Refactor `R/traits.R` into `SpecimenMap` class methods

[jasonratcliff]

Replace currently exported functions in R/traits.R with comparable methods for mapping continuous and discrete trait data.

Lifecycle Deprecation

• range_split()

  • data-raw/specimens/vouchers.R (d7fc40c)

Occurrences

Targets
    Occurrences of 'range_split(' in Project with mask '!*.Rd'
Found Occurrences in Project with mask '!*.Rd'  (17 usages found)
    Unclassified  (10 usages found)
        thesis  (10 usages found)
              (1 usage found)
                NEWS.md  (1 usage found)
                    348 - `range_split()` returns only min / max values (i.e. two column tibble)
            data-raw/descriptions  (1 usage found)
                index.Rmd  (1 usage found)
                    48 thesis::range_split(trait_tbl = ., split_var = trait) %>%
            data-raw/specimens  (1 usage found)
                vouchers.R  (1 usage found)
                    208 thesis::range_split(
            docs/descriptions  (1 usage found)
                index.Rmd  (1 usage found)
                    48 thesis::range_split(trait_tbl = ., split_var = trait) %>%
            docs/thesis/chapters  (2 usages found)
                _morphometrics.qmd  (2 usages found)
                    14 bind_cols(range_split(trait_tbl = ., split_var = "Ovule_number")) %>%
                    21 bind_cols(range_split(trait_tbl = ., split_var = "Stem_length_dm")) %>%
            inst/scripts  (4 usages found)
                ResultsPhysariaFruits.R  (1 usage found)
                    22 thesis::range_split(trait_tbl = ., split_var = "Mature_fruit_length_mm")
                ResultsPhysariaHabit.R  (2 usages found)
                    24 thesis::range_split(trait_tbl = ., split_var = "Stem_length_dm"),
                    25 thesis::range_split(trait_tbl = ., split_var = "Basal_leaf_length_cm")
                ResultsPhysariaOvules.R  (1 usage found)
                    21 thesis::range_split(trait_tbl = ., split_var = "Ovule_number")
    Usage in comments  (7 usages found)
        thesis  (7 usages found)
            R  (7 usages found)
                data.R  (4 usages found)
                    31 #'   \item{Elev_var,Elev_raw}{Non-missing elevation data for `range_split()`}
                    33 #'   `range_split()` function.}
                    77 #'   \item{Elev_var,Elev_raw}{Non-missing elevation data for `range_split()`}
                    79 #'     Split elevation range output by `range_split()` function.
                traits.R  (3 usages found)
                    20 #'   range_split(trait_tbl = ., split_var = "Ovule_number")
                    130 #'     range_split(trait_tbl = ., split_var = "Ovule_number")
                    271 #'     range_split(trait_tbl = ., split_var = "Mature_fruit_length_mm")

• map_trait_distribution()

  • R/traits.R
  • man/map_trait_distribution.Rd
  • inst/scripts/DiscussionTrait*.R
  • NAMESPACE
  • NEWS.md

Occurrences

Targets
    Occurrences of 'map_trait_distribution' in Project with mask '!*.json,!*.html,!*.txt,!*.xml'
Found Occurrences in Project with mask '!*.json,!*.html,!*.txt,!*.xml'  (12 usages found)
    Unclassified  (10 usages found)
        thesis  (10 usages found)
              (2 usages found)
                NAMESPACE  (1 usage found)
                    31 export(map_trait_distribution)
                NEWS.md  (1 usage found)
                    328 * New `map_trait_distribution()` provides a convenient wrapper for displaying
            inst/scripts  (3 usages found)
                DiscussionTraitApices.R  (1 usage found)
                    41 thesis::map_trait_distribution(tidy_trait = traits$counts) +
                DiscussionTraitMargins.R  (1 usage found)
                    21 thesis::map_trait_distribution(tidy_trait = ., .identifier = "prior_id") +
                DiscussionTraitTrichomes.R  (1 usage found)
                    24 thesis::map_trait_distribution(tidy_trait = ., .identifier = "prior_id") +
            man  (4 usages found)
                map_trait_distribution.Rd  (4 usages found)
                    3 \name{map_trait_distribution}
                    4 \alias{map_trait_distribution}
                    7 map_trait_distribution(
                    39 map_trait_distribution(tidy_trait = tidied) +
            R  (1 usage found)
                traits.R  (1 usage found)
                    140 map_trait_distribution <- function(tidy_trait, .identifier = "prior_id",
    Usage in comments  (2 usages found)
        thesis  (2 usages found)
            inst/scripts  (1 usage found)
                DiscussionTraitFruits.R  (1 usage found)
                    18 # thesis::map_trait_distribution(tidy_trait = .) +
            R  (1 usage found)
                traits.R  (1 usage found)
                    135 #' map_trait_distribution(tidy_trait = tidied) +