Installation
# install.packages("devtools")
devtools::install_github('iobis/obistools')
library(obistools)
Help and issues
2018-02-09
Getting started
Generate a report
View points on a map and check missing fields, event dates, depth values, points on land, …
report(abra, file="abra_report.html", dir=".")
Check required fields
check_fields(abra)
## field level message ## 1 occurrenceStatus error Required field occurrenceStatus is missing
occurrenceStatus: A statement about the presence or absence of a Taxon at a Location.
http://rs.tdwg.org/dwc/terms/#occurrenceStatus
Map column names to Darwin Core terms
data <- data.frame(
id = c("cruise_1", "station_1", "station_2", "sample_1", "sample_2", "sample_3", "sample_4", "subsample_1", "subsample_2"),
date = c(NA, NA, NA, "2017-01-01", "2017-01-02", "2017-01-03", "2017-01-04", NA, NA),
locality = rep("North Sea", 9),
lon = c(NA, 2.9, 4.7, NA, NA, NA, NA, NA, NA),
lat = c(NA, 54.1, 55.8, NA, NA, NA, NA, NA, NA),
stringsAsFactors = FALSE)
mapping <- list(
decimalLongitude = "lon", decimalLatitude = "lat",
datasetName = "dataset", eventID = "id", eventDate = "date")
Map column names to Darwin Core terms
map_fields(data, mapping)
## eventID eventDate locality decimalLongitude decimalLatitude ## 1 cruise_1 <NA> North Sea NA NA ## 2 station_1 <NA> North Sea 2.9 54.1 ## 3 station_2 <NA> North Sea 4.7 55.8 ## 4 sample_1 2017-01-01 North Sea NA NA ## 5 sample_2 2017-01-02 North Sea NA NA ## 6 sample_3 2017-01-03 North Sea NA NA ## 7 sample_4 2017-01-04 North Sea NA NA ## 8 subsample_1 <NA> North Sea NA NA ## 9 subsample_2 <NA> North Sea NA NA
Taxon matching
Interactive taxon matching with the World Register of Marine Species (WoRMS)
taxa <- c("Abra alva", "Buccinum fusiforme", "Buccinum fusiforme", "hlqsdkf")
matched_taxa <- match_taxa(taxa)
matched_taxa
3 names, 1 without matches, 1 with multiple matches Proceed to resolve names (y/n/p)? y AphiaID scientificname authority status match_type 1 531014 Buccinum fusiforme Kiener, 1834 unaccepted exact 2 510389 Buccinum fusiforme Broderip, 1830 unaccepted exact Multiple matches, pick a number or leave empty to skip: 2
## scientificName scientificNameID matche_type ## 1 Abra alba urn:lsid:marinespecies.org:taxname:141433 near_1 ## 2 Buccinum fusiforme urn:lsid:marinespecies.org:taxname:510389 exact ## 3 Buccinum fusiforme urn:lsid:marinespecies.org:taxname:510389 exact ## 4 <NA> <NA> <NA>
Checking points on land
onland <- check_onland(abra) onland[,1:5]
## id decimalLongitude decimalLatitude basisOfRecord ## 31 365512845 -0.9092748 54.57467 Occurrence ## eventDate ## 31 2011-09-03 10:00:00
plot_map(onland, zoom = TRUE)
robis::leafletmap(onland)
Checking depth values
depthreport <- check_depth(abra, report = TRUE) depthreport[1:10, ]
## field level row ## 1 minimumDepthInMeters warning 34 ## 2 minimumDepthInMeters warning 35 ## 3 minimumDepthInMeters warning 36 ## 4 minimumDepthInMeters warning 37 ## 5 minimumDepthInMeters warning 47 ## 6 minimumDepthInMeters warning 51 ## 7 minimumDepthInMeters warning 52 ## 8 minimumDepthInMeters warning 54 ## 9 minimumDepthInMeters warning 55 ## 10 minimumDepthInMeters warning 56 ## message ## 1 Depth value (15.9) is greater than the value found in the bathymetry raster (depth=14.6, margin=0) ## 2 Depth value (15.9) is greater than the value found in the bathymetry raster (depth=14.6, margin=0) ## 3 Depth value (23.7) is greater than the value found in the bathymetry raster (depth=20.2, margin=0) ## 4 Depth value (24.8) is greater than the value found in the bathymetry raster (depth=20.2, margin=0) ## 5 Depth value (19.4) is greater than the value found in the bathymetry raster (depth=18.6, margin=0) ## 6 Depth value (23.4) is greater than the value found in the bathymetry raster (depth=18.6, margin=0) ## 7 Depth value (23.8) is greater than the value found in the bathymetry raster (depth=18.6, margin=0) ## 8 Depth value (8.5) is greater than the value found in the bathymetry raster (depth=7.2, margin=0) ## 9 Depth value (8.75) is greater than the value found in the bathymetry raster (depth=7.2, margin=0) ## 10 Depth value (8.9) is greater than the value found in the bathymetry raster (depth=7.2, margin=0)
Checking depth values
robis::leafletmap(abra[depthreport$row,])
Checking depth values
Extra parameters for check_depth:
depthmargin: How much can the given depth deviate from the bathymetry in the rasters (in meters).shoremargin: How far offshore (in meters) should a record be to have a bathymetry greater than 0. If NA (default) then this test is ignored.bathymetry: Raster* object that you want to use to check the depth against. If NULL (default) then the bathymetry from the xylookup service is used.
Lookup XY
Data for on land and depth checks is provided by the xylookup service which can be called trough the lookup_xy function.
env <- lookup_xy(abra) head(env)
## shoredistance sstemperature sssalinity bathymetry ## 1 30 10.2863 34.7627 -4.0 ## 2 1080 10.3324 34.9062 61.4 ## 3 1184 10.7220 34.8890 122.2 ## 4 290 10.7920 34.2934 20.6 ## 5 259 10.7220 34.8890 51.0 ## 6 506 10.7710 34.3070 32.4
Check event date
data_nodate <- data.frame(
scientificName = c("Abra alba", "Lanice conchilega"),
stringsAsFactors = FALSE)
check_eventdate(data_nodate)
## level message ## 1 error Column eventDate missing
Check event date
data_goodformats <- data.frame(
eventDate = c(
"2016",
"2016-01",
"2016-01-02",
"2016-01-02 13:00",
"2016-01-02T13:00",
"2016-01-02 13:00:00/2016-01-02 14:00:00",
"2016-01-02 13:00:00/14:00:00"),
stringsAsFactors = FALSE)
check_eventdate(data_goodformats)
## data frame with 0 columns and 0 rows
Check event date
data_badformats <- data.frame(
eventDate = c(
"2016/01/02",
"2016-01-02 13h00"),
stringsAsFactors = FALSE)
check_eventdate(data_badformats)
## level row field ## 1 error 1 eventDate ## 2 error 2 eventDate ## message ## 1 eventDate 2016/01/02 does not seem to be a valid date ## 2 eventDate 2016-01-02 13h00 does not seem to be a valid date
Dataset structure
archive <- hyperbenthos$data
tree <- treeStructure(archive$event.txt, archive$occurrence.txt,
archive$extendedmeasurementorfact.txt)
exportTree(tree, "hyperbenthos_tree.html")
Check eventID and parentEventID
check_eventids() checks if both eventID() and parentEventID fields are present in an event table, and if al parentEventIDs have a corresponding eventID.
data <- data.frame(
eventID = c("a", "b", "c", "d", "e", "f"),
parentEventID = c("", "", "a", "a", "z", "b"),
stringsAsFactors = FALSE
)
check_eventids(data)
## field level row message ## 1 parentEventID error 5 parentEventID z has no corresponding eventID
Check eventID in an extension
check_extension_eventids() checks if all eventIDs in an extension have matching eventIDs in the core table.
event <- data.frame(
eventID = c("cruise_1", "station_1", "station_2",
"sample_1", "sample_2", "sample_3", "sub_1", "sub_2"),
parentEventID = c(NA, "cruise_1", "cruise_1", "station_1", "station_1", "station_2",
"sample_3", "sample_3"),
eventDate = c(NA, NA, NA, "2017-01-01", "2017-01-02", "2017-01-03", NA, NA),
decimalLongitude = c(NA, 2.9, 4.7, NA, NA, NA, NA, NA),
decimalLatitude = c(NA, 54.1, 55.8, NA, NA, NA, NA, NA),
stringsAsFactors = FALSE)
event
## eventID parentEventID eventDate decimalLongitude decimalLatitude ## 1 cruise_1 <NA> <NA> NA NA ## 2 station_1 cruise_1 <NA> 2.9 54.1 ## 3 station_2 cruise_1 <NA> 4.7 55.8 ## 4 sample_1 station_1 2017-01-01 NA NA ## 5 sample_2 station_1 2017-01-02 NA NA ## 6 sample_3 station_2 2017-01-03 NA NA ## 7 sub_1 sample_3 <NA> NA NA ## 8 sub_2 sample_3 <NA> NA NA
Check eventID in an extension
occurrence <- data.frame(
eventID = c("sample_1","sample_1","sample_28","sample_2","sample_3","sub_1"),
scientificName = c("Abra alba", "Lanice conchilega", "Pectinaria koreni",
"Nephtys hombergii", "Pectinaria koreni", "Abra alba"),
stringsAsFactors = FALSE)
occurrence
## eventID scientificName ## 1 sample_1 Abra alba ## 2 sample_1 Lanice conchilega ## 3 sample_28 Pectinaria koreni ## 4 sample_2 Nephtys hombergii ## 5 sample_3 Pectinaria koreni ## 6 sub_1 Abra alba
Check eventID in an extension
check_extension_eventids(event, occurrence)
## field level row ## 1 eventID error 3 ## message ## 1 eventID sample_28 has no corresponding eventID in the core
Flatten event records
flatten_event() recursively adds event information from parent to child events.
event
## eventID parentEventID eventDate decimalLongitude decimalLatitude ## 1 cruise_1 <NA> <NA> NA NA ## 2 station_1 cruise_1 <NA> 2.9 54.1 ## 3 station_2 cruise_1 <NA> 4.7 55.8 ## 4 sample_1 station_1 2017-01-01 NA NA ## 5 sample_2 station_1 2017-01-02 NA NA ## 6 sample_3 station_2 2017-01-03 NA NA ## 7 sub_1 sample_3 <NA> NA NA ## 8 sub_2 sample_3 <NA> NA NA
flatten_event(event)
## eventID parentEventID eventDate decimalLongitude decimalLatitude ## 1 cruise_1 <NA> <NA> NA NA ## 2 station_1 cruise_1 <NA> 2.9 54.1 ## 3 station_2 cruise_1 <NA> 4.7 55.8 ## 4 sample_1 station_1 2017-01-01 2.9 54.1 ## 5 sample_2 station_1 2017-01-02 2.9 54.1 ## 6 sample_3 station_2 2017-01-03 4.7 55.8 ## 7 sub_1 sample_3 2017-01-03 4.7 55.8 ## 8 sub_2 sample_3 2017-01-03 4.7 55.8
Flatten occurrence and event records
flatten_occurrence() will add event information to occurrence records.
occurrence
## eventID scientificName ## 1 sample_1 Abra alba ## 2 sample_1 Lanice conchilega ## 3 sample_28 Pectinaria koreni ## 4 sample_2 Nephtys hombergii ## 5 sample_3 Pectinaria koreni ## 6 sub_1 Abra alba
occurrence[occurrence$eventID=="sample_28",] <- "sample_2" flatten_occurrence(event, occurrence)
## eventID scientificName eventDate decimalLatitude decimalLongitude ## 1 sample_1 Abra alba 2017-01-01 54.1 2.9 ## 2 sample_1 Lanice conchilega 2017-01-01 54.1 2.9 ## 3 sample_2 sample_2 2017-01-02 54.1 2.9 ## 4 sample_2 Nephtys hombergii 2017-01-02 54.1 2.9 ## 5 sample_3 Pectinaria koreni 2017-01-03 55.8 4.7 ## 6 sub_1 Abra alba 2017-01-03 55.8 4.7
Calculate centroid and radius for WKT geometries
WKT: text representation for geometries https://en.wikipedia.org/wiki/Well-known_text
POINT (30 10) LINESTRING (30 10, 10 30, 40 40) POLYGON ((30 10, 40 40, 20 40, 10 20, 30 10))
calculate_centroid() calculates a centroid and radius for WKT strings. This is useful for populating decimalLongitiude, decimalLatitude and coordinateUncertaintyInMeters.
wkt <- c( "POLYGON ((2.5378 51.1242, 2.9937 51.3203, 3.3453 51.3957, 2.2741 51.6998, 2.5378 51.1242))", "POLYGON ((3.1558 42.2356, 3.1324 42.1420, 3.2203 42.1124, 3.2601 42.2153, 3.1558 42.2356))" ) centroid <- calculate_centroid(wkt) centroid
## decimalLongitude decimalLatitude coordinateUncertaintyInMeters ## 1 2.719067 51.40717 44860.608 ## 2 3.193506 42.17714 7524.069
Centroid and radius for WKT
if(!requireNamespace("sf")){
install.packages(sf)
}
features <- sf::st_as_sfc(wkt)
map <- robis::leafletmap(centroid)
leaflet::addPolygons(map, data = features)