align_pft

align_pft

align_pft(con, observation_one, observation_two, custom_table = NULL,
  format_one, format_two, subset_is_ok = FALSE,
  comparison_type = "data_to_data", ...)

Arguments

con	database connection
observation_one	a vector of plant fucntional types, or species
observation_two	anouther vector of plant fucntional types, or species
custom_table	a table that either maps two pft's to one anouther or maps custom species codes to bety id codes. In the second case, must be passable to match_species_id.
format_one	The output of query.format.vars() of observation one of the form output$vars$bety_names
format_two	The output of query.format.vars() of observation two of the form output$vars$bety_names
subset_is_ok	When aligning two species lists, this allows for alignement when species lists aren't identical. set to FALSE by default.

Value

list containing the following columns:

$original

Will spit back out original vectors pre-alignment

$aligned$aligned_by_observation_one

Where possible, will return a vector of observation_one pft's/species in the order of observation_two

species

Where possible, will return a vector of observation_two's pft's/species in the order of observation_one

$bety_species_id

Where possible, will return the bety_species_id's for one or both observations

Details

Aligns vectors of Plant Fucntional Typed and species. Can align: - two vectors of plant fucntional types (pft's) if a custom map is provided - a list of species (usda, fia, or latin_name format) to a plant fucntional type - a list of species in a custom format, with a table mapping it to bety_species_id's

Will return a list of what was originally provided, bety_speceis_codes if possible, and an aligned output. Becuase some alignement is order-sensitive, alignment based on observation_one and observation_two are both provided.

comparison_type can be one of the following:

data_to_data

Will align lists of pfts and species. Must be assosiated with inputs.

data_to_model

Not yet implemented

model_to_model

Not yet implemented

Examples

# NOT RUN {

#------------ A species to PFT alignment -----------
observation_one<-c("AMCA3","AMCA3","AMCA3","AMCA3")
observation_two<-c("a", "b", "a", "a") #

format_one<-"species_USDA_symbol"
format_two<-"plant_funtional_type"

table<-list()
table$plant_functional_type_one<- c("AMCA3","AMCA3","ARHY", "ARHY")
table$plant_functional_type_two<- c('a','a','b', 'b') # PFT groupings
table<-as.data.frame(table)


aligned<-align_pft(con = con, observation_one = observation_one, observation_two = observation_two,
format_one = format_one, format_two = format_two, custom_table = table)
# }# NOT RUN {
# }