cboettig
commented
3 years ago Thanks for the report. Yes, it looks like the duckdb backend (that recently replaced MonetDBLite as the default backend when the latter was removed from CRAN) still doesn't support some dplyr verbs, including top_n.
Meanwhile, I think it's easier if you stick with the filter_* functions instead, e.g. like so
library(dplyr)
found_name <-taxadb::filter_name("Leporinus reinhardti", provider = 'fb')
matches <- taxadb::filter_id(found_name$acceptedNameUsageID, 'fb')
matches %>% filter(taxonomicStatus == "accepted") %>% pull(scientificName)Taxonomic naming provider data isn't always as clean as we'd like it to be, so working with the table-based verbs can help spot potential issues or inconsistencies.
Geiziane
Hi, I'm running the folowing comand:
found_name <-taxadb::filter_name("Leporinus reinhardti", provider = 'fb') taxadb::get_names(found_name$acceptedNameUsageID, 'fb')
But I get the error: no such function: top_n_rank
Matrix products: default BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
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=C
[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
attached base packages: [1] stats graphics grDevices utils datasets [6] methods base
other attached packages: [1] dbplyr_1.4.4 Hmisc_4.4-0
[3] Formula_1.2-3 survival_3.1-12
[5] lattice_0.20-41 flora_0.3.4
[7] data.table_1.12.8 rgnparser_0.1.0.91 [9] here_0.1 vroom_1.2.1
[11] forcats_0.5.0 stringr_1.4.0
[13] dplyr_1.0.0 purrr_0.3.4
[15] readr_1.3.1 tidyr_1.1.0
[17] tibble_3.0.1 ggplot2_3.3.1
[19] tidyverse_1.3.0 taxadb_0.1.0
loaded via a namespace (and not attached): [1] colorspace_1.4-1 ellipsis_0.3.1
[3] class_7.3-16 rprojroot_1.3-2
[5] htmlTable_1.13.3 base64enc_0.1-3
[7] fs_1.4.1 rstudioapi_0.11
[9] remotes_2.1.1 bit64_0.9-7
[11] fansi_0.4.1 lubridate_1.7.8
[13] xml2_1.3.2 codetools_0.2-16
[15] splines_4.0.0 knitr_1.28
[17] pkgload_1.1.0 jsonlite_1.6.1
[19] broom_0.5.6 cluster_2.1.0
[21] png_0.1-7 compiler_4.0.0
[23] httr_1.4.1 backports_1.1.7
[25] assertthat_0.2.1 Matrix_1.2-18
[27] cli_2.0.2 acepack_1.4.1
[29] htmltools_0.4.0 prettyunits_1.1.1
[31] tools_4.0.0 gtable_0.3.0
[33] glue_1.4.1 rappdirs_0.3.1
[35] Rcpp_1.0.4.6 cellranger_1.1.0
[37] raster_3.1-5 vctrs_0.3.1
[39] countrycode_1.2.0 nlme_3.1-147
[41] xfun_0.14 ps_1.3.3
[43] testthat_2.3.2 rvest_0.3.5
[45] lifecycle_0.2.0 sys_3.3
[47] devtools_2.3.0 stringdist_0.9.5.5 [49] scales_1.1.1 hms_0.5.3
[51] parallel_4.0.0 RColorBrewer_1.1-2 [53] curl_4.3 memoise_1.1.0
[55] gridExtra_2.3 rpart_4.1-15
[57] latticeExtra_0.6-29 stringi_1.4.6
[59] RSQLite_2.2.0 desc_1.2.0
[61] e1071_1.7-3 checkmate_2.0.0
[63] pkgbuild_1.0.8 rlang_0.4.6
[65] pkgconfig_2.0.3 sf_0.9-3
[67] htmlwidgets_1.5.1 bit_1.1-15.2
[69] tidyselect_1.1.0 processx_3.4.2
[71] magrittr_1.5 R6_2.4.1
[73] generics_0.0.2 DBI_1.1.0
[75] arkdb_0.0.5 pillar_1.4.4
[77] haven_2.3.1 foreign_0.8-78
[79] withr_2.2.0 units_0.6-6
[81] sp_1.4-2 nnet_7.3-13
[83] modelr_0.1.8 crayon_1.3.4
[85] KernSmooth_2.23-16 utf8_1.1.4
[87] usethis_1.6.1 jpeg_0.1-8.1
[89] progress_1.2.2 rnaturalearth_0.1.0 [91] grid_4.0.0 readxl_1.3.1
[93] blob_1.2.1 callr_3.4.3
[95] reprex_0.3.0 digest_0.6.25
[97] classInt_0.4-3 munsell_0.5.0
[99] sessioninfo_1.1.1
Thank you.