To install ggbiplot, the code is now (17, Jan, 2020): library(devtools) install_github("vqv/ggbiplot") source: github.com/vqv/ggbiplot Excellent video and well explained these concepts. Thanks.
Thanks a lot Sir for your nice presentation. You saved my time. Earlier I used your R codes on Kohonen NN and now for PCA for my training lectures. Your explanation is so lucid. I appreciate your noble service of sharing knowledge
19:12 It is only for purpose to show another way to get the principal component related to training because : identical(pc$x, predict(pc,training)) gives TRUE meaning that pc$x is same as predict(pc,training).
Very informative and nice presentation sir, sir can we estimate PCA for factor (for eg species) with unequal no. of observation. And we want to see the correlations in terms of each species viz for setosa or other two, how to do it? Please explain...Thank You
Thank you for the material. It is very clear and actually very relevant to my current work. As I understand, the conversion of the data comprises addition products of notmalized predictors and loadings. Maybe you would have time to post a PLS regression video, please? The intriguing part is the explanation of the model itself
Your videos have been constant companions during the last months of my master thesis. It seemed as if every time I had to switch to another analysis technique you were allready waiting here. So thank you a lot for your guidance and clear explanations! The only thing I would appreciate would be if you could provide the basic R scripts. Even though the copying process might help with understanding each command due to step by step application, to type text of a tiny youtube screen shown in one half of my monitor to r studio in the other half is troublesome. Thanks!
Thank you for this nice video Dr. Rai. I have a doubt. Why the predict function was used multiple times. After the prcomp function, all the data of Principle components were available in: pc$x. Why do we have to do: trg
Thank you for sharing, I get an error "Error in plot_label(p = p, data = plot.data, label = label, label.label = label.label, : Unsupported class: prcomp"", when I try to run the ggbiplot. Would you please advise how to fix it?
Great video. Do you have a suggested package for running binary logistic regression? From a brief scan of nnet it appears to only have arguments for multinomial response variables. Thank you.
@@bkrai sorry I was unclear in my message. I was hoping for a suggested package to run a binary logistic regression using PCA components as predictors - similar to what you have done here with multinomial. Any suggestions are welcome.
If I just use addEllipses =TRUE, what determines the size of those ellipses? Also, if I specify ellipse.type = “confidence”, what confidence level is used to generate the ellipses? I used factoextra if that helps.
Thanks for this video sir, very good class but I can´t get it. because Error ... could not find function "ggbiplot". Excuse me, which is your R version ?
Thank you Dr. Bharatendra Rai for explaining PCA in detail. Can you please explain how to find weights of a variable by PCA for making a composite index? Is it rotation values that are for PC1, PC2, etc.? For example, if I have (I=w1*X+w2*Y+w3*Z) then how to find w1, w2, w3 by PCA.
Sir why have you predicted the training and test data with respect to PC? can use trg data for making neural model and test using tst data set? and find correlation b/w act and predicted values?
When there are many variables, chances of having multicollinearity problem increases. And PCA helps to solve that problem. And yes, you can use neural network model.
@@bkrai sir can you please explain me the significance of the lines under the heading: prediction with principle components.As I am unable to understand why we are predicting twice on test data set. Please explain sir
Nice video and very helpful, I have challenges while installing the ggbiplot and mnet packages (am using R version 3.6.3) please any advice on how to over come such challenge?
For machine learning such random forest, neural networks, support vector machines, and extreme gradient boosting, you can refer to following: ua-cam.com/play/PL34t5iLfZddu8M0jd7pjSVUjvjBOBdYZ1.html
Awesome video sir...kudos... :) 1 doubt though .... 20:48 - why are we using 2 components only? How do we know how many principal components to use?(species ~ PC1 + PC2)
2 PCs capture more than 95% of the variability in the data. Other 2 only add about 5%. So you can choose to have PCs that capture over 80% or 90% of the variability.
Awesome video! Could you plz add Partial least squares regression and principal components regression to your playlist! That would be of great help. Thanks in advance!
Dear Sir..thanks for a wonderful video. I have some questions. 1) At 20:18, why did u choose to reorder by setosa? 2)Why did you choose to use data as trg and not training to build mymodel given that trg has predictions from training 3) Can PCA be used to choose k in kmeans. If so, how to go about it? Thanks again. Regards
In universities, business students usually use R and computer science students mostly use Python. If you are mainly looking to apply various machine learning and statistical methodologies, R is perfect.
Hi Sir,Could you take one session on SVD in R and also some theoretical explanation on it. I m finding it very difficult to understand it with most of the material available on the net.
Thanks for the video Please publish video on Exploratory Factor Analysis,Confirmatory Factor Analysis application in a model Also please explain the difference from PCA
Sir, I am doing PCA analysis on DJ 30 Stocks and when I view pca$loadings for 30 variables, I noticed that some were not displayed. For example, Component 1 has -0.218 for Apple but then shows none for JPM, what does this mean?
Firstly thank you for your helpful video. I have problem to add ellipse in the plot. I have 30 variables, first 29 is the numeric and last one is the factor variables. But i can,t plot the ellipse in the PCA plot. How can i solve this? Please help.
Dear Respected Sir, I wanted to install ggbiplot using the command you provided with us. but it gives me another message. The message is (Installation failed: SSL certificate problem: self signed certificate in certificate chain Warning message: Username parameter is deprecated. Please use vqv/ggbiplot) I used vqv/ggbiplot as well, but no good results. please guide me what shall I do?
Hello. I dont know anything about Principal Component Analysis in R: Example with Predictive Model & Biplot Interpretation and i will never need to since thats not in my line of work. I Appreciate your Intromusic though. You are a true champ Bharatendra and enrich this world with your presence. Also that intro music fucking slaps.
thank you a lot for this support sir. If you could provide further guidance it would be very helpful. I am trying to build a models for metastasis prediction using single cell gene expression levels. kindly let me know if it would be possible for you. thanks again
Thanks for good video. Sir I am using R 3.6.1 version unable to install devtools and ggbiplot also. If devtools install then show that usethis package is missing please solve my issue.
Great video. I have one doubt. What does the stddev attribute of PC contain? Standard deviations of the variables are already in scale..so what does stddev represent? Thanks a lot
Bharatendra Rai sorry it’s sdev attribute of pc and in 9:48 while showing the summary of pc, I would like to know what the standard deviation row denote..thanks a lot
Dr. Rai, Thanks for this informative video. I am having a problem getting the predict function to work with the model created on the training dataset. I am getting two errors(paraphrased): 1. NAs not allowed in subscripted assignments; 2. newdata has 1900 rows but variables found have 8100 rows. I think it is looking for the same number of rows in the test dataset. Is there something I am doing wrong? Appreciate any feedback.
Hello great video as always! However one question i had (even though you warned against hard interpretability of results) relates to how to interpret the coefficients. If we look at the coefficient table and read the first line (after the intercept), does that mean that with every increase of Sepal.Length there is a log odd increase of 14.05 in the probability of categorizing the specie as Versicolor, relative to a Setosa? Thanks!
To install ggbiplot, the code is now (17, Jan, 2020):
library(devtools)
install_github("vqv/ggbiplot")
source: github.com/vqv/ggbiplot
Excellent video and well explained these concepts. Thanks.
Thanks for the update!
This is the best PCA explanation I have seen anywhere so far. Thank you for sharing your knowledge.
Thanks for the feedback!
I revisited your video for interpretation of biplots in PCA. Many thanks.
You are welcome!
Thanks a lot Sir for your nice presentation. You saved my time. Earlier I used your R codes on Kohonen NN and now for PCA for my training lectures. Your explanation is so lucid. I appreciate your noble service of sharing knowledge
You are most welcome!
The Bio-plot was explained very clearly, thank you Dr. Rai!
You are welcome!
Awesome video. Every R enthusiast needs to keep an eye on your channel. Thank you and keep up with great work!
+Model Michael thanks👍
Sir,
Can we get code file ?
Thank you!!Best explanation on Biplot on UA-cam .
Glad it was helpful!
one really good video i have found. After watching few of your video now your videos are becoming a "turn to" when require. thanks
Glad to hear that!
Many thanks for you Dr. God bless you.
You are most welcome!
Thank you for this extremely helpful, and easily understood tutorial, particularly the clear interpretation of the Bi-Plot. Much appreciated
You're very welcome!
19:12 It is only for purpose to show another way to get the principal component related to training because :
identical(pc$x, predict(pc,training)) gives TRUE meaning that pc$x is same as predict(pc,training).
That's correct!
You are too good sir. An absolute treat for ML enthusiasts.
Thanks for your comments!
Orthogonality of principal component- 10:17
Thx
Fantastic session.Perfectly understood Biplot
Thanks for comments!
Thanks for the video! It helped me a lot doing the forecasting for future values using PCA.
Very welcome!
Great Video! Excellent walk though on PCA and how it can be useful for actual classifications. Thanks for the upload.
+theeoddname thanks for the feedback!
Very useful video sir. Could you explain me what is the need to partition the data into training and testing data?
You may review this:
ua-cam.com/video/aS1O8EiGLdg/v-deo.html
@@bkrai thank you sir.
This is great. I was looking for PCA and you have done it. Many many thanks to you sir.
Very informative and nice presentation sir, sir can we estimate PCA for factor (for eg species) with unequal no. of observation.
And we want to see the correlations in terms of each species viz for setosa or other two, how to do it? Please explain...Thank You
Thank you so much Professor🙏
You are very welcome!
One of the best PCA videos i ever seen, Thank you Mr. Rai.
Thanks for comments!
Thank you for this amazing video. Better than my university lectures
Thanks for comments!
I really like your explanations in your videos. Keep them coming! Thanks
Thanks for the feedback!
Thank you so much Dr. Rai. Detailed teaching
Thanks for comments!
This video is worth its weight in gold
R PCA IS VERY GOOD PACKAGE AND VERY HELPFULL
Yes, I agree!
Thank you for the material. It is very clear and actually very relevant to my current work.
As I understand, the conversion of the data comprises addition products of notmalized predictors and loadings.
Maybe you would have time to post a PLS regression video, please? The intriguing part is the explanation of the model itself
Fabulous work in PCA ! Keep it up
Thanks for the feedback!
scatter Plat and Correlation- 2:04
Thx
Wonderful job explaining the material.
Thanks for your comments and finding it useful!
Awesome Explanation
make sure you run following before installing:
library(devtools)
Your videos have been constant companions during the last months of my master thesis. It seemed as if every time I had to switch to another analysis technique you were allready waiting here. So thank you a lot for your guidance and clear explanations!
The only thing I would appreciate would be if you could provide the basic R scripts. Even though the copying process might help with understanding each command due to step by step application, to type text of a tiny youtube screen shown in one half of my monitor to r studio in the other half is troublesome. Thanks!
Thanks for the feedback!
Really really great explanation sir, Thank you so much for making it very simple
Thanks for comments!
Thank you for this nice video Dr. Rai.
I have a doubt. Why the predict function was used multiple times. After the prcomp function, all the data of Principle components were available in:
pc$x.
Why do we have to do:
trg
In R you can get same thing in multiple ways. This is just for illustration.
@@bkrai Thank you Sir. That makes it clear.
@@abhishek894 You are welcome!
sir, please make a session on factor analysis with prediction
Thanks for the suggestion!
Seriously awesome explanations! Thank you again.
Thanks!
Thank you for sharing, I get an error "Error in plot_label(p = p, data = plot.data, label = label, label.label = label.label, : Unsupported class: prcomp"", when I try to run the ggbiplot. Would you please advise how to fix it?
Thank you. Learned a lot from your channel
Thanks!
Great video. Do you have a suggested package for running binary logistic regression? From a brief scan of nnet it appears to only have arguments for multinomial response variables. Thank you.
You can refer to this:
ua-cam.com/video/AVx7Wc1CQ7Y/v-deo.html
@@bkrai sorry I was unclear in my message. I was hoping for a suggested package to run a binary logistic regression using PCA components as predictors - similar to what you have done here with multinomial. Any suggestions are welcome.
Yes, you can use the PCA components as predictors and run binary logistic regression as shown in the link that I sent earlier.
Thanks sir, why in this video use linear regression? Can i use k means to clustering from pc1 and pc2?
Which line are you referring to?
Sorry, i mean logistic regression in line 59
If I just use addEllipses =TRUE, what determines the size of those ellipses? Also, if I specify ellipse.type = “confidence”, what confidence level is used to generate the ellipses? I used factoextra if that helps.
Thanks for this video sir, very good class but I can´t get it. because Error ... could not find function "ggbiplot". Excuse me, which is your R version ?
Try this:
library(devtools)
install_github("vqv/ggbiplot")
Great Explanation....
Thanks!
Good evening
If you want to show the first dimension (Dim1) and the third dimension (Dim3)
What to do or if you can provide the code for that
Thanks
Thank you Dr. Bharatendra Rai for explaining PCA in detail. Can you please explain how to find weights of a variable by PCA for making a composite index? Is it rotation values that are for PC1, PC2, etc.? For example, if I have (I=w1*X+w2*Y+w3*Z) then how to find w1, w2, w3 by PCA.
For calculations you can refer to any textbook.
Great video! Thanks for sharing your knowledge.
Thanks for comments!
Sir why have you predicted the training and test data with respect to PC? can use trg data for making neural model and test using tst data set? and find correlation b/w act and predicted values?
When there are many variables, chances of having multicollinearity problem increases. And PCA helps to solve that problem. And yes, you can use neural network model.
@@bkrai sir can you please explain me the significance of the lines under the heading: prediction with principle components.As I am unable to understand why we are predicting twice on test data set. Please explain sir
To avoid over-fitting where you get very good result from training data but not so from testing.
Nice video and very helpful, I have challenges while installing the ggbiplot and mnet packages (am using R version 3.6.3) please any advice on how to over come such challenge?
OK for the nnet package it was successfully installed. but still struggling with the ggbiplot (despite using your codes). thanks
too good!! plz make more such videos...plz!
Thanks for comments! You may find this useful too:
ua-cam.com/play/PL34t5iLfZddu8M0jd7pjSVUjvjBOBdYZ1.html
Awesome video. Thank you. As time permits can you do a video on use of caret package? thank you
Saw this today. Thanks for comments!
great lecture..please share your thoughts on machine learning introduction too
For machine learning such random forest, neural networks, support vector machines, and extreme gradient boosting, you can refer to following:
ua-cam.com/play/PL34t5iLfZddu8M0jd7pjSVUjvjBOBdYZ1.html
Thank you, this video will be really helpful to complete my thesis :)
Good luck!
Add a video on non negative matrix factorization like intNMF
Thanks, I've added it to my list of future videos.
Awesome video sir...kudos... :)
1 doubt though .... 20:48 - why are we using 2 components only? How do we know how many principal components to use?(species ~ PC1 + PC2)
2 PCs capture more than 95% of the variability in the data. Other 2 only add about 5%. So you can choose to have PCs that capture over 80% or 90% of the variability.
can a dataset consisting of the principal components and the target variable be used to perform machine learning techniques?
Yes, this video shows an example of doing it.
your videos are great :)
Thank you!
Awesome video! Could you plz add Partial least squares regression and principal components regression to your playlist! That would be of great help. Thanks in advance!
Thanks for suggestions!
Thank You - this was extremely useful.
Very nice channel you have here - easy sub.
Thanks for comments!
Dear Sir..thanks for a wonderful video. I have some questions.
1) At 20:18, why did u choose to reorder by setosa?
2)Why did you choose to use data as trg and not training to build mymodel given that trg has predictions from training
3) Can PCA be used to choose k in kmeans. If so, how to go about it?
Thanks again.
Regards
Can you upload a video describing independent component analysis in R
I've added it to my list.
Sir can I use boruta function instead of pca in r..
Yes certainly. Here is the link:
ua-cam.com/video/VEBax2WMbEA/v-deo.html
@@bkrai sir what do you like between r and python..i find r code more easy to understand and write..
In universities, business students usually use R and computer science students mostly use Python. If you are mainly looking to apply various machine learning and statistical methodologies, R is perfect.
brilliant sir..simple and sweet..thanks...nice music....if i have 10 DISCRETE VARIABLEShow to reduce to 2 or 3 components, please explain?
Thanks for comments! Note that this method is only for numeric variables.
Hi, I want to know from where can I get the iris example data ? thank you!
It's inbuilt in R itself. You can access it by running first 3 lines shown in the video.
Great lecture. Thanks.
Thanks!
Hello very nice video!!! i have a question. Do you how i choose how many PC i have to use and which ones ???
When you have many PCs, you can select first few that capture almost all variability contained in data.
@@bkrai thank you for your response! So I have to test every possible model , right? Do you know if I can use something like a criterion ?
It is good to capture over 80% of the variability.
Great video.. What if we want to include factor-like "Control and Heat" for genotypes? Please suggest
It should work fine.
Excellent demonstration of PCA, really helpful. I just don't understand why in pc object, you use only training data instead of the entire data.
We only use training data so that we can later use test data to assess prediction model.
Hi Sir,Could you take one session on SVD in R and also some theoretical explanation on it. I m finding it very difficult to understand it with most of the material available on the net.
Can you please show back propagation algorithm in r
Refer to this:
ua-cam.com/video/-Vs9Vae2KI0/v-deo.html
Awesome explanation sir...👍👍can you make a video for independent component analysis using r in the same way sir?
Thanks, I've have added it to my list.
sir my data is showing [ reached getOption("max.print") -- omitted 10 rows ]. the last 10 rows are omitted, how to fix this, please
That's just how much gets printed. But all data still remains intact.
is there any other alternative package for ggbiplot ?
Try this for biplot ( I just now ran this in RStudio cloud, and it worked fine):
library(devtools)
install_github("fawda123/ggord")
library(ggord)
Thanks for the video
Please publish video on Exploratory Factor Analysis,Confirmatory Factor Analysis application in a model
Also please explain the difference from PCA
Thanks for the suggestion, I've added this to my list.
Great work! Thank you
It was a fruitful video.Can you please share the code.
Great video, thanks for uploading.
Thanks for comments!
Cool video! Can you do a video about Multiple Correspondance Analysis(MCA) for cualitative data? It would help me a lot
Thanks, I've added this to my list.
Sir, I am doing PCA analysis on DJ 30 Stocks and when I view pca$loadings for 30 variables, I noticed that some were not displayed. For example, Component 1 has -0.218 for Apple but then shows none for JPM, what does this mean?
Firstly thank you for your helpful video. I have problem to add ellipse in the plot. I have 30 variables, first 29 is the numeric and last one is the factor variables. But i can,t plot the ellipse in the PCA plot. How can i solve this? Please help.
thank you for the amazing video!
Thanks for comments!
Dear Respected Sir,
I wanted to install ggbiplot using the command you provided with us. but it gives me another message. The message is (Installation failed: SSL certificate problem: self signed certificate in certificate chain
Warning message:
Username parameter is deprecated. Please use vqv/ggbiplot) I used vqv/ggbiplot as well, but no good results.
please guide me what shall I do?
Not sure what went wrong. May be some typo or something else. Probably you can try running commands using my R file.
Hi Dr, How to I use PCA to generate a score based on several variables? Regards
Hello. I dont know anything about Principal Component Analysis in R: Example with Predictive Model & Biplot Interpretation and i will never need to since thats not in my line of work. I Appreciate your Intromusic though. You are a true champ Bharatendra and enrich this world with your presence. Also that intro music fucking slaps.
Thanks for comments!
Do you have a video on PCA for unsupervised learning via clustering and similarity ranking?
not yet.
Can you please help with combined pca and ann model?
I'm adding to the list of future videos.
@5:47 He says the Average of the variables are converted to zeroes
@6:34 The means(Average) are non-zero
I Don't understand can anyone Explain?/
@5.47 refers to standardizing process before principal component analysis.
@6.34 provides means of original dataset
thanks for the video sir... helped a lot :)
Thanks for the feedback!
Thank you so much for this video. Will you please make a video on Broken-line regression in R?
Thanks for the suggestion, I've added this to my list.
thank you a lot for this support sir.
If you could provide further guidance it would be very helpful. I am trying to build a models for metastasis prediction using single cell gene expression levels.
kindly let me know if it would be possible for you. thanks again
You may find this useful:
ua-cam.com/video/Uil2GZa8gbg/v-deo.html
Sir - Requesting you to kindly give a lecture advanced r programming like on H20 packages etc..
Thanks for the suggestion, I've added this to my list.
Thanks for good video. Sir I am using R 3.6.1 version unable to install devtools and ggbiplot also. If devtools install then show that usethis package is missing please solve my issue.
I would suggest upgrade R. Currently it is around 4.
@@bkrai I upgrade it but still this problem happen
Try this:
library(devtools)
install_github("vqv/ggbiplot")
@@bkrai I used these codes but not install error occured
After intalling make sure to run library.
sir can u please make one video on k means clustering and classification and regression tree analysis
See this link:
ua-cam.com/video/5eDqRysaico/v-deo.html
@@bkrai thank you sir
You are welcome!
@@bkrai Sir do you know about WRF model
yes
Great job, same as always. Can I use PCA for 2 or more categorical variables? Can I define those variables as 0 and 1 in PCA?
You can only use numeric variables. You can try using 0 and 1 and see if it works ok.
Sir, can you please suggest how I can perform PCA on my Panel Data? -Regards
Great video. I have one doubt. What does the stddev attribute of PC contain? Standard deviations of the variables are already in scale..so what does stddev represent? Thanks a lot
At what point in time do you see this?
Bharatendra Rai sorry it’s sdev attribute of pc and in 9:48 while showing the summary of pc, I would like to know what the standard deviation row denote..thanks a lot
It is standard deviation related to principal components. It helps to estimate what percentage of variability is captured by each principal component.
Bharatendra Rai thanks a lot. I understand this now
5:01 Principal component Analysis
Thx
Dr. Rai,
Thanks for this informative video. I am having a problem getting the predict function to work with the model created on the training dataset. I am getting two errors(paraphrased): 1. NAs not allowed in subscripted assignments; 2. newdata has 1900 rows but variables found have 8100 rows. I think it is looking for the same number of rows in the test dataset. Is there something I am doing wrong? Appreciate any feedback.
NAs occur when there is missing data. For handling missing values, refer to:
ua-cam.com/video/An7nPLJ0fsg/v-deo.html
Hello great video as always! However one question i had (even though you warned against hard interpretability of results) relates to how to interpret the coefficients. If we look at the coefficient table and read the first line (after the intercept), does that mean that with every increase of Sepal.Length there is a log odd increase of 14.05 in the probability of categorizing the specie as Versicolor, relative to a Setosa? Thanks!
Your interpretation is correct.
Thank you! Keep up the good work! Your r videos are great!
Sir ..ggbiplot is not installed hence cant work on this ..though i followed the video throughly
Hi Sir, your materials are simple and wonderful. Pls do one video for xgboost. that would be great.
Thanks for the suggestion!
Bharatendra Rai Thanks a lot sir.
I agree with sathish ravi, Sir please make a video on xgboost. You are one stop solution for every problem and I will remember you all my life.
Thanks much appreciated..
it worked