sdtaylor / phenometr Goto Github PK

inside get_credentials()

if prompted for info:
  get info  
  test_connection (just grab a small table)
  failed?
     password failure?
         re-enter
     connection failure?
         ping server to check

instead of start and end dates be able to call a single or multiple years.

What if they're are consecutive? ie. years = c(2015,2019)

like the phenophase page

species, pp code, common name, sites

Phenophases with a percent cover are categorical, but need to be mapped to a percent cover.

Need to ensure it's only done on the correct phenophases.

The bins:

Midpoints

percent_cover_values = tribble(
  ~PHENOPHASE, ~STATUS, ~PERCENT_COVER,
  'DS_202',     0,       0,
  'DS_202',     1,       2.5,
  'DS_202',     2,       14.5,
  'DS_202',     3,       37,
  'DS_202',     4,       57,
  'DS_202',     5,       84,
  'DS_202',     6,       97.5
)

dplyr, tidyr, dbplyr, DBI, RMariaDB, yaml

req. for testing with the included sqlite db: RSQLite, testthat

wrote this but didn't end up using it. could be useful at some point.
where functional_groups can be 'all' or some combination of c('GR','DS','BE','CA')

some_function = function(functional_groups='all'){
  available_fg = c('GR','DS','BE','CA')
  if((functional_groups == 'all')[1]){
    functional_groups <- available_fg
  } else if(!all(functional_groups %in% available_fg)){
    stop('unknown functional groups: ', paste(functional_groups, collapse = ','))
  }
}

Most are just marked with a -99. Potentially make the na or remove entirely.

Potentially different NA values with different phenophases. need to check on that.

Just a single to run. Also emphasize the clear_credential() function in case of login problems.

in get_site_phenophase and get_fg_phenophase

get_species_phenophase()

inside

get plant info
filter to species
catch if nothing found/not valid
for each individual
     get_plant_phenophase