R/internal_functions.R

In adamhsparks/fulcrum: 'Fulcrum' Client to Query and Tidy Data and Other Tools and Data for Reporting

#' @noRd
`%notin%` <- function(x, table) {
  # Same as !(x %in% table)
  match(x, table, nomatch = 0L) == 0L
}

#' Read Fulcrum Data from Fulcrum Site
#' @param .url A url of a shared 'CSV' file of Fulcrum data
#' @note The \code{.url} may either be provided by the user or taken from the
#' .Renviron/.bashrc/bash_profile files
#' @noRd
.fetch_data <- function(.url) {
  # CRAN note avoidance (even though it's never going to CRAN) -----------------
  "fulcrum_id" <- #nocov start
    "created_at" <-
    "updated_at" <-
    "created_by" <-
    "updated_by" <-
    "system_created_at" <-
    "system_updated_at" <-
    "version" <-
    "status" <-
    "project" <-
    "assigned_to" <-
    "latitude" <-
    "longitude" <-
    "geometry" <-
    "season" <-
    "paddockproperty" <-
    "location_description" <-
    "location_description_other" <-
    "landform" <-
    "nearest_town" <-
    "region" <-
    "grower" <-
    "growers_phone_number" <-
    "agronomist" <-
    "agronomists_phone_number" <-
    "crop" <-
    "cultivar" <-
    "canola_growth_stage_" <-
    "chickpea_growth_stage_" <-
    "maize_growth_stage_" <-
    "mungbean_growth_stage_" <-
    "peanut_growth_stage_" <-
    "sorghum_growth_stage_" <-
    "soybean_growth_stage_" <-
    "sunflower_growth_stage_" <-
    "winter_cereal_growth_stage_" <-
    "total_plant_count" <-
    "barley_fusarium_head_blightscab" <-
    "barley_net_form_net_blotch" <-
    "barley_spot_form_net_blotch" <-
    "barley_powdery_mildew" <-
    "barley_stem_rust" <-
    "barley_virus" <-
    "barley_other" <-
    "describe_barley_other" <-
    "canola_powdery_mildew" <-
    "canola_blackleg" <-
    "canola_sclerotinia_stem_rot" <-
    "canola_virus" <-
    "canola_other" <-
    "describe_canola_other" <-
    "chickpea_ascochyta_blight" <-
    "chickpea_botrytis_grey_mould" <-
    "chickpea_fusarium_wilt" <-
    "chickpea_phytoplasma" <-
    "chickpea_phytophthora_root_rot" <-
    "chickpea_virus" <-
    "chickpea_other" <-
    "describe_chickpea_other" <-
    "maize_bacterial_stalk_rot_and_bacterial_top_rot" <-
    "maize_charcoal_rot" <-
    "maize_common_rust" <-
    "maize_commonboil_smut" <-
    "maize_crazy_top" <-
    "maize_damping_off" <-
    "maize_diplodia_cob_rot" <-
    "maize_downy_mildew" <-
    "maize_dwarf_mosaic_virus" <-
    "maize_fusarium_ear_rot" <-
    "maize_fusarium_stalk_rot" <-
    "maize_head_smut" <-
    "maize_pythium_stalk_rot" <-
    "maize_turcica_leaf_blight" <-
    "maize_maydis_leaf_blight" <-
    "maize_southern_rust" <-
    "maize_virus" <-
    "maize_other" <-
    "describe_maize_other" <-
    "mungbean_alternaria_leaf_spot" <-
    "mungbean_bacterial_blight" <-
    "mungbean_charcoal_rot" <-
    "mungbean_damping_off" <-
    "mungbean_fusarium_wilt" <-
    "mungbean_gummy_pod" <-
    "mungbean_halo_blight" <-
    "mungbean_phytoplasma" <-
    "mungbean_powdery_mildew" <-
    "mungbean_puffy_pod" <-
    "mungbean_rhizoctonia_rot" <-
    "mungbean_root_lesion_nematode" <-
    "mungbean_sclerotinia_stem_rot" <-
    "mungbean_sclerotium_stem_rot" <-
    "mungbean_tan_spot" <-
    "mungbean_tsv" <-
    "mungbean_virus" <-
    "mungbean_other" <-
    "describe_mungbean_other" <-
    "peanut_fusarium_root_rot" <-
    "peanut_neocosmospora_root_rot" <-
    "peanut_net_blotch" <-
    "peanut_kernel_shrivel_syndrome" <-
    "peanut_root_lesion_nematode" <-
    "peanut_rust" <-
    "peanut_sclerotium_base_rot" <-
    "peanut_tsv" <-
    "peanut_virus" <-
    "peanut_other" <-
    "describe_peanut_other" <-
    "sorghum_bacterial_top_and_stalk_rot" <-
    "sorghum_charcoal_rot" <-
    "sorghum_damping_off" <-
    "sorghum_ergot" <-
    "sorghum_fusarium_head_blight" <-
    "sorghum_fusarium_stalk_rot" <-
    "sorghum_grain_mould" <-
    "sorghum_head_smut" <-
    "sorghum_johnsongrass_mosaic_virus" <-
    "sorghum_leaf_blight" <-
    "sorghum_root_lesion_nematode" <-
    "sorghum_rust" <-
    "sorghum_sclerotium_base_rot" <-
    "sorghum_tar_spot" <-
    "sorghum_other" <-
    "describe_sorghum_other" <-
    "soybean_bacterial_blight_bacterial_pustule" <-
    "soybean_charcoal_rot" <-
    "soybean_damping_off" <-
    "soybean_peanut_mottle_virus" <-
    "soybean_phomopsis_seed_decay" <-
    "soybean_phytophthora_root_stem_and_root_rot" <-
    "soybean_phytoplasma" <-
    "soybean_pod_stem_cankerblight" <-
    "soybean_powdery_mildew" <-
    "soybean_purple_seed_stain" <-
    "soybean_rhizoctonia_rot" <-
    "soybean_root_lesion_nematode" <-
    "soybean_rust" <-
    "soybean_sclerotinia_rot" <-
    "soybean_mosaic_virus" <-
    "soybean_virus" <-
    "soybean_other" <-
    "describe_soybean_other" <-
    "sunflower_apical_chlorosis" <-
    "sunflower_botrytis_head_rot_grey_mould" <-
    "sunflower_charcoal_rot" <-
    "sunflower_powdery_mildew" <-
    "sunflower_rhizopus_head_rot" <-
    "sunflower_rust" <-
    "sunflower_sclerotinia_rot" <-
    "sunflower_sclerotium_base_rot" <-
    "sunflower_stem_cankerblight" <-
    "sunflower_tsv" <-
    "sunflower_verticillium_wilt" <-
    "sunflower_other" <-
    "describe_sunflower_other" <-
    "wheat_fusarium_head_blightscab" <-
    "wheat_crown_rot" <-
    "wheat_common_root_rot" <-
    "wheat_leafbrown_rust" <-
    "wheat_root_lesion_nematode" <-
    "wheat_septoria_nodorum_blotch" <-
    "wheat_stemblack_rust" <-
    "wheat_stripeyellow_rust" <-
    "wheat_yellow_spot" <-
    "wheat_white_grain" <-
    "wheat_other" <-
    "describe_wheat_other" <-
    "notes" <-
    "photos" <-
    "photos_caption" <-
    "photos_url" <-
    "gps_altitude" <-
    "gps_horizontal_accuracy" <-
    "gps_vertical_accuracy" <-
    "gps_speed" <-
    "gps_course" <-
    "crop_gs" <-
    "growth_stage" <-
    "incidence" <-
    "disease" <-
    "disease.x" <-
    "disease.y" <-
    "." <- NULL #nocov end

  readr::read_csv(
    .url,
    na = c(""),
    col_types = readr::cols(
      fulcrum_id = readr::col_character(),
      created_at = readr::col_character(),
      updated_at = readr::col_character(),
      created_by = readr::col_character(),
      updated_by = readr::col_character(),
      system_created_at = readr::col_character(),
      system_updated_at = readr::col_character(),
      version = readr::col_integer(),
      status = readr::col_character(),
      project = readr::col_character(),
      assigned_to = readr::col_character(),
      latitude = readr::col_double(),
      longitude = readr::col_double(),
      geometry = readr::col_character(),
      season = readr::col_character(),
      paddockproperty = readr::col_character(),
      location_description = readr::col_character(),
      location_description_other = readr::col_logical(),
      landform = readr::col_character(),
      nearest_town = readr::col_character(),
      region = readr::col_character(),
      grower = readr::col_character(),
      growers_phone_number = readr::col_character(),
      agronomist = readr::col_character(),
      agronomists_phone_number = readr::col_character(),
      crop = readr::col_character(),
      cultivar = readr::col_character(),
      canola_growth_stage_ = readr::col_character(),
      chickpea_growth_stage_ = readr::col_character(),
      maize_growth_stage_ = readr::col_character(),
      mungbean_growth_stage_ = readr::col_character(),
      peanut_growth_stage_ = readr::col_character(),
      sorghum_growth_stage_ = readr::col_character(),
      soybean_growth_stage_ = readr::col_character(),
      sunflower_growth_stage_ = readr::col_character(),
      winter_cereal_growth_stage_ = readr::col_character(),
      total_plant_count = readr::col_integer(),
      barley_fusarium_head_blightscab = readr::col_integer(),
      barley_net_form_net_blotch = readr::col_integer(),
      barley_spot_form_net_blotch = readr::col_integer(),
      barley_powdery_mildew = readr::col_integer(),
      barley_stem_rust = readr::col_integer(),
      barley_virus = readr::col_integer(),
      barley_other = readr::col_integer(),
      describe_barley_other = readr::col_character(),
      canola_powdery_mildew = readr::col_integer(),
      canola_blackleg = readr::col_integer(),
      canola_sclerotinia_stem_rot = readr::col_integer(),
      canola_virus = readr::col_integer(),
      canola_other = readr::col_integer(),
      describe_canola_other = readr::col_character(),
      chickpea_ascochyta_blight = readr::col_integer(),
      chickpea_botrytis_grey_mould = readr::col_integer(),
      chickpea_fusarium_wilt = readr::col_integer(),
      chickpea_phytoplasma = readr::col_integer(),
      chickpea_phytophthora_root_rot = readr::col_integer(),
      chickpea_virus = readr::col_integer(),
      chickpea_other = readr::col_integer(),
      describe_chickpea_other = readr::col_character(),
      maize_bacterial_stalk_rot_and_bacterial_top_rot = readr::col_integer(),
      maize_charcoal_rot = readr::col_integer(),
      maize_common_rust = readr::col_integer(),
      maize_commonboil_smut = readr::col_integer(),
      maize_crazy_top = readr::col_integer(),
      maize_damping_off = readr::col_integer(),
      maize_diplodia_cob_rot = readr::col_integer(),
      maize_downy_mildew = readr::col_integer(),
      maize_dwarf_mosaic_virus = readr::col_integer(),
      maize_fusarium_ear_rot = readr::col_integer(),
      maize_fusarium_stalk_rot = readr::col_integer(),
      maize_head_smut = readr::col_integer(),
      maize_pythium_stalk_rot = readr::col_integer(),
      maize_turcica_leaf_blight = readr::col_integer(),
      maize_maydis_leaf_blight = readr::col_integer(),
      maize_southern_rust = readr::col_integer(),
      maize_virus = readr::col_integer(),
      maize_other = readr::col_integer(),
      describe_maize_other = readr::col_character(),
      mungbean_alternaria_leaf_spot = readr::col_integer(),
      mungbean_bacterial_blight = readr::col_integer(),
      mungbean_charcoal_rot = readr::col_integer(),
      mungbean_damping_off = readr::col_integer(),
      mungbean_fusarium_wilt = readr::col_integer(),
      mungbean_gummy_pod = readr::col_integer(),
      mungbean_halo_blight = readr::col_integer(),
      mungbean_phytoplasma = readr::col_integer(),
      mungbean_powdery_mildew = readr::col_integer(),
      mungbean_puffy_pod = readr::col_integer(),
      mungbean_rhizoctonia_rot = readr::col_integer(),
      mungbean_root_lesion_nematode = readr::col_integer(),
      mungbean_sclerotinia_stem_rot = readr::col_integer(),
      mungbean_sclerotium_stem_rot = readr::col_integer(),
      mungbean_tan_spot = readr::col_integer(),
      mungbean_tsv = readr::col_integer(),
      mungbean_virus = readr::col_integer(),
      mungbean_other = readr::col_integer(),
      describe_mungbean_other = readr::col_character(),
      peanut_fusarium_root_rot = readr::col_integer(),
      peanut_neocosmospora_root_rot = readr::col_integer(),
      peanut_net_blotch = readr::col_integer(),
      peanut_kernel_shrivel_syndrome = readr::col_integer(),
      peanut_root_lesion_nematode = readr::col_integer(),
      peanut_rust = readr::col_integer(),
      peanut_sclerotium_base_rot = readr::col_integer(),
      peanut_tsv = readr::col_integer(),
      peanut_virus = readr::col_integer(),
      peanut_other = readr::col_integer(),
      describe_peanut_other = readr::col_character(),
      sorghum_bacterial_top_and_stalk_rot = readr::col_integer(),
      sorghum_charcoal_rot = readr::col_integer(),
      sorghum_damping_off = readr::col_integer(),
      sorghum_ergot = readr::col_integer(),
      sorghum_fusarium_head_blight = readr::col_integer(),
      sorghum_fusarium_stalk_rot = readr::col_integer(),
      sorghum_grain_mould = readr::col_integer(),
      sorghum_head_smut = readr::col_integer(),
      sorghum_johnsongrass_mosaic_virus = readr::col_integer(),
      sorghum_leaf_blight = readr::col_integer(),
      sorghum_root_lesion_nematode = readr::col_integer(),
      sorghum_rust = readr::col_integer(),
      sorghum_sclerotium_base_rot = readr::col_integer(),
      sorghum_tar_spot = readr::col_integer(),
      sorghum_other = readr::col_integer(),
      describe_sorghum_other = readr::col_character(),
      soybean_bacterial_blight_bacterial_pustule = readr::col_integer(),
      soybean_charcoal_rot = readr::col_integer(),
      soybean_damping_off = readr::col_integer(),
      soybean_peanut_mottle_virus = readr::col_integer(),
      soybean_phomopsis_seed_decay = readr::col_integer(),
      soybean_phytophthora_root_stem_and_root_rot = readr::col_integer(),
      soybean_phytoplasma = readr::col_integer(),
      soybean_pod_stem_cankerblight = readr::col_integer(),
      soybean_powdery_mildew = readr::col_integer(),
      soybean_purple_seed_stain = readr::col_integer(),
      soybean_rhizoctonia_rot = readr::col_integer(),
      soybean_root_lesion_nematode = readr::col_integer(),
      soybean_rust = readr::col_integer(),
      soybean_sclerotinia_rot = readr::col_integer(),
      soybean_mosaic_virus = readr::col_integer(),
      soybean_virus = readr::col_integer(),
      soybean_other = readr::col_integer(),
      describe_soybean_other = readr::col_character(),
      sunflower_apical_chlorosis = readr::col_integer(),
      sunflower_botrytis_head_rot_grey_mould = readr::col_integer(),
      sunflower_charcoal_rot = readr::col_integer(),
      sunflower_powdery_mildew = readr::col_integer(),
      sunflower_rhizopus_head_rot = readr::col_integer(),
      sunflower_rust = readr::col_integer(),
      sunflower_sclerotinia_rot = readr::col_integer(),
      sunflower_sclerotium_base_rot = readr::col_integer(),
      sunflower_stem_cankerblight = readr::col_integer(),
      sunflower_tsv = readr::col_integer(),
      sunflower_verticillium_wilt = readr::col_integer(),
      sunflower_other = readr::col_integer(),
      describe_sunflower_other = readr::col_character(),
      wheat_fusarium_head_blightscab = readr::col_integer(),
      wheat_crown_rot = readr::col_integer(),
      wheat_common_root_rot = readr::col_integer(),
      wheat_leafbrown_rust = readr::col_integer(),
      wheat_root_lesion_nematode = readr::col_integer(),
      wheat_septoria_nodorum_blotch = readr::col_integer(),
      wheat_stemblack_rust = readr::col_integer(),
      wheat_stripeyellow_rust = readr::col_integer(),
      wheat_yellow_spot = readr::col_integer(),
      wheat_white_grain = readr::col_integer(),
      wheat_other = readr::col_integer(),
      describe_wheat_other = readr::col_character(),
      notes = readr::col_character(),
      photos = readr::col_character(),
      photos_caption = readr::col_character(),
      photos_url = readr::col_character(),
      gps_altitude = readr::col_double(),
      gps_horizontal_accuracy = readr::col_double(),
      gps_vertical_accuracy = readr::col_double(),
      gps_speed = readr::col_double(),
      gps_course = readr::col_character()
    )
  )
}

#' Capitalises Only the First Letter
#' @param .sc Text to be cleaned to "Upper and lower case only" format.
#' @noRd
.simple_cap <- function(sc) {
  sub("(.)", ("\\U\\1"), tolower(sc), perl = TRUE)
}