Haha. To be honest, I'd rather that people use a combination of species richness and an independent evenness measure, instead of these indices. If you like that idea, take a look at my Evar video, which is a nice evenness index
Thanks for making this video! It really helped me a lot and saved me a lot of time. People like you are making a difference in other people's studies. Greetings from Turkey.
This is wonderful! Thank you. I will add that if you copy the two columns of cells, you can right click on where you want to put them next and "insert copied cells" so that you eliminate the inserting two columns step.
You're a life saver, I know there is a website which makes this easy but doing it manually negates any worries regarding how legitimate it is. I feel like I owe you!
Happy to help! And hopefully now you know how to use Excel in some interesting ways too. Sometimes, having someone do something for you isn't as helpful in the end.
Precisely my point! It's worth a lot more to learn. I have to analyse 13 years of data for my ecology dissertation and one aspect is to look at the species diversity, so this video is priceless.
ahhh when you showed us the formula trick so we don't need to write the formula over and over and don't have to worry about 0 !! life saver thank you :D
I've been trying to avoid QIIME/R to obtain this index for a microbiome dataset, and your explanation through this video was incredibly helpful! Thank you so much!
If you calculate the diversity of each plot/sample, you can simply take the standard deviation of this value across plots/samples in Excel using the STDEV function
@kater81bln The highest we got for that data set was 2.14, but I haven't used it for much more than that. In general, I prefer to simply measure species richness and evenness separately.
My pleasure. Sorry about all the clicks etc. This was the first video I ever made this way and RUclips won't let me edit it now. Oh well. I'm glad it was helpful.
Joe, are you trying to test for differences between two sites or treatments? If so, probably an ANOVA would suffice. I'm glad you found the video helpful.
This is an index of diversity, and so is not the same as Evar, which is an index of evenness. If you wish to use two indices, one for diversity and one for evenness, I would suggest the combination of Species Richness, and Evar.
Hi Dr Schamp, thanks for this video! It was very clear and I learnt some new Excel tricks. I am doing a germination trial, with different heat treatments applied to some soil/seed samples. Soil was collected from each site and I wanted to do the average diversity across sites for each treatment. When there is only 1 species present, the diversity index is zero. I have some sites where there was no germination. What is the Shannon-Wiener index when there are no species present?
ANOVA would be useful for data like those presented in my example, with multiple plots in different treatments. Then you could test for differences across treatments using the plots within treatments as replicates that provide the variance. If you've only got one sample, I'm afraid you're not likely to have any good way to statistically test whether two numbers are from different parent distributions.
thank you for this, very helpful.Following on from Francois below, I have 2 different vegetation types where I am looking at invertebrates in each. Each veg type has 5 sites with 10 sub-plots in each. I have done the calculation for each sub-plot. To me it looks like there is a difference within the plots of both the vegetation types but how do I back this up and show that it is a significant difference? Is there another test I could use perhaps?
@youtubing8286 Hi there. This is equivalent to the blanks in each quadrat (site) in the example video. You wouldn't calculate the diversity in plots using the number of species in the community, just those in that site. So S would not be equal for both of your cites. I hope this is helpful.
Hey Dr, what if I have data for 3 sites (low, medium and high) by the environment gradient, and there are 12 quadrats for each site and 30 meters between each 2 as transects. How can i get both alpha and beta differences? Is that right to boxplot with low, medium and high as the x-axis and shannon diversity as y-axis? Furthermore, i want the beta diversity as well, Not sure if i made it clear or not.
Thanks for this video great help. I don't suppose anyone knows what statistical test to run to see if there is a significant difference in the shannon-weiner diversity index?
Hi there, sorry for the delay in responding. I didn't see this comment until now. You could certainly just compare alpha diversity across 'treatments' (low, med, high). As for beta diversity, there are a lot of different ways to do that. I'm afraid getting into that wouldn't be possible here. You'll have to do some digging and reading! Good luck.
This video is extremely helpful. I was wondering whether the S-W index can be calculated by just using averaged species data (of quadrats/plots). Or would the S-W index have to be calculated for each plot/quadrat? And if you want to obtain an overall S-W index for the entire community, would you average out each of the S-W indexes calculated on a plot-by-plot basis? Thank you!
Off hand, I'm not sure if the average would be the same as calculating the index across all the plots. But you can certainly just add up all the plot data and calculate it for the whole community to check! That's probably pretty easy if you've already done the plots. Good luck!
Thank you for the video, it is very helpful. I've read that the meaning of the values is very limited and doesn't tell you much. What would be a good interpretation of the values obtained? Thank you
That's a good question. This index arbitrarily weights richness and evenness here. I admit that while it's a commonly taught metric, I tend to prefer to use species richness, and a separate and independent measure of relative abundance in assessments of diversity. Combining the two the way several diversity indices do may be useful for comparisons, but if you're trying to understand what drives patterns, I think it's better to examine the two aspects of diversity separately. I'm not sure that's a simple answer, but there you are!
Actually, it definitely helped me decide for my second option, which was discussing species richness and relative abundance. It was fun learning those tricks in excel anyways! Thank you
Great. Consider the Evar index of relative abundance, which I have another video for. It is not correlated with richness, and so when you examine each, they are not conflated. Good luck
excellent description, it helped a lot. thank you. however, i do have one question if you don't mind, i sampled 8 marshes (each marsh for 12 months) for phytoplankton biomass; in this case do i have to calculate SW from monthly or can i calculate it using the annual biomass? thanks again
Glad you found it helpful. I would say you could do both. That said, it's worth noting that phytoplankton species are seasonal, so you might get different answers from each of the analyses. Both address different questions. Also, if you want to know in more detail what the nature of the differences between the marshes are, I would recommend examining species richness patterns and evenness patterns separately. I'd also recommend an evenness metric that is independent of species richness variation, like Evar (I have a video on how to calculate Evar). Good luck!
thanks Dr. Brandon. i did calculate the Evar as well as SW and simpson index. if you have time would you be interested to post a video describe the best method to select the most dominant species within a system. for example, in your demonstration above you have many plant species collected from an environment where some of them have very low abundance comparing to others. lets awesome, that you want to chose only the most dominant (abundant) species to do CAA analysis. what method (test) you should use that allows you to chose some species than others? i will be grateful if you helped me in this case.... best regards
I have abundance data in the form of the Domin scale of percentage cover (a scale of 1-10). I understand that this loses a lot of information, but can I still calculate a diversity index with this domin cover data or will it be meaningless?
I see no reason not to use these values. The loss of information happens whenever we use an index, and there are many discussions about how best to record abundance data. Just about all approaches can be criticized, depending on how they are used. As long as you make it clear what you have done and interpret the data reasonably, I think you are fine.
Hi Brandon, I have 2 plots to compare - each plot is divided in 16 sublots. Is it enough to calculate the indice for the entire plot or is it worth looking at the indice at the subplot level ? Francois
+François Tron Hi there. You've got options there, but I think the most informative option would be to calculate it for all sub-plots and compare the sub-plots across the two main plots. Of course, there may be some issues related to how independent the subplots are, depending on whether they are randomly placed. For example, two subplots may be pseudoreplicates if they are similar because they are side-by-side. I hope this helps
@luanswan2002 I'd advise just calculating the index for plants and animals separately; it would be a bit fishy to try to scale the two measures together. Good luck
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You're a savior to all Environmental Technicians
Haha. To be honest, I'd rather that people use a combination of species richness and an independent evenness measure, instead of these indices. If you like that idea, take a look at my Evar video, which is a nice evenness index
I learned more from this than any of the similar statistics workshops I attended to help me with my Marine Zoology course. Thank you.
Thanks for making this video! It really helped me a lot and saved me a lot of time. People like you are making a difference in other people's studies. Greetings from Turkey.
This is wonderful! Thank you. I will add that if you copy the two columns of cells, you can right click on where you want to put them next and "insert copied cells" so that you eliminate the inserting two columns step.
You're a life saver, I know there is a website which makes this easy but doing it manually negates any worries regarding how legitimate it is.
I feel like I owe you!
Happy to help! And hopefully now you know how to use Excel in some interesting ways too. Sometimes, having someone do something for you isn't as helpful in the end.
Precisely my point! It's worth a lot more to learn. I have to analyse 13 years of data for my ecology dissertation and one aspect is to look at the species diversity, so this video is priceless.
ahhh when you showed us the formula trick so we don't need to write the formula over and over and don't have to worry about 0 !! life saver thank you :D
Thank you for the video, Dr. Schamp. It's very well explained, short, clear, and very helpful.
Thank you so much! You were 100X more helpful then my professor was when I asked for help on analyzing my data for a conference presentation.
You're very welcome, and I'm sorry about your professor. All the best!
Extremely helpful for our IPM/applied ecology group, especially for our students. Thanks.
I've been trying to avoid QIIME/R to obtain this index for a microbiome dataset, and your explanation through this video was incredibly helpful! Thank you so much!
You're very welcome.
Thank you for sharing your knowledge. This saved me a lot of stressing.
This was a MASSIVE help. I have species diversity coursework I have to do and this has benefited me greatly. Thank you!
No problem. Share it!
Dude, you saved me on the all nighter I had to do to complete my assignment, and for that I thank you :)
Thanks so much. This was exactly what I needed for my last lab of 12th grade before winter break!!
You are an excel god, and now i am a subscriber
Thanks a lot, it's so great to you showed also the excel shortcuts, they help massively with huge datasets!
Thank you so much for the tutorial. Became more familair with excel than ever before
Great. I'm glad it helped
Thank you so much! This video is beyond helpful! I'm sharing it with my class tomorrow!
Just analysing my dissertation data and this helped a lot. Thank you!
A trick: watch movies at Flixzone. I've been using it for watching loads of movies during the lockdown.
@Quinton Ayaan yea, I have been watching on flixzone} for months myself =)
Thank you so much dude, you helped me save a lot of time on my AP Environmental Class with this video :)
I've used this video for doing my homework, thanks a lot Mr Brandon Schamp
this was amazing clear and simple, made a supposedly difficult calculation appear simple and straight forward, top job xx
Thanks! I'm glad it was helpful.
This was very helpful, I managed to finish my project thanks to this video
Cheers :D
This has saved me so much time thank you!!
You're very welcome.
This was wonderful, really showed me the many different features of excel! thanks!!
I hope you answered that email at 5:09, you may be a winner!
In all seriousness, thank you for helping me study for my Ecology final :)
Thank you! This has made my life so much easier!
...dude...just...dude, i love you more than anything right now!
I also did this on fishery data - thank you so much!
By far! Phew, made our lives easier!
Thank you so much!
This is the most genius thing I've ever encountered !!
Appreciate it and thanks for sharing :)
@Bitchyology
You're welcome! I'm glad you found it helpful. There's another one for an index of evenness if you're interested. (Evar)
I'm glad you found it useful, and thanks for passing it on
If you calculate the diversity of each plot/sample, you can simply take the standard deviation of this value across plots/samples in Excel using the STDEV function
Great video, very informative and easy to understand. thanks
Thank you so much for sharing your knowledge.Helped me a lot.
Did this with counts data for fish. Thank you so much!
Glad it was helpful!
Thank you so much, this was very helpful.
This helped me so much. Thank you for making this video!
Thank you for this. It help me to understand more. Cheers!
AMZING!!!!!!!Thanks!!!U saved my life!!!!!
@kater81bln The highest we got for that data set was 2.14, but I haven't used it for much more than that. In general, I prefer to simply measure species richness and evenness separately.
Thanks Dr. Schamp! Very helpful!
Katherine Barry You're very welcome. Glad I could help
My pleasure. Sorry about all the clicks etc. This was the first video I ever made this way and RUclips won't let me edit it now. Oh well. I'm glad it was helpful.
No problem everyone. I'm glad it was helpful
I wish I had known these tricks in Excel when I was in undergrad :)
Hey Brandon you may already be a winner!
Thanks so much for this video, incredibly useful!
I love you! Saved my life. My Allah bless you and your family!
You're very welcome.
Joe, are you trying to test for differences between two sites or treatments? If so, probably an ANOVA would suffice. I'm glad you found the video helpful.
I'm glad you found it helpful!
This is an index of diversity, and so is not the same as Evar, which is an index of evenness. If you wish to use two indices, one for diversity and one for evenness, I would suggest the combination of Species Richness, and Evar.
No problem. I'm glad it helped
You're very welcome. Good luck as you finish up.
Wow, that was incredibly helpful. Thank you!
Cheers Man awesome help
if i use the shannon diversity index to find the species evenness, can i get the same answer if i use the EVAR? thanks
Gracias por compartir, Claro y sencillo. Fue de mucha ayuda.
Hi Dr Schamp, thanks for this video! It was very clear and I learnt some new Excel tricks. I am doing a germination trial, with different heat treatments applied to some soil/seed samples. Soil was collected from each site and I wanted to do the average diversity across sites for each treatment. When there is only 1 species present, the diversity index is zero. I have some sites where there was no germination. What is the Shannon-Wiener index when there are no species present?
thank you so much:)) great video.
thanks a lot! I figure if you reverse the species and plot, it might be easier to speed up.
This was so helpful, thank you!
Does this work as well with number of individuals counted instead of biomass. I tried it out and it seems fine, but I'm a statistics novice.
Thanks a lot, helped by a ton!
Glad to hear it!
Same!
ANOVA would be useful for data like those presented in my example, with multiple plots in different treatments. Then you could test for differences across treatments using the plots within treatments as replicates that provide the variance. If you've only got one sample, I'm afraid you're not likely to have any good way to statistically test whether two numbers are from different parent distributions.
thank you for this, very helpful.Following on from Francois below, I have 2 different vegetation types where I am looking at invertebrates in each. Each veg type has 5 sites with 10 sub-plots in each. I have done the calculation for each sub-plot. To me it looks like there is a difference within the plots of both the vegetation types but how do I back this up and show that it is a significant difference? Is there another test I could use perhaps?
@youtubing8286 Hi there. This is equivalent to the blanks in each quadrat (site) in the example video. You wouldn't calculate the diversity in plots using the number of species in the community, just those in that site. So S would not be equal for both of your cites. I hope this is helpful.
My pleasure. I'm glad it helped
Hey Dr, what if I have data for 3 sites (low, medium and high) by the environment gradient, and there are 12 quadrats for each site and 30 meters between each 2 as transects. How can i get both alpha and beta differences? Is that right to boxplot with low, medium and high as the x-axis and shannon diversity as y-axis? Furthermore, i want the beta diversity as well, Not sure if i made it clear or not.
With all the plots you have, would you take the mean of every H' or as you have it SW Divers. value to get a H' value that you can report?
Thank you Brandon!
Thanks for this video great help. I don't suppose anyone knows what statistical test to run to see if there is a significant difference in the shannon-weiner diversity index?
Was wondering if you knew how to normalize the Shannon-Wiener Index or do you do that already in the fourth column by taking the natual log of the Pi?
Hi there, sorry for the delay in responding. I didn't see this comment until now. You could certainly just compare alpha diversity across 'treatments' (low, med, high). As for beta diversity, there are a lot of different ways to do that. I'm afraid getting into that wouldn't be possible here. You'll have to do some digging and reading! Good luck.
Well explained, thanks a lot!
Wouw!! Its wonderful
You're very welcome.
Thanks, this was really helpful :)
Incredible advice, thanks mano!
My pleasure.
Honestly... I love you for this... I do...
Thank you!
I'm glad it was helpful!
This video is extremely helpful. I was wondering whether the S-W index can be calculated by just using averaged species data (of quadrats/plots). Or would the S-W index have to be calculated for each plot/quadrat? And if you want to obtain an overall S-W index for the entire community, would you average out each of the S-W indexes calculated on a plot-by-plot basis? Thank you!
Off hand, I'm not sure if the average would be the same as calculating the index across all the plots. But you can certainly just add up all the plot data and calculate it for the whole community to check! That's probably pretty easy if you've already done the plots. Good luck!
Thank you for the video, it is very helpful. I've read that the meaning of the values is very limited and doesn't tell you much. What would be a good interpretation of the values obtained? Thank you
That's a good question. This index arbitrarily weights richness and evenness here. I admit that while it's a commonly taught metric, I tend to prefer to use species richness, and a separate and independent measure of relative abundance in assessments of diversity. Combining the two the way several diversity indices do may be useful for comparisons, but if you're trying to understand what drives patterns, I think it's better to examine the two aspects of diversity separately. I'm not sure that's a simple answer, but there you are!
Actually, it definitely helped me decide for my second option, which was discussing species richness and relative abundance. It was fun learning those tricks in excel anyways! Thank you
Great. Consider the Evar index of relative abundance, which I have another video for. It is not correlated with richness, and so when you examine each, they are not conflated. Good luck
mate you are great! thnks a lot
You've very welcome. Please feel free to share with anyone who could use it.
Please how do I find overall Sharnon Weiner index
No problem! Glad it helped.
excellent description, it helped a lot. thank you. however, i do have one question if you don't mind, i sampled 8 marshes (each marsh for 12 months) for phytoplankton biomass; in this case do i have to calculate SW from monthly or can i calculate it using the annual biomass? thanks again
Glad you found it helpful. I would say you could do both. That said, it's worth noting that phytoplankton species are seasonal, so you might get different answers from each of the analyses. Both address different questions. Also, if you want to know in more detail what the nature of the differences between the marshes are, I would recommend examining species richness patterns and evenness patterns separately. I'd also recommend an evenness metric that is independent of species richness variation, like Evar (I have a video on how to calculate Evar). Good luck!
thanks Dr. Brandon. i did calculate the Evar as well as SW and simpson index. if you have time would you be interested to post a video describe the best method to select the most dominant species within a system. for example, in your demonstration above you have many plant species collected from an environment where some of them have very low abundance comparing to others. lets awesome, that you want to chose only the most dominant (abundant) species to do CAA analysis. what method (test) you should use that allows you to chose some species than others? i will be grateful if you helped me in this case.... best regards
how would I go about doing this if I used percent cover for abundance?
When using ANOVA, how does one calculate the variance of the index. It is a single number, after all.
Thank you very much men!!!
I have abundance data in the form of the Domin scale of percentage cover (a scale of 1-10). I understand that this loses a lot of information, but can I still calculate a diversity index with this domin cover data or will it be meaningless?
I see no reason not to use these values. The loss of information happens whenever we use an index, and there are many discussions about how best to record abundance data. Just about all approaches can be criticized, depending on how they are used. As long as you make it clear what you have done and interpret the data reasonably, I think you are fine.
Geez thank you!!!
Hi Brandon, I have 2 plots to compare - each plot is divided in 16 sublots. Is it enough to calculate the indice for the entire plot or is it worth looking at the indice at the subplot level ?
Francois
+François Tron Hi there. You've got options there, but I think the most informative option would be to calculate it for all sub-plots and compare the sub-plots across the two main plots. Of course, there may be some issues related to how independent the subplots are, depending on whether they are randomly placed. For example, two subplots may be pseudoreplicates if they are similar because they are side-by-side. I hope this helps
Ha! I know about the duplicates. Funny that you caught that. Damn Lycopus!
Thanks a lot! :)
Thank you very much, great video!!! (y)
@luanswan2002 I'd advise just calculating the index for plants and animals separately; it would be a bit fishy to try to scale the two measures together. Good luck
Thanks ! Really usefull :)