Journal archives for August 2019

August 09, 2019

BioCaching with iNaturalist Trips

https://apps.apple.com/us/app/biocaching/id827737251

BioCaching: Rediscover Nature
https://forum.inaturalist.org/t/trips-feature-on-inat/3061/12
BioCaching puts the power to conduct a biodiversity resurvey in your hands. Search for and revisit places where plants and animals have been observed in your community, or anywhere in the world. By using this app you will update our knowledge of current biodiversity distributions.

Our app works together with iNaturalist (an online platform for recording and sharing biodiversity observations). Learn more about the iNaturalist community and sign-up to the platform at http://www.inaturalist.org (you can also sign-up through the BioCaching app if you're not already a member).

With one click, you will see all of the plants and animals that have been observed around you. Next, choose previously observed species that you can recognize and would like to try and resurvey. You are now ready to conduct a ‘trip’, attempting to re-document those species. Start looking and record whether or not you are able to relocate each frog, toad, tree, bee, spider, shrub or whatever comes up on your list. If you find what you are looking for, record new field observations. Your entire trip and your finds will be recorded on iNaturalist.org and all verified reports will become new records available to scientists. The BioCaching app is a concrete way for you to connect with nature and bear witness to habitat loss and biodiversity change.


The BioCaching app, was developed and designed by Andy Jeffrey in partnership with the California Academy of Sciences Library, Academy Citizen Science and iNaturalist and was funded by the Institute of Museum and Library Studies National Leadership Grant, Connecting Content: A Collaboration to Link Field Notes to Specimens and Published Literature, LG- 05-010-0048.

https://apps.apple.com/us/app/biocaching/id827737251

https://forum.inaturalist.org/t/trips-feature-on-inat/3061/12

Posted on August 09, 2019 17:35 by ahospers ahospers | 3 comments | Leave a comment

August 10, 2019

Find/Exclude observations without a location?

Find/Exclude observations without a location?
https://forum.inaturalist.org/t/find-exclude-observations-without-a-location/3571
https://forum.inaturalist.org/t/how-to-use-inaturalists-search-urls-wiki/63
, weird twist on place exclusion: While searching through casual, I know how to exclude humans, pets, potted plants. and records without photos. If I also want to exclude ones without any location given, what is the proper exclusion term? These might not work: place_id=null or not_in_place=true (heh)

Then, I might as well also ask what the term is for excluding ones with no observation date. Thanks for advice!

Hm reading back over my post, it’s confusingly written. To be clear I want to search for observations that definitively do have a location, and exclude the ones without a location. These might not work for that: place_id=any or not_in_place=false

But since others may even specifically want to search for records without place or without date to help people get those particular orphaned observations in shape, I’ll leave the prior unclear post as an implied question about that too.
Find/Exclude observations without a location?
https://forum.inaturalist.org/t/find-exclude-observations-without-a-location/3571
https://forum.inaturalist.org/t/how-to-use-inaturalists-search-urls-wiki/63

To your question about location vs. place, the version released next week will say "Places" instead of "Locations" for clarity (and other changes needed to be consistent with the explanation text—these were the designs used to create the feel and core functions, but not the final copy).

?interpolate_coordinates=true

photos/?advanced=on

Here's the link for creating a traditional project: https://www.inaturalist.org/projects/new_traditional

Posted on August 10, 2019 16:08 by ahospers ahospers | 0 comments | Leave a comment

August 11, 2019

20190811 Drielanden KNNV Groningen InventarisatieProject (Trip)

20190811 Drielanden KNNV Groningen InventarisatieProject Ilse, Hugo, Thorhold, Andre, Wil, Stella

Posted on August 11, 2019 17:29 by ahospers ahospers | 26 observations | 0 comments | Leave a comment

August 17, 2019

KNNV Drielanden Lepidoptera night (Trip)

KNNV Nachtvlinder nacht

Posted on August 17, 2019 22:53 by ahospers ahospers | 0 comments | Leave a comment

KNNV Drielanden Lepidoptera night (Trip)

KNNV Nachtvlinder nacht

https://www.inaturalist.org/identifications?user_id=juliereid 3

Other parameters you can add:

&taxon_id=1234
&category=maverick|supporting|improving|leading Default: any
&current=false|any Default: true
&for=self|others|any Default: any
?interpolate_coordinates=true

Find observations missing a location
https://www.inaturalist.org/observations?quality_grade=any&place_id=any&not_in_place=91708,97391&user_id=ahospers&verifiable=any works!

https://www.inaturalist.org/identifications?user_id=juliereid&for=others
You can play with the other parameters, as well – adding different &PARAMETER=SETTING options. Choose between options separated by the “|”. It’s safe; you shouldn’t be able to break anything, just get

But there is still a huge need for classical projects: i.e. projects to which observations are manually added, or added by virtue of observation fields that are required. To my mind these are "tagged" projects. (in iNat logic one traditionally "added observations to projects", but for similar projects on iSpot we added tags and created projects to filter on the tags - the net effect is the same, a lookup table of project-tag and observation, that can be used as a filter - either alone or with other filters).
The addition of a project-tag filter to the new projects will make the "traditional" projects into "collection type" projects too, while preserving the Project Icons on the observations.
((the additional functionality of defining observation fields from within a project is an extremely useful feature.))

A nitpick: is the central filter a Location filter (using google places) or a Place filter (using user-created iNat polygons) or both? It would help if the terminology was standardized with the observations pages and its filters.

Posted on August 17, 2019 22:54 by ahospers ahospers | 2 comments | Leave a comment

August 22, 2019

Define import fields from Observation to iNaturalist like Number, ObservadoUr.

Waarnemingen.be In the old project one could add additional observation fields like 'Number', 'Observado Url' , 'Sex' etc. How can i import this into this project field ? The project leaf-and-plant-galls.csv has additional fields like ,Tags,Geoprivacy,Host,Reference URL,Gall Location.
Is it possible to do some nice conversion stuff with the TAG fields ?

OBSERVATION FIELD &field:Observado%20URL
https://www.inaturalist.org/observations?verifiable=any&place_id=any&field:Observado%20URL

blockquote OBSERVATION FIELD &field:Observado%20URL
https://www.inaturalist.org/observations?verifiable=any&place_id=any&field:Observado%20URL
blockquote

https://www.inaturalist.org/observations/import

Posted on August 22, 2019 07:31 by ahospers ahospers | 0 comments | Leave a comment

Locations are different than Places, don’t work l for searches.

the place_id numbers in the above examples can be found by using the Filters button on the Explore or Identify screens, then clicking More Filters near bottom, then starting to type a name into the Place box. (Caution: do not use the Location box above the filters, and make sure it is clear and blank - Locations are different than Places, oddly enough, and don’t work as well for searches.)

If what you are looking for comes up as a Place, select it and then you will see your browser address change to include place_id=XXXX, giving you the number for future use. If you plan to search that place a lot, you can set the Place (and any other Filter options) just as you like, then bookmark the resulting page in your browser for future use.

https://www.inaturalist.org/observations/import

Posted on August 22, 2019 07:39 by ahospers ahospers | 0 comments | Leave a comment

https://www.inaturalist.org/pages/extra_fields_nz

https://www.inaturalist.org/pages/extra_fields_nz

For all fields in iNaturalist NZ — Mātaki Taiao (and the global iNaturalist network), see https://inaturalist.nz/observation_fields/. Any of these fields can also be added to Projects as required or recommended fields for people to fill in. This is a great way to add value to the observations in a project.

If you cannot find the field you need, you can create it. Any field you create will be available to everyone across iNaturalist NZ — Mātaki Taiao and the whole iNaturalist Network. If you do create a new field, please take the time first to ensure that a field doesn't already exist with the same function. You can search all of the existing fields at https://inaturalist.nz/observation_fields/.

Recommended fields

Observation fields work best when everyone uses the same one field for a particular purpose. With that in mind, we list here our favourite fields that are commonly used throughout iNaturalist NZ.

General monitoring fields

For how long did you search? What did you look for? How many did you find?

Activity duration (minutes) (How long did you spend observing? Values are in hours and minutes.)
Count
Dead or alive
Is it wild?
Bands observed (For recording band combinations of banded individuals, like bird leg bands.)
Casual or planned observation (Was this observation an incidental, "casual" observation or the result of a planned search or survey for this species?)
Area searched (m2)
Searched for all birds (This observation was part of a survey for all birds.)
Searched for all dragonflies and damselflies (This observation was part of a survey for all dragonflies and damselflies.)
Searched for all butterflies (This observation was part of a survey for all butterflies.)
Searched for all plants (This observation was part of a survey for all plants, with or without mosses and liverworts.)
Searched for all (Specify the taxonomic group that you searched for in your survey.)
Taxon sought but not found (Specify the taxonomic group that you searched for in your survey, when you found none of them at all. Add this to an observation with no species ID.)
Identification uncertain
(For observations where you didn't get a photo/recording and you're pretty sure of your ID but not 100% certain.)
Sampling methods

Method of surveying for invertebrates
Five minute bird count method
Botany sampling method
Mammal tracking method
Monitoring_Plot/Site Non-Species Data (Add this to the Key observation in a series of observations that contains all of your Plot/Site data — this observation gets all of the non-biological and/or non-species-specific site data (e.g., weather data, soil type, slope, bare ground, moss cover, etc.))
People fields

Your name will automatically be added to your observation. However, sometimes you may also want to add names of other observers.

Original observer If you're not the person who originally made this observation, you can add their name in this field.
Photographer If you didn't take the photo, you can add the name of the photographer in this field.
Additional observers You can list the names of the people with you when you made the observation.
Number of observers If the number of observers is an important measure of collection effort for your project, you can include it with this field.
Substrate

Substrate refers to the kind of thing a species is growing on.

Lichen substrate
Substrate of fungus
Substrate_detail2 (drop down list of primarily epiphyte substrates)
Substrate type (dropdown list of bare ground textures)
Topography

Elevation (m) (You can usually get this later from maps but if you have more accurate on site information you can add it.)
Weather and Noise

The weather conditions can influence what species you find. The following are the standard weather fields used in NZ 5-minute bird counts.

Simple temperature (from " freezing (less than 0 degrees C)" to "hot (greater than 22 degrees C)")
Simple wind (from " Leaves still or move without noise (Beaufort 0 and 1)" to "Branches or trees sway (Beaufort 5, 6 and 7) ")
Direct sunshine (minutes) (make sure that you also use Activity duration (minutes), so that the proportion of time with direct sun can be calculated)
Preciptiation type (from "None" to "Snow")
Precipitation intensity (from "None" to "Heavy")
Noise (from "Not important" to "Loud")
Lifestage/Behaviour

Insect life stage
Bird life stage
Plant life stage
Fungi life stage
Simple life stage: adult or juvenile
Sex
Animal sign and song (useful if you just found tracks, or scat, or an empty nest, etc.)
Oviposition (was a female laying eggs?)
Plant phenology

Plant flower buds
Plant flowering
Plant immature fruit/seeds
Plant mature fruit/seeds
Plant seeds dispersed
Plant phenology: most common flowering/fruiting reproductive stage
Interactions

Nature is filled with species interacting with other species. These interactions are often poorly documented (what eats what, what pollinates what, etc.) so it's really helpful to add these fields to observations of species interacting. It's best to add each appropriate interaction to an observation using the relevant field starting with "Interaction->".

You can also add the link to another observation using the "associated observation" field.

Interaction->Flower visited by
Interaction->Visited flower of
Interaction->Fruit eaten by
Interaction->Ate fruit of
Interaction->Dispersed seed of
Interaction->Seed dispersed by
Interaction->Ate seed of
Interaction->Seed eaten by
Interaction->Preyed upon by
Interaction->Preyed on
Interaction->Herbivory by
Interaction->Herbivore of
type of herbivory
Interaction->Parasite of
Interaction->Parasitoid of
Interaction->Hemiparasite of
Interaction->Parasitised by
Interaction->Infected by
Interaction->Pathogen of
Interaction->Nested in
Interaction->Used as nest by
Interaction->Decomposer of
Interaction->Decomposed by
Interaction->Carcass scavenged by
Interaction->Scavenged carcass of
Interaction->Competition with
Interaction->Chasing
Interaction->Chased by
Mobbing
Mobbed by
Interaction->Egg(s) laid on/in
Interaction->Damaged
Interaction->Damaged by
Host
Is Host For
Perching on
Five minute bird count fields

Five minute bird count method
Count
Minimum number of individuals SEEN (If you're having trouble counting the exact number of individuals, it can be easier to provide a minimum and maximum for the number of individuals of a species that you see.)
Maximum number of individuals SEEN
Minimum number of individuals HEARD ONLY
Maximum number of individuals HEARD ONLY
Bird using habitat (Was the bird you saw using the local habitat or just flying by?)
Simple temperature (Which of the following best describes the temperature at your site?)
Simple wind (Which of the following best matches the wind conditions at your site?)
Noise (Noise can make it harder to detect some species (e.g. hear bird calls).)
Direct sunshine in 5 minutes (To the nearest minute, how much of your five minutes of sampling was the sun not blocked by cloud?)
Precipitation type
Precipitation intensity
Or, for including five minute counts inside longer bird counts:

Minimum number of individuals seen in first five minutes (Counts for just the first five minutes of your duration)
Maximum number of individuals seen in first five minutes (Counts for just the first five minutes of your duration. If one bird is seen and goes away and another of the same species is later seen, then the maximum is 2 and the minimum is 1.)
Minimum number of individuals HEARD ONLY in the first five minutes (Counts for just the first five minutes of your duration)
Maximum number of individuals HEARD ONLY in the first five minutes (Counts for just the first five minutes of your duration)
Minimum number of individuals seen after the first five minutes (Counts from the first five minutes to the end of the duration of your count)
Maximum number of individuals seen after the first five minutes (Counts from the first five minutes to the end of the duration of your count. If one bird is seen and goes away and another of the same species is later seen, then the maximum is 2 and the minimum is 1.)
Minimum number of individuals HEARD ONLY after the first five minutes (Counts from after the first five minutes to the end of your count duration)
Maximum number of individuals HEARD ONLY after the first five minutes (Counts for just the first five minutes of your duration)
Seen after the first five minutes (For simpler recording after the first five minutes: did you see this species only after the first five minutes of recording? Yes/No)
HEARD ONLY after the first five minutes (For simpler recording after the first five minutes: did you HEAR but not see this species only after the first five minutes of recording? Yes/No)
Pest mammal trapping

Trap Types The NZ standard trap types for mammalian pest control trap monitoring.
Other Trap Type This is the specified other trap type in the NZ standard trap types for mammalian pest control trap monitoring.
Trap Bait Type The NZ standard trap bait types for mammalian pest control pest trap monitoring.
Other trap bait type This is the specified other trap bait type in the NZ standard trap bait types for mammalian pest control trap monitoring.
Trap status The NZ standard trap status for mammalian pest control pest trap monitoring.
Bait Station target species The NZ standard bait station target species for mammalian pest control bait station monitoring.
Other bait station target species This is the specified other bait station target species in the NZ standard trap bait types for mammalian pest control trap monitoring.
Bait formulation The NZ standard bait formulation for mammalian pest control bait station monitoring.
Other bait formulation This is the specified other bait formulation in the NZ standard trap bait types for mammalian pest control trap monitoring.
Bait Station Type The NZ standard bait station type for mammalian pest control bait station monitoring.
Other Bait Station Type This is the specified other bait station type in the NZ standard trap bait types for mammalian pest control trap monitoring.
Bait active ingredient The NZ standard bait active ingredients for mammalian pest control bait station monitoring.
Other bait active ingredient This is the specified other bait active ingredient in the NZ standard trap bait types for mammalian pest control trap monitoring.
Taxonomy fields

These fields are for people good with names. Many NZ species don't have scientific names yet. Taxonomists say that species without formal names and scientific descriptions are "undescribed". Some are easily recognised and expected to be real species when the taxonomic work is done. These are given "tag names" in the mean time. To make observations of probable species

https://www.inaturalist.org/pages/extra_fields_nz

= = = = = =
https://www.inaturalist.org/pages/add-an-observation-nz
Don't be surprised if other users also add your observation to Projects on iNaturalist NZ — Mātaki Taiao, or add extra fields to your observation that can make it more useful to researchers. There are lots of Projects in iNaturalist NZ dedicated to gathering together particular kinds of observations. Extra fields are things like life stage, associated species, and reproductive state (like whether a plant is flowering). You can also add extra field information to your observations. See here for details.

We've only covered the essentials of adding an observation via the webpage. There are other features there too for power users. Import lets you upload lots of observations at once from your photo library on Facebook or Flickr, or you can bulk upload a whole spreadsheet. From photos lets you upload lots of photos at once from your hard-drive and iNaturalist NZ will look inside the file info of each photo for the date, time, location (from a camera GPS) and any recognisable species names added to the photo metadata.
https://www.inaturalist.org/pages/add-an-observation-nz
= = = = = =

Posted on August 22, 2019 11:47 by ahospers ahospers | 0 comments | Leave a comment

August 23, 2019

Analysing iNat data

While I haven’t done it with iNaturalist data, if you are trying to start doing data analysis on large datasets I suggest learning some python. Packages in python such as Numpy, Pandas, Scipy, Scikit-learn and Matplotlib go awfully far for data analysis.

I suspect it is possible to use pyinaturalist 3 and the API reference 1 for getting data out of iNaturalist as well, but it seems like you were already able to extract to excel already. https://pypi.org/project/pyinaturalist/ https://www.inaturalist.org/pages/api+reference Data analysis and visualization is really a field of its own. There are many different software applications, like R, python, etc, but you really need to have a working knowledge of these programming languages. If you’re only familiar with Excel, that might be the best place to start. There are not any programs specifically for easily working with iNat data.

https://forum.inaturalist.org/t/analysing-inat-data/6001/3

https://pypi.org/project/pyinaturalist/

https://www.inaturalist.org/pages/api+reference

?interpolate_coordinates=true

Find observations missing a location
https://www.inaturalist.org/observations?quality_grade=any&place_id=any&not_in_place=91708,97391&user_id=ahospers&verifiable=any works!

But there is still a huge need for classical projects: i.e. projects to which observations are manually added, or added by virtue of observation fields that are required. To my mind these are "tagged" projects. (in iNat logic one traditionally "added observations to projects", but for similar projects on iSpot we added tags and created projects to filter on the tags - the net effect is the same, a lookup table of project-tag and observation, that can be used as a filter - either alone or with other filters).
The addition of a project-tag filter to the new projects will make the "traditional" projects into "collection type" projects too, while preserving the Project Icons on the observations.
((the additional functionality of defining observation fields from within a project is an extremely useful feature.))

A nitpick: is the central filter a Location filter (using google places) or a Place filter (using user-created iNat polygons) or both? It would help if the terminology was standardized with the observations pages and its filters.

?interpolate_coordinates=true

photos/?advanced=on

Here's the link for creating a traditional project: https://www.inaturalist.org/projects/new_traditional

Posted on August 23, 2019 14:55 by ahospers ahospers | 0 comments | Leave a comment