m
#>
[K
#> • Closest occurrence: 58.98 km
#>
#> ■■■■■ 12% | ETA: 4m
#>
■■■■■ 13% | ETA: 4m
[K
#>
[K
#> ℹ Processing GPS point: "1.60122818798864_47.8599313706998"
#>
#> ■■■■■ 13% | ETA: 4m
#> Cleaning suppress 19 taxa and 0 samples.
#>
#>
[K
#> ! No taxonomic names found at the specified taxonomic rank.Please check the `taxonomic_rank` parameter and your phyloseq object.
#>
#> ■■■■■ 13% | ETA: 4m
#>
[K
#> ℹ Processing GPS point: "1.98980478971632_48.0790437367661"
#>
#> ■■■■■ 13% | ETA: 4m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■ 13% | ETA: 4m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■ 13% | ETA: 4m
#>
[K
#> • Closest occurrence: 44.76 km
#>
#> ■■■■■ 13% | ETA: 4m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 29 occurrences remain(s)
#> - Total original: 32
#> - Retention rate: 90.6%
#>
#> ■■■■■ 13% | ETA: 4m
#>
[K
#> ✔ Found 29 occurrences for species Cerocorticium molare:
#>
#> ■■■■■ 13% | ETA: 4m
#>
[K
#> • Closest occurrence: 52.75 km
#>
#> ■■■■■ 13% | ETA: 4m
#>
■■■■■ 15% | ETA: 4m
[K
#>
[K
#> ℹ Processing GPS point: "2.04364455202932_48.3227813435762"
#>
#> ■■■■■ 15% | ETA: 4m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■ 15% | ETA: 4m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■ 15% | ETA: 4m
#>
[K
#> • Closest occurrence: 21.24 km
#>
#> ■■■■■ 15% | ETA: 4m
#>
■■■■■■ 15% | ETA: 4m
[K
#>
[K
#> ℹ Processing GPS point: "1.9251944020232_47.7722906194223"
#>
#> ■■■■■■ 15% | ETA: 4m
#> Cleaning suppress 19 taxa and 0 samples.
#>
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■ 15% | ETA: 4m
#>
■■■■■■ 16% | ETA: 4m
[K
#>
[K
#> ℹ Processing GPS point: "1.87206048896544_47.7724218267879"
#>
#> ■■■■■■ 16% | ETA: 4m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■ 16% | ETA: 4m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■ 16% | ETA: 4m
#>
[K
#> • Closest occurrence: 79.38 km
#>
#> ■■■■■■ 16% | ETA: 4m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■ 16% | ETA: 4m
#>
■■■■■■ 17% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.74062920158094_47.9138174489072"
#>
#> ■■■■■■ 17% | ETA: 3m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■ 17% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■ 17% | ETA: 3m
#>
[K
#> • Closest occurrence: 70.15 km
#>
#> ■■■■■■ 17% | ETA: 3m
#>
■■■■■■ 18% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.97431155666963_47.8919119497415"
#>
#> ■■■■■■ 18% | ETA: 3m
#> Cleaning suppress 18 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■ 18% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■ 18% | ETA: 3m
#>
[K
#> • Closest occurrence: 64.23 km
#>
#> ■■■■■■ 18% | ETA: 3m
#>
■■■■■■ 18% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.48263441603355_48.0261924844287"
#>
#> ■■■■■■ 18% | ETA: 3m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■ 18% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■ 18% | ETA: 3m
#>
[K
#> • Closest occurrence: 74.3 km
#>
#> ■■■■■■ 18% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 4 occurrences remain(s)
#> - Total original: 4
#> - Retention rate: 100%
#>
#> ■■■■■■ 18% | ETA: 3m
#>
[K
#> ✔ Found 4 occurrences for species Basidiodendron eyrei:
#>
#> ■■■■■■ 18% | ETA: 3m
#>
[K
#> • Closest occurrence: 78.3 km
#>
#> ■■■■■■ 18% | ETA: 3m
#>
■■■■■■■ 19% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.57243356349822_48.0868322859995"
#>
#> ■■■■■■■ 19% | ETA: 3m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■ 19% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■ 19% | ETA: 3m
#>
[K
#> • Closest occurrence: 64.91 km
#>
#> ■■■■■■■ 19% | ETA: 3m
#>
■■■■■■■ 20% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.0292250789377_48.0726171498082"
#>
#> ■■■■■■■ 20% | ETA: 3m
#> Cleaning suppress 19 taxa and 0 samples.
#>
#>
[K
#> ! No taxonomic names found at the specified taxonomic rank.Please check the `taxonomic_rank` parameter and your phyloseq object.
#>
#> ■■■■■■■ 20% | ETA: 3m
#>
[K
#> ℹ Processing GPS point: "2.29209124736533_47.8283733758595"
#>
#> ■■■■■■■ 20% | ETA: 3m
#> Cleaning suppress 19 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■ 20% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■ 20% | ETA: 3m
#>
[K
#> • Closest occurrence: 67.2 km
#>
#> ■■■■■■■ 20% | ETA: 3m
#>
■■■■■■■ 21% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.61470233209667_48.0988313611085"
#>
#> ■■■■■■■ 21% | ETA: 3m
#> Cleaning suppress 15 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■ 21% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■ 21% | ETA: 3m
#>
[K
#> • Closest occurrence: 61.6 km
#>
#> ■■■■■■■ 21% | ETA: 3m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■ 21% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 389 occurrences remain(s)
#> - Total original: 402
#> - Retention rate: 96.8%
#>
#> ■■■■■■■ 21% | ETA: 3m
#>
[K
#> ✔ Found 350 occurrences for species Stereum hirsutum:
#>
#> ■■■■■■■ 21% | ETA: 3m
#>
[K
#> • Closest occurrence: 26.46 km
#>
#> ■■■■■■■ 21% | ETA: 3m
#>
■■■■■■■■ 22% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.21498966421748_48.295972436813"
#>
#> ■■■■■■■■ 22% | ETA: 3m
#> Cleaning suppress 16 taxa and 0 samples.
#>
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■ 22% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■ 22% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Sistotrema oblongisporum:
#>
#> ■■■■■■■■ 22% | ETA: 3m
#>
[K
#> • Closest occurrence: 35.96 km
#>
#> ■■■■■■■■ 22% | ETA: 3m
#>
■■■■■■■■ 23% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.89493312259817_48.01884545766"
#>
#> ■■■■■■■■ 23% | ETA: 3m
#> Cleaning suppress 19 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■ 23% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■ 23% | ETA: 3m
#>
[K
#> • Closest occurrence: 54.09 km
#>
#> ■■■■■■■■ 23% | ETA: 3m
#>
■■■■■■■■ 23% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.25486553201844_47.7644966605838"
#>
#> ■■■■■■■■ 23% | ETA: 3m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■ 23% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■ 23% | ETA: 3m
#>
[K
#> • Closest occurrence: 74.31 km
#>
#> ■■■■■■■■ 23% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 22 occurrences remain(s)
#> - Total original: 22
#> - Retention rate: 100%
#>
#> ■■■■■■■■ 23% | ETA: 3m
#>
[K
#> ✔ Found 22 occurrences for species Hypochnicium analogum:
#>
#> ■■■■■■■■ 23% | ETA: 3m
#>
[K
#> • Closest occurrence: 74.65 km
#>
#> ■■■■■■■■ 23% | ETA: 3m
#>
■■■■■■■■ 24% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.03049928179273_47.8518325317124"
#>
#> ■■■■■■■■ 24% | ETA: 3m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■ 24% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■ 24% | ETA: 3m
#>
[K
#> • Closest occurrence: 67.16 km
#>
#> ■■■■■■■■ 24% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■ 24% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Sistotrema oblongisporum:
#>
#> ■■■■■■■■ 24% | ETA: 3m
#>
[K
#> • Closest occurrence: 79.02 km
#>
#> ■■■■■■■■ 24% | ETA: 3m
#>
■■■■■■■■ 25% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.01390756079847_48.1646937552455"
#>
#> ■■■■■■■■ 25% | ETA: 3m
#> Cleaning suppress 19 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■ 25% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■ 25% | ETA: 3m
#>
[K
#> • Closest occurrence: 35.66 km
#>
#> ■■■■■■■■ 25% | ETA: 3m
#>
■■■■■■■■■ 26% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.38329502714333_47.9179197636477"
#>
#> ■■■■■■■■■ 26% | ETA: 3m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■ 26% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■ 26% | ETA: 3m
#>
[K
#> • Closest occurrence: 57.75 km
#>
#> ■■■■■■■■■ 26% | ETA: 3m
#>
■■■■■■■■■ 26% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.79653093345683_48.0116087875764"
#>
#> ■■■■■■■■■ 26% | ETA: 3m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■ 26% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■ 26% | ETA: 3m
#>
[K
#> • Closest occurrence: 58.89 km
#>
#> ■■■■■■■■■ 26% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 22 occurrences remain(s)
#> - Total original: 22
#> - Retention rate: 100%
#>
#> ■■■■■■■■■ 26% | ETA: 3m
#>
[K
#> ✔ Found 22 occurrences for species Hypochnicium analogum:
#>
#> ■■■■■■■■■ 26% | ETA: 3m
#>
[K
#> • Closest occurrence: 76.4 km
#>
#> ■■■■■■■■■ 26% | ETA: 3m
#>
■■■■■■■■■ 27% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.80452770460834_48.0072137534363"
#>
#> ■■■■■■■■■ 27% | ETA: 3m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■ 27% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■ 27% | ETA: 3m
#>
[K
#> • Closest occurrence: 58.93 km
#>
#> ■■■■■■■■■ 27% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 350 occurrences remain(s)
#> - Total original: 375
#> - Retention rate: 93.3%
#>
#> ■■■■■■■■■ 27% | ETA: 3m
#>
[K
#> ✔ Found 305 occurrences for species Stereum hirsutum:
#>
#> ■■■■■■■■■ 27% | ETA: 3m
#>
[K
#> • Closest occurrence: 15.54 km
#>
#> ■■■■■■■■■ 27% | ETA: 3m
#>
■■■■■■■■■ 28% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.00024748559981_47.7333852356941"
#>
#> ■■■■■■■■■ 28% | ETA: 3m
#> Cleaning suppress 19 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■ 28% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■ 28% | ETA: 3m
#>
[K
#> • Closest occurrence: 80.46 km
#>
#> ■■■■■■■■■ 28% | ETA: 3m
#>
■■■■■■■■■■ 28% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.87981820501418_48.1128645586334"
#>
#> ■■■■■■■■■■ 28% | ETA: 3m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■ 28% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■ 28% | ETA: 3m
#>
[K
#> • Closest occurrence: 46.22 km
#>
#> ■■■■■■■■■■ 28% | ETA: 3m
#>
■■■■■■■■■■ 29% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.44862432057724_47.8143614451431"
#>
#> ■■■■■■■■■■ 29% | ETA: 3m
#> Cleaning suppress 19 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■ 29% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■ 29% | ETA: 3m
#>
[K
#> • Closest occurrence: 69.89 km
#>
#> ■■■■■■■■■■ 29% | ETA: 3m
#>
■■■■■■■■■■ 30% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.8952190532575_47.7112928397872"
#>
#> ■■■■■■■■■■ 30% | ETA: 3m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■ 30% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■ 30% | ETA: 3m
#>
[K
#> • Closest occurrence: 85.12 km
#>
#> ■■■■■■■■■■ 30% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 17 occurrences remain(s)
#> - Total original: 17
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■ 30% | ETA: 3m
#>
[K
#> ✔ Found 17 occurrences for species Cerocorticium molare:
#>
#> ■■■■■■■■■■ 30% | ETA: 3m
#>
[K
#> • Closest occurrence: 21.89 km
#>
#> ■■■■■■■■■■ 30% | ETA: 3m
#>
■■■■■■■■■■ 31% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.89928147562711_47.888655500778"
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#>
[K
#> • Closest occurrence: 66.72 km
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#>
■■■■■■■■■■ 31% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.96107944701493_47.6767521091196"
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#> Cleaning suppress 19 taxa and 0 samples.
#>
#>
[K
#> ! No taxonomic names found at the specified taxonomic rank.Please check the `taxonomic_rank` parameter and your phyloseq object.
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#>
[K
#> ℹ Processing GPS point: "2.00396596832688_47.9267196096506"
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#>
[K
#> • Closest occurrence: 59.83 km
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Sistotrema oblongisporum:
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#>
[K
#> • Closest occurrence: 73.74 km
#>
#> ■■■■■■■■■■ 31% | ETA: 3m
#>
■■■■■■■■■■■ 33% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.98038288416931_48.0538816328756"
#>
#> ■■■■■■■■■■■ 33% | ETA: 3m
#> Cleaning suppress 19 taxa and 0 samples.
#>
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■ 33% | ETA: 3m
#>
■■■■■■■■■■■ 34% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.03951410085234_47.8141564719444"
#>
#> ■■■■■■■■■■■ 34% | ETA: 3m
#> Cleaning suppress 15 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■ 34% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■ 34% | ETA: 3m
#>
[K
#> • Closest occurrence: 71.03 km
#>
#> ■■■■■■■■■■■ 34% | ETA: 3m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■ 34% | ETA: 3m
#>
■■■■■■■■■■■ 34% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "1.91916129044248_47.9690486959801"
#>
#> ■■■■■■■■■■■ 34% | ETA: 2m
#> Cleaning suppress 19 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 336 occurrences remain(s)
#> - Total original: 361
#> - Retention rate: 93.1%
#>
#> ■■■■■■■■■■■ 34% | ETA: 2m
#>
[K
#> ✔ Found 304 occurrences for species Stereum hirsutum:
#>
#> ■■■■■■■■■■■ 34% | ETA: 2m
#>
[K
#> • Closest occurrence: 6.07 km
#>
#> ■■■■■■■■■■■ 34% | ETA: 2m
#>
■■■■■■■■■■■■ 35% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.75249793897135_47.9626277044037"
#>
#> ■■■■■■■■■■■■ 35% | ETA: 3m
#> Cleaning suppress 19 taxa and 0 samples.
#>
#>
[K
#> ! No taxonomic names found at the specified taxonomic rank.Please check the `taxonomic_rank` parameter and your phyloseq object.
#>
#> ■■■■■■■■■■■■ 35% | ETA: 3m
#>
[K
#> ℹ Processing GPS point: "2.01614424799679_48.1580134942152"
#>
#> ■■■■■■■■■■■■ 35% | ETA: 3m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■ 35% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■ 35% | ETA: 3m
#>
[K
#> • Closest occurrence: 36.2 km
#>
#> ■■■■■■■■■■■■ 35% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 364 occurrences remain(s)
#> - Total original: 388
#> - Retention rate: 93.8%
#>
#> ■■■■■■■■■■■■ 35% | ETA: 3m
#>
[K
#> ✔ Found 330 occurrences for species Stereum hirsutum:
#>
#> ■■■■■■■■■■■■ 35% | ETA: 3m
#>
[K
#> • Closest occurrence: 14.6 km
#>
#> ■■■■■■■■■■■■ 35% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 29 occurrences remain(s)
#> - Total original: 32
#> - Retention rate: 90.6%
#>
#> ■■■■■■■■■■■■ 35% | ETA: 3m
#>
[K
#> ✔ Found 29 occurrences for species Cerocorticium molare:
#>
#> ■■■■■■■■■■■■ 35% | ETA: 3m
#>
[K
#> • Closest occurrence: 43.86 km
#>
#> ■■■■■■■■■■■■ 35% | ETA: 3m
#>
■■■■■■■■■■■■ 36% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.05760676880779_48.4208011005223"
#>
#> ■■■■■■■■■■■■ 36% | ETA: 3m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■ 36% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■ 36% | ETA: 3m
#>
[K
#> • Closest occurrence: 16.38 km
#>
#> ■■■■■■■■■■■■ 36% | ETA: 3m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■■ 36% | ETA: 3m
#>
■■■■■■■■■■■■ 37% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.96750508635991_48.2583979892214"
#>
#> ■■■■■■■■■■■■ 37% | ETA: 3m
#> Cleaning suppress 19 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 3 occurrences remain(s)
#> - Total original: 3
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■ 37% | ETA: 3m
#>
[K
#> ✔ Found 3 occurrences for species Basidiodendron eyrei:
#>
#> ■■■■■■■■■■■■ 37% | ETA: 3m
#>
[K
#> • Closest occurrence: 55.25 km
#>
#> ■■■■■■■■■■■■ 37% | ETA: 3m
#>
■■■■■■■■■■■■ 38% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.6648152807142_47.6512805131074"
#>
#> ■■■■■■■■■■■■ 38% | ETA: 3m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■ 38% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■ 38% | ETA: 3m
#>
[K
#> • Closest occurrence: 98.14 km
#>
#> ■■■■■■■■■■■■ 38% | ETA: 3m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■■ 38% | ETA: 3m
#>
■■■■■■■■■■■■■ 39% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "2.0208957460923_47.8011478160344"
#>
#> ■■■■■■■■■■■■■ 39% | ETA: 2m
#> Cleaning suppress 15 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■ 39% | ETA: 2m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■ 39% | ETA: 2m
#>
[K
#> • Closest occurrence: 72.78 km
#>
#> ■■■■■■■■■■■■■ 39% | ETA: 2m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■■■ 39% | ETA: 2m
#>
■■■■■■■■■■■■■ 39% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "2.14252394307795_48.2639421994398"
#>
#> ■■■■■■■■■■■■■ 39% | ETA: 2m
#> Cleaning suppress 18 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 405 occurrences remain(s)
#> - Total original: 418
#> - Retention rate: 96.9%
#>
#> ■■■■■■■■■■■■■ 39% | ETA: 2m
#>
[K
#> ✔ Found 357 occurrences for species Stereum hirsutum:
#>
#> ■■■■■■■■■■■■■ 39% | ETA: 2m
#>
[K
#> • Closest occurrence: 9.53 km
#>
#> ■■■■■■■■■■■■■ 39% | ETA: 2m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 3 occurrences remain(s)
#> - Total original: 3
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■ 39% | ETA: 2m
#>
[K
#> ✔ Found 3 occurrences for species Basidiodendron eyrei:
#>
#> ■■■■■■■■■■■■■ 39% | ETA: 2m
#>
[K
#> • Closest occurrence: 42.84 km
#>
#> ■■■■■■■■■■■■■ 39% | ETA: 2m
#>
■■■■■■■■■■■■■ 40% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "1.72377103410667_47.9989421202064"
#>
#> ■■■■■■■■■■■■■ 40% | ETA: 2m
#> Cleaning suppress 14 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■ 40% | ETA: 2m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■ 40% | ETA: 2m
#>
[K
#> • Closest occurrence: 63.38 km
#>
#> ■■■■■■■■■■■■■ 40% | ETA: 2m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 350 occurrences remain(s)
#> - Total original: 377
#> - Retention rate: 92.8%
#>
#> ■■■■■■■■■■■■■ 40% | ETA: 2m
#>
[K
#> ✔ Found 313 occurrences for species Stereum hirsutum:
#>
#> ■■■■■■■■■■■■■ 40% | ETA: 2m
#>
[K
#> • Closest occurrence: 19.36 km
#>
#> ■■■■■■■■■■■■■ 40% | ETA: 2m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 4 occurrences remain(s)
#> - Total original: 4
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■ 40% | ETA: 2m
#>
[K
#> ✔ Found 4 occurrences for species Basidiodendron eyrei:
#>
#> ■■■■■■■■■■■■■ 40% | ETA: 2m
#>
[K
#> • Closest occurrence: 83.58 km
#>
#> ■■■■■■■■■■■■■ 40% | ETA: 2m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 481 occurrences remain(s)
#> - Total original: 500
#> - Retention rate: 96.2%
#>
#> ■■■■■■■■■■■■■ 40% | ETA: 2m
#>
[K
#> ✔ Found 388 occurrences for species Fomes fomentarius:
#>
#> ■■■■■■■■■■■■■ 40% | ETA: 2m
#>
[K
#> • Closest occurrence: 9.43 km
#>
#> ■■■■■■■■■■■■■ 40% | ETA: 2m
#>
■■■■■■■■■■■■■ 41% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.210883969947_47.8377142602746"
#>
#> ■■■■■■■■■■■■■ 41% | ETA: 3m
#> Cleaning suppress 18 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■ 41% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■ 41% | ETA: 3m
#>
[K
#> • Closest occurrence: 66.34 km
#>
#> ■■■■■■■■■■■■■ 41% | ETA: 3m
#>
■■■■■■■■■■■■■ 42% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.29943018778344_47.9222739558244"
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#> Cleaning suppress 19 taxa and 0 samples.
#>
#>
[K
#> ! No taxonomic names found at the specified taxonomic rank.Please check the `taxonomic_rank` parameter and your phyloseq object.
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> ℹ Processing GPS point: "2.00686588187344_47.9354214811856"
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> • Closest occurrence: 58.85 km
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 329 occurrences remain(s)
#> - Total original: 340
#> - Retention rate: 96.8%
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> ✔ Found 303 occurrences for species Stereum hirsutum:
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> • Closest occurrence: 0.9 km
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 3 occurrences remain(s)
#> - Total original: 3
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> ✔ Found 3 occurrences for species Basidiodendron eyrei:
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> • Closest occurrence: 70.58 km
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Sistotrema oblongisporum:
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> • Closest occurrence: 72.88 km
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 494 occurrences remain(s)
#> - Total original: 500
#> - Retention rate: 98.8%
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> ✔ Found 455 occurrences for species Fomes fomentarius:
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> • Closest occurrence: 1.43 km
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 29 occurrences remain(s)
#> - Total original: 32
#> - Retention rate: 90.6%
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> ✔ Found 28 occurrences for species Cerocorticium molare:
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> • Closest occurrence: 54.94 km
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 5 occurrences remain(s)
#> - Total original: 5
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> ✔ Found 5 occurrences for species Aporpium canescens:
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> • Closest occurrence: 70.66 km
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 22 occurrences remain(s)
#> - Total original: 22
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> ✔ Found 22 occurrences for species Hypochnicium analogum:
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
[K
#> • Closest occurrence: 70.54 km
#>
#> ■■■■■■■■■■■■■ 42% | ETA: 3m
#>
■■■■■■■■■■■■■■ 43% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.91217774869042_47.5174079690895"
#>
#> ■■■■■■■■■■■■■■ 43% | ETA: 3m
#> Cleaning suppress 19 taxa and 0 samples.
#>
#>
[K
#> ! No taxonomic names found at the specified taxonomic rank.Please check the `taxonomic_rank` parameter and your phyloseq object.
#>
#> ■■■■■■■■■■■■■■ 43% | ETA: 3m
#>
[K
#> ℹ Processing GPS point: "1.80985723692523_47.9575478589018"
#>
#> ■■■■■■■■■■■■■■ 43% | ETA: 3m
#> Cleaning suppress 14 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■ 43% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■ 43% | ETA: 3m
#>
[K
#> • Closest occurrence: 63.24 km
#>
#> ■■■■■■■■■■■■■■ 43% | ETA: 3m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 345 occurrences remain(s)
#> - Total original: 363
#> - Retention rate: 95%
#>
#> ■■■■■■■■■■■■■■ 43% | ETA: 3m
#>
[K
#> ✔ Found 297 occurrences for species Stereum hirsutum:
#>
#> ■■■■■■■■■■■■■■ 43% | ETA: 3m
#>
[K
#> • Closest occurrence: 11.55 km
#>
#> ■■■■■■■■■■■■■■ 43% | ETA: 3m
#>
■■■■■■■■■■■■■■ 45% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.83395870853466_48.1219315017671"
#>
#> ■■■■■■■■■■■■■■ 45% | ETA: 3m
#> Cleaning suppress 18 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■ 45% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■ 45% | ETA: 3m
#>
[K
#> • Closest occurrence: 47.72 km
#>
#> ■■■■■■■■■■■■■■ 45% | ETA: 3m
#>
■■■■■■■■■■■■■■■ 45% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.93395637851301_48.0678563568902"
#>
#> ■■■■■■■■■■■■■■■ 45% | ETA: 3m
#> Cleaning suppress 15 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■ 45% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■■ 45% | ETA: 3m
#>
[K
#> • Closest occurrence: 47.93 km
#>
#> ■■■■■■■■■■■■■■■ 45% | ETA: 3m
#>
■■■■■■■■■■■■■■■ 46% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.24290765102149_48.2813810125112"
#>
#> ■■■■■■■■■■■■■■■ 46% | ETA: 3m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■ 46% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■■ 46% | ETA: 3m
#>
[K
#> • Closest occurrence: 17.02 km
#>
#> ■■■■■■■■■■■■■■■ 46% | ETA: 3m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■■■■■ 46% | ETA: 3m
#>
■■■■■■■■■■■■■■■ 47% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.05872540028937_48.302394701658"
#>
#> ■■■■■■■■■■■■■■■ 47% | ETA: 3m
#> Cleaning suppress 18 taxa and 0 samples.
#>
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■■■■■ 47% | ETA: 3m
#>
■■■■■■■■■■■■■■■ 47% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "2.07311192398735_47.9918603563432"
#>
#> ■■■■■■■■■■■■■■■ 47% | ETA: 3m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■ 47% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■■ 47% | ETA: 3m
#>
[K
#> • Closest occurrence: 51.33 km
#>
#> ■■■■■■■■■■■■■■■ 47% | ETA: 3m
#>
■■■■■■■■■■■■■■■ 48% | ETA: 3m
[K
#>
[K
#> ℹ Processing GPS point: "1.79423545440676_47.7104884597658"
#>
#> ■■■■■■■■■■■■■■■ 48% | ETA: 3m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■ 48% | ETA: 3m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■■ 48% | ETA: 3m
#>
[K
#> • Closest occurrence: 88 km
#>
#> ■■■■■■■■■■■■■■■ 48% | ETA: 3m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■■■■■ 48% | ETA: 3m
#>
■■■■■■■■■■■■■■■■ 49% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "2.27351268065882_48.0048125639325"
#>
#> ■■■■■■■■■■■■■■■■ 49% | ETA: 2m
#> Cleaning suppress 19 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■ 49% | ETA: 2m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■■■ 49% | ETA: 2m
#>
[K
#> • Closest occurrence: 47.57 km
#>
#> ■■■■■■■■■■■■■■■■ 49% | ETA: 2m
#>
■■■■■■■■■■■■■■■■ 50% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "2.24363797030147_47.9447549477189"
#>
#> ■■■■■■■■■■■■■■■■ 50% | ETA: 2m
#> Cleaning suppress 19 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■ 50% | ETA: 2m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■■■ 50% | ETA: 2m
#>
[K
#> • Closest occurrence: 54.31 km
#>
#> ■■■■■■■■■■■■■■■■ 50% | ETA: 2m
#>
■■■■■■■■■■■■■■■■ 50% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "2.12716836153844_48.0187295951851"
#>
#> ■■■■■■■■■■■■■■■■ 50% | ETA: 2m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■ 50% | ETA: 2m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■■■ 50% | ETA: 2m
#>
[K
#> • Closest occurrence: 47.37 km
#>
#> ■■■■■■■■■■■■■■■■ 50% | ETA: 2m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■■■■■■ 50% | ETA: 2m
#>
■■■■■■■■■■■■■■■■ 51% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "2.26372728935724_48.0897399170468"
#>
#> ■■■■■■■■■■■■■■■■ 51% | ETA: 2m
#> Cleaning suppress 19 taxa and 0 samples.
#>
#>
[K
#> ! No taxonomic names found at the specified taxonomic rank.Please check the `taxonomic_rank` parameter and your phyloseq object.
#>
#> ■■■■■■■■■■■■■■■■ 51% | ETA: 2m
#>
[K
#> ℹ Processing GPS point: "2.19121953447668_48.0927592222255"
#>
#> ■■■■■■■■■■■■■■■■ 51% | ETA: 2m
#> Cleaning suppress 19 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■ 51% | ETA: 2m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■■■ 51% | ETA: 2m
#>
[K
#> • Closest occurrence: 38.34 km
#>
#> ■■■■■■■■■■■■■■■■ 51% | ETA: 2m
#>
■■■■■■■■■■■■■■■■■ 53% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "2.01782252475527_48.0515538003913"
#>
#> ■■■■■■■■■■■■■■■■■ 53% | ETA: 2m
#> Cleaning suppress 19 taxa and 0 samples.
#>
#>
[K
#> ! No taxonomic names found at the specified taxonomic rank.Please check the `taxonomic_rank` parameter and your phyloseq object.
#>
#> ■■■■■■■■■■■■■■■■■ 53% | ETA: 2m
#>
■■■■■■■■■■■■■■■■■ 53% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "1.94832418800796_48.08649070254"
#>
#> ■■■■■■■■■■■■■■■■■ 53% | ETA: 2m
#> Cleaning suppress 17 taxa and 0 samples.
#>
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■■■■■■■ 53% | ETA: 2m
#>
■■■■■■■■■■■■■■■■■ 54% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "2.15250303422653_48.1201888916157"
#>
#> ■■■■■■■■■■■■■■■■■ 54% | ETA: 2m
#> Cleaning suppress 17 taxa and 0 samples.
#>
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■■■■■■■ 54% | ETA: 2m
#>
■■■■■■■■■■■■■■■■■ 55% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "2.16927616560517_48.2311025328875"
#>
#> ■■■■■■■■■■■■■■■■■ 55% | ETA: 2m
#> Cleaning suppress 15 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■■ 55% | ETA: 2m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■■■■ 55% | ETA: 2m
#>
[K
#> • Closest occurrence: 23.83 km
#>
#> ■■■■■■■■■■■■■■■■■ 55% | ETA: 2m
#>
■■■■■■■■■■■■■■■■■■ 55% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "2.01210694162616_48.3020599305486"
#>
#> ■■■■■■■■■■■■■■■■■■ 55% | ETA: 2m
#> Cleaning suppress 18 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■■■ 55% | ETA: 2m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■■■■■ 55% | ETA: 2m
#>
[K
#> • Closest occurrence: 24.48 km
#>
#> ■■■■■■■■■■■■■■■■■■ 55% | ETA: 2m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■■■■■■■■ 55% | ETA: 2m
#>
■■■■■■■■■■■■■■■■■■ 56% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "1.9350825812771_47.8597752773594"
#>
#> ■■■■■■■■■■■■■■■■■■ 56% | ETA: 2m
#> Cleaning suppress 18 taxa and 0 samples.
#>
#>
■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "2.20507678326343_47.5035734427658"
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> ! No occurrences found for Stereum ostrea
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> ! No occurrences found for Ossicaulis lachnopus
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 112 occurrences remain(s)
#> - Total original: 112
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> ✔ Found 70 occurrences for species Stereum hirsutum:
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> • Closest occurrence: 13.69 km
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 2 occurrences remain(s)
#> - Total original: 2
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> ✔ Found 0 occurrences for species Basidiodendron eyrei:
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> • Closest occurrence: 102.69 km
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> ! No occurrences found for Sistotrema oblongisporum
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 277 occurrences remain(s)
#> - Total original: 277
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> ✔ Found 214 occurrences for species Fomes fomentarius:
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> • Closest occurrence: 3.41 km
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 9 occurrences remain(s)
#> - Total original: 9
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> ✔ Found 4 occurrences for species Cerocorticium molare:
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> • Closest occurrence: 13.69 km
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> ! No occurrences found for Aporpium canescens
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 4 occurrences remain(s)
#> - Total original: 4
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> ✔ Found 0 occurrences for species Hypochnicium analogum:
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
[K
#> • Closest occurrence: 102.7 km
#>
#> ■■■■■■■■■■■■■■■■■■ 57% | ETA: 2m
#>
■■■■■■■■■■■■■■■■■■ 58% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "1.90686590016618_48.0168820455305"
#>
#> ■■■■■■■■■■■■■■■■■■ 58% | ETA: 2m
#> Cleaning suppress 16 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■■■ 58% | ETA: 2m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■■■■■ 58% | ETA: 2m
#>
[K
#> • Closest occurrence: 53.82 km
#>
#> ■■■■■■■■■■■■■■■■■■ 58% | ETA: 2m
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 481 occurrences remain(s)
#> - Total original: 500
#> - Retention rate: 96.2%
#>
#> ■■■■■■■■■■■■■■■■■■ 58% | ETA: 2m
#>
[K
#> ✔ Found 421 occurrences for species Fomes fomentarius:
#>
#> ■■■■■■■■■■■■■■■■■■ 58% | ETA: 2m
#>
[K
#> • Closest occurrence: 3.02 km
#>
#> ■■■■■■■■■■■■■■■■■■ 58% | ETA: 2m
#>
■■■■■■■■■■■■■■■■■■■ 58% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "2.07324487271148_48.0290363016356"
#>
#> ■■■■■■■■■■■■■■■■■■■ 58% | ETA: 2m
#> Cleaning suppress 18 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■■■■ 58% | ETA: 2m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■■■■■■ 58% | ETA: 2m
#>
[K
#> • Closest occurrence: 47.39 km
#>
#> ■■■■■■■■■■■■■■■■■■■ 58% | ETA: 2m
#>
■■■■■■■■■■■■■■■■■■■ 59% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "1.80635420214086_48.1394888162458"
#>
#> ■■■■■■■■■■■■■■■■■■■ 59% | ETA: 2m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 1 occurrences remain(s)
#> - Total original: 1
#> - Retention rate: 100%
#>
#> ■■■■■■■■■■■■■■■■■■■ 59% | ETA: 2m
#>
[K
#> ✔ Found 1 occurrences for species Stereum ostrea:
#>
#> ■■■■■■■■■■■■■■■■■■■ 59% | ETA: 2m
#>
[K
#> • Closest occurrence: 47.8 km
#>
#> ■■■■■■■■■■■■■■■■■■■ 59% | ETA: 2m
#>
■■■■■■■■■■■■■■■■■■■ 60% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "1.98340127563098_47.9824995895498"
#>
#> ■■■■■■■■■■■■■■■■■■■ 60% | ETA: 2m
#> Cleaning suppress 18 taxa and 0 samples.
#>
#>
[K
#> ! No taxonomic names found at the specified taxonomic rank.Please check the `taxonomic_rank` parameter and your phyloseq object.
#>
#> ■■■■■■■■■■■■■■■■■■■ 60% | ETA: 2m
#>
■■■■■■■■■■■■■■■■■■■ 61% | ETA: 2m
[K
#>
[K
#> ℹ Processing GPS point: "2.13000863474002_48.0893193893191"
#>
#> ■■■■■■■■■■■■■■■■■■■ 61% | ETA: 2m
#> Cleaning suppress 19 taxa and 0 samples.
#>
#>
[K
#> ! No taxonomic names found at the specified taxonomic rank.Please check the `taxonomic_rank` parameter and your phyloseq object.
#>
#> ■■■■■■■■■■■■■■■■■■■ 61% | ETA: 2m
#>
[K
#> ℹ Processing GPS point: "2.19752469900431_48.0808515338862"
#>
#> ■■■■■■■■■■■■■■■■■■■ 61% | ETA: 2m
#> Cleaning suppress 17 taxa and 0 samples.
#> Reading 'ne_50m_land.zip' from naturalearth...
#>
[K
#> ℹ After cleaning with CoordinateCleaner::clean_coordinates:
#> - 358 occurrences remain(s)
#> - Total original: 385
#> - Retention rate: 93%
#>
#> ■■■■■■■■■■■■■■■■■■■ 61% | ETA: 2m
#>
[K
#> ✔ Found 331 occurrences for species Stereum hirsutum:
#>
#> ■■■■■■■■■■■■■■■■■■■ 61% | ETA: 2m
#>
[K
#> • Closest occurrence: 4.92 km
#>
#> ■■■■■■■■■■■■■■■■■■■ 61% | ETA: 2m
#>
[K
</pre></div>
<div id='warn-popup-unnamed-chunk-12' class='popup' role='dialog' aria-hidden='true' onclick='event.stopPropagation();'><button class='popup-close' aria-label='Close'>×</button><div class='popup-header'><strong>Warnings</strong></div><pre class='popup-pre'>#> Warning: [vect] guessed crs
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</pre></div>
``` r
sample_locations <- data.frame(
longitude = rnorm(nsamples(data_clean), mean = 2, sd = 0.2),
latitude = rnorm(nsamples(data_clean), mean = 48, sd = 0.2)
)
# Check occurrences for multiple locations
multi_location_check <- tax_occur_multi_check_pq(
data_clean,
longitudes = sample_locations$longitude,
latitude = sample_locations$latitude,
radius_km = 100,
n_occur = 500
)#> Error in `h()`:
#> ! error in evaluating the argument 'x' in selecting a method for function 't': Service Unavailable
# Summarize by site
site_summary <- multi_location_check[[1]] |>
group_by(sample_name) |>
summarise(
taxa_with_occurrences = sum(count_in_radius > 0),
mean_nb_occurrences = mean(count_in_radius),
.groups = "drop"
) |>
arrange(desc(taxa_with_occurrences), desc(mean_nb_occurrences))#> Error:
#> ! object 'multi_location_check' not found
site_summary#> Error:
#> ! object 'site_summary' not foundSample Site Validation
Validate your sampling sites against known distributions:
# Define your sampling coordinates
sample_coords <- data.frame(
longitude = c(2.3, 5.4, -1.6), # Example coordinates
latitude = c(48.9, 50.6, 47.2)
)
# Check if sampling sites overlap with known ranges
site_validation <- purrr::map_dfr(1:nrow(sample_coords), function(i) {
tax_occur_check_pq(data_clean,
longitude = sample_coords$longitude[i],
latitude = sample_coords$latitude[i],
radius_km = 50,
add_to_phyloseq = FALSE
)
})#> Error in `map()`:
#> ℹ In index: 1.
#> Caused by error in `h()`:
#> ! error in evaluating the argument 'x' in selecting a method for function 't': Service Unavailable
# Summarize validation results
validation_summary <- site_validation |>
group_by(sample_point_lon, sample_point_lat) |>
summarise(
taxa_with_occurrences = sum(count_in_radius > 0),
mean_nb_occurrences = mean(count_in_radius),
.groups = "drop"
)#> Error:
#> ! object 'site_validation' not found
validation_summary#> Error:
#> ! object 'validation_summary' not foundIntegration with Phyloseq
Add occurrence information directly to your phyloseq object:
# Add occurrence data to phyloseq tax_table
data_with_occurrence <- tax_occur_check_pq(data_clean,
longitude = longitude,
latitude = latitude,
radius_km = 100
)#> Error in `h()`:
#> ! error in evaluating the argument 'x' in selecting a method for function 't': Service Unavailable
# View enhanced tax_table with occurrence columns
head(data_with_occurrence@tax_table)#> Error:
#> ! object 'data_with_occurrence' not foundInterpreting Results
Occurrence Patterns
- High local, high global: Cosmopolitan species, expected presence
- High local, low global: Regionally endemic species
- Low local, high global: Cosmopolitan but locally rare
- Low local, low global: Rare species or potential errors
Quality Control Applications
Use occurrence checking for:
- Contamination detection: Taxa with zero local occurrences may be contaminants
- Sample validation: Ensure detected communities match biogeographic expectations
- Filtering decisions: Remove unlikely taxa from downstream analyses
- Hypothesis generation: Identify interesting biogeographic patterns
Best Practices
- Use appropriate radii for your study system and organism dispersal capability
- Consider temporal factors - GBIF data spans many years
- Account for sampling bias in GBIF data (some regions/taxa better sampled)
- Validate results with ecological knowledge of your study system
- Document thresholds used for filtering decisions
Integration with Other Functions
Occurrence checking works well with other taxinfo functions:
data_complete <- data_fungi_mini |>
# 1. Clean names
gna_verifier_pq(data_sources = 210) |>
# 2. Check occurrences
tax_occur_check_pq(
longitude = 2.3, latitude = 48.8,
radius_km = 100
) |>
subset_taxa(as.numeric(count_in_radius) > 0) |> # Keep only taxa known in a radius of 100km
# 3. Add GBIF occurrence data
tax_gbif_occur_pq() |>
# 4. Filter based on frequency in samples (Keep taxa in >2 samples)
filter_taxa(function(x) sum(x > 0) > 2, prune = TRUE) |>
# 5. Remove empty samples and taxa
clean_pq()#> Error in `h()`:
#> ! error in evaluating the argument 'object' in selecting a method for function 'tax_table': error in evaluating the argument 'x' in selecting a method for function 't': Service Unavailable
data_complete@tax_table[1:5, ]#> Error:
#> ! object 'data_complete' not foundThis approach provides a robust framework for validating taxa presence and improving the reliability of your microbiome or environmental DNA analyses.
Session information
#> R version 4.6.0 (2026-04-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Pop!_OS 24.04 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: Europe/Paris
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] leafpop_0.1.0 leaflet_2.2.3 taxinfo_0.1.2 MiscMetabar_0.16.8
#> [5] dplyr_1.2.1 ggplot2_4.0.3 phyloseq_1.56.0
#>
#> loaded via a namespace (and not attached):
#> [1] RColorBrewer_1.1-3 wk_0.9.5 jsonlite_2.0.0
#> [4] magrittr_2.0.5 farver_2.1.2 CoordinateCleaner_3.0.1
#> [7] vctrs_0.7.3 multtest_2.68.0 RCurl_1.98-1.19
#> [10] base64enc_0.1-6 terra_1.9-27 htmltools_0.5.9
#> [13] forcats_1.0.1 curl_7.1.0 s2_1.1.11
#> [16] raster_3.6-32 divent_0.5-4 KernSmooth_2.23-26
#> [19] htmlwidgets_1.6.4 plyr_1.8.9 zoo_1.8-15
#> [22] uuid_1.2-2 whisker_0.4.1 igraph_2.3.2
#> [25] lifecycle_1.0.5 iterators_1.0.14 pkgconfig_2.0.3
#> [28] Matrix_1.7-5 R6_2.6.1 fastmap_1.2.0
#> [31] rbibutils_2.4.1 digest_0.6.39 mapview_2.11.4
#> [34] S4Vectors_0.50.1 leafem_0.2.5 textshaping_1.0.5
#> [37] crosstalk_1.2.2 vegan_2.7-5 labeling_0.4.3
#> [40] urltools_1.7.3.1 httr_1.4.8 NMOF_2.11-0
#> [43] mgcv_1.9-4 compiler_4.6.0 proxy_0.4-29
#> [46] bit64_4.8.2 withr_3.0.2 brew_1.0-10
#> [49] S7_0.2.2 DBI_1.3.0 maps_3.4.3
#> [52] MASS_7.3-65 gbif.range_1.6.0 classInt_0.4-11
#> [55] biomformat_1.40.0 permute_0.9-10 oai_0.4.0
#> [58] tools_4.6.0 units_1.0-1 otel_0.2.0
#> [61] ape_5.8-1 zip_3.0.0 rgbif_3.8.5
#> [64] satellite_1.0.6 glue_1.8.1 nlme_3.1-169
#> [67] grid_4.6.0 sf_1.1-1 cluster_2.1.8.2
#> [70] reshape2_1.4.5 ade4_1.7-24 generics_0.1.4
#> [73] leaflet.providers_3.0.0 gtable_0.3.6 tzdb_0.5.0
#> [76] class_7.3-23 tidyr_1.3.2 data.table_1.18.4
#> [79] hms_1.1.4 sp_2.2-1 xml2_1.5.2
#> [82] utf8_1.2.6 XVector_0.52.0 BiocGenerics_0.58.1
#> [85] ggrepel_0.9.8 foreach_1.5.2 pillar_1.11.1
#> [88] stringr_1.6.0 vroom_1.7.1 rglobi_0.3.4
#> [91] splines_4.6.0 lattice_0.22-9 survival_3.8-6
#> [94] FNN_1.1.4.1 gmp_0.7-5.1 bit_4.6.0
#> [97] tidyselect_1.2.1 pbapply_1.7-4 Biostrings_2.80.1
#> [100] knitr_1.51 IRanges_2.46.0 Seqinfo_1.2.0
#> [103] svglite_2.2.2 crul_1.6.0 stats4_4.6.0
#> [106] xfun_0.58 wikitaxa_0.5.0 Biobase_2.72.0
#> [109] taxize_0.10.1 stringi_1.8.7 lazyeval_0.2.3
#> [112] evaluate_1.0.5 codetools_0.2-20 httpcode_0.3.0
#> [115] tibble_3.3.1 cli_3.6.6 RcppParallel_5.1.11-2
#> [118] systemfonts_1.3.2 Rdpack_2.6.6 jquerylib_0.1.4
#> [121] Rcpp_1.1.1-1.1 rnaturalearth_1.2.0 triebeard_0.4.1
#> [124] png_0.1-9 parallel_4.6.0 readr_2.2.0
#> [127] openalexR_3.0.1 mclust_6.1.2 ClusterR_1.3.6
#> [130] WikipediR_1.7.1 bitops_1.0-9 scales_1.4.0
#> [133] e1071_1.7-17 purrr_1.2.2 crayon_1.5.3
#> [136] geosphere_1.6-8 rlang_1.2.0