NMDS (Non-metric multidimensional scaling) Clearly Explained | R Studio

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  • เผยแพร่เมื่อ 12 ธ.ค. 2024

ความคิดเห็น • 40

  • @mohanakrishnanlogan2379
    @mohanakrishnanlogan2379 3 ปีที่แล้ว +6

    Madhu, you are excellent!
    The code for others:
    library(vegan)
    library(tidyverse)
    set.seed(100)
    nmds

  • @aftabalamusmani2020
    @aftabalamusmani2020 2 หลายเดือนก่อน

    Very informative and simple to understand. Even better than chatGPT.

  • @danielgarnique1800
    @danielgarnique1800 ปีที่แล้ว +4

    Excelente aporte, aunque el vídeo no esta en mi idioma nativo, es completamente entendible, les doy una solucion al problema nmdsscores

  • @petacone
    @petacone 2 หลายเดือนก่อน +1

    The rooster in the back is the best 😄

  • @mdmoinuddinsheam3111
    @mdmoinuddinsheam3111 ปีที่แล้ว +1

    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?

  • @multitaskprueba1
    @multitaskprueba1 ปีที่แล้ว

    Fantastic video! Thank you so much!

  • @saramashhadinejad5082
    @saramashhadinejad5082 2 หลายเดือนก่อน

    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.

    • @Researchocrat
      @Researchocrat  2 หลายเดือนก่อน

      Thank you! Check out this playlist for inkscape tutorials: th-cam.com/video/8f011wdiW7g/w-d-xo.htmlsi=ew4zaviTYpjMO-IF

  • @isabell2383
    @isabell2383 ปีที่แล้ว

    Thank you so much for the video! :))
    How did you perform the bar chart? Do you have a code? :D

  • @dorrarjaibi
    @dorrarjaibi ปีที่แล้ว

    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 .

  • @rachitsingh98
    @rachitsingh98 3 ปีที่แล้ว

    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!

  • @FlowCutie
    @FlowCutie 2 ปีที่แล้ว

    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?

    • @Researchocrat
      @Researchocrat  2 ปีที่แล้ว

      First you have to extract the NMDS scores (X and Y values as NMDS1 and NMDS2)
      nmdsscores

  • @jeanevanscodjia606
    @jeanevanscodjia606 2 ปีที่แล้ว +2

    Nice video. I appreciate. I tried to run your script as exercise. But I'm getting this error:
    > nmdsscores

    • @philippjeske163
      @philippjeske163 2 ปีที่แล้ว +5

      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

    • @Researchocrat
      @Researchocrat  2 ปีที่แล้ว

      @@philippjeske163 Great. This will work too : scores(nmds_result, display="site")

    • @AM-yf4pi
      @AM-yf4pi 2 ปีที่แล้ว

      Solved using this line: nmdsscores

  • @mac2663
    @mac2663 2 ปีที่แล้ว

    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?

    • @Researchocrat
      @Researchocrat  2 ปีที่แล้ว

      Hope this will help : www.statology.org/r-arguments-imply-differing-number-of-rows/

  • @kassiocastroo
    @kassiocastroo 3 ปีที่แล้ว

    How did you do the species composition graph, could you give the script, please?

    • @Researchocrat
      @Researchocrat  3 ปีที่แล้ว +1

      I used the function barplot() to generate the basic black and white plot. And colours were added using Inkscape.

    • @kassiocastroo
      @kassiocastroo 3 ปีที่แล้ว

      I really liked your video and it was very useful! It would be interesting you did a tutorial also about the barplot graph! thanks!

    • @Researchocrat
      @Researchocrat  3 ปีที่แล้ว

      @@kassiocastroo Thank you..... And Sure, I will post more videos on data visualisation.

  • @mdumar6479
    @mdumar6479 6 หลายเดือนก่อน

    Sir, if we get poor fit, what to do then

    • @Researchocrat
      @Researchocrat  6 หลายเดือนก่อน

      It means that your sample size may be inadequate (you need to have more samples), or there is no grouping pattern in your dataset.

    • @mdumar6479
      @mdumar6479 6 หลายเดือนก่อน

      @@Researchocrat , kindly make video on pcoa cca and rda also, the way u expalin is very informative,

  • @marianaqueiroz6751
    @marianaqueiroz6751 2 ปีที่แล้ว

    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?

    • @Researchocrat
      @Researchocrat  2 ปีที่แล้ว

      Hope this will help : www.statology.org/r-arguments-imply-differing-number-of-rows/

    • @Dr.munna89
      @Dr.munna89 2 ปีที่แล้ว

      @@Researchocrat not helping

    • @Dr.munna89
      @Dr.munna89 2 ปีที่แล้ว

      as example if i replace with NA then the code is not running

    • @Researchocrat
      @Researchocrat  2 ปีที่แล้ว

      @@Dr.munna89 Try this instead : scores(nmds_result, display="site")

  • @jpoblete11
    @jpoblete11 3 ปีที่แล้ว

    why i need to use the set.seed code?

    • @Researchocrat
      @Researchocrat  3 ปีที่แล้ว +1

      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 .

    • @jpoblete11
      @jpoblete11 3 ปีที่แล้ว

      @@Researchocrat i get it, thanks for the explanation and thanks for the video to

  • @mwdasja1127
    @mwdasja1127 7 หลายเดือนก่อน

    Thanks for the Video, very useful for nob like me..
    Btw, i am getting stag at this line: nmdsscores

    • @Researchocrat
      @Researchocrat  7 หลายเดือนก่อน

      Hi
      Please make the following changes to your code.
      nmdsscores

    • @mwdasja1127
      @mwdasja1127 7 หลายเดือนก่อน +1

      @@Researchocrat Thanks brother, it finally work..😄

  • @doing_it_my_way
    @doing_it_my_way 3 ปีที่แล้ว

    Very useful video

  • @elaichahmed102
    @elaichahmed102 ปีที่แล้ว

    Reading in the black is very difficult.