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b-cubed-eu / pdindicatoR

Repository for the phylogenetic indicator calculation workflow as part of the Bcubed project.
MIT License
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While using the PAFTOL tree, NAs error #8

Open mtrekels opened 3 months ago

mtrekels commented 3 months ago

matched <- taxonmatch(tree) Error in check_ott_ids(ott_id) : NAs are not allowed In addition: Warning message: Gnetales_Gnetaceae_Gnetum_montanum_GTHK, Ephedrales_Ephedraceae_Ephedra_sinica_VDAO, Ginkgoales_Ginkgoaceae_Ginkgo_biloba_SGTW, Cycadales_Cycadaceae_Cycas_micholitzii_XZUY, Pinales_Araucariaceae_Araucaria_rulei_XTZO, Pinales_Cupressaceae_Thuja_plicata_VFYZ, Pinales_Cupressaceae_Sequoia_sempervirens_HBGV, Pinales_Pinaceae_Cedrus_libani_GGEA, Pinales_Pinaceae_Picea_engelmannii_AWQB, Pinales_Pinaceae_Pinus_ponderosa_JBND, Amborellales_Amborellaceae_Amborella_trichopoda_SRR7451104, Amborellales_Amborellaceae_Amborella_trichopoda_URDJ, Amborellales_Amborellaceae_Amborella_trichopoda_PRJNA212863, Nymphaeales_Hydatellaceae_Trithuria_austinensis_ERR4179984, Nymphaeales_Hydatellaceae_Trithuria_filamentosa_ERR4180047, Nymphaeales_Cabombaceae_Cabomba_caroliniana_ERR4180008, Nymphaeales_Cabombaceae_Brasenia_schreberi_ERR7618329, Nymphaeales_Nymphaeaceae_Nuphar_advena_WTKZ, Nymphaeales_Nymphaeaceae_Nuphar_lutea_ERR7618331, Nymphaeales_Nymphaeaceae_Barclaya_longifolia_ERR5033816, Nymphaeales_Nymphae [... truncated]

mtrekels commented 3 months ago

Troubleshooting: problem is in the "taxa <- rotl::tnrs_match_names(tree_labels)", the tip labels are not giving matches, since they also contain higher taxonomies

LBreugelmans commented 1 month ago

Using tnrs_match_names() should be possible with higher taxonomies according to the documentation, needs to be further checked.

LBreugelmans commented 4 weeks ago

On further inspection, tnrs_match_names() does not result in good matches when higher taxons are part of the tip.labels. This is a specific case of issue #19