Merge pull request #17 from RobLBaker/master

add get_custom_flags

Author: RobLBaker

DESCRIPTION

@@ -39,7 +39,8 @@ Imports:
     ODataQuery,
     magrittr,
     stringr,
-    base
+    base,
+    readr
 RoxygenNote: 7.2.1
 Suggests: 
     knitr,

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(DC_col_check)
 export(fuzz_location)
+export(get_custom_flags)
 export(get_dc_flags)
 export(get_df_flags)
 export(get_dp_flags)

R/DC_col_check.R

@@ -16,8 +16,8 @@
 #' DC_col_check(yourdataframe)
 #' }
 DC_col_check <- function(working_df) {
-  #dwc_terms<-read.csv("https://raw.githubusercontent.com/tdwg/dwc/master/dist/simple_dwc_vertical.csv", header=FALSE) #does not include measurementOrFact or resourceRelationship classes and thus has 179 items vs 196 in the list below.  
-  
+  # dwc_terms<-read.csv("https://raw.githubusercontent.com/tdwg/dwc/master/dist/simple_dwc_vertical.csv", header=FALSE) #does not include measurementOrFact or resourceRelationship classes and thus has 179 items vs 196 in the list below.
+
   dwcterms <- data.frame(DarwinCore = c("type", "modified", "language", "license", "rightsHolder", "accessRights", "bibliographicCitation", "references", "institutionID", "collectionID", "datasetID", "institutionCode", "collectionCode", "datasetName", "ownerInstitutionCode", "basisOfRecord", "informationWithheld", "dataGeneralizations", "dynamicProperties", "occurrenceID", "catalogNumber", "recordNumber", "recordedBy", "recordedByID", "individualCount", "organismQuantity", "organismQuantityType", "sex", "lifeStage", "reproductiveCondition", "behavior", "establishmentMeans", "degreeOfEstablishment", "pathway", "georeferenceVerificationStatus", "occurrenceStatus", "preparations", "disposition", "associatedMedia", "associatedOccurrences", "associatedReferences", "associatedSequences", "associatedTaxa", "otherCatalogNumbers", "occurrenceRemarks", "organismID", "organismName", "organismScope", "associatedOrganisms", "previousIdentifications", "organismRemarks", "materialSampledID", "eventID", "parentEventID", "fieldNumber", "eventDate", "eventTime", "startDayOfYear", "endDayOfYear", "year", "month", "day", "verbatimEventDate", "habitat", "samplingProtocol", "sampleSizeValue", "sampleSizeUnit", "samplingEffort", "fieldNotes", "eventRemarks", "locationID", "higherGeographyID", "higherGeography", "continent", "waterBody", "islandGroup", "island", "country", "countryCode", "stateProvince", "county", "municipality", "locality", "verbatimLocality", "minimumElevationInMeters", "maximumElevationInMeters", "verbatimElevation", "verticalDatum", "minimumDepthInMeters", "maximumDepthInMeters", "verbatimDepth", "minimumDistanceAboveSurfaceInMeters", "maximumDistanceAboveSurfaceInMeters", "locationAccordingTo", "locationRemarks", "decimalLatitude", "decimalLongitude", "geodeticDatum", "coordinateUncertaintyInMeters", "coordinatePrecision", "pointRadiusSpatialFit", "verbatimCoordinates", "verbatimLatitude", "verbatimLongitude", "verbatimCoordinateSystem", "verbatimSRS", "footprintWKT", "footprintSRS", "footprintSpatialFit", "georeferencedBy", "georeferencedDate", "georeferenceProtocol", "georeferenceSources", "georeferenceRemarks", "geologicalContextID", "earliestEonOrLowestEonothem", "latestEonOrHighestEonothem", "earliestEraOrLowestErathem", "latestEraOrHighestErathem", "earliestPeriodOrLowestSystem", "latestPeriodOrHighestSystem", "earliestEpochOrLowestSeries", "latestEpochOrHighestSeries", "earliestAgeOrLowestStage", "latestAgeOrHighestStage", "lowestBiostratigraphicZone", "highestBiostratigraphicZone", "lithostratigraphicTerms", "group", "formation", "member", "bed", "identificationID", "verbatimIdentification", "identificationQualifier", "typeStatus", "identifiedBy", "identifiedByID", "dateIdentified", "ientificationReferences", "identificationVerificationStatus", "identificationRemarks", "taxonID", "scientificNameID", "acceptedNameUsageID", "parentNameUsageID", "originalNameUsageID", "naemAccordingToID", "naemPublishedInID", "taxonConceptID", "scientificName", "acceptedNameUsage", "parentNameUsage", "originalNameUsage", "nameAccordingTo", "namePublishedIn", "namePublishedInYear", "higherClassification", "kingdom", "phylum", "class", "order", "family", "subfamily", "genus", "genericName", "subgenus", "infragenericEpithet", "specificEpithet", "infraspecificEpithet", "cultivarEpithet", "taxonRank", "verbatimTaxonRank", "scientificNameAuthorship", "vernacularName", "nomenclaturalCode", "taxonomicStatus", "nomenclaturalStatus", "taxonRemarks", "measurementID", "measurementType", "measurementValue", "measurementAccuracy", "measurementUnit", "measurementDeterminedBy", "measurementDeterminedDate", "measurementMethod", "measurementRemarks", "resourceRelationshipID", "resourceID", "reationshipOfResourceID", "relatedResourceID", "relationshipOfResource", "relationshipAccordingTo", "relationshipEstablishedDate", "relationshipRemarks"))
 
 

R/geography.R

@@ -35,7 +35,6 @@ get_park_polygon <- function(unit_code) {
 #' qc_ValidateCoordinates("OBRI", 36.07951, -84.65610)
 #' }
 validate_coord <- function(unit_code, lat, lon) {
-
   # get geography from NPS Rest Services
   park <- get_park_polygon(unit_code)
 
@@ -75,13 +74,13 @@ fuzz_location <- function(lat, lon, coord_ref_sys, fuzz_level) {
       ## Function to get the UTM zone for a given longitude
       (floor((long + 180) / 6) %% 60) + 1
     }
-    
+
     tempcrs <- if (lat > 0) {
       long2UTM(lon) + 32600
     } else {
       long2UTM(lon) + 32700
     }
-    
+
     point <- sf::st_point(c(lon, lat))
     point <- sf::st_sfc(point, crs = 4326)
     pointutm <- sf::st_transform(x = point, crs = tempcrs)
@@ -91,7 +90,7 @@ fuzz_location <- function(lat, lon, coord_ref_sys, fuzz_level) {
     locationlat <- lat
     locationlon <- lon
   }
-  
+
   # do rounding of UTMs based on fuzz_level
   if (fuzz_level == "Fuzzed - 1km") {
     fuzzfactor <- 1000
@@ -100,14 +99,14 @@ fuzz_location <- function(lat, lon, coord_ref_sys, fuzz_level) {
   } else {
     fuzzfactor <- 1
   }
-  
+
   locationlat <- locationlat / fuzzfactor
   locationlon <- locationlon / fuzzfactor
   locationlathi <- ceiling(locationlat) * fuzzfactor
   locationlatlo <- floor(locationlat) * fuzzfactor
   locationlonhi <- ceiling(locationlon) * fuzzfactor
   locationlonlo <- floor(locationlon) * fuzzfactor
-  
+
   # construct simple feature geometry polygon from UTM points
   polygon_list <- list(rbind(
     c(locationlatlo, locationlonlo),
@@ -117,18 +116,18 @@ fuzz_location <- function(lat, lon, coord_ref_sys, fuzz_level) {
     c(locationlatlo, locationlonlo)
   ))
   utmsfg <- sf::st_polygon(polygon_list)
-  
+
   # convert sfg to sfc with appropriate crs
   if (coord_ref_sys == 4326) {
     utmsfc <- sf::st_sfc(utmsfg, crs = tempcrs)
   } else {
     utmsfc <- sf::st_sfc(utmsfg, crs = coord_ref_sys)
   }
-  
+
   # convert polygon to decimal degrees
   wkt <- sf::st_transform(x = utmsfc, crs = 4326)
   wkt <- sf::st_as_text(wkt)
-  
+
   # return WKT string
   return(wkt)
 }
@@ -148,14 +147,15 @@ fuzz_location <- function(lat, lon, coord_ref_sys, fuzz_level) {
 #' @return The function returns your dataframe, mutated with an additional two columns of decimal Longitude and decimal Latitude.
 #' @export
 #'
-#' @examples 
+#' @examples
 #' \dontrun{
-#' utm_to_ll(df = mydataframe, 
-#'           EastingCol = "EastingCoords", 
-#'           NorthingCol = "NorthingCoords", 
-#'           zone = "17", 
-#'           datum = "WGS84"
-#'           )
+#' utm_to_ll(
+#'   df = mydataframe,
+#'   EastingCol = "EastingCoords",
+#'   NorthingCol = "NorthingCoords",
+#'   zone = "17",
+#'   datum = "WGS84"
+#' )
 #' }
 utm_to_ll <- function(df, EastingCol, NorthingCol, zone, datum = "WGS84") {
   Base <- as.data.frame(df)
@@ -166,24 +166,26 @@ utm_to_ll <- function(df, EastingCol, NorthingCol, zone, datum = "WGS84") {
   Final[1:2] <- lapply(Final[1:2], FUN = function(z) {
     as.numeric(z)
   })
-  
+
   Final <- cbind(Final$b, Final$a)
-  
-  v <- terra::vect(Final, crs = paste0("+proj=utm +zone=",
-                                       zone, 
-                                       " +datum=", 
-                                       datum, "
-                                       +units=m"))
-  
+
+  v <- terra::vect(Final, crs = paste0(
+    "+proj=utm +zone=",
+    zone,
+    " +datum=",
+    datum, "
+                                       +units=m"
+  ))
+
   converted <- terra::project(v, "+proj=longlat +datum=WGS84")
-  
+
   lonlat <- terra::geom(converted)[, c("x", "y")]
 
   df <- cbind(Mid, lonlat)
   df <- plyr::rbind.fill(df, Mid2)
-  df <- dplyr::rename(df, EastingCol = "b", NorthingCol = "a",
-                      "decimalLongitude" = x, "decimalLatitude" = y)
+  df <- dplyr::rename(df,
+    EastingCol = "b", NorthingCol = "a",
+    "decimalLongitude" = x, "decimalLatitude" = y
+  )
   return(df)
 }
-
-