01 de diciembre de 2020

Using iNaturalist data for research

Things to be aware of


Certainty of ID.
iNat does not have a reputation system. So it is impossible to know what "research grade" means. Basically if someone proposes an ID, and someone agrees, then it is research grade. But double IDs can come about for many reasons, despite the guidelines (https://www.inaturalist.org/pages/help#identification). for instance:

  • people may agree with someone they know (or trust), often just supporting a friend;
  • to get their own (or a friends, associates) observation to research grade;
  • to stop getting messages about identifications on observations they have contributed to.
  • to up their profile in identifications posted.

If you are interested in quality of observations here are some fields that you can use:
(in downloads)

  • num_identification_agreements
  • num_identification_disagreements

Another option is to see if any experts or acclaimed enthusiasts have contributed to the ID, if you know of any. You can do this by adding the &ident_user_id= phrase to your filter.
By similar token, you may want to use observations that are not research grade, but that have been identified by certain users (experts, enthusiasts). [Although why not just agree to these observations and make them research grade, if they are not too many?].
If you dont know who experts are, look at the identifications tab on a filter for the group. But beware that regular observers may be high up the list, even if they dont know the group, and that some identifiers may be interested in a group, but not particularly competent.

Alternatively, if you are knowledgeable in a group, and there are not too many observations, it is worthwhile using the curation tool to check any identifications before using the data (e.g. https://www.inaturalist.org/observations/identify?quality_grade=needs_id%2Cresearch%2Ccasual&verifiable=true&taxon_id=563588&place_id=any)
If you intend using data regularly, then it is worthwhile also adding to the DQA at the end of each observation (or the last tab on the curation tool).
If you have special data needs, you can always add an Observation Field and annotate the observations, and then include these fields with any downloads you make.


Obscuration on iNaturalist is necessary, but the bane of research. Obtaining obscured data is virtually impossible. (note that private data is useless for most research as even the country is not accessible.) You can see obscured data with the following phrase

Note that the coordinates provided in any download are meaningless if the field coordinates_obscured=True if you require a locality resolution less than 30km radius. Make sure that you download the field " coordinates_obscured" and exclude any such data if you need to have accurate localities.
The best way to obtain taxon-obscured data (and all IUCN Red List species are obscured by default) is to requrest data from your community administrator (or California if you are not part of an iNaturalist Community). Note that this will not include any observations additionally obscured by users.
Obtaining user obscured data is nigh impossible. The problem is simply the volume of users that need to be contacted, and the number of dead, inactive or unresponsive users. These data are effectively forever lost. (users can manage their obscuration rights at https://www.inaturalist.org/relationships - but they cannot add new people there.
There are several ways to access user obscured data:

  • request the user to trust you. There are many ways of doing this, but the best is via a message to the user, explaining why you need access to their obscured localities.
  • create a traditional project and ask users to join the project and to trust you (and to allow you do add your project to their observations and see the coordinates: it is useless if users only trust you if they add the observation to the project themselves, because the amount of chasing up required is impossible - they need to allow anyone to add the project to the observation). This is the most efficient, and the only option if you want the data to be useful in the long term (just make sure that curation of project is passed on the next generation of researchers).

Location Accuracy
(An unfortunate term, as higher values are more inaccurate; think of it as Location Error or Location Uncertainty. On iNaturalist it is measured as the radius (in m) in which the given location point is likely to occur).
Some useful filters:

There are two issues here:

  1. What resolution of location do your require?
    If your work requires resolution to m or km accuracy, then add in a filter to exclude values of less certainty. For instance, modelling distributions using a climate model at minute scale is about 2000m in South Africa. Discard courser data.

  2. Are you working with smaller nature reserves?
    The place filters exclude data that are too course. Conceptually, one does not want a locality to be considered inside a reserve if the possibility that it is outside the reserve exceeds 50%. So iNaturalist excludes observations were the uncertainty is too large (details here: ).

    This means that for very small reserves, lots of good data can be discarded where users are not aware of the implications. Many naive observers assume that making the circle of uncertainty just larger than the reserve will indicate that the data are from (somewhere in) the reserve. In reality, if the area outside of the actual reserve is too large while doing this, then the point will be considered probably outside.
    This requires educating users, and especially educating users as to the significance and importance of Locality Accuracy. For app users, it is merely an awareness that they need to let the app find their locality to a reasonable accuracy, as the app is quite precise thereafter. But for users adding in data and doing their own mapwork, need to be aware of the significance of not recording the Location Accuracy, or making it too precise or too imprecise.

Dont forget the DQA: mark up any localities that have dubious localities, especially if you plan to download the data in the future for further research

Anotado en diciembre 01, martes 11:35 por tonyrebelo tonyrebelo | 3 comentarios | Deja un comentario

13 de octubre de 2019

New Functionality: taxon counts on taxon page.

There is new functionailty on the taxon pages: so now we can easily see:

In the genus Protea we dont have any observations of
In South Africa;
Protea curvata
In Tropical Africa:
(10 spp: Protea argyrea , P dekindtiana, P flavopilosa, P kibarensis, P linearifolia, P matonchiana, P micans, P minima, P ongotium, P praticola)

Anotado en octubre 13, domingo 16:36 por tonyrebelo tonyrebelo | 2 comentarios | Deja un comentario

22 de julio de 2019

Proforma - Cribsheet

For posting comments

Anotado en julio 22, lunes 10:30 por tonyrebelo tonyrebelo | 10 comentarios | Deja un comentario

17 de abril de 2019

Publications using iNaturalist data in southern Africa.


Recent records of fruit chafers (Scarabaeidae: Cetoniinae: Cetoniini) in the southwestern Cape region of South Africa suggest that range expansions were facilitated by human- mediated jump-dispersal and pre-adaptation to transformed landscapes.
F. Roets, J.D. Allison & R.J. Basson. 2019. African Entomology 27(1): 135–145 DOI: https://doi.org/10.4001/003.027.0135


Invasive potential and management of naturalised ornamentals across an urban environmental gradient with a focus on Centranthus ruber
Patricia M. Holmes, Anthony G. Rebelo, & Ulrike M. Irlich 2018. Bothalia 48 https://doi.org/10.4102/abc.v48i1.2345



The harlequin ladybird, Harmonia axyridis: global perspectives on invasion history and ecology.

Helen E. Roy, Peter M. J. Brown, Tim Adriaens, Nick Berkvens, Isabel Borges, Susana Clusella-Trullas, Richard F. Comont, Patrick De Clercq, Rene Eschen, Arnaud Estoup, Edward W. Evans, Benoit Facon, Mary M. Gardiner, Artur Gil, Audrey A. Grez, Thomas Guillemaud, Danny Haelewaters, Annette Herz, Alois Honek, Andy G. Howe, Cang Hui, William D. Hutchison, Marc Kenis, Robert L. KochJan Kulfan, Lori Lawson Handley, Eric Lombaert, Antoon Loomans, John Losey, Alexander O. Lukashuk, Dirk Maes,, Alexandra Magro, Katie M. Murray, Gilles San Martin, Zdenka Martinkova, Ingrid A. Minnaar, Oldřich Nedved, Marina J. Orlova-Bienkowskaja, Naoya Osawa, Wolfgang Rabitsch, Hans Peter Ravn, Gabriele Rondoni, Steph L. Rorke, Sergey K. Ryndevich, May-Guri Saethre, John J. Sloggett, Antonio Onofre Soares, Riaan Stals, Matthew C. Tinsley, Axel Vandereycken, Paul van Wielink, Sandra Viglášová, Peter ZachIlya A. Zakharov, Tania Zaviezo & Zihua Zhao. 2016. Biological Invasions 18, 997–1044 DOI: 10.1007/s10530-016-1077-6

Anotado en abril 17, miércoles 06:50 por tonyrebelo tonyrebelo | 1 comentario | Deja un comentario

26 de febrero de 2019

Leader Boards

Top observers in southern Africa as of today.
(using: https://www.inaturalist.org/observations?hrank=species&lrank=variety&place_id=113055&subview=grid&verifiable=any&view=observers - select iconic group from the filters, and click on the species column.

Numbers of "species" in southern Africa (eligible for research grade)

Amphibians (136 species observed)
84 alexanderr

32 jouberth

30 scbc

29 robert_taylor

26 tonyrebelo

Reptiles (428 species observed)
156 alexanderr

117 scbc
99 jouberth

90 toby

89 herpguy
89 nick_schaller

Mammals (400 species observed)
107 tonyrebelo
101 markuslilje
93 joachim
89 henrydelange
87 johnnybirder

Birds (877species observed)
630 markuslilje
422 mr_fab

381 johnnybirder

367 happyasacupcake
363 carmelo_lopez

Fish (794 species observed)
296 nevillea

234 seastung

210 rosepalmer
165 robert_taylor

152 andrewdeacon

152 rowanwattpringle

Molluscs (641 species observed)
132 mr_fab
130 seastung

125 pbsouthwood

103 maddyo
83 diveinn_capetown

Arachnids (433 species observed)
71 wynand_uys

67 jouberth

52 alexanderr

43 sallyslak

43 tuli

Insects ( 4 370 species observed)
1 101 wolfachim

609 riana60

608 magdastlucia

587 ricky_taylor

545 botswanabugs
539 tonyrebelo

513 robert_taylor

454 qgrobler

398 jaheymans

391 bushboy

Plants (14 811 species observed)
5 146 tonyrebelo
3 660 botaneek
3 278 nicky
2 142 vynbos
1 934 mr_fab
1 620 outramps
1 338 linkie

1 272 richardadcock
1 265 gerhardmalan
1 181 peterrwarren

Fungi (543 species observed)
194 lizziepop

167 gabymeyer

133 nicky

122 tonyrebelo
115 colin25

Bacteria and Viruses (18 species observed)
10 lizziepop

9 gabymeyer

5 colin25
4 tonyrebelo

3 nicky

Mosses (60 species observed)
17 tonyrebelo

5 magdastlucia
5 nicky

5 ricky_taylor
4 barnabas

Ferns (168 species observed)
48 tonyrebelo

45 nicky

41 outramps

37 jaheymans

35 ricky_taylor

Gymnosperms (23 species observed)
18 tonyrebelo

9 vynbos

8 nicky

6 muonmo

6 outramps
6 shauns

Monocots (3 552 species observed)
1 103 tonyrebelo

1 023 botaneek

694 nicky

553 vynbos

444 gerhardmalan

Dicots (10 912 species observed)
3 936 tonyrebelo

2 623 botaneek
2 500 nicky

1 561 vynbos

1 477 mr_fab

1 244 outramps

Moths & Butterflies (2 106 species observed)
796 wolfachim

351 qgrobler

347 ricky_taylor
304 magdastlucia

247 mr_fab

Beetles (1 517 species observed)
276 riana60

214 wolfachim

196 fubr

189 botswanabugs

134 magdastlucia

Wasps Bees & Ants (388 species observed)
74 flippie1971
71 tonyrebelo
63 peterslingsby

51 magdastlucia

41 robert_taylor

Bugs (488 species observed)
95 botswanabugs

53 magdastlucia

42 colin25
38 jane_trembath

33 tonyrebelo

Anotado en febrero 26, martes 10:48 por tonyrebelo tonyrebelo | 0 comentarios | Deja un comentario

29 de noviembre de 2018

Species complexes

Examples of where species complexes would be useful.

Tomopterna cryptotis complex
Field guide says: "morphologically indistinguishable from (each other), but chromosome number and call differ." - about 60% of range overlaps, so some IDs can be based on distribution.
Tomopterna cryptotis 36 (no range map on iNat)
Tomopterna tandyi 21
IDs only to genus level (8 spp s Afr): 21 (out of 161: = 13%) - many of the notes refer to a "T. cryptotis, T. krugerensis, T. tandyi." issue - ID of krugerensis requires pictures of hand underside.

Amietia fuscigula complex
IDs only to genus level (7 spp s Afr): 36 (out of 692: = 5%)
Amietia fuscigula 472
Amietia poyntoni 13 (no range map on iNat; not in 2009 field guide)

Amietia angolensis complex
Amietia drakensbergensis was indistinghishable except by call, but this got sunk into Amietia delalandii (A. d.: no range map on iNat, not in 2009 field guide - 124 observations)
Taxonomic Notes from AmphibiaWeb (sourced IUCN Red List):
"(Amietia delalandii) was resurrected from synonymy with Amietia angolensis by Channing et al. (2016) and now also includes the names Amietia dracomontana and Amietia quecketti. It occurs in sympatry with Amietia inyangae, A. fuscigula, A. vertebralis and A. poyntoni.
(Note:) A. quecketti records from Namibia have been assigned to A. poyntoni."
Amietia angolensis, as the new species concept is restricted to Angola, so the complex is redundant. However the range maps on iNat is now incorrrect, and at least 10 of the 18 observations are still incorrectly identified as A. angolensis (a geographical taxonomic swap is called for))

Leptopelis bocagei complex
IDs only to genus level (6 spp s Afr - this complex is north of us, so no mentions in field guides): 27 (out of 193: = 14%)
Leptopelis bocagei 8
Leptopelis parbocagei 1

Some rules for species complexes:

  • do not add superspecies which are synonymous with their genus, subspecies, section or series: merely use those instead.
  • use the earliest published species name for the superspecies name.
  • dont use compound names (such as Hypsiboas calcaratus–fasciatus group - especially when there are six species in the group).
  • the complex must be recognized in the literature - dont create complexes for observations where IDs can be done, but diagnostic features are often missing from some photographs - rather inform and train users to provide the additional evidence.
  • dont go overboard with adding "complexes" to the dictionary unless there are observations present for them.
  • complexes should be exclusive: any species can only belong to a single complex - in the event of complications: merge.
  • complexes are complex: subcomplexes are not an option - rationalize.

Anotado en noviembre 29, jueves 07:31 por tonyrebelo tonyrebelo | 0 comentarios | Deja un comentario

15 de octubre de 2018

The Ants and Bees: or AB See of Citizen Science

"I have had a look at iNaturalist to see what South African bee species are recorded - am I right that there are only 9 species: Apis mellifera, Xylocopa caffra, X. flavorufa, Megachile maxillosa, Halictus jucundus (which I believe is now Seladonia), Amegilla atrocincta, Xylocopa capensis, Xylocopa nigrita, Megachile felina. There is Plebeina hildebrandt - but it has only been recorded in Namibia so far.
I see that ants feature much more than bees (and wasps) - how many ant species would you say are recorded on iNaturalist SA so far?"

That is not quite a fair comparison on several grounds. Let us expand to southern Africa and look at the details:
See Ants: https://www.inaturalist.org/observations?place_id=113055&taxon_id=47336&view=species
See Bees: https://www.inaturalist.org/observations?place_id=113055&taxon_id=630955&view=species


Bees: 1,486 observations 43 species 117 identifiers 200 Observers
Ants: 2,836 observations 176 species 115 identifiers 220 Observers

So Ants have twice as many observations. But the same number of identifiers and observers. The big difference is the identifications and the enthusiasm of those making the IDs (shown: more than 200 IDs). (to see this click on the “Identifiers” tab on the pages above)

1 peterslingsby 2,755
2 rjpretor 907
3 tonyrebelo 449
4 meldem 342
5 alexdreyer 276
6 colin25 202
1 rjpretor 726
2 johnascher 524
3 tonyrebelo 368
4 colin25 218

That is all it takes: 1 champion! Someone willing to adopt a group and run with it and get everyone excited and all cued up. Apart from this champion there is not much different between the two.
But what does help is someone willing to make IDs to species level:

Rank of identifications
Observations (taxa):

Level of ID: Ants Bees
Family 90 (1) 133 (6)
Tribe 44 (6) 129 (12)
Genus 551 (22) 381 (23)
Species 2228 (176) 849 (28)

So: 79% of ants are identified to species, and 57% of bees!

Bees: Top 5 (but > 10 obs):
Apis mellifera: 583
Xylocopa caffra: 93
Xylocopa flavorufa: 73
Halictus (Seladonia): 18
Ants: (> 100 obs)
Camponotis niveosetosus: 188
Camponotis fulvopilosus: 154
Lepisota capensis: 125
Crematogaster peringuei: 124
Anoplolepis custodiens: 122

So – the Honeybees accounts for 69% of bee observations, and only 4 species have 10 or more observations.
But ants have 5 species with more than 100 observations, and 46 species with ten or more observations

So that is the difference: the ants have the more charismatic identifiers and identifications (and they don’t fly away).

The solution is simple. We need a Bee Champion on iNaturalist for the region!

Anotado en octubre 15, lunes 09:39 por tonyrebelo tonyrebelo | 5 comentarios | Deja un comentario

29 de junio de 2018

Filter Cribsheet

Some shortcuts to filtering data
(this does not include simple terms accessible in the grey filter box: explore there)

Searching comments:
your own comments:
https://www.inaturalist.org/comments?commit=Search&q=robin 1

Searching Identifications:
maverick IDs:
IDs not current:
e.g. observations that are currently falsely identified by me relative to community ID.
Inactive taxa:

Searching others:
&search_on=names (for taxa)
&search_on=place (for localities)

Useful extra terms to add to filters in filter bar:

(for multiple taxa, users, projects, fields separate values with a comma, note "ids" not "id")
&taxon_ids=12345,67890 &geoprivacy=open,obscured

With & without: &photos=true or &photos= or &has=photos ; &photos=false

Observations without any ID:
&iconic_taxa=unknown (includes Bacteria)

Observations identified by a particular user (e.g. tony_rebelo):

Instances of any ID made (community or not) :


To exclude:
&without_term_id=1 [NB: only works in Identify tool - not in Explore, use the Annotations tab to add]


Observation Fields:
with a field:
with a field and value:

Observation field view:
Observation field view for a value: (e.g. Fynbos in Habitats-s-afr):
https://www.inaturalist.org/observation_fields/7498?value=Fynbos (case sensitive)

Plant phenology:

&term_id=9 (male: &term_value_id=11 female: &term_value_id=10)
Life stage:
&term_id=1 (juvenile: &term_value_id=6)
Full listing:
Life Stage: 2=Adult, 3=Teneral, 4=Pupa, 5=Nymph, 6=Larva, 7=Egg, 8=Juvenile, 16=Subimago
Sex: 10=Female, 11=Male
Plant Phenology: 13=Flowering, 14=Fruiting, 15=Budding

OBSCURED DATA: (observations and identify)
no positional data: https://www.inaturalist.org/observations?acc=false
above: https://www.inaturalist.org/observations?acc_above=10000
below: https://www.inaturalist.org/observations?acc_below=3

no localities: &geo=false

user private: https://www.inaturalist.org/observations?geoprivacy=private
user obscured: https://www.inaturalist.org/observations?geoprivacy=obscured
user obscured or private: https://www.inaturalist.org/observations?geoprivacy=obscured_private
taxon private: https://www.inaturalist.org/observations?taxon_geoprivacy=private
taxon obscured: https://www.inaturalist.org/observations?user_id=kueda&taxon_geoprivacy=obscured

?list_id=1471294 (e.g. https://www.inaturalist.org/lists/1471294-Trees-of-South-Africas-Check-List)
trees: https://www.inaturalist.org/observations?list_id=1471294

compare lists (can use projects, places, dates and such)
e.g. CT List : place_id=52355&taxon_id=489493&d2=2019-04-25

exclude a taxon:
e.g. Moths

via flags: https://www.inaturalist.org/flags?taxon_id=129714
via taxa: https://www.inaturalist.org/taxa/129714/flags
all children: https://www.inaturalist.org/flags?flaggable_type=Taxon&taxon_id=64517
query inactive: https://www.inaturalist.org/taxa/search?is_active=any&q=corycium&utf8=%E2%9C%93

projects in a place: (restricted to those with a centroid in the place)

center map and zoom: #1 out #9 close, latitude, longitude


e.g. https://www.inaturalist.org/taxa/map?taxa=74191,74190,68137,74189,74188,43523#7/5.791/41.797

TABS: opening pages on special tabs:
for Places add: #observationstab #peoplestab
for Taxa add:

  • also /map#2/0/0
    for Observations add: ?view=species view=observers


&user_after=2w (d, w, m, y)

&order_by=updated_at (for sequence by updates)

can add users and other features:

Your statistics:
Site usage statistics

To find a value of a project or field or user: add ".json" to the url, or use chrome > inspect

using APIs: http://api.inaturalist.org/v1/docs/#!/Observations/get_observations

Anotado en junio 29, viernes 07:53 por tonyrebelo tonyrebelo | 1 observación | 25 comentarios | Deja un comentario

14 de mayo de 2018


With the help of more than 100 IUCN Species Survival Commission Specialist Groups, Global Wildlife Conservation has compiled the following list of lost species, spanning more than 160 countries, as part of the Search for Lost Species. We welcome additional nominations and encourage conservationists, scientists and naturalists to launch searches for species on this broad list.

more at https://www.lostspecies.org/

Our LOST southern African species are:

• South-East African Burrowing Grasshopper Acrotylus mossambicus last seen unknown Mozambique, South Africa, Tanzania, Zimbabwe

• Mt. Coke False Shieldback Acilacris furcatus last seen: 1965 South Africa CR
• Peringueys Seedpod Shieldback Thoracistus peringueyi last seen: 1879 South Africa CR(PE)
• Imperiled Grass False Shieldback Paracilacris periclitatus last seen: 2008 South Africa CR
• Zulu Ambush Katydid Peringueyella zulu last seen: 1922 South Africa CR(PE)
• Elusive Skimmer Orthetrum rubens last seen: 1977 South Africa CR(PE)

• Suspect Rivercrab Potamonautes dubius last seen: 1890 Angola, Namibia DD

• Shortridges Rat Thallomys shortridgei last seen: 1932 South Africa DD
• De Wintons Golden Mole Cryptochloris wintoni last seen: 1937 South Africa CR(PE)
• Visagies Golden Mole Chrysochloris visagiei (incertae sedis) Only one specimen South Africa DD
• Karoo Rock Sengi Elephantulus pilicaudus last seen: 2008 South Africa DD
• Dusky Sengi Elephantulus fuscus One specimen from 2005, others pre-date 1968. Malawi, Mozambique, Zimbabwe DD

• Small Pipefish Campichthys nanus last seen: 1956? Mozambique DD

• Watergrass Button Cotula myriophylloides last seen: 1971 South Africa CR(PE) Found by Nick Feb 2014: revised status: CR
• Pretoria Dolldaisy Dicoma pretoriensis last seen: 1925 South Africa CR(PE) [Macledium pretoriense on BODATSA]
• Lost Fingersedge Eleocharis lepta last seen: 1897 South Africa CR(PE)
• Waxen Cycad Encephalartos cerinus last seen: before 2000 South Africa CR(PE)
• Venda Cycad Encephalartos hirsutus last seen: 2004 South Africa CR(PE)
• Pearsons Panicum Panicum pearsonii last seen: 1913 Namibia CR(PE)

Are there any other species that should be included. Tell us and we will nominate them.

• Mini Threadorchid Holothrix micrantha last collected: 1925 - Southern Gauteng endemic CR(PE) - Casper

Anotado en mayo 14, lunes 23:23 por tonyrebelo tonyrebelo | 10 comentarios | Deja un comentario

13 de abril de 2018

iSpot migration issues.

Please log any migration issues here. Things such as

No pictures
Missing pictures
Funny commenting
Missing content.
Deleted observations loaded:

We will fix these in the mop up!

Please note:
Note yet uploaded - still coming:

  • Projects (those that worked by tags! - NOT those by area: create a place for those)
  • Observation Fields (e.g. Habitats, interactions, project fields).

Please DONT post:

  • Pictures to be rotated.
  • Pictures in the wrong order.
    (But please do fix them if you can).

Please use a heading and then the url:

No pictures:
Missing pictures:
https://www.inaturalist.org/observations/10840705 (1 out of 4, added 2, still 1)
Deleted observations loaded:
https://www.inaturalist.org/observations/10838105 (deleted on iSpot & now iNat duplicate - will delete)

(no need to report or do anything with these: these are on the mop-up list)

To see observations that migrated without pictures please see:

(note: in the url box add &user_id=XXX to see yours or use the filter box to select a Location that you know, e.g. place=Cape Peninsula or George (to add to url box you will need to know the place code)

No IDs:
Weak IDs:


(and substitute your user name in the url box)

(and substitute your user name in the url box)

Anotado en abril 13, viernes 16:37 por tonyrebelo tonyrebelo | 59 comentarios | Deja un comentario