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Tools for data enhancement and quality control

Home Page: https://iobis.github.io/obistools

License: Other

R 100.00%

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obistools's Issues

check records against known OBIS distributions

Either fetch full distribution or check for records in box around given coordinates.

taxon matching: show input name

Error in completing the function in R Studio

Just writing the function in the RStudio console and after the underscore (autocompletion is trying to guess the command) a small window appears with the message "R code Execution Error". None of the functions of the obistools are working after a fresh install

check fossil taxa

check if eventDate value in future

flatten event and occurrence records

offline taxon matching

tree structure issue

This dataset should have 18 occurrences and thousands of Location events.

require(finch)
require(obistools)

archive <- dwca_read("http://arobis.cenpat-conicet.gob.ar:8081/archive.do?r=mleonina_adufem&v=1.0", read = TRUE, na.strings = "")
event <- archive$data$event.txt
occurrence <- archive$data$occurrence.txt
emof <- archive$data$extendedmeasurementorfact.txt
emof$eventID <- emof$id

flat <- flatten_occurrence(event, occurrence)
plot_map_leaflet(flat)

tree <- treeStructure(event, occurrence, emof)
exportTree(tree, "tree.html")

check_depth() problem

aa <- robis::occurrence("Abra alba")
check_depth(aa)

Retrieved 39657 records of 39657 (100%)
 Error in lookup_xy(data, shoredistance = TRUE, areas = FALSE) : 
  7b227469746c65223a20224572726f72206c6f6f6b696e67207570206461746120666f722070726f766964656420706f696e7473222c20226465736372697074696f6e223a2022696e6465782039343830206973206f7574206f6620626f756e647320666f722061786973203120776974682073697a652039343830227d

tree structure: issue warning for empty strings in identifier fields

check ISO 8601 dates

generate DwC-A

check points on land

add bottom depth

taxon matching: document y/n/p

Add option for eventid column name

incorrect hyperbenthos tree

See number of cruise records.

 ### Level 1 ###
     event type:  ###
     example: 
     measurement types: 
     records: 
   ### Level 2 ###
       event type:  ###
       example: Cruise68
       measurement types: Platform Name
       records: 1
     ### Level 3 ###
         event type:  ###
         example: Cruise6:Station19:EventSorbeSledge910:Subsample69
         measurement types:  
         records: 124
       ### Level 4 ###
           event type:  ###
           example: Cruise6:Station19:EventSorbeSledge910
           measurement types: Sampling device, Sieve mesh size
           records: 112
         ### Level 5 ###
             event type:  ###
             example: Cruise6:Station19:EventSorbeSledge910:Subsample69
             measurement types:  
             records: 242
       ### Level 4 ###
           event type:  ###
           example: Cruise68:Station622:EventBowers-Connell10020
           measurement types: Grain-size mean in sediment by particle sizer, Grain-size median in sediment by particle sizer, Percentage of the volume of the sediment with a grainsize between 0 µm and 63 µm, Percentage of the volume of the sediment with a grainsize between 125 µm and 250 µm, Percentage of the volume of the sediment with a grainsize between 250 µm and 500 µm, Percentage of the volume of the sediment with a grainsize between 500 µm and 900 µm, Percentage of the volume of the sediment with a grainsize between 63 µm and 125 µm, Sampling device
           records: 86
       ### Level 4 ###
           event type:  ###
           example: Cruise68:Station622:EventSea-Bird SBE21_10019
           measurement types: Salinity, Sampling device, water temperature
           records: 93
       ### Level 4 ###
           event type:  ###
           example: Cruise65:Station560:EventSea-Bird SBE09_9767
           measurement types: Dissolved oxygen, Salinity, Sampling device, water temperature
           records: 5
       ### Level 4 ###
           event type:  ###
           example: Cruise68:Station622:EventSecchi disc_10021
           measurement types: Sampling device, Secchi depth
           records: 62

fix dependencies

Including rgeos::readWKT.

depth check issue

What's up with point 5? Should be ok?

library(obistools)
library(robis)

pol <- occurrence("Polychaeta", geometry = "POLYGON ((6.50391 54.59753, 6.45996 53.14677, 8.26172 53.17312, 8.08594 54.54658, 6.50391 54.59753))")
problems <- check_depth(pol[1:1500,], depthmargin = 10)
bathymetry <- lookup_xy(problems, shoredistance = FALSE, grids = TRUE, areas = FALSE)$bathymetry

rbind(
  problems$minimumDepthInMeters,
  problems$maximumDepthInMeters,
  problems$depth,
  bathymetry
)

            [,1] [,2] [,3] [,4] [,5] [,6]
           448.0   51   73  159 18.1 19.0
           448.0   51   73  159 15.1 19.0
           448.0   51   73  159 16.6 19.0
bathymetry  12.2    5   11   17 18.4  1.4

dataset tree only event core and occurrence extension

enable building dataset tree when no (e)MoF is available. e.g. http://ipt.ala.org.au/archive.do?r=global

online taxon matching

Provide offline version as well if supported by WoRMS.

convert eventDate from and to UTC or local time

check parentEventIDs

support scientific name labels on Leaflet map

open tree in browser

browseURL

generate ISO 8601 dates

check foreign keys between core and extensions

Better check_depth/check_onland output

Related to the output from check_depth/check_onland I would propose two changes:

remove the report=true parameter and always return both the dataframe and the report in a list with two elements: "problems" and "report"
in the report add 4 additional columns: lon, lat, value, comparison_value (= name to be discussed)

These changes would allow two things:

prevent running the xylookup twice with the same data
new inspection functions and plotting functions e.g. plot the difference between bathymetry and the depth values on a map

calculate distance to coast

OBIS env to GBIF Event data transformation script

Just a thought. Do you think this is possible?
A GBIF event data to OBIS-env script seems much more difficult to me.

typo in check_depth documentation

Hey,

When I ?check_depth (obistools v 0.0.4), the documentation says

Check which points are located on land.

Description

Check which points are located on land.

Usage

check_depth(data, depthmargin = 0, shoremargin = NA, report = FALSE)

check date value, not just format

1948-03/50

calculate_centroid needs rgeos

the rgeos package is needed for readWKT and other rgeos functions, but it is not loaded by default.

flatten out measurements or facts

Add an function to create a single flat table with measurementsorfacts present as columns pasted to the event/occurrence.
Column header should be measurementtype or preferable concatenation of measurementtype and measurementunit.

Reason: scientist are likely to need data in a single matrix form for their analyses.

event tree HTML output

match_taxa output: includes original names

The output of the function match_taxa should include the original names and the same order of the vector of names submitted.

HTML data quality report

check_depth: add option to provide additional bathymetry layers

enter LSID manually during taxonmatching

check required fields

depth check issue

library(robis)
library(obistools)

pol <- occurrence("Polychaeta", geometry = "POLYGON ((6.50391 54.59753, 6.45996 53.14677, 8.26172 53.17312, 8.08594 54.54658, 6.50391 54.59753))")
problems <- check_depth(pol)

Error in data.frame(field = column, level = "error", row = i, message = message,  : 
  arguments imply differing number of rows: 2, 1, 3

map fields to Darwin Core

xylookup fails

library(robis)
library(obistools)

calfin <- occurrence("Calanus finmarchicus", fields = c("decimalLongitude", "decimalLatitude"))
lookup_xy(calfin, shoredistance = FALSE, grids = TRUE, areas = FALSE)

Error in lookup_xy(calfin[1:2e+05, ], shoredistance = FALSE, grids = TRUE,  : 
  3c68746d6c3e0d0a3c686561643e3c7469746c653e343133205265717565737420456e7469747920546f6f204c617267653c2f7469746c653e3c2f686561643e0d0a3c626f6479206267636f6c6f723d227768697465223e0d0a3c63656e7465723e3c68313e343133205265717565737420456e7469747920546f6f204c617267653c2f68313e3c2f63656e7465723e0d0a3c68723e3c63656e7465723e6e67696e782f312e31302e3320285562756e7475293c2f63656e7465723e0d0a3c2f626f64793e0d0a3c2f68746d6c3e0d0a

fix xylookup endpoint in tests

https://github.com/iobis/obistools/blob/master/tests/testthat/test_check_onland.R#L6

Unless there's a good reason?

fix crosstalk warnings

Warning: replacing previous import by ‘stringr::%>%’ when loading ‘data.tree’
Warning: replacing previous import by ‘tidyr::%>%’ when loading ‘obistools’
Warning: replacing previous import by ‘shiny::validateCssUnit’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::br’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::tags’ when loading ‘crosstalk’
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Warning: replacing previous import by ‘shiny::h5’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::h6’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::knit_print.html’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::tagSetChildren’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::includeScript’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::em’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::tagAppendChild’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::is.singleton’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::includeHTML’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::includeMarkdown’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::code’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::tagList’ when loading ‘crosstalk’
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Warning: replacing previous import by ‘shiny::tagAppendAttributes’ when loading ‘crosstalk’
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Warning: replacing previous import by ‘shiny::hr’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::p’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::suppressDependencies’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::tagAppendChildren’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::includeText’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::pre’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::span’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::withTags’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::htmlTemplate’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::img’ when loading ‘crosstalk’
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Warning: replacing previous import by ‘shiny::includeCSS’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::knit_print.shiny.tag’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::knit_print.shiny.tag.list’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::strong’ when loading ‘crosstalk’
Warning: replacing previous import by ‘shiny::HTML’ when loading ‘crosstalk’

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obistools's Issues

Check which points are located on land.

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