Add GBIF check presence, startende vanaf phyloseq object

source/rmarkdown/annelida_data_analyse.Rmd

@@ -213,10 +213,20 @@ glimpse(otu_table(physeq_rarefied) %>% as.data.frame %>% as_tibble())
 
 ## Taxonomie tabel
 
+
 ```{r verken-taxonomie-data}
 glimpse(tax_table(physeq_rarefied) %>% as.data.frame %>% as_tibble())
 ```
 
+```{r GBIF-check-presence}
+
+species <- as.vector(tax_table(physeq)[, "species"])
+species <- species[!grepl("_otu", species)]
+species <- gsub("_", " ", species)
+source("source/r/check_presence.R")
+check_presence(species)
+```
+
 Unieke en gedeelde taxa per diepte:
 
 ```{r}
@@ -251,6 +261,7 @@ psadd::plot_krona(physeq_rarefied, "MBAG_Olig01_Annelida_rar_species_alle_stalen
 
 ```
 
+
 ```{r}
 tidy_physeq_rarefied %>%
   tidytacos::tacoplot_stack(x = Landgebruik_MBAG)