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v04_metadata.html
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v04_metadata.html
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<main id="main"><div class="page-header">
<img src="../logo.png" class="logo" alt=""><h1>Metadata</h1>
<h4 data-toc-skip class="author">William K. Morris</h4>
<small class="dont-index">Source: <a href="https://github.com/luomus/finbif/blob/HEAD/vignettes/v04_metadata.Rmd" class="external-link"><code>vignettes/v04_metadata.Rmd</code></a></small>
<div class="d-none name"><code>v04_metadata.Rmd</code></div>
</div>
<p>Much of the information in the FinBIF database consists of metadata that helps provide context for occurrence records and other information in FinBIF.</p>
<div class="section level2">
<h2 id="general-metadata">General metadata<a class="anchor" aria-label="anchor" href="#general-metadata"></a>
</h2>
<p>You can see some of the metadata available in <a href="https://github.com/luomus/finbif" class="external-link">finbif</a> by calling the <code>finbif_metadata</code> function without any arguments.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/finbif_metadata.html">finbif_metadata</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<details closed><summary>
Click to show/hide output.
</summary><div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co">#> metadata_name </span>
<span class="co">#> 1 admin_status </span>
<span class="co">#> 2 red_list </span>
<span class="co">#> 3 country </span>
<span class="co">#> 4 province </span>
<span class="co">#> 5 municipality </span>
<span class="co">#> 6 bird_assoc_area </span>
<span class="co">#> 7 finnish_occurrence_status</span>
<span class="co">#> 8 habitat_type </span>
<span class="co">#> 9 habitat_qualifier </span>
<span class="co">#> 10 life_stage </span>
<span class="co">#> 11 record_basis </span>
<span class="co">#> 12 restriction_level </span>
<span class="co">#> 13 restriction_reason </span>
<span class="co">#> 14 sex_category </span>
<span class="co">#> 15 source </span>
<span class="co">#> 16 taxon_rank </span></code></pre></div>
</details><p><br></p>
<p>Calling <code><a href="../reference/finbif_metadata.html">finbif_metadata()</a></code> and specifying one of the metadata categories will display a <code>data.frame</code> with the requested metadata.</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/finbif_metadata.html">finbif_metadata</a></span><span class="op">(</span><span class="st">"red_list"</span><span class="op">)</span></code></pre></div>
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<code class="sourceCode R">
<span class="co">#> status_name status_code</span>
<span class="co">#> 1 Critically Endangered CR </span>
<span class="co">#> 2 Data Deficient DD </span>
<span class="co">#> 3 Endangered EN </span>
<span class="co">#> 4 Extinct EX </span>
<span class="co">#> 5 Extinct in the Wild EW </span>
<span class="co">#> 6 Least Concern LC </span>
<span class="co">#> 7 Near Threatened NT </span>
<span class="co">#> 8 Not Applicable NA </span>
<span class="co">#> 9 Not Evaluated NE </span>
<span class="co">#> 10 Regionally Extinct RE </span>
<span class="co">#> 11 Vulnerable VU </span></code></pre></div>
</details><p><br></p>
</div>
<div class="section level2">
<h2 id="special-cases">Special cases<a class="anchor" aria-label="anchor" href="#special-cases"></a>
</h2>
<p>Some more complex metadata is accessed with other <a href="https://github.com/luomus/finbif" class="external-link">finbif</a> functions</p>
<div class="section level3">
<h3 id="informal-groups">Informal groups<a class="anchor" aria-label="anchor" href="#informal-groups"></a>
</h3>
<p>Informal taxonomic groups and their relationships can be displayed with <code><a href="../reference/finbif_informal_groups.html">finbif_informal_groups()</a></code></p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/finbif_informal_groups.html">finbif_informal_groups</a></span><span class="op">(</span>limit <span class="op">=</span> <span class="fl">6</span><span class="op">)</span></code></pre></div>
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<code class="sourceCode R">
<span class="co">#> [1] "Algae" </span>
<span class="co">#> [2] "Macro algae" </span>
<span class="co">#> [3] "Brown algae and yellow green algae" </span>
<span class="co">#> [4] "Green algae" </span>
<span class="co">#> [5] "Red algae" </span>
<span class="co">#> [6] "Stoneworts" </span>
<span class="co">#> [7] "Birds" </span>
<span class="co">#> [8] "Birds of prey and owls" </span>
<span class="co">#> [9] "Birds of prey" </span>
<span class="co">#> [10] "Owls" </span>
<span class="co">#> [11] "Bryophytes" </span>
<span class="co">#> [12] "Hornworts" </span>
<span class="co">#> [13] "Liverworts" </span>
<span class="co">#> [14] "Mosses" </span>
<span class="co">#> [15] "Crustaceans" </span>
<span class="co">#> [16] "Macrocrustaceans" </span>
<span class="co">#> [17] "Amphipods, isopods, opossum shrimps" </span>
<span class="co">#> [18] "Crabs, shrimps and crayfishes" </span>
<span class="co">#> [19] "Other macrocrustaceans" </span>
<span class="co">#> [20] "Woodlice" </span>
<span class="co">#> [21] "Microcrustaceans" </span>
<span class="co">#> [22] "Branchiopoda" </span>
<span class="co">#> [23] "Copepods" </span>
<span class="co">#> [24] "Seed shrimps" </span>
<span class="co">#> [25] "Fishes" </span>
<span class="co">#> [26] "Fungi and lichens" </span>
<span class="co">#> [27] "Ascomycota" </span>
<span class="co">#> [28] "Erysiphales" </span>
<span class="co">#> [29] "Non-lichenized Ascomycota" </span>
<span class="co">#> [30] "Lichenized and lichenicolous fungi" </span>
<span class="co">#> [31] "Lichenicolous fungi" </span>
<span class="co">#> [32] "Lichenized fungi" </span>
<span class="co">#> [33] "Macrofungi" </span>
<span class="co">#> [34] "Agaricoid fungi" </span>
<span class="co">#> [35] "Aphyllophoroid fungi" </span>
<span class="co">#> [36] "Cantharelloid fungi" </span>
<span class="co">#> [37] "Clavarioid fungi" </span>
<span class="co">#> [38] "Corticioid fungi" </span>
<span class="co">#> [39] "Hydnoid fungi" </span>
<span class="co">#> [40] "Jelly fungi, tremelloid fungi" </span>
<span class="co">#> [41] "Polypores" </span>
<span class="co">#> [42] "Ramarioid fungi" </span>
<span class="co">#> [43] "Boletoid fungi" </span>
<span class="co">#> [44] "Cyphelloid fungi" </span>
<span class="co">#> [45] "Gastroid fungi, puffballs" </span>
<span class="co">#> [46] "Parasitic microfungi" </span>
<span class="co">#> [47] "Exobasibium" </span>
<span class="co">#> [48] "Rust fungi" </span>
<span class="co">#> [49] "Smut fungi" </span>
<span class="co">#> [50] "Insects and arachnids" </span>
<span class="co">#> [51] "Aquatic insects" </span>
<span class="co">#> [52] "Caddisflies" </span>
<span class="co">#> [53] "Mayflies" </span>
<span class="co">#> [54] "Stoneflies" </span>
<span class="co">#> [55] "Archaeognatha and Zygentoma" </span>
<span class="co">#> [56] "Beetles" </span>
<span class="co">#> [57] "Booklice" </span>
<span class="co">#> [58] "Cockroaches" </span>
<span class="co">#> [59] "Dragonflies" </span>
<span class="co">#> [60] "Earwigs" </span>
<span class="co">#> [61] "Fleas" </span>
<span class="co">#> [62] "Harvestmen" </span>
<span class="co">#> [63] "Katydids, crickets, grasshopper" </span>
<span class="co">#> [64] "Lice" </span>
<span class="co">#> [65] "Mites and ticks" </span>
<span class="co">#> [66] "Moths and butterflies" </span>
<span class="co">#> [67] "Butterflies" </span>
<span class="co">#> [68] "Geometer moths" </span>
<span class="co">#> [69] "Macrolepidoptera" </span>
<span class="co">#> [70] "Microlepidoptera" </span>
<span class="co">#> [71] "Owlet moths" </span>
<span class="co">#> [72] "Sphinx moths" </span>
<span class="co">#> [73] "Net-winged insects, megalopterans, snakeflies, mecopterans"</span>
<span class="co">#> [74] "Pseudoscorpions" </span>
<span class="co">#> [75] "Sawflies, wasps, ants and bees" </span>
<span class="co">#> [76] "Spiders" </span>
<span class="co">#> [77] "Thrips" </span>
<span class="co">#> [78] "True bugs" </span>
<span class="co">#> [79] "Aphids" </span>
<span class="co">#> [80] "Auchenorrhynchans" </span>
<span class="co">#> [81] "Bladloppor" </span>
<span class="co">#> [82] "Heteropterans" </span>
<span class="co">#> [83] "Soft scales" </span>
<span class="co">#> [84] "Whiteflies" </span>
<span class="co">#> [85] "True flies" </span>
<span class="co">#> [86] "Brachyceran flies" </span>
<span class="co">#> [87] "Nematoceran flies" </span>
<span class="co">#> [88] "Twisted-wing parasites" </span>
<span class="co">#> [89] "Mammals" </span>
<span class="co">#> [90] "Bats" </span>
<span class="co">#> [91] "Small mammals" </span>
<span class="co">#> [92] "Molluscs" </span>
<span class="co">#> [93] "Aquatic snails" </span>
<span class="co">#> [94] "Bivalves" </span>
<span class="co">#> [95] "Landsnails and slugs" </span>
<span class="co">#> [96] "Myriapods" </span>
<span class="co">#> [97] "Chilopods, centipedes" </span>
<span class="co">#> [98] "Millipedes" </span>
<span class="co">#> [99] "Pauropods" </span>
<span class="co">#> [100] "Symphylans" </span>
<span class="co">#> [101] "Other organisms" </span>
<span class="co">#> [102] "Bacteria" </span>
<span class="co">#> [103] "Entognatha" </span>
<span class="co">#> [104] "Slime molds" </span>
<span class="co">#> [105] "Sponges, bryozoans and cnidarians" </span>
<span class="co">#> [106] "Viruses and viroids" </span>
<span class="co">#> [107] "Reptiles and amphibians" </span>
<span class="co">#> [108] "Amphibians" </span>
<span class="co">#> [109] "Reptiles" </span>
<span class="co">#> [110] "Vascular plants" </span>
<span class="co">#> [111] "Berry plants" </span>
<span class="co">#> [112] "Carnivorous plants" </span>
<span class="co">#> [113] "Plant life forms" </span>
<span class="co">#> [114] "Aquatic plants" </span>
<span class="co">#> [115] "Elodeids" </span>
<span class="co">#> [116] "Helophytes" </span>
<span class="co">#> [117] "Isoetids" </span>
<span class="co">#> [118] "Lemnids" </span>
<span class="co">#> [119] "Nympheids" </span>
<span class="co">#> [120] "Submerged plants" </span>
<span class="co">#> [121] "Chamaephytes" </span>
<span class="co">#> [122] "Deciduous chamaephytes" </span>
<span class="co">#> [123] "Evergreen chamaephytes" </span>
<span class="co">#> [124] "Climbers" </span>
<span class="co">#> [125] "Deciduous climbers" </span>
<span class="co">#> [126] "Evergreen climbers" </span>
<span class="co">#> [127] "Geophytes" </span>
<span class="co">#> [128] "Hemicryptophytes" </span>
<span class="co">#> [129] "Shore plants" </span>
<span class="co">#> [130] "Shrubs" </span>
<span class="co">#> [131] "Deciduous shrubs" </span>
<span class="co">#> [132] "Evergreen bushes" </span>
<span class="co">#> [133] "Therophytes" </span>
<span class="co">#> [134] "Trees" </span>
<span class="co">#> [135] "Deciduous trees" </span>
<span class="co">#> [136] "Evergreen trees" </span>
<span class="co">#> [137] "Spring flowers" </span>
<span class="co">#> [138] "Worms" </span>
<span class="co">#> [139] "Annelids" </span>
<span class="co">#> [140] "Earthworms, oligochaetes" </span>
<span class="co">#> [141] "Leeches" </span>
<span class="co">#> [142] "Polychaetes" </span>
<span class="co">#> [143] "Parasitic worms" </span>
<span class="co">#> [144] "Monogeneans" </span>
<span class="co">#> [145] "Tapeworms" </span>
<span class="co">#> [146] "Priapulid worms" </span>
<span class="co">#> [147] "Ribbon worms" </span>
<span class="co">#> [148] "Turbellarians" </span>
<span class="co">#> attr(,"class")</span>
<span class="co">#> [1] "translation"</span></code></pre></div>
</details><p><br></p>
<p>You can select a subgroup by specifying a parent informal group as a function argument.</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/finbif_informal_groups.html">finbif_informal_groups</a></span><span class="op">(</span><span class="st">"Crustaceans"</span><span class="op">)</span>
<span class="co">#> Crustaceans </span>
<span class="co">#> ¦--Macrocrustaceans </span>
<span class="co">#> ¦ ¦--Amphipods, isopods, opossum shrimps </span>
<span class="co">#> ¦ ¦--Crabs, shrimps and crayfishes </span>
<span class="co">#> ¦ ¦--Other macrocrustaceans </span>
<span class="co">#> ¦ °--Woodlice </span>
<span class="co">#> °--Microcrustaceans </span>
<span class="co">#> ¦--Branchiopoda </span>
<span class="co">#> ¦--Copepods </span>
<span class="co">#> °--Seed shrimps</span></code></pre></div>
</div>
</div>
<div class="section level2">
<h2 id="collections">Collections<a class="anchor" aria-label="anchor" href="#collections"></a>
</h2>
<p>Another special case of metadata is <code><a href="../reference/finbif_collections.html">finbif_collections()</a></code>. Collections are the highest level of record aggregation in the FinBIF database.</p>
<p>You can subset collection metadata by using the <code>filter</code> and <code>select</code> arguments.</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/finbif_collections.html">finbif_collections</a></span><span class="op">(</span>
filter <span class="op">=</span> <span class="va">geographic_coverage</span> <span class="op">==</span> <span class="st">"Finland"</span>,
select <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"collection_name"</span>, <span class="st">"taxonomic_coverage"</span>, <span class="st">"count"</span><span class="op">)</span>
<span class="op">)</span></code></pre></div>
<details closed><summary>
Click to show/hide output.
</summary><div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co">#> collection_name taxonomic_coverage count </span>
<span class="co">#> HR.1227 Coll Mikko Heikkinen Biota 67</span>
<span class="co">#> HR.1349 JYV - Fungal collections <NA> 13399</span>
<span class="co">#> HR.1350 JYV - Lichen collections <NA> 398</span>
<span class="co">#> HR.1351 JYV - Bryophyte collections <NA> 4369</span>
<span class="co">#> HR.1467 Per-Eric Grankvist´s butterly co… Lepidoptera 5</span>
<span class="co">#> HR.1487 JYV - Fish collections <NA> 1371</span>
<span class="co">#> HR.1507 Lingonblad Birger och Hjördis bu… Lepidoptera 2796</span>
<span class="co">#> HR.157 Point counts of breeding terrest… Birds, landbirds 376833</span>
<span class="co">#> HR.1592 Herbarium of The Ark Nature Cent… <NA> 7806</span>
<span class="co">#> HR.1687 Papilionoidea of Coll. Lauro Papilionoidea 525</span>
<span class="co">#> HR.1688 Noctuidae I of Coll. Lauro Noctuidae 614</span>
<span class="co">#> HR.1689 Noctuidae II of Coll. Lauro Noctuidae 839</span>
<span class="co">#> HR.1690 Noctuidae III, Bombycoidea, Sphi… Noctuidae, Bombycoidea, Geometri… 521</span>
<span class="co">#> HR.1691 Drepanidae & Geometridae of Coll… Drepanidae, Geometridae 1408</span>
<span class="co">#> HR.175 National Finnish butterfly monit… Lepidoptera 408864</span>
<span class="co">#> HR.200 Finnish Insect Database Insecta 3725818</span>
<span class="co">#> HR.2049 Invasive alien species control Invasive species 471</span>
<span class="co">#> HR.206 The Finnish Nature League's Spri… biota 107275</span>
<span class="co">#> HR.2089 Håkan Lindberg collection Hymenoptera 2400</span>
<span class="co">#> HR.209 Atlas of Finnish Macrolepidoptera Macrolepidoptera 1218544</span>
<span class="co">#> HR.2209 KUO Arachnida collection Arachnida 3</span>
<span class="co">#> HR.2289 Specimens that lack collecting i… <NA> 109</span>
<span class="co">#> HR.2691 Line transect censuses of breedi… Aves 603950</span>
<span class="co">#> HR.2692 Censuses of breeding birds - Are… Aves 14963</span>
<span class="co">#> HR.3051 VieKas LIFE project invasive spe… <NA> 1349</span>
<span class="co">#> HR.3071 Observing species on milk farms <NA> 529</span>
<span class="co">#> HR.3211 iNaturalist Suomi Finland biota 417052</span>
<span class="co">#> HR.3491 LajiGIS: Aquatic species survey Biota 518824</span>
<span class="co">#> HR.3553 LajiGIS: Species monitoring sites Biota 657410</span>
<span class="co">#> HR.3671 Bird of prey nests for protection Aves 10246</span>
<span class="co">#> HR.3691 eBird Aves 528002</span>
<span class="co">#> HR.3791 Invasive species observations Biota 1385</span>
<span class="co">#> HR.39 Winter Bird Census Aves 1404097</span>
<span class="co">#> HR.3911 Bumblebee census Bumblebees 4154</span>
<span class="co">#> HR.3991 Waterbird counts, Luomus dataset Aves 2424</span>
<span class="co">#> HR.3992 Waterbird counts, Luke dataset Aves 15012</span>
<span class="co">#> HR.4011 Salmonidae in streams Salmonidae 12630</span>
<span class="co">#> HR.4051 LajiGIS: Species monitoring site… Aquila chrysaetos; Haliaeetus al… 7780</span>
<span class="co">#> HR.4091 Retkikasvio <NA> 1227</span>
<span class="co">#> HR.4131 Butterflies in Finnish agricultu… Papilionoidea, Others 356560</span>
<span class="co">#> HR.435 Löydös Open Invasive Species Obs… Biota 17157</span>
<span class="co">#> HR.60 Monitoring scheme of birds and m… Aves, Mammalia 826341</span>
<span class="co">#> HR.627 Invasive mammal species of Finla… Mammalia 228</span>
<span class="co">#> HR.808 E. Sjöholm´s butterfly collection Lepidoptera 4951</span>
<span class="co">#> HR.847 Atlas of amphibians and reptiles… Amphibia, Reptilia 6233</span></code></pre></div>
</details><p><br></p>
<p>By default, <code><a href="../reference/finbif_collections.html">finbif_collections()</a></code> only displays the lowest level collections. Higher level, “supercollections” can be viewed by setting <code>supercollections = TRUE</code> and you can limit the output to collections with a minimum number of records in them with the <code>nmin</code> argument.</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">collections</span> <span class="op"><-</span> <span class="fu"><a href="../reference/finbif_collections.html">finbif_collections</a></span><span class="op">(</span>supercollections <span class="op">=</span> <span class="cn">TRUE</span>, nmin <span class="op">=</span> <span class="fl">10000</span><span class="op">)</span></code></pre></div>
<p>The <code><a href="../reference/finbif_collections.html">finbif_collections()</a></code> function returns a <code>data.frame</code> where the row names are the ID number of the collection.</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/finbif_collections.html">finbif_collections</a></span><span class="op">(</span>supercollections <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">[</span><span class="st">"HR.128"</span>, <span class="st">"collection_name"</span><span class="op">]</span></code></pre></div>
<details closed><summary>
Click to show/hide output.
</summary><div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co">#> Collections of the Finnish Museum of Natural History Luomus</span></code></pre></div>
</details><p><br></p>
<p>You can see the child collections of a supercollection by specifying the ID as a filter. Note that the children of supercollections may also be supercollections</p>
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/finbif_collections.html">finbif_collections</a></span><span class="op">(</span><span class="va">is_part_of</span> <span class="op">==</span> <span class="st">"HR.128"</span>, supercollections <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
<details closed><summary>
Click to show/hide output.
</summary><div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="co">#> collection_name abbreviation description online_url has_children is_part_of data_quality</span>
<span class="co">#> HR.129 Collections of… H Herbarium … <NA> TRUE HR.128 MY.dataQual…</span>
<span class="co">#> HR.160 Zoological col… MZH The collec… http://ww… TRUE HR.128 MY.dataQual…</span>
<span class="co">#> HR.173 Zoological mon… <NA> Monitoring… <NA> TRUE HR.128 MY.dataQual…</span>
<span class="co">#> HR.1849 Genomic resour… <NA> Genomic re… <NA> TRUE HR.128 MY.dataQual…</span>
<span class="co">#> HR.203 Löydös Open Fi… <NA> A service … http://ws… TRUE HR.128 MY.dataQual…</span>
<span class="co">#> HR.447 Hatikka.fi obs… <NA> Hatikka.fi… http://ha… FALSE HR.128 MY.dataQual…</span>
<span class="co">#> HR.48 Ringing and re… TIPU Database o… <NA> TRUE HR.128 MY.dataQual…</span>
<span class="co">#> methods collection_type taxonomic_coverage geographic_coverage temporal_coverage</span>
<span class="co">#> HR.129 <NA> MY.collectionT… <NA> <NA> <NA> </span>
<span class="co">#> HR.160 <NA> MY.collectionT… Animalia World 1700 to present </span>
<span class="co">#> HR.173 <NA> MY.collectionT… <NA> Finland 1950- </span>
<span class="co">#> HR.1849 Sampling… MY.collectionT… Biota World 2000- </span>
<span class="co">#> HR.203 <NA> MY.collectionT… biota world 2013- </span>
<span class="co">#> HR.447 <NA> MY.collectionT… Biota World <NA> </span>
<span class="co">#> HR.48 <NA> MY.collectionT… <NA> Ringing data: Finl… 1913- </span>
<span class="co">#> secure_level count </span>
<span class="co">#> HR.129 <NA> 1513</span>
<span class="co">#> HR.160 MX.secureLe… 940</span>
<span class="co">#> HR.173 <NA> 4765423</span>
<span class="co">#> HR.1849 <NA> 1</span>
<span class="co">#> HR.203 <NA> 26650</span>
<span class="co">#> HR.447 <NA> 2010389</span>
<span class="co">#> HR.48 <NA> 12456603</span></code></pre></div>
</details><p><br></p>
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