In martonelab/ptm: Custom Functions for the Martone Lab

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
library(gt)

library(ptm)

Some dataframe with species names

df <- readxl::read_xlsx("yourfile.xlsx")

df <- tibble::tribble(
                      ~Final.determination,                         ~`genetic.match/notes`,              ~Determination.in.the.field,
    "Corallina officinalis var. chilensis",                                             NA,                  "Corallina officinalis",
                       "Bossiella plumosa",                                  "no more DNA",                      "Bossiella plumosa",
           "Calliarthron cheilosporioides",                                             NA,          "Calliarthron cheilosporioides"
  )

gt::gt(df)

Get the higher taxonomy

taxa <- taxonomy(df$Final.determination)

Add it back to the original data

cbind(taxa, df)

gt::gt(cbind(taxa, df))

martonelab/ptm documentation built on July 13, 2020, 10:36 p.m.