This has been the most helpful vid I've found and goddamn it could've saved me so much frustration if I had just clicked on this one first instead of the others. Thank you, and also for the references at the end
Thank you for this, I've been looking all over the place trying to find out how to do species accumulation curves using PAST, SPSS and R, but this is so straightforward and well-explained.
Hello! Thank you for this tutorial. Is there any data that shows confidence that enough samples have been collected at each site for the infrequency data? would this be when SC> 0.95. I am trying to see if a sight has been visited enough to have seen all of the species statistically.
No, I don't think there is. If you don't want to do it in R, some colour changes can be done in Photoshop by manipulating the 'hue'. But that might not be an easy fix for most people.
Thank you very much for the excellent tutorial. I was able to use a lot of it as a handrail for working with the package in R. I have noticed that the R package returns some ridiculous estimates for Shannon/Simpson. For example, in my first grouping, where I had an observed sp rich of 22, the observed Shannon score was 16.8, which is ridiculous/wrong. And that is for an observed value, not inter/extrapolated. Have I missed something or is there a problem with the back-end calculation in the function? Thanks again heaps!
Your video was great and helpful, thank you! If my input data is species incidence frequencies (trap captures), is my understanding correct that the data I'll be inputting are the number of captures? Also, are all the data input non-zeroes, and does that mean I should remove out my zeroes? For example, at a certain elevation no individuals were captured for a certain species so do I remove this 0 data entry? Should my data entry for example be: h250m 1000 2 10 5 instead of: h250m 1000 0 2 10 0 5 Hope I made sense and would appreciate your help!
I don't have all information I need to help you here, but if you are using 'incidence' rather than abundance, each entry (after the number of traps or trap days) is the number of traps/days/units that a species occurred in. If a species was absent from ALL traps at a site, then it did not occur so is not included in the data for that site. I think this agrees with what you are saying!
Thank you very much, very helpful video indeed. In the video, you describe the method of using bootstrapping to estimate a value of expected richness, and averaging the value to get a rarefied value. Is there a way to extract these averaged values from the output, so that they can be used in generalised linear/linear modelling in addition to creating an accumulation curve?
For me it was useful to read the vignette, which has more detailed descriptions. Just type "vignette("Introduction", package = "iNEXT")" in R console. In it you will also find how to manipulate the ggiNEXT() function to handle the plot
Thank you for this video, it helped me very much. Of course much thanks as well to the great team that made this online software work. i have one question though: When i put the data for three different sites the first graph seemed very logical. But the completness one i didnt understand. it was showing me that a site with less species was more complete than the ones with more species. If anyone knows what might be the problem please let me know.
Hi there,Thanks a lot for the video, it's very useful! I would like to ask you a question: if i have camera trap data, how should i build my data frame to get a rarefied species accumulation curve using camera trap days?. For example, if i use 8 cameras for 30 days, would i have to account for species appearing when i have 8 camera trap days (8 cameras on day 1), then when i have16 camera trap days (8 cameras on day 2) and so on until i reach the 30x8 camera trap days? Or should i start when i have 1 camera trap day (1 camera on day 1)? Because i can imagine how to relate the appearing of species when i start at 1 camera trap day :((( Thank u so much.
Great question! We treat each camera as a separate sampling unit, but you have the option of using each camera day as you say above (and as we have used in our papers), or having a sampling unit that lasts longer (say six days as we use with occupancy modelling). I agree that 1 camera day makes more sense intuitively, and suggest starting with that.
@@uoswildlife Thank you so much for answering me! Now i have other question: If i choose start at 1 camera trap day, how should i build my data frame? would i have to record species appearing at each day the camera 1 was functioning, and then the same with each camera? I mean, for example, that if i had 3 cameras for 3 days and i found species A, B, C, i would make something like this: First, i organize my data as follow: Camera 1 Camera 2 Camera 3 1 2 3 4 5 6 7 8 9 ← camera trap days: 4 represents camera 2 on day 1, Species A 2 0 2 4 4 1 1 0 2 7 represents camera 3 on day 1 Species B 0 2 1 0 0 0 4 3 8 Species C 0 0 1 0 0 0 4 7 8 And then, the data i would put on iNext would be: Bosque1 9 7 5 4 Where the first number represents the total camera trap days i got, and the next numbers represent the number of sampling units (ie. camera trap days) in which i recorded each species. I'm really confused with this, because i don't know if the order i assign to my cameras could affect the estimate or if that can be corrected by bootstrapping or if i'm completely wrong. Thank you so much. I'm apologyze for asking such a long question
This has been the most helpful vid I've found and goddamn it could've saved me so much frustration if I had just clicked on this one first instead of the others. Thank you, and also for the references at the end
Thank you!
Thank you for this, I've been looking all over the place trying to find out how to do species accumulation curves using PAST, SPSS and R, but this is so straightforward and well-explained.
Thank you!! And thanks Anne Chao!
Nice thank you very much! Great help!
Does it make sense to do this for equal sample sizes of N=40 in let's say 3 groups?
Hello! Thank you for this tutorial. Is there any data that shows confidence that enough samples have been collected at each site for the infrequency data? would this be when SC> 0.95. I am trying to see if a sight has been visited enough to have seen all of the species statistically.
Thank you so much for your video! really! :)
Great video but one question: do i also have make a rarefaction if my data is binary (present/absent of taxa in different geological time units?)
That's not a usage I've seen before... testing sample completeness within a geological time period sounds like it might be appropriate though.
Great video! Is there a way to change the color of the plots directly in iNEXT Online (as opposed to in R)?
No, I don't think there is. If you don't want to do it in R, some colour changes can be done in Photoshop by manipulating the 'hue'. But that might not be an easy fix for most people.
@@uoswildlife Okay, thanks so much!
Thank you very much for the excellent tutorial. I was able to use a lot of it as a handrail for working with the package in R. I have noticed that the R package returns some ridiculous estimates for Shannon/Simpson. For example, in my first grouping, where I had an observed sp rich of 22, the observed Shannon score was 16.8, which is ridiculous/wrong. And that is for an observed value, not inter/extrapolated. Have I missed something or is there a problem with the back-end calculation in the function? Thanks again heaps!
Try to search exponential of Shannon entropy Exp(H')
Would you please tell what is the meaning of the shaded region around the rarefaction curve? thank you!
thank you for the video. I want to have species diversity on x-axis and no. of sampling units on y-axis. will that be possible???
Your video was great and helpful, thank you! If my input data is species incidence frequencies (trap captures), is my understanding correct that the data I'll be inputting are the number of captures? Also, are all the data input non-zeroes, and does that mean I should remove out my zeroes? For example, at a certain elevation no individuals were captured for a certain species so do I remove this 0 data entry?
Should my data entry for example be:
h250m
1000
2
10
5
instead of:
h250m
1000
0
2
10
0
5
Hope I made sense and would appreciate your help!
I don't have all information I need to help you here, but if you are using 'incidence' rather than abundance, each entry (after the number of traps or trap days) is the number of traps/days/units that a species occurred in. If a species was absent from ALL traps at a site, then it did not occur so is not included in the data for that site. I think this agrees with what you are saying!
Thank you very much, very helpful video indeed. In the video, you describe the method of using bootstrapping to estimate a value of expected richness, and averaging the value to get a rarefied value. Is there a way to extract these averaged values from the output, so that they can be used in generalised linear/linear modelling in addition to creating an accumulation curve?
The values you need should be given on the other tabs when you run the analysis
How can i change axis label after i download the figure??
Hey bro, thanks!!!
problem with bigger data with online plots. I had to use R, yet still trying to learn how to handle plots (modify text size etc)
For me it was useful to read the vignette, which has more detailed descriptions. Just type "vignette("Introduction", package = "iNEXT")" in R console. In it you will also find how to manipulate the ggiNEXT() function to handle the plot
I can not select my sites together, I copy pasted my data from excel
Thank you for this video, it helped me very much. Of course much thanks as well to the great team that made this online software work.
i have one question though: When i put the data for three different sites the first graph seemed very logical. But the completness one i didnt understand. it was showing me that a site with less species was more complete than the ones with more species.
If anyone knows what might be the problem please let me know.
Hi there,Thanks a lot for the video, it's very useful! I would like to ask you a question: if i have camera trap data, how should i build my data frame to get a rarefied species accumulation curve using camera trap days?. For example, if i use 8 cameras for 30 days, would i have to account for species appearing when i have 8 camera trap days (8 cameras on day 1), then when i have16 camera trap days (8 cameras on day 2) and so on until i reach the 30x8 camera trap days? Or should i start when i have 1 camera trap day (1 camera on day 1)? Because i can imagine how to relate the appearing of species when i start at 1 camera trap day :((( Thank u so much.
Great question! We treat each camera as a separate sampling unit, but you have the option of using each camera day as you say above (and as we have used in our papers), or having a sampling unit that lasts longer (say six days as we use with occupancy modelling). I agree that 1 camera day makes more sense intuitively, and suggest starting with that.
@@uoswildlife Thank you so much for answering me! Now i have other question: If i choose start at 1 camera trap day, how should i build my data frame? would i have to record species appearing at each day the camera 1 was functioning, and then the same with each camera? I mean, for example, that if i had 3 cameras for 3 days and i found species A, B, C, i would make something like this: First, i organize my data as follow:
Camera 1 Camera 2 Camera 3
1 2 3 4 5 6 7 8 9 ← camera trap days: 4 represents camera 2 on day 1,
Species A 2 0 2 4 4 1 1 0 2 7 represents camera 3 on day 1
Species B 0 2 1 0 0 0 4 3 8
Species C 0 0 1 0 0 0 4 7 8
And then, the data i would put on iNext would be:
Bosque1 9 7 5 4
Where the first number represents the total camera trap days i got, and the next numbers represent the number of sampling units (ie. camera trap days) in which i recorded each species.
I'm really confused with this, because i don't know if the order i assign to my cameras could affect the estimate or if that can be corrected by bootstrapping or if i'm completely wrong.
Thank you so much. I'm apologyze for asking such a long question
@@valentinaecheverry9957 looks correct!
@@uoswildlife thank u so much for answering me c:
Species diversity as in for animals or plants?? Ot both?? Please help
it can be used for plants, but more commonly for animals where sampling means we are not sure if we have seen all the species yet.
Is this software freely available
Yes, just use the URL shown at the start - it runs over the web
Thank you