cast scientificName error

[Jegelewicz]

@vijaybarve when I try to use the cast_scientificname function, I get this:

Error in is.empty(sciname) : could not find function "is.empty"

Any idea what I am missing?

[vijaybarve]

Can you please share code snippet / complete function call.

[Jegelewicz]

library(taxotools)

# if no genus, but scientificName need to parse scientificName

df <- melt_scientificname (df,
                           sciname = "scientificName",
                           genus = "genus",
                           species = "specificEpithet",
                           subspecies = "infraspecificEpithet",
                           author = "scientificNameAuthorship")

[Jegelewicz]

Let me start this one over, because actually when I try to use:

  library(taxotools)
  df <- cast_scientificname (df,
                           genus = "genus",
                           subgenus = "subgenus",
                           species = "species", 
                           subspecies = "subspecies",
                           author = "scientificNameAuthorship")

I get this error

Error in cast_scientificname(df, genus = "genus", subgenus = "subgenus", : could not find function "cast_scientificname"

I made sure to have taxotools library loaded.

[Jegelewicz]

I took this part of the code

for(i in 1:nrow(newdat)){
    if(!is.empty(newdat$genus_[i])){
      scn <- toproper(newdat$genus_[i])
    }
    if(!is.empty(newdat$subgenus_[i])){
      scn <- paste(scn," (",toproper(newdat$genus_[i]),") ",sep = "")
    }
    if(!is.empty(newdat$species_[i])){
      scn <- paste(scn,newdat$species_[i])
    }
    if(!is.empty(newdat$subspecies_[i])){
      scn <- paste(scn,newdat$subspecies_[i])
    }
    if(!is.empty(newdat$author_[i])){
      scn <- paste(scn,trimws(newdat$author_[i]))
    }
    newdat$sciname_[i] <- scn

I made a few changes, but it works for me like this

df$scientificName[i] <- for(i in 1:nrow(df)){
    if(!is.na(df$genus[i])){
      scn <- df$genus[i]
    }
    if(!is.na(df$subgenus[i])){
      scn <- paste(scn," (",df$subgenus[i],")",sep = "")
    }
    if(!is.na(df$specificEpithet[i])){
      scn <- paste(scn,df$specificEpithet[i], sep = " ")
    }
    if(!is.na(df$infraspecificEpithet[i])){
      scn <- paste(scn,df$infraspecificEpithet[i], sep = " ")
    }
    if(!is.na(df$scientificNameAuthorship[i])){
      scn <- paste(scn,trimws(df$scientificNameAuthorship[i]), sep = " ")
    }
    df$scientificName[i] <- scn
}

[vijaybarve]

I think this was just due to trying to run single function rather than installing the package again.