I’m trying to use the API to download some data using the rinat package. I’m using the following code to get observations from one species per day, then binding the data together for one month. require(rinat) days <- c(1:31) firstDay <- min(days) obsMnt <- data.frame() for(d in days){ obsDay <- …

this thread probably shouldn’t be classified as a bug report since there’s not much iNat staff can do to address issues in rinat or in your own code. is there a particular reason you want to use rinat? as far as i can tell, that package seems to hit the deprecated iNat API. you could get data direc…

That’s a good point thanks for your feedback. I switched the classification to general. I didn’t realize that rinat seems to hit the depreciated iNat API. I’ll try spocc and see if that works.

A little tip I give for debugging loops in R is to manually set the iterator variable (“d”, here) to 1, and then go line by line and run the code inside the for-loop. After running each line you can print the result to console and make sure it looks like what you’re going for. Although, also lookin…

This way you are making 31 requests to get the data. Would it be possible to make only one API request (possibly with paging) and then loop through the observations?

I’ve found that if you make too many requests in rapid succession with rinat, the API starts throwing up errors. It might be better to just do one big call that gets all the observations of your taxon within your desired time frame and then filter that down in R.

Yes, that’s a good point about making one big request. I normally end up doing one big request, but sometimes it’s handy to use loops. This example could easily be done in one big request, but I think it’s useful for figuring out the problem because it’s small and doesn’t take long to reproduce.

Thanks for the tip! I actually tried that approach and each iterator seems to work if they’re run independently. I also tried experimenting with different numbers of days and the loop seems to break between roughly the 6th and 20th day, but not consistently with a particular number of days. It seems…

[image] kentross: or use the spocc package instead for what it’s worth, i don’t think using the spocc package will address API throttling by iNat, although i still think it’s better for you to get data from the current API (either directly or via a package like spocc), as opposed to getting d…

API (rinat) with for-loop has error that breaks loop in R

General

Topic		Replies	Views
Download +10.000 pictures from iNat user General question	5	465	April 23, 2024
R scripts to help analyse iNat content General	16	2234	December 10, 2020
R package rinat. User experiences? General	5	1899	May 5, 2021
Using R to extract observations of a specific phenological state General	7	2607	December 5, 2019
iNaturalist User Trends with R General third-party-tools	23	3112	July 24, 2020

API (rinat) with for-loop has error that breaks loop in R

Related topics