R - Nonmetric Multidimensional scaling (NMDS)

Рет қаралды 35,295

5 жыл бұрын

IMPORTANT UPDATE:
Internal R coding/language was recently changed, so that the color and shape scheme as explained in the tutorial no longer works.
The script has therefore been rewritten using ggplot2 for visualization. The updated code can be found and downloaded here (Make sure you have the file "nmdsUPDATED.r"):
R script download: rstatisticsandresearch.weebly...
Real-life example
Assumptions
Output interpretation
R studio tutorial
NMDS
Multivariate statistics

Пікірлер: 64

@valeriiadedus3594 3 жыл бұрын

Thank you a lot for this video. I did everything definitely the same, but when I pressed "run" for plot I didn't have a plot with red and blue dots. It's just empty field. After I pressed "run" for ordispider and I got the line in different directions but without red or blue dots. Could you please tell me what I did wrong ?

@RStatisticsandResearch 3 жыл бұрын

Hello, internal R code had recently been changed. I therefore rewrote the script using ggplot for visualization. You can find the updated script here: rstatisticsandresearch.weebly.com/nonmetric-multidimensional-scaling-nmds.html

@valeriiadedus3594 3 жыл бұрын

@@RStatisticsandResearch perfect, thank you very much!

@ekkirizkiramadhan3553 5 ай бұрын

hi, i got error while convert to data frame 🙏@@RStatisticsandResearch

@backyardbiology5894 3 жыл бұрын

This is absolutely amazing! You have clarified a problem that I have been struggling to understand for months. I was so close to scrapping this analysis from my thesis. You are a hero!

@hibitrithibitrit7264 Жыл бұрын

You did a fantastic job explaining this. Thanks for helping with my r-stat homework! I have proven that cougars found in boreal forests have a different environmental features in comparison to cougars found in prairie habitat. Yes, it is very obvious which makes it excellent practice data.

@hanhnguyen84 4 жыл бұрын

Thank you so much! This the best instruction so far for NMDS!

@yelenasofiapajaroesquivia3634 2 жыл бұрын

This was exactly what I was needing. Thank you so much!

@jalrox123 4 жыл бұрын

This is best tutorial. Very simple to understand. Thank you.

@diahidvegi8536 4 жыл бұрын

How sweet! Thank you so much for this explanation. Very clear. :)

@raflikamil9403 3 жыл бұрын

Thank you so much. Your work definitely helps me a lot.

@TheJremple 3 жыл бұрын

This is a great tutorial. Thank you for making this video.

@videogrillo 5 жыл бұрын

I am a master student in Tel Aviv University and this video has helped me more than anyone here, thanks for your submission, I will immediately subscribe to your channel.

@megha7564 5 жыл бұрын

hey, im planning on interning at tel aviv university next year, mind if we talk about the university a little ?

@videogrillo 5 жыл бұрын

@@megha7564 sure but please do consider other places too ♡ write to me in youtube chat before they take it off

@zarashine2543 3 жыл бұрын

The best tutorial ...thanks a ton

@ynattirb3 7 ай бұрын

Thank you so much for this video!!!

@loriscapria6757 4 жыл бұрын

Great video! very clear and well explained! thanks! What if you have n groups instead of 2 (habitats)?

@ellaromanspedersen600 3 жыл бұрын

Such a great video thank-you!! do you know what i'd do to change the points to three colours instead of two?

@kestutiskatilius7841 3 жыл бұрын

Amazing stuff! Very helpful and understandabe.

@RStatisticsandResearch 3 жыл бұрын

Thanks!

@khanofficial2249 3 жыл бұрын

Thanks for this amazing video.

@Acropora09 4 жыл бұрын

Very well explained, than you

@deprofundis3293 3 жыл бұрын

Hi, thanks for the video! I was hoping to use ANOSIM and SIMPER but have trouble finding any tutorials. Is there any reason why you chose adonis instead? I tried adonis2 once on my data, and it was absolutely terrible, while anosim was significant (but I'm not sure if I ran either of them correctly. I suspect that I didn't meet the assumptions for the permanova). But I also am having trouble figuring out how to interpret the ANOSIM results. :(

@JibHyourinmaru 2 жыл бұрын

I got the visual using my own data. thanks! will you also do for other multivariate analysis like PCA, CA, PCO etc?

@nadineali2780 3 жыл бұрын

Hi I am trying this tutorial with my data set But in trying to plot the ordination, an error message is displayed "x and y length differ" What does mean that? Thanks in advance for your reply.

@yxliew8331 3 жыл бұрын

Is it possible to show the species name in the plot?

@fede8327 2 жыл бұрын

How to choose the number of permutations if n=24 ?

@rachelneff5837 5 жыл бұрын

I am trying to do this for 9 different habitat types (sites), how would I do this?

@RStatisticsandResearch 4 жыл бұрын

Hello, in exactly the same manner (just add more factor names to your factor column (here "habitat").

@marybethweihbrecht7949 2 жыл бұрын

Hello, I am following along but am getting the error - in if (autotransform && xam > 50) { : missing value where TRUE/FALSE needed. I have no NAs or blank cells in my dataset. Can anyone help me with this?

@yuktitaneja2179 2 жыл бұрын

The plots/samples with 0 species, shall they be part of the matrix?

@liamhughes1998 4 жыл бұрын

Hi thank you very much for this, have tried it with my own data but when I visualised it no points came up, do you know why this might be the case?

@4Katt7 4 жыл бұрын

I am experiencing the same problem. I have tried editing the code but to no avail.

@kweenny5224 4 жыл бұрын

The fonts are so small 😔

@diegosimijacas4466 3 жыл бұрын

Thanks for your instructions. May you help me with adding name of centroids in the new version of your code... Once more, so much Thanks...

@marlonedy55 2 жыл бұрын

I can use Euclidean distance instead of Bray Curtis... I told you this because I was trying to do with an abundance base but at the time of running NMDS I was not able to do it. (mnds

@elinegomes403 4 жыл бұрын

O meu está dando um erro fatal

@IanMahetiMbano 5 жыл бұрын

Hello Sir, l am trying this Tutorial with my data set. I keep on getting the error input must be numeric when l try the ordination. I have checked all all the data and all seems fine. Wanted to ask if u have faced such an issue and how u got around it.

@RStatisticsandResearch 4 жыл бұрын

Most likely R will think that one of your columns is not numeric. So, select your input datamatrix, and type and run the code str(dataname) to find out which one it is (note that you need to replace [datanama] with the name of your dataset). When you have found the particular column, then type dataname$columnname -> as.numeric(dataname$columnname) (again replacing with the actual names of your dataset and the corresponding column name).

@nellllsooon1 3 жыл бұрын

I have a question. what can I do if I do not met the assumptions of the Permanova?

@khanofficial2249 3 жыл бұрын

If your permanova is significant and permadisp is not then their is location effect and if both of them are significant then their is surely dispersion effect and might (not always ) have location effect.

@kimki-fitlifestyle1361 4 жыл бұрын

I tried the code with my data and the figures generated were nice, however for the assumption of homogeneity of multivariate dispersion, I got an extremely small p-value, what I am supposed to do to modify it? Please give me some advice! Thank you!

@RStatisticsandResearch 4 жыл бұрын

Hello, this happens sometimes, and cannot always be solved. However, you could try to transform your input matrix prior to analysis, e.g. square root transformation to downsize larger values.

@shumonaakther9416 4 жыл бұрын

can you please provide the link to download the dataset

@RStatisticsandResearch 4 жыл бұрын

The link can be found below the video!

@baburao8511 5 жыл бұрын

I tried but every time I'm getting xy.coords have different lengths please help me

@sandrezzalima7661 5 жыл бұрын

Me too

@molliepage1054 5 жыл бұрын

@@sandrezzalima7661 This happened to me to but then it worked when I copy and pasted his exact script, I was obviously writing it wrong.

@RStatisticsandResearch 4 жыл бұрын

This suggests that there is an error in the format of your input file. Indeed, copy-paste my file (and add in your data), and it should work.

@chitrarajagopal8434 Жыл бұрын

Sir, Thank you so much for this well-explained tutorial on NMDS. I tried to do it with my data and successfully did up to NMDS calculation. when I ran the code datascores

@sofiavivas2050 Жыл бұрын

Hello! i have the same problem..were you able to solve it?

@barry6129 10 ай бұрын

I also have this problem.

@pipe919 Ай бұрын

Hello! i have the same problem..were you able to solve it?

@user-or4cq1ij3c 3 жыл бұрын

Hello, I follow the tutorial, but I cannot get the plot. Can I send my my data for your reference?

@RStatisticsandResearch 3 жыл бұрын

@katz9649 3 жыл бұрын

I LOVE YOU.. you just saved my paper.. i could kiss you right now

@BLooDy21HD 3 жыл бұрын

Is there anyway to get blue/red again? I am trying to run the command but i get the solution with every item being black

@pgpsp41 3 жыл бұрын

I am not a pro in R, so I don´t know if it works for you too... But with "with" after the normal plotting you can ink some communities/species. veg.mds

@RStatisticsandResearch 3 жыл бұрын

@BLooDy21HD 3 жыл бұрын

@@RStatisticsandResearch Thank you for that, is there anyway that we can display the names of the dots in the plot?

@BLooDy21HD 3 жыл бұрын

@@pgpsp41 Thank you for y our time, i ll try the main script first and if it won't work, i ll try yours! Your's seems a little complicated, this is why i ll let it as my final choice