Thanks for the video. However, when I try to nmdsscore and make a dataframe it shows: "arguments imply differing number of rows: 7, 5". Is there any probable soulution?
Very nice and informative viedo. Very simple to understood. Could you please strat makeing a viedo or at leat sharing some good resources about Inkscape softeware as well? That will be very useful as well.
Thank u for this video , it 's really helpful. I have a question : if my data is a multiple kraken reports each report is for a sample, how to deal with that ? i tried to combine the reports and to analyse them to know the most abandoned one . bacteria in them but i failed .
Thank you for the video, this was really helpful and clear. Though it doesn't explain the basic working behind it in that much detail, we can still understand the basics and how to perform it. For other complicated stuff there are other videos of course. :-D Cheers!
Is there anyway in which you can add the species data to the final NDMS plot? Similar to the basic plot which is shown at the beginning with the plot function, but with the GGplot function?
Finally I found the problem: "The newest version of the vegan package (>2.6-2) changed the format of the scores(nmds) object to a list, and so the above code will throw an error saying arguments imply differing number of rows. If you get this error try the following code instead to extract your site scores" data.scores = as.data.frame(scores(nmds)$sites) so just add $sites and it should work. At least it worked in my case
Great video! However, I have a problem with the "as.data.frame" function, it would not let me plot scores in nmds_result because arguments imply differing number of rows; 29, 88, because I have 88 species in 29 plots. How do I solve this error?
this error appeared. Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, : arguments imply differing number of rows: 9, 40. Can you help me?
NMDS is a random process. Every time you run the model you will get a different result. set.seed command makes sure that you obtain the same results each time you run your nmds model. You can try running NMDS with out set.seed command to find out the difference in stress values and arrangement of samples every time you run the modle .
Madhu, you are excellent!
The code for others:
library(vegan)
library(tidyverse)
set.seed(100)
nmds
Very informative and simple to understand. Even better than chatGPT.
Excelente aporte, aunque el vídeo no esta en mi idioma nativo, es completamente entendible, les doy una solucion al problema nmdsscores
The rooster in the back is the best 😄
Thanks for the video. However, when I try to nmdsscore and make a dataframe it shows: "arguments imply differing number of rows: 7, 5". Is there any probable soulution?
Fantastic video! Thank you so much!
Very nice and informative viedo. Very simple to understood. Could you please strat makeing a viedo or at leat sharing some good resources about Inkscape softeware as well? That will be very useful as well.
Thank you! Check out this playlist for inkscape tutorials: th-cam.com/video/8f011wdiW7g/w-d-xo.htmlsi=ew4zaviTYpjMO-IF
Thank you so much for the video! :))
How did you perform the bar chart? Do you have a code? :D
Thank u for this video , it 's really helpful. I have a question : if my data is a multiple kraken reports each report is for a sample, how to deal with that ? i tried to combine the reports and to analyse them to know the most abandoned one . bacteria in them but i failed .
Thank you for the video, this was really helpful and clear. Though it doesn't explain the basic working behind it in that much detail, we can still understand the basics and how to perform it. For other complicated stuff there are other videos of course. :-D Cheers!
Thanks bro👍👍
Is there anyway in which you can add the species data to the final NDMS plot? Similar to the basic plot which is shown at the beginning with the plot function, but with the GGplot function?
First you have to extract the NMDS scores (X and Y values as NMDS1 and NMDS2)
nmdsscores
Nice video. I appreciate. I tried to run your script as exercise. But I'm getting this error:
> nmdsscores
Finally I found the problem:
"The newest version of the vegan package (>2.6-2) changed the format of the scores(nmds) object to a list, and so the above code will throw an error saying arguments imply differing number of rows. If you get this error try the following code instead to extract your site scores"
data.scores = as.data.frame(scores(nmds)$sites)
so just add $sites and it should work. At least it worked in my case
@@philippjeske163 Great. This will work too : scores(nmds_result, display="site")
Solved using this line: nmdsscores
Great video! However, I have a problem with the "as.data.frame" function, it would not let me plot scores in nmds_result because arguments imply differing number of rows; 29, 88, because I have 88 species in 29 plots. How do I solve this error?
Hope this will help : www.statology.org/r-arguments-imply-differing-number-of-rows/
How did you do the species composition graph, could you give the script, please?
I used the function barplot() to generate the basic black and white plot. And colours were added using Inkscape.
I really liked your video and it was very useful! It would be interesting you did a tutorial also about the barplot graph! thanks!
@@kassiocastroo Thank you..... And Sure, I will post more videos on data visualisation.
Sir, if we get poor fit, what to do then
It means that your sample size may be inadequate (you need to have more samples), or there is no grouping pattern in your dataset.
@@Researchocrat , kindly make video on pcoa cca and rda also, the way u expalin is very informative,
this error appeared. Error in (function (..., row.names = NULL, check.rows = FALSE, check.names = TRUE, :
arguments imply differing number of rows: 9, 40. Can you help me?
Hope this will help : www.statology.org/r-arguments-imply-differing-number-of-rows/
@@Researchocrat not helping
as example if i replace with NA then the code is not running
@@Dr.munna89 Try this instead : scores(nmds_result, display="site")
why i need to use the set.seed code?
NMDS is a random process. Every time you run the model you will get a different result.
set.seed command makes sure that you obtain the same results each time you run your nmds model.
You can try running NMDS with out set.seed command to find out the difference in stress values and arrangement of samples every time you run the modle .
@@Researchocrat i get it, thanks for the explanation and thanks for the video to
Thanks for the Video, very useful for nob like me..
Btw, i am getting stag at this line: nmdsscores
Hi
Please make the following changes to your code.
nmdsscores
@@Researchocrat Thanks brother, it finally work..😄
Very useful video
Reading in the black is very difficult.