Updates the entire metadata for receivers and tags from Motus server.
Contrary to tagme(), this function retrieves the entire set of metadata for
tags and receivers, and not only those pertinent to the detections in your
local file.
Arguments
- src
SQLite connection. Result of
tagme(XXX)orDBI::dbConnect(RSQLite::SQLite(), "XXX.motus").- projectIDs
optional integer vector of Motus projects IDs for which metadata should be obtained; default: NULL, meaning obtain metadata for all tags and receivers that your permissions allow.
- replace
logical scalar; if TRUE (default), existing data replace the existing metadata with the newly acquired ones.
- delete
logical scalar; Default = FALSE. if TRUE, the entire metadata tables are cleared (for all projects) before re-importing the metadata.
See also
tagme() provides an option to update only the metadata
relevant to a specific project or receiver file.
Examples
# Download sample project 176 to .motus database (username/password are "motus.sample")
if (FALSE) sql_motus <- tagme(176, new = TRUE)
# Or use example data base in memory
sql_motus <- tagmeSample()
# Add extended metadata to your file
if (FALSE) metadata(sql_motus)
# Access different metadata tables
library(dplyr)
tbl(sql_motus, "species")
#> # Source: table<`species`> [10 x 6]
#> # Database: sqlite 3.45.2 [:memory:]
#> id english french scientific group sort
#> <int> <chr> <chr> <chr> <chr> <int>
#> 1 4180 Semipalmated Plover Pluvier semipalmé Charadriu… BIRDS NA
#> 2 4670 Red Knot Bécasseau maubèche Calidris … BIRDS NA
#> 3 4680 Sanderling Bécasseau sanderling Calidris … BIRDS NA
#> 4 4690 Semipalmated Sandpiper Bécasseau semipalmé Calidris … BIRDS NA
#> 5 4760 White-rumped Sandpiper Bécasseau à croupion bla… Calidris … BIRDS NA
#> 6 4780 Pectoral Sandpiper Bécasseau à poitrine cen… Calidris … BIRDS NA
#> 7 4820 Dunlin Bécasseau variable Calidris … BIRDS NA
#> 8 4980 American Woodcock Bécasse d'Amérique Scolopax … BIRDS NA
#> 9 15560 Gray-cheeked Thrush Grive à joues grises Catharus … BIRDS NA
#> 10 19050 White-crowned Sparrow Bruant à couronne blanche Zonotrich… BIRDS NA
tbl(sql_motus, "projs")
#> # Source: table<`projs`> [5 x 5]
#> # Database: sqlite 3.45.2 [:memory:]
#> id name label tagsPermissions sensorsPermissions
#> <int> <chr> <chr> <int> <int>
#> 1 47 Red Knot staging and migration… Niles NA NA
#> 2 57 Selva Colombia Selva NA NA
#> 3 82 Maine - American Woodcock RBro… NA NA
#> 4 146 Neonicotinoid insecticides and… NEON… NA NA
#> 5 176 Sample Data Samp… NA NA
tbl(sql_motus, "tagDeps")
#> # Source: table<`tagDeps`> [?? x 24]
#> # Database: sqlite 3.45.2 [:memory:]
#> tagID deployID projectID tsStart tsEnd deferSec speciesID markerType
#> <int> <int> <int> <dbl> <dbl> <dbl> <int> <chr>
#> 1 10811 1077 47 1414479600 1438585200 0 4670 metal band
#> 2 16011 1798 176 1438515600 1450352400 0 4690 metal band
#> 3 17357 1818 176 1439277600 1451114400 0 4760 metal band
#> 4 16035 1823 176 1439371200 1451208000 0 4690 metal band
#> 5 16036 1824 176 1439371200 1451208000 0 4690 metal band
#> 6 16037 1825 176 1439807400 1451644200 0 4690 metal band
#> 7 16038 1826 176 1439807400 1451644200 0 4690 metal band
#> 8 16039 1827 176 1439804400 1451641200 0 4690 metal band
#> 9 16044 1832 176 1439362800 1451199600 0 4760 metal band
#> 10 16047 1839 176 1441908000 1457632800 0 4670 metal band
#> # ℹ more rows
#> # ℹ 16 more variables: markerNumber <chr>, sex <chr>, age <chr>,
#> # latitude <dbl>, longitude <dbl>, elevation <dbl>, comments <chr>,
#> # test <int>, attachment <chr>, tsStartCode <chr>, tsEndCode <chr>,
#> # bandNumber <chr>, id <int>, bi <int>, fullID <chr>, status <chr>
# Etc.