Last updated on 2024-12-22 13:49:12 CET.
| Package | ERROR | OK |
|---|---|---|
| BeeBDC | 2 | 11 |
Current CRAN status: ERROR: 2, OK: 11
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [33s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> requireNamespace("testthat")
Loading required namespace: testthat
> requireNamespace("BeeBDC")
Loading required namespace: BeeBDC
>
> testthat::test_check("BeeBDC")
Loading required package: BeeBDC
Loading required namespace: mgsub
Starting taxonomy report...
Nomia maneei is an accpeted name with the taxon id number 37446.
- 'Nomia maneei' has the synonyms:
Starting checklist report...
- Nomia maneei Cockerell, 1910 is reportedly found in:
United States
The output will be returned as a list with the elements: 'taxonomyReport', 'SynonymReport', and 'checklistReport'.
These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, 'output'$checklistReport, or 'output'$failedReport.
Starting taxonomy report...
Ceratina nanula Cockerell, 1897 is an accpeted name with the taxon id number 12061.
Nomia maneei is an accpeted name with the taxon id number 37446.
Bombus hypnorum is an accpeted name with the taxon id number 9667.
- 'Ceratina nanula Cockerell, 1897' has the synonyms:
- 'Nomia maneei' has the synonyms:
- 'Bombus hypnorum' has the synonyms:
Starting checklist report...
- Bombus hypnorum (Linnaeus, 1758) is reportedly found in:
Austria, Belarus, Brussels, Belize, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, Central African Republic, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, New Caledonia, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, United Kingdom, Colombia, Canada
- Bombus hypnorum (Linnaeus, 1758) is reportedly found in:
Austria, Belarus, Brussels, Belize, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, Central African Republic, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, New Caledonia, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, United Kingdom, Colombia, Canada
- Bombus hypnorum (Linnaeus, 1758) is reportedly found in:
Austria, Belarus, Brussels, Belize, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, Central African Republic, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, New Caledonia, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, United Kingdom, Colombia, Canada
The output will be returned as a list with the elements: 'taxonomyReport', 'SynonymReport', and 'checklistReport'.
These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, 'output'$checklistReport, or 'output'$failedReport.
Starting taxonomy report...
Ceratina nanula Cockerell, 1897 is an accpeted name with the taxon id number 12061.
Nomia maneei is an accpeted name with the taxon id number 37446.
Bombus hypnorum is an accpeted name with the taxon id number 9667.
- 'Ceratina nanula Cockerell, 1897' has the synonyms:
- 'Nomia maneei' has the synonyms:
- 'Bombus hypnorum' has the synonyms:
The output will be returned as a list with the elements: 'taxonomyReport' and 'SynonymReport'.
These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, or 'output'$failedReport.
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
- jbd_GBIFissues:
Flagged 5
The .GBIFflags column was added to the database.
- Formatting taxonomy for matching...
The names_clean column was not found and will be temporarily copied from scientificName
- Harmonise the occurrence data with unambiguous names...
- Attempting to harmonise the occurrence data with ambiguous names...
- Formatting merged datasets...
Removing the names_clean column...
- We matched valid names to 91 of 100 occurrence records. This leaves a total of 9 unmatched occurrence records.
harmoniseR:
9
records were flagged.
The column, '.invalidName' was added to the database.
- We updated the following columns: scientificName, species, family, subfamily, genus, subgenus, specificEpithet, infraspecificEpithet, and scientificNameAuthorship. The previous scientificName column was converted to verbatimScientificName
- Completed in 0.42 secs
- Formatting taxonomy for matching...
The names_clean column was not found and will be temporarily copied from scientificName
- Harmonise the occurrence data with unambiguous names...
- Attempting to harmonise the occurrence data with ambiguous names...
checkVerbatim = TRUE. Checking the verbatimScientificName column...
- Formatting merged datasets...
Removing the names_clean column...
- We matched valid names to 93 of 102 occurrence records. This leaves a total of 9 unmatched occurrence records.
harmoniseR:
9
records were flagged.
The column, '.invalidName' was added to the database.
- We updated the following columns: scientificName, species, family, subfamily, genus, subgenus, specificEpithet, infraspecificEpithet, and scientificNameAuthorship. The previous scientificName column was converted to verbatimScientificName
- Completed in 0.82 secs
- INITIAL match with occurrenceID only 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
- Starting iteration 1
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 2
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 3
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 4
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 5
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 6
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 7
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 8
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 9
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Updating Paige datasheet to merge...
- Updating the final datasheet with new information from Paige...
- No dates in file name(s). Finding most-recent from file save time...
- Found the following file(s):
/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//Rtmp1imbE3/19-Nov-22_USGS_DRO_flat.txt
- Reading in data file. This should not take too long.
There may be some errors upon reading in depending on the state of the data.
One might consider reporting errors to Sam Droege to improve the dataset.
Rows: 7 Columns: 35
── Column specification ────────────────────────────────────────────────────────
Delimiter: "$"
chr (22): ID., name, sex, DeterminedBy, WhoScanned, COLLECTION.db, ip, coun...
dbl (7): gmt, latitude, longitude, accuracy, elevation, position, how1
lgl (3): SpeciesNotes, days, note
dttm (1): DateEntered
date (2): DeterminedWhen, DateScanned
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
- Formatting the USGS dataset...
- Formatting the dateTime...
- Creating samplingProtocol and samplingEffort columns...
- Creating the fieldNotes and dataSource columns...
- Renaming and selecting columns...
- Checking for existing out_file directory...
- No existing,out_file directory found. Creating directory...
- Writing occurrence data file...
Number of rows (records): 7
Written to file called USGS_formatted_2024-12-22.csv at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//Rtmp1imbE3/out_file
- Writing attributes file...
Written to file called USGS_attribute_files2024-12-22.xml at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//Rtmp1imbE3/out_file
- Fin.
trying URL 'https://figshare.com/ndownloader/files/47092720'
Content type 'application/octet-stream' length 797948 bytes (779 KB)
==================================================
downloaded 779 KB
trying URL 'https://open.flinders.edu.au/ndownloader/files/47089969'
Content type 'application/octet-stream' length 1106932 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
Loading required namespace: rnaturalearthdata
Spherical geometry (s2) switched off
- Extracting continent data from points...
- Prepare the neighbouring continent dataset...
although coordinates are longitude/latitude, st_intersects assumes that they
are planar
- Compare points with the checklist...
- Combining data...
- Finished.
We have matched 74 records to their exact continent and 2 to an adjacent continent
We failed to match 3 occurrences to any 'exact' or 'neighbouring' continent
There are 21 'NA' occurrences for the .continentOutlier column.
continentOutlieRs:
Flagged 5 for continent outlier and flagged 2 for in the .sea records.
Three columns were added to the database:
1. The '.continentOutlier' column was added which is a filtering column.
2. The 'continentMatch' columns indicates exact, neighbour, or noMatch.
3. The '.sea' column was added as a filtering column for points in the ocean. The '.sea' column includes the user input buffer in its calculation.
- Completed in 2.74 secs
\coordUncerFlagR:
Flagged 3 geographically uncertain records:
The column '.uncertaintyThreshold' was added to the database.
- Using default country names and codes from https:en.wikipedia.org/wiki/ISO_3166-1_alpha-2 - static version from July 2022.
- Extracting country data from points...
- Prepare the neighbouring country dataset...
although coordinates are longitude/latitude, st_intersects assumes that they
are planar
- Compare points with the checklist...
- Combining data...
- Finished.
We have matched 72 records to their exact country and 2 to an adjacent country
We failed to match 3 occurrences to any 'exact' or 'neighbouring' country.
There are 23 'NA' occurrences for the .countryOutlier column.
countryOutlieRs:
Flagged 5 for country outlier and flagged 2 for in the .sea records.
Three columns were added to the database:
1. The '.countryOutlier' column was added which is a filtering column.
2. The 'countryMatch' columns indicates exact, neighbour, or noMatch.
3. The '.sea' column was added as a filtering column for points in the ocean. The '.sea' column includes the user input buffer in its calculation.
- Completed in 1.28 secs
Loading required namespace: emld
- Checking for existing out_file directory...
- Existing out_filedirectory found. Data will be saved here.
- We have removed empty columns. This is standard, but as an FYI, these columns are:
- Writing occurrence, attribute, and EML data file in .rds format...
Number of records: 5
Number of attribute sources: 1
The 0 eml sources are
Writing to file called BeeData_2024-12-22.rds at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//Rtmp1imbE3/out_file...
- dataSaver. Fin.
- Checking for existing out_file directory...
- Existing out_filedirectory found. Data will be saved here.
- We have removed empty columns. This is standard, but as an FYI, these columns are:
- Writing occurrence data file in csv format...
Number of rows (records): 5
Writing to file called BeeData_combined_2024-12-22.csv at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//Rtmp1imbE3/out_file...
- Writing attribute data file in csv format...
Number of rows (sources): 1
Written to file called BeeData_attributes_2024-12-22.csv at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//Rtmp1imbE3/out_file
- dataSaver. Fin.
Rows: 5 Columns: 15
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (10): catalog_number, pollinator_family, pollinator_genus, pollinator_sp...
dbl (5): collector_number, day_collected, year_collected, latitude, longitude
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 1 Columns: 11
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (11): dataSource, alternateIdentifier, title, pubDate, dateStamp, doi, d...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
- Preparing data...
- Extracting dates from year, month, day columns...
- Extracting dates from fieldNotes, locationRemarks, and verbatimEventDate columns in unambiguous ymd, dmy, mdy, and my formats...
- Extracting year from fieldNotes, locationRemarks, and verbatimEventDate columns in ambiguous formats...
- Formating and combining the new data..
- Merging all data, nearly there...
- Finished.
We now have -1 more full eventDate cells than in the input data.
We modified dates in
9 occurrences.
- As it stands, there are 9 complete eventDates and 1 missing dates.
- There are also 9 complete year occurrences to filter from. This is up from an initial count of 2 At this rate, you will stand to lose 1 occurrences on the basis of missing year - Operation time: 0.129679918289185 secs
- Preparing data...
- Extracting dates from year, month, day columns...
- Extracting dates from fieldNotes, locationRemarks, and verbatimEventDate columns in unambiguous ymd, dmy, mdy, and my formats...
- Extracting year from fieldNotes, locationRemarks, and verbatimEventDate columns in ambiguous formats...
- Formating and combining the new data..
- Merging all data, nearly there...
- Finished.
We now have 8 more full eventDate cells than in the input data.
We modified dates in
18 occurrences.
- As it stands, there are 18 complete eventDates and 1 missing dates.
- There are also 19 complete year occurrences to filter from. This is up from an initial count of 6 At this rate, you will stand to lose 0 occurrences on the basis of missing year - Operation time: 0.202357053756714 secs
Removing rounded coordinates with BeeBDC::jbd_coordinates_precision...
jbd_coordinates_precision:
Removed 5 records.
- Starting the latitude sequence...
- Starting the longitude sequence...
- Merging results and adding the .sequential column...
diagonAlley:
Flagged 17 records
The .sequential column was added to the database.
- Completed in 0.21 secs
Loading required namespace: forcats
Loading required namespace: cowplot
Loading required namespace: igraph
- Generating a basic completeness summary from the decimalLatitude, decimalLongitude, scientificName, eventDate columns.
This summary is simply the sum of complete.cases in each column. It ranges from zero to the N of columns. This will be used to sort duplicate rows and select the most-complete rows.
- Updating the .summary column to sort by...
- We will NOT flag the following columns. However, they will remain in the data file.
.gridSummary, .lonFlag, .latFlag, .uncer_terms, .uncertaintyThreshold, .unLicensed
- summaryFun:
Flagged 0
The .summary column was added to the database.
- Working on CustomComparisonsRAW duplicates...
Completed iteration 1 of 1:
- Identified 2 duplicate records and kept 1 unique records using the column(s):
catalogNumber, institutionCode, scientificName
- Working on CustomComparisons duplicates...
Completed iteration 1 of 4:
- Identified 0 duplicate records and kept 0 unique records using the column(s):
gbifID, scientificName
Completed iteration 2 of 4:
- Identified 1 duplicate records and kept 1 unique records using the column(s):
occurrenceID, scientificName
Completed iteration 3 of 4:
- Identified 0 duplicate records and kept 0 unique records using the column(s):
recordId, scientificName
Completed iteration 4 of 4:
- Identified 0 duplicate records and kept 0 unique records using the column(s):
id, scientificName
- Working on collectionInfo duplicates...
Completed iteration 1 of 2:
- Identified 0 duplicate records and kept 0 unique records using the columns:
decimalLatitude, decimalLongitude, scientificName, eventDate, recordedBy, and catalogNumber
Completed iteration 2 of 2:
- Identified 0 duplicate records and kept 0 unique records using the columns:
decimalLatitude, decimalLongitude, scientificName, eventDate, recordedBy, and otherCatalogNumbers
- Clustering duplicate pairs...
Duplicate pairs clustered. There are 3 duplicates across 2 kept duplicates.
- Ordering prefixs...
- Ordering data by 1. dataSource, 2. completeness and 3. .summary column...
- Find and FIRST duplicate to keep and assign other associated duplicates to that one (i.e., across multiple tests a 'kept duplicate', could otherwise be removed)...
- Duplicates have been saved in the file and location: /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//Rtmp1imbE3duplicateRun_collectionInfo_2024-12-22.csv
- Across the entire dataset, there are now 3 duplicates from a total of 12 occurrences.
- Completed in 0.31 secs
- No dates in file name(s). Finding most-recent from file save time...
- Found the following file(s):
/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//Rtmp1imbE3/testData.csv
\.occurrenceAbsent:
Flagged 18 absent records:
One column was added to the database.
No dataSource provided. Filling this column with NAs...
No license provided. Filling this column with NAs...
\.unLicensed:
Flagged 11 records that may NOT be used.
One column was added to the database.
- We will flag all columns starting with '.'
- summaryFun:
Flagged 77
The .summary column was added to the database.
The percentages of species impacted by each flag in your analysis are as follows:
.coordinates_empty = 23.46%
.coordinates_outOfRange = 0%
.basisOfRecords_notStandard = 1.23%
.coordinates_country_inconsistent = 1.23%
.occurrenceAbsent = 8.64%
.unLicensed = 0%
.GBIFflags = 0%
.uncer_terms = 0%
.rou = 29.63%
.val = 0%
.equ = 0%
.zer = 0%
.cap = 0%
.cen = 0%
.gbf = 0%
.inst = 0%
.sequential = 0%
.lonFlag = 0%
.latFlag = 2.47%
.gridSummary = 0%
.uncertaintyThreshold = 12.35%
.countryOutlier = 0%
.sea = 1.23%
.eventDate_empty = 13.58%
.year_outOfRange = 13.58%
.duplicates = 56.79%
- Great, R has detected some files. These files include:
/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//Rtmp1imbE3/USGS_attribute_files2023-01-27.csv
/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//Rtmp1imbE3/USGS_formatted_2023-01-27.csv - .csv export version found. Loading this file...
Warning message:
- No completeness_cols provided. Using default of: c('decimalLatitude', 'decimalLongitude', 'scientificName', and 'eventDate')
- Generating a basic completeness summary from the decimalLatitude, decimalLongitude, scientificName, eventDate columns.
This summary is simply the sum of complete.cases in each column. It ranges from zero to the N of columns. This will be used to sort duplicate rows and select the most-complete rows.
- Starting core loop...
- we matched 26 records using gbifID.
This leaves 24 unmatched data in the priorData file
- we matched 20 records using catalogNumber, institutionCode, dataSource.
This leaves 4 unmatched data in the priorData file
- we matched 4 records using occurrenceID, dataSource.
This leaves 0 unmatched data in the priorData file
- we matched 0 records using recordId, dataSource.
This leaves 0 unmatched data in the priorData file
- we matched 0 records using id.
This leaves 0 unmatched data in the priorData file
- we matched 0 records using catalogNumber, institutionCode.
This leaves 0 unmatched data in the priorData file
- Combining ids and assigning new ones where needed...
- We matched a total of 50 database_id numbers. We then assigned new database_id numbers to 49 unmatched occurrences.
Warning message:
- No completeness_cols provided. Using default of: c('decimalLatitude', 'decimalLongitude', 'scientificName', and 'eventDate')
- Generating a basic completeness summary from the decimalLatitude, decimalLongitude, scientificName, eventDate columns.
This summary is simply the sum of complete.cases in each column. It ranges from zero to the N of columns. This will be used to sort duplicate rows and select the most-complete rows.
- Starting core loop...
- we matched 26 records using gbifID.
This leaves 24 unmatched data in the priorData file
- we matched 20 records using catalogNumber, institutionCode, dataSource.
This leaves 4 unmatched data in the priorData file
- we matched 4 records using occurrenceID, dataSource.
This leaves 0 unmatched data in the priorData file
- we matched 0 records using recordId, dataSource.
This leaves 0 unmatched data in the priorData file
- we matched 0 records using id.
This leaves 0 unmatched data in the priorData file
- we matched 0 records using catalogNumber, institutionCode.
This leaves 0 unmatched data in the priorData file
- Combining ids and assigning new ones where needed...
- We matched a total of 50 database_id numbers. We then assigned new database_id numbers to 50 unmatched occurrences.
Loading required namespace: leaflet
The column .expertOutlier was not found. One will be created with all values = TRUE.
- Running chunker with:
stepSize = 50
chunkStart = 1
chunkEnd = 50
- Starting parallel operation. Unlike the serial operation (mc.cores = 1) , a parallel operation will not provide running feedback. Please be patient as this function may take some time to complete. Each chunk will be run on a seperate thread so also be aware of RAM usage.
Loading required package: rnaturalearth
- Completed in 0.57 secs
- We have updated the country names of 0 occurrences that previously had no country name assigned.
- Running chunker with:
stepSize = 50
chunkStart = 1
chunkEnd = 50
- Starting parallel operation. Unlike the serial operation (mc.cores = 1) , a parallel operation will not provide running feedback. Please be patient as this function may take some time to complete. Each chunk will be run on a seperate thread so also be aware of RAM usage.
- Completed in 0.59 secs
- We have updated the country names of 0 occurrences that previously had no country name assigned.
- Running chunker with:
stepSize = 100
chunkStart = 1
chunkEnd = 100
append = FALSE
- Starting chunk 1...
From 1 to 100
Loading required package: readr
Attaching package: 'readr'
The following objects are masked from 'package:testthat':
edition_get, local_edition
Spherical geometry (s2) switched on
Correcting latitude and longitude transposed
8 occurrences will be tested
jbd_coordinates_transposed:
Corrected 3 records.
One columns were added to the database.
- Finished chunk 1 of 1. Total records examined: 91
- Completed in 2.84 secs
Loading required package: cowplot
Loading required package: ggspatial
Loading required namespace: bdc
Check figures in /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//Rtmp1imbE3
Check figures in /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//Rtmp1imbE3
Check figures in /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//Rtmp1imbE3
- Preparing data to plot...
- Building plot...
Loading required namespace: openxlsx
A .csv data type was chosen...
Rows: 5 Columns: 15
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (10): catalog_number, pollinator_family, pollinator_genus, pollinator_sp...
dbl (5): collector_number, day_collected, year_collected, latitude, longitude
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 4 Columns: 21
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (15): family, subfamily, Tribe, genus, subgenus, Morphospecies, specific...
dbl (5): catalogNumber, decimalLatitude, decimalLongitude, coordinateUncert...
lgl (1): associatedTaxa
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 4 Columns: 24
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (20): catalogNumber, Phylum, higherClassification, Order, family, genus,...
dbl (2): decimalLatitude, decimalLongitude
lgl (2): dateIdentified, county
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 6 Columns: 41
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (30): occurence_lsid, language, basisOfRecord, catalogNumber, scientifi...
dbl (4): organismQuantity, decimalLatitude, decimalLongitude, dateIdentified
lgl (6): municipality, eventTime, fieldNumber, typeStatus, infraspecificEp...
dttm (1): modified
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 4 Columns: 91
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (27): institutionCode, collectionCode, basisOfRecord, occurrenceID, high...
dbl (12): id, taxonID, year, month, day, startDayOfYear, cultivationStatus, ...
lgl (52): ownerInstitutionCode, catalogNumber, otherCatalogNumbers, subgenus...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 4 Columns: 48
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (34): institutionCode, Collection Code, collection.var, catalogNumber, ...
dbl (10): Other Catalog Number, SampleRound, TempStart, TempEnd, WindStart,...
lgl (2): sex, subspecies
time (2): eventTime, EndTime
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .xlsx data type was chosen...
A .csv data type was chosen...
A .csv data type was chosen...
Rows: 6 Columns: 6
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (2): Collection, Species
dbl (4): ID_project, Longitude, Latitude, Year
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
- We have read in 6 occurrence records from the 'GEOLOCATE HIGH' sheet.
- We have read in 5 occurrence records from the 'BELS High' sheet.
- We have kept 6 occurrences from GeoLocate, and 5 records from BELS (11 in total). BELS was given preference over GeoLocate
A .csv data type was chosen...
A .xlsx data type was chosen...
A .xlsx data type was chosen...
A .csv data type was chosen...
Rows: 4 Columns: 91
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (32): institutionCode, collectionCode, basisOfRecord, catalogNumber, hig...
dbl (10): id, taxonID, year, month, day, startDayOfYear, localitySecurity, d...
lgl (49): ownerInstitutionCode, occurrenceID, otherCatalogNumbers, subgenus,...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 5 Columns: 18
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (13): organismName, county, stateProvince, locale, observationDate, coll...
dbl (3): individualCount, latitude, longitude
lgl (2): determiner, Notes
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .xlsx data type was chosen...
A .csv data type was chosen...
Rows: 6 Columns: 25
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (17): eventID, occurrenceID, basisOfRecord, eventDate, Kingdom, Order, F...
dbl (5): Morphospecies, individualCount, sampleSizeValue, decimalLatitude, ...
lgl (3): Species, adult, sex
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .xlsx data type was chosen...
A .csv data type was chosen...
Rows: 6 Columns: 30
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (23): basisOfRecord, recordNumber, locationID, family, subfamily, genus...
dbl (5): individualCount, decimalLatitude, decimalLongitude, elevationInMe...
lgl (1): catalogNumber
time (1): eventTime
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .xlsx data type was chosen...
A .csv data type was chosen...
Rows: 5 Columns: 36
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (22): CodeBBdatabase_curated, Scientific name corrected, Native.to.Brazi...
dbl (8): Day, Month, Year, Latitude_dec.degrees, Longitude_dec.degrees, Spc...
lgl (6): Date_precision, NotasLatLong, NotesOnLocality, Spcslink.county, Sp...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .xlsx data type was chosen...
A .csv data type was chosen...
Rows: 3 Columns: 92
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (28): institutionCode, collectionCode, collectionID, basisOfRecord, occu...
dbl (8): Catalognumber, taxonID, year, month, day, startDayOfYear, decimalL...
lgl (56): ownerInstitutionCode, catalogNumber, otherCatalogNumbers, subgenus...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 3 Columns: 19
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (15): Country, Muninciplaity, Gender, Site, Latitud, Longitude, elevatio...
lgl (4): Type, othercatalognumber, AssociatedTaxa, Citation
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .xlsx data type was chosen...
A .xlsx data type was chosen...
- We will flag all columns starting with '.'
- summaryFun:
Flagged 30
The .summary column was added to the database.
Spherical geometry (s2) switched off
- Extracting country data from points...
although coordinates are longitude/latitude, st_intersects assumes that they
are planar
although coordinates are longitude/latitude, st_intersects assumes that they
are planar
Extraction complete.
- Buffering naturalearth map by pointBuffer...
dist is assumed to be in decimal degrees (arc_degrees).
although coordinates are longitude/latitude, st_intersects assumes that they
are planar
although coordinates are longitude/latitude, st_intersects assumes that they
are planar
- Downloading taxonomy...
- taxadb save the taxonomy to: /Users/pkgbuild/Library/Application Support/org.R-project.R/R/taxadb
Removing previous flags generated with this function
- 0 duplicates found in the data.
- Cleaning complete! From an initial dataset of 196 names, there remain 196 names.
- We removed:
0 source1 accepted names,
0 source2 'accepted' names,
0 source2 synonyms internally duplicated,
0 source2 synonyms duplicated with the source1 list,
0 subsequent duplicates after merging,
- We flagged:
0 ambiguous validName,
0 ambiguous canonical_withFlags names,
4 ambiguous canonical names,
0 NON-ambiguous, but duplicated, canonical_withFlags names,
4 NON-ambiguous, but duplicated, canonical names,
- We removed:
0 ambiguous synonyms associated with accepted names.
- We re-assigned:
0 duplicated [non-duplicate] ids
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 244 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-formattedCombiner.R:69:1'): (code run outside of `test_that()`) ──
Error in `file(.)`: invalid 'description' argument
Backtrace:
▆
1. ├─BeeBDC::formattedCombiner(...) at test-formattedCombiner.R:69:1
2. │ └─... %>% xml2::read_xml()
3. ├─xml2::read_xml(.)
4. └─base::file(.)
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 244 ]
Error: Test failures
Execution halted
Flavor: r-release-macos-arm64
Version: 1.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [33s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
>
> requireNamespace("testthat")
Loading required namespace: testthat
> requireNamespace("BeeBDC")
Loading required namespace: BeeBDC
>
> testthat::test_check("BeeBDC")
Loading required package: BeeBDC
Loading required namespace: mgsub
Starting taxonomy report...
Nomia maneei is an accpeted name with the taxon id number 37446.
- 'Nomia maneei' has the synonyms:
Starting checklist report...
- Nomia maneei Cockerell, 1910 is reportedly found in:
United States
The output will be returned as a list with the elements: 'taxonomyReport', 'SynonymReport', and 'checklistReport'.
These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, 'output'$checklistReport, or 'output'$failedReport.
Starting taxonomy report...
Ceratina nanula Cockerell, 1897 is an accpeted name with the taxon id number 12061.
Nomia maneei is an accpeted name with the taxon id number 37446.
Bombus hypnorum is an accpeted name with the taxon id number 9667.
- 'Ceratina nanula Cockerell, 1897' has the synonyms:
- 'Nomia maneei' has the synonyms:
- 'Bombus hypnorum' has the synonyms:
Starting checklist report...
- Bombus hypnorum (Linnaeus, 1758) is reportedly found in:
Austria, Belarus, Brussels, Belize, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, Central African Republic, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, New Caledonia, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, United Kingdom, Colombia, Canada
- Bombus hypnorum (Linnaeus, 1758) is reportedly found in:
Austria, Belarus, Brussels, Belize, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, Central African Republic, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, New Caledonia, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, United Kingdom, Colombia, Canada
- Bombus hypnorum (Linnaeus, 1758) is reportedly found in:
Austria, Belarus, Brussels, Belize, Federation of Bosnia and Herzegovina, Bulgaria, Myanmar, Central African Republic, China, Croatia, Czech Republic, Denmark, Estonia, Finland, France, Georgia, Germany, Greece, Guernsey, Hungary, Iceland, Italy, Japan, Kazakhstan, Latvia, Liechtenstein, Lithuania, Luxembourg, Mongolia, Montenegro, Netherlands, New Caledonia, Dem. Rep. Korea, Norway, Pakistan, Poland, Romania, Russian Federation, Kosovo, Slovakia, Slovenia, Republic of Korea, Spain, Sweden, Switzerland, Ukraine, India, Nepal, Taiwan, United Kingdom, Colombia, Canada
The output will be returned as a list with the elements: 'taxonomyReport', 'SynonymReport', and 'checklistReport'.
These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, 'output'$checklistReport, or 'output'$failedReport.
Starting taxonomy report...
Ceratina nanula Cockerell, 1897 is an accpeted name with the taxon id number 12061.
Nomia maneei is an accpeted name with the taxon id number 37446.
Bombus hypnorum is an accpeted name with the taxon id number 9667.
- 'Ceratina nanula Cockerell, 1897' has the synonyms:
- 'Nomia maneei' has the synonyms:
- 'Bombus hypnorum' has the synonyms:
The output will be returned as a list with the elements: 'taxonomyReport' and 'SynonymReport'.
These can be accessed using 'output'$taxonomyReport, 'output'$SynonymReport, or 'output'$failedReport.
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
- jbd_GBIFissues:
Flagged 5
The .GBIFflags column was added to the database.
- Formatting taxonomy for matching...
The names_clean column was not found and will be temporarily copied from scientificName
- Harmonise the occurrence data with unambiguous names...
- Attempting to harmonise the occurrence data with ambiguous names...
- Formatting merged datasets...
Removing the names_clean column...
- We matched valid names to 91 of 100 occurrence records. This leaves a total of 9 unmatched occurrence records.
harmoniseR:
9
records were flagged.
The column, '.invalidName' was added to the database.
- We updated the following columns: scientificName, species, family, subfamily, genus, subgenus, specificEpithet, infraspecificEpithet, and scientificNameAuthorship. The previous scientificName column was converted to verbatimScientificName
- Completed in 0.34 secs
- Formatting taxonomy for matching...
The names_clean column was not found and will be temporarily copied from scientificName
- Harmonise the occurrence data with unambiguous names...
- Attempting to harmonise the occurrence data with ambiguous names...
checkVerbatim = TRUE. Checking the verbatimScientificName column...
- Formatting merged datasets...
Removing the names_clean column...
- We matched valid names to 93 of 102 occurrence records. This leaves a total of 9 unmatched occurrence records.
harmoniseR:
9
records were flagged.
The column, '.invalidName' was added to the database.
- We updated the following columns: scientificName, species, family, subfamily, genus, subgenus, specificEpithet, infraspecificEpithet, and scientificNameAuthorship. The previous scientificName column was converted to verbatimScientificName
- Completed in 0.63 secs
- INITIAL match with occurrenceID only 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
- Starting iteration 1
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 2
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 3
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 4
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 5
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 6
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 7
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 8
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Starting iteration 9
Matched 2 of 15 Paige occurrences.
There are 13 occurrences remaining to match.
This step has found 0 extra occurrences from the last iteration.
- Updating Paige datasheet to merge...
- Updating the final datasheet with new information from Paige...
- No dates in file name(s). Finding most-recent from file save time...
- Found the following file(s):
/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpkVoGDC/19-Nov-22_USGS_DRO_flat.txt
- Reading in data file. This should not take too long.
There may be some errors upon reading in depending on the state of the data.
One might consider reporting errors to Sam Droege to improve the dataset.
Rows: 7 Columns: 35
── Column specification ────────────────────────────────────────────────────────
Delimiter: "$"
chr (22): ID., name, sex, DeterminedBy, WhoScanned, COLLECTION.db, ip, coun...
dbl (7): gmt, latitude, longitude, accuracy, elevation, position, how1
lgl (3): SpeciesNotes, days, note
dttm (1): DateEntered
date (2): DeterminedWhen, DateScanned
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
- Formatting the USGS dataset...
- Formatting the dateTime...
- Creating samplingProtocol and samplingEffort columns...
- Creating the fieldNotes and dataSource columns...
- Renaming and selecting columns...
- Checking for existing out_file directory...
- No existing,out_file directory found. Creating directory...
- Writing occurrence data file...
Number of rows (records): 7
Written to file called USGS_formatted_2024-12-22.csv at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpkVoGDC/out_file
- Writing attributes file...
Written to file called USGS_attribute_files2024-12-22.xml at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpkVoGDC/out_file
- Fin.
trying URL 'https://figshare.com/ndownloader/files/47092720'
Content type 'application/octet-stream' length 797948 bytes (779 KB)
==================================================
downloaded 779 KB
trying URL 'https://open.flinders.edu.au/ndownloader/files/47089969'
Content type 'application/octet-stream' length 1106932 bytes (1.1 MB)
==================================================
downloaded 1.1 MB
Loading required namespace: rnaturalearthdata
Spherical geometry (s2) switched off
- Extracting continent data from points...
- Prepare the neighbouring continent dataset...
although coordinates are longitude/latitude, st_intersects assumes that they
are planar
- Compare points with the checklist...
- Combining data...
- Finished.
We have matched 74 records to their exact continent and 2 to an adjacent continent
We failed to match 3 occurrences to any 'exact' or 'neighbouring' continent
There are 21 'NA' occurrences for the .continentOutlier column.
continentOutlieRs:
Flagged 5 for continent outlier and flagged 2 for in the .sea records.
Three columns were added to the database:
1. The '.continentOutlier' column was added which is a filtering column.
2. The 'continentMatch' columns indicates exact, neighbour, or noMatch.
3. The '.sea' column was added as a filtering column for points in the ocean. The '.sea' column includes the user input buffer in its calculation.
- Completed in 2.33 secs
\coordUncerFlagR:
Flagged 3 geographically uncertain records:
The column '.uncertaintyThreshold' was added to the database.
- Using default country names and codes from https:en.wikipedia.org/wiki/ISO_3166-1_alpha-2 - static version from July 2022.
- Extracting country data from points...
- Prepare the neighbouring country dataset...
although coordinates are longitude/latitude, st_intersects assumes that they
are planar
- Compare points with the checklist...
- Combining data...
- Finished.
We have matched 72 records to their exact country and 2 to an adjacent country
We failed to match 3 occurrences to any 'exact' or 'neighbouring' country.
There are 23 'NA' occurrences for the .countryOutlier column.
countryOutlieRs:
Flagged 5 for country outlier and flagged 2 for in the .sea records.
Three columns were added to the database:
1. The '.countryOutlier' column was added which is a filtering column.
2. The 'countryMatch' columns indicates exact, neighbour, or noMatch.
3. The '.sea' column was added as a filtering column for points in the ocean. The '.sea' column includes the user input buffer in its calculation.
- Completed in 1.38 secs
Loading required namespace: emld
- Checking for existing out_file directory...
- Existing out_filedirectory found. Data will be saved here.
- We have removed empty columns. This is standard, but as an FYI, these columns are:
- Writing occurrence, attribute, and EML data file in .rds format...
Number of records: 5
Number of attribute sources: 1
The 0 eml sources are
Writing to file called BeeData_2024-12-22.rds at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpkVoGDC/out_file...
- dataSaver. Fin.
- Checking for existing out_file directory...
- Existing out_filedirectory found. Data will be saved here.
- We have removed empty columns. This is standard, but as an FYI, these columns are:
- Writing occurrence data file in csv format...
Number of rows (records): 5
Writing to file called BeeData_combined_2024-12-22.csv at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpkVoGDC/out_file...
- Writing attribute data file in csv format...
Number of rows (sources): 1
Written to file called BeeData_attributes_2024-12-22.csv at location /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpkVoGDC/out_file
- dataSaver. Fin.
Rows: 5 Columns: 15
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (10): catalog_number, pollinator_family, pollinator_genus, pollinator_sp...
dbl (5): collector_number, day_collected, year_collected, latitude, longitude
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 1 Columns: 11
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (11): dataSource, alternateIdentifier, title, pubDate, dateStamp, doi, d...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
- Preparing data...
- Extracting dates from year, month, day columns...
- Extracting dates from fieldNotes, locationRemarks, and verbatimEventDate columns in unambiguous ymd, dmy, mdy, and my formats...
- Extracting year from fieldNotes, locationRemarks, and verbatimEventDate columns in ambiguous formats...
- Formating and combining the new data..
- Merging all data, nearly there...
- Finished.
We now have -1 more full eventDate cells than in the input data.
We modified dates in
9 occurrences.
- As it stands, there are 9 complete eventDates and 1 missing dates.
- There are also 9 complete year occurrences to filter from. This is up from an initial count of 2 At this rate, you will stand to lose 1 occurrences on the basis of missing year - Operation time: 0.166344165802002 secs
- Preparing data...
- Extracting dates from year, month, day columns...
- Extracting dates from fieldNotes, locationRemarks, and verbatimEventDate columns in unambiguous ymd, dmy, mdy, and my formats...
- Extracting year from fieldNotes, locationRemarks, and verbatimEventDate columns in ambiguous formats...
- Formating and combining the new data..
- Merging all data, nearly there...
- Finished.
We now have 8 more full eventDate cells than in the input data.
We modified dates in
18 occurrences.
- As it stands, there are 18 complete eventDates and 1 missing dates.
- There are also 19 complete year occurrences to filter from. This is up from an initial count of 6 At this rate, you will stand to lose 0 occurrences on the basis of missing year - Operation time: 0.164690017700195 secs
Removing rounded coordinates with BeeBDC::jbd_coordinates_precision...
jbd_coordinates_precision:
Removed 5 records.
- Starting the latitude sequence...
- Starting the longitude sequence...
- Merging results and adding the .sequential column...
diagonAlley:
Flagged 17 records
The .sequential column was added to the database.
- Completed in 0.15 secs
Loading required namespace: forcats
Loading required namespace: cowplot
Loading required namespace: igraph
- Generating a basic completeness summary from the decimalLatitude, decimalLongitude, scientificName, eventDate columns.
This summary is simply the sum of complete.cases in each column. It ranges from zero to the N of columns. This will be used to sort duplicate rows and select the most-complete rows.
- Updating the .summary column to sort by...
- We will NOT flag the following columns. However, they will remain in the data file.
.gridSummary, .lonFlag, .latFlag, .uncer_terms, .uncertaintyThreshold, .unLicensed
- summaryFun:
Flagged 0
The .summary column was added to the database.
- Working on CustomComparisonsRAW duplicates...
Completed iteration 1 of 1:
- Identified 2 duplicate records and kept 1 unique records using the column(s):
catalogNumber, institutionCode, scientificName
- Working on CustomComparisons duplicates...
Completed iteration 1 of 4:
- Identified 0 duplicate records and kept 0 unique records using the column(s):
gbifID, scientificName
Completed iteration 2 of 4:
- Identified 1 duplicate records and kept 1 unique records using the column(s):
occurrenceID, scientificName
Completed iteration 3 of 4:
- Identified 0 duplicate records and kept 0 unique records using the column(s):
recordId, scientificName
Completed iteration 4 of 4:
- Identified 0 duplicate records and kept 0 unique records using the column(s):
id, scientificName
- Working on collectionInfo duplicates...
Completed iteration 1 of 2:
- Identified 0 duplicate records and kept 0 unique records using the columns:
decimalLatitude, decimalLongitude, scientificName, eventDate, recordedBy, and catalogNumber
Completed iteration 2 of 2:
- Identified 0 duplicate records and kept 0 unique records using the columns:
decimalLatitude, decimalLongitude, scientificName, eventDate, recordedBy, and otherCatalogNumbers
- Clustering duplicate pairs...
Duplicate pairs clustered. There are 3 duplicates across 2 kept duplicates.
- Ordering prefixs...
- Ordering data by 1. dataSource, 2. completeness and 3. .summary column...
- Find and FIRST duplicate to keep and assign other associated duplicates to that one (i.e., across multiple tests a 'kept duplicate', could otherwise be removed)...
- Duplicates have been saved in the file and location: /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpkVoGDCduplicateRun_collectionInfo_2024-12-22.csv
- Across the entire dataset, there are now 3 duplicates from a total of 12 occurrences.
- Completed in 0.23 secs
- No dates in file name(s). Finding most-recent from file save time...
- Found the following file(s):
/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpkVoGDC/testData.csv
\.occurrenceAbsent:
Flagged 18 absent records:
One column was added to the database.
No dataSource provided. Filling this column with NAs...
No license provided. Filling this column with NAs...
\.unLicensed:
Flagged 11 records that may NOT be used.
One column was added to the database.
- We will flag all columns starting with '.'
- summaryFun:
Flagged 77
The .summary column was added to the database.
The percentages of species impacted by each flag in your analysis are as follows:
.coordinates_empty = 23.46%
.coordinates_outOfRange = 0%
.basisOfRecords_notStandard = 1.23%
.coordinates_country_inconsistent = 1.23%
.occurrenceAbsent = 8.64%
.unLicensed = 0%
.GBIFflags = 0%
.uncer_terms = 0%
.rou = 29.63%
.val = 0%
.equ = 0%
.zer = 0%
.cap = 0%
.cen = 0%
.gbf = 0%
.inst = 0%
.sequential = 0%
.lonFlag = 0%
.latFlag = 2.47%
.gridSummary = 0%
.uncertaintyThreshold = 12.35%
.countryOutlier = 0%
.sea = 1.23%
.eventDate_empty = 13.58%
.year_outOfRange = 13.58%
.duplicates = 56.79%
- Great, R has detected some files. These files include:
/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpkVoGDC/USGS_attribute_files2023-01-27.csv
/var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpkVoGDC/USGS_formatted_2023-01-27.csv - .csv export version found. Loading this file...
Warning message:
- No completeness_cols provided. Using default of: c('decimalLatitude', 'decimalLongitude', 'scientificName', and 'eventDate')
- Generating a basic completeness summary from the decimalLatitude, decimalLongitude, scientificName, eventDate columns.
This summary is simply the sum of complete.cases in each column. It ranges from zero to the N of columns. This will be used to sort duplicate rows and select the most-complete rows.
- Starting core loop...
- we matched 26 records using gbifID.
This leaves 24 unmatched data in the priorData file
- we matched 20 records using catalogNumber, institutionCode, dataSource.
This leaves 4 unmatched data in the priorData file
- we matched 4 records using occurrenceID, dataSource.
This leaves 0 unmatched data in the priorData file
- we matched 0 records using recordId, dataSource.
This leaves 0 unmatched data in the priorData file
- we matched 0 records using id.
This leaves 0 unmatched data in the priorData file
- we matched 0 records using catalogNumber, institutionCode.
This leaves 0 unmatched data in the priorData file
- Combining ids and assigning new ones where needed...
- We matched a total of 50 database_id numbers. We then assigned new database_id numbers to 49 unmatched occurrences.
Warning message:
- No completeness_cols provided. Using default of: c('decimalLatitude', 'decimalLongitude', 'scientificName', and 'eventDate')
- Generating a basic completeness summary from the decimalLatitude, decimalLongitude, scientificName, eventDate columns.
This summary is simply the sum of complete.cases in each column. It ranges from zero to the N of columns. This will be used to sort duplicate rows and select the most-complete rows.
- Starting core loop...
- we matched 26 records using gbifID.
This leaves 24 unmatched data in the priorData file
- we matched 20 records using catalogNumber, institutionCode, dataSource.
This leaves 4 unmatched data in the priorData file
- we matched 4 records using occurrenceID, dataSource.
This leaves 0 unmatched data in the priorData file
- we matched 0 records using recordId, dataSource.
This leaves 0 unmatched data in the priorData file
- we matched 0 records using id.
This leaves 0 unmatched data in the priorData file
- we matched 0 records using catalogNumber, institutionCode.
This leaves 0 unmatched data in the priorData file
- Combining ids and assigning new ones where needed...
- We matched a total of 50 database_id numbers. We then assigned new database_id numbers to 50 unmatched occurrences.
Loading required namespace: leaflet
The column .expertOutlier was not found. One will be created with all values = TRUE.
- Running chunker with:
stepSize = 50
chunkStart = 1
chunkEnd = 50
- Starting parallel operation. Unlike the serial operation (mc.cores = 1) , a parallel operation will not provide running feedback. Please be patient as this function may take some time to complete. Each chunk will be run on a seperate thread so also be aware of RAM usage.
Loading required package: rnaturalearth
- Completed in 0.69 secs
- We have updated the country names of 0 occurrences that previously had no country name assigned.
- Running chunker with:
stepSize = 50
chunkStart = 1
chunkEnd = 50
- Starting parallel operation. Unlike the serial operation (mc.cores = 1) , a parallel operation will not provide running feedback. Please be patient as this function may take some time to complete. Each chunk will be run on a seperate thread so also be aware of RAM usage.
- Completed in 0.68 secs
- We have updated the country names of 0 occurrences that previously had no country name assigned.
- Running chunker with:
stepSize = 100
chunkStart = 1
chunkEnd = 100
append = FALSE
- Starting chunk 1...
From 1 to 100
Loading required package: readr
Attaching package: 'readr'
The following objects are masked from 'package:testthat':
edition_get, local_edition
Spherical geometry (s2) switched on
Correcting latitude and longitude transposed
8 occurrences will be tested
jbd_coordinates_transposed:
Corrected 3 records.
One columns were added to the database.
- Finished chunk 1 of 1. Total records examined: 91
- Completed in 2.93 secs
Loading required package: cowplot
Loading required package: ggspatial
Loading required namespace: bdc
Check figures in /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpkVoGDC
Check figures in /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpkVoGDC
Check figures in /var/folders/k4/0jwzxmln0nb8y6rkzprptb640000gq/T//RtmpkVoGDC
- Preparing data to plot...
- Building plot...
Loading required namespace: openxlsx
A .csv data type was chosen...
Rows: 5 Columns: 15
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (10): catalog_number, pollinator_family, pollinator_genus, pollinator_sp...
dbl (5): collector_number, day_collected, year_collected, latitude, longitude
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 4 Columns: 21
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (15): family, subfamily, Tribe, genus, subgenus, Morphospecies, specific...
dbl (5): catalogNumber, decimalLatitude, decimalLongitude, coordinateUncert...
lgl (1): associatedTaxa
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 4 Columns: 24
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (20): catalogNumber, Phylum, higherClassification, Order, family, genus,...
dbl (2): decimalLatitude, decimalLongitude
lgl (2): dateIdentified, county
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 6 Columns: 41
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (30): occurence_lsid, language, basisOfRecord, catalogNumber, scientifi...
dbl (4): organismQuantity, decimalLatitude, decimalLongitude, dateIdentified
lgl (6): municipality, eventTime, fieldNumber, typeStatus, infraspecificEp...
dttm (1): modified
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 4 Columns: 91
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (27): institutionCode, collectionCode, basisOfRecord, occurrenceID, high...
dbl (12): id, taxonID, year, month, day, startDayOfYear, cultivationStatus, ...
lgl (52): ownerInstitutionCode, catalogNumber, otherCatalogNumbers, subgenus...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 4 Columns: 48
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (34): institutionCode, Collection Code, collection.var, catalogNumber, ...
dbl (10): Other Catalog Number, SampleRound, TempStart, TempEnd, WindStart,...
lgl (2): sex, subspecies
time (2): eventTime, EndTime
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .xlsx data type was chosen...
A .csv data type was chosen...
A .csv data type was chosen...
Rows: 6 Columns: 6
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (2): Collection, Species
dbl (4): ID_project, Longitude, Latitude, Year
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
- We have read in 6 occurrence records from the 'GEOLOCATE HIGH' sheet.
- We have read in 5 occurrence records from the 'BELS High' sheet.
- We have kept 6 occurrences from GeoLocate, and 5 records from BELS (11 in total). BELS was given preference over GeoLocate
A .csv data type was chosen...
A .xlsx data type was chosen...
A .xlsx data type was chosen...
A .csv data type was chosen...
Rows: 4 Columns: 91
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (32): institutionCode, collectionCode, basisOfRecord, catalogNumber, hig...
dbl (10): id, taxonID, year, month, day, startDayOfYear, localitySecurity, d...
lgl (49): ownerInstitutionCode, occurrenceID, otherCatalogNumbers, subgenus,...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 5 Columns: 18
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (13): organismName, county, stateProvince, locale, observationDate, coll...
dbl (3): individualCount, latitude, longitude
lgl (2): determiner, Notes
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .xlsx data type was chosen...
A .csv data type was chosen...
Rows: 6 Columns: 25
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (17): eventID, occurrenceID, basisOfRecord, eventDate, Kingdom, Order, F...
dbl (5): Morphospecies, individualCount, sampleSizeValue, decimalLatitude, ...
lgl (3): Species, adult, sex
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .xlsx data type was chosen...
A .csv data type was chosen...
Rows: 6 Columns: 30
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (23): basisOfRecord, recordNumber, locationID, family, subfamily, genus...
dbl (5): individualCount, decimalLatitude, decimalLongitude, elevationInMe...
lgl (1): catalogNumber
time (1): eventTime
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .xlsx data type was chosen...
A .csv data type was chosen...
Rows: 5 Columns: 36
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (22): CodeBBdatabase_curated, Scientific name corrected, Native.to.Brazi...
dbl (8): Day, Month, Year, Latitude_dec.degrees, Longitude_dec.degrees, Spc...
lgl (6): Date_precision, NotasLatLong, NotesOnLocality, Spcslink.county, Sp...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .xlsx data type was chosen...
A .csv data type was chosen...
Rows: 3 Columns: 92
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (28): institutionCode, collectionCode, collectionID, basisOfRecord, occu...
dbl (8): Catalognumber, taxonID, year, month, day, startDayOfYear, decimalL...
lgl (56): ownerInstitutionCode, catalogNumber, otherCatalogNumbers, subgenus...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .csv data type was chosen...
Rows: 3 Columns: 19
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (15): Country, Muninciplaity, Gender, Site, Latitud, Longitude, elevatio...
lgl (4): Type, othercatalognumber, AssociatedTaxa, Citation
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
A .xlsx data type was chosen...
A .xlsx data type was chosen...
- We will flag all columns starting with '.'
- summaryFun:
Flagged 30
The .summary column was added to the database.
Spherical geometry (s2) switched off
- Extracting country data from points...
although coordinates are longitude/latitude, st_intersects assumes that they
are planar
although coordinates are longitude/latitude, st_intersects assumes that they
are planar
Extraction complete.
- Buffering naturalearth map by pointBuffer...
dist is assumed to be in decimal degrees (arc_degrees).
although coordinates are longitude/latitude, st_intersects assumes that they
are planar
although coordinates are longitude/latitude, st_intersects assumes that they
are planar
- Downloading taxonomy...
- taxadb save the taxonomy to: /Users/pkgbuild/Library/Application Support/org.R-project.R/R/taxadb
Removing previous flags generated with this function
- 0 duplicates found in the data.
- Cleaning complete! From an initial dataset of 196 names, there remain 196 names.
- We removed:
0 source1 accepted names,
0 source2 'accepted' names,
0 source2 synonyms internally duplicated,
0 source2 synonyms duplicated with the source1 list,
0 subsequent duplicates after merging,
- We flagged:
0 ambiguous validName,
0 ambiguous canonical_withFlags names,
4 ambiguous canonical names,
0 NON-ambiguous, but duplicated, canonical_withFlags names,
4 NON-ambiguous, but duplicated, canonical names,
- We removed:
0 ambiguous synonyms associated with accepted names.
- We re-assigned:
0 duplicated [non-duplicate] ids
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 244 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-formattedCombiner.R:69:1'): (code run outside of `test_that()`) ──
Error in `file(.)`: invalid 'description' argument
Backtrace:
▆
1. ├─BeeBDC::formattedCombiner(...) at test-formattedCombiner.R:69:1
2. │ └─... %>% xml2::read_xml()
3. ├─xml2::read_xml(.)
4. └─base::file(.)
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 244 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-macos-arm64
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