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
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?
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.
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
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.
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
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.
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 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
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$x. Why do we have to do: trg
Nice video and very helpful, I have challenges while installing the ggbiplot and mnet packages (am using R version 3.6.3) please any advice on how to over come such challenge?
Your videos have been constant companions during the last months of my master thesis. It seemed as if every time I had to switch to another analysis technique you were allready waiting here. So thank you a lot for your guidance and clear explanations! The only thing I would appreciate would be if you could provide the basic R scripts. Even though the copying process might help with understanding each command due to step by step application, to type text of a tiny youtube screen shown in one half of my monitor to r studio in the other half is troublesome. Thanks!
Thanks for good video. Sir I am using R 3.6.1 version unable to install devtools and ggbiplot also. If devtools install then show that usethis package is missing please solve my issue.
Dear Respected Sir, I wanted to install ggbiplot using the command you provided with us. but it gives me another message. The message is (Installation failed: SSL certificate problem: self signed certificate in certificate chain Warning message: Username parameter is deprecated. Please use vqv/ggbiplot) I used vqv/ggbiplot as well, but no good results. please guide me what shall I do?
19:12 It is only for purpose to show another way to get the principal component related to training because : identical(pc$x, predict(pc,training)) gives TRUE meaning that pc$x is same as predict(pc,training).
Firstly thank you for your helpful video. I have problem to add ellipse in the plot. I have 30 variables, first 29 is the numeric and last one is the factor variables. But i can,t plot the ellipse in the PCA plot. How can i solve this? Please help.
Thank you Dr. Bharatendra Rai for explaining PCA in detail. Can you please explain how to find weights of a variable by PCA for making a composite index? Is it rotation values that are for PC1, PC2, etc.? For example, if I have (I=w1*X+w2*Y+w3*Z) then how to find w1, w2, w3 by PCA.
Sir, I am doing PCA analysis on DJ 30 Stocks and when I view pca$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?
Thanks, I also found other way to plot the PCA: library(ggfortify) autoplot(pc, data = training_set, colour = 'Species', loadings = TRUE, loadings.colour = 'blue', loadings.label = TRUE, loadings.label.size = 3)
Using predict function we are generating principal components. Later, we are using these principal components for developing a classification model. This is a small dataset just to illustrate the process. And will be useful for high dimensional data where one deals with 1000s of variables.
I'm using stata, are there any specific commands for principal component analysis PCA in PANEL DATA Or Just simply run PCA after standardizing variables?
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.
@@bkrai Thank you for your kindly replying When I ran it, it would shown like this. Error in install_github("ggbiplot", "vqv") : could not find function "install_github"
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
Thank you Sir, I understood so many things. While I was checking with my dataset, I facing little bit problem at nnet library function, the error is coming by saying like that; trg$Depth
Thanks Sir. Yes, it might be the reason... I have three different depths (Sur, Mid, Bot) where I am measuring different chemical compounds/parameters. I want to classify the different parameters with respect to different depths and try to check how efficiently PCA is classifying.
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.
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!
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.
For machine learning such random forest, neural networks, support vector machines, and extreme gradient boosting, you can refer to following: ruclips.net/p/PL34t5iLfZddu8M0jd7pjSVUjvjBOBdYZ1
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.
Many thanks for you Dr. God bless you.
You are most welcome!
I revisited your video for interpretation of biplots in PCA. Many thanks.
You are welcome!
Thank you so much Professor🙏
You are very welcome!
Awesome Explanation
make sure you run following before installing:
library(devtools)
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!
R PCA IS VERY GOOD PACKAGE AND VERY HELPFULL
Yes, I agree!
This is the best PCA explanation I have seen anywhere so far. Thank you for sharing your knowledge.
Thanks for the feedback!
The Bio-plot was explained very clearly, thank you Dr. Rai!
You are welcome!
Thank you!!Best explanation on Biplot on RUclips .
Glad it was helpful!
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!
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!
Thank you for this extremely helpful, and easily understood tutorial, particularly the clear interpretation of the Bi-Plot. Much appreciated
You're very 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 ?
You are too good sir. An absolute treat for ML enthusiasts.
Thanks for your comments!
Great Explanation....
Thanks!
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!
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?
This is great. I was looking for PCA and you have done it. Many many thanks to you sir.
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:
ruclips.net/video/aS1O8EiGLdg/видео.html
@@bkrai thank you sir.
I really like your explanations in your videos. Keep them coming! Thanks
Thanks for the feedback!
Thanks for the video! It helped me a lot doing the forecasting for future values using PCA.
Very welcome!
Fantastic session.Perfectly understood Biplot
Thanks for comments!
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
One of the best PCA videos i ever seen, Thank you Mr. Rai.
Thanks for comments!
This video is worth its weight in gold
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
Thank you for this amazing video. Better than my university lectures
Thanks for comments!
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.
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.
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)
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.
Can you please show back propagation algorithm in r
Refer to this:
ruclips.net/video/-Vs9Vae2KI0/видео.html
sir, please make a session on factor analysis with prediction
Thanks for the suggestion!
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.
Sir can I use boruta function instead of pca in r..
Yes certainly. Here is the link:
ruclips.net/video/VEBax2WMbEA/видео.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.
Thank you so much Dr. Rai. Detailed teaching
Thanks for comments!
Fabulous work in PCA ! Keep it up
Thanks for the feedback!
Can you upload a video describing independent component analysis in R
I've added it to my list.
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
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 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:
ruclips.net/video/AVx7Wc1CQ7Y/видео.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.
Wonderful job explaining the material.
Thanks for your comments and finding it useful!
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")
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
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!
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
Really really great explanation sir, Thank you so much for making it very simple
Thanks for comments!
your videos are great :)
Thank you!
Seriously awesome explanations! Thank you again.
Thanks!
Can you please help with combined pca and ann model?
I'm adding to the list of future videos.
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!
Thank you. Learned a lot from your channel
Thanks!
Why u partition the data into 80 and 20 % please answer
It can be any other ratio too. Eg., 60:40, 70:30, 75:25 or 90:10.
@@bkrai my question is that what's the reason behind splitting the data into parts in testing and training either its 8o to 20 or 60 to 40. Thanks
To avoid over-fitting where you get very good result from training data but not so from testing.
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.
Where can I find the raw data of this project?
Data used here is available within R.
Hi Dr, How to I use PCA to generate a score based on several variables? Regards
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.
Great video! Thanks for sharing your knowledge.
Thanks for comments!
Orthogonality of principal component- 10:17
Thx
sir can u please make one video on k means clustering and classification and regression tree analysis
See this link:
ruclips.net/video/5eDqRysaico/видео.html
@@bkrai thank you sir
You are welcome!
@@bkrai Sir do you know about WRF model
yes
Add a video on non negative matrix factorization like intNMF
Thanks, I've added it to my list of future videos.
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!
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.
> install_github("ggbiplot","vqv")
Error in parse_repo_spec(repo) :
Invalid git repo specification: 'ggbiplot'
what should i do sir
Check if you ran library(devtools)
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.
Sir, I am doing PCA analysis on DJ 30 Stocks and when I view pca$loadings for 30 variables, I noticed that some were not displayed. For example, Component 1 has -0.218 for Apple but then shows none for JPM, what does this mean?
ggbiplot not getting installed when tried the way in the video,please advise how to install
You can try this:
library(devtools)
install_github("vqv/ggbiplot")
@@bkrai
try this
install.packages("remotes")
remotes::install_github("vqv/ggbiplot")
it will help.
Thanks!
Hi..good day bharatendra..I want to replace one my columns with value 1 for all its elements,what is the code in R studio..thanks for your time?
suppose you are using following data:
data(iris)
To add what you indicated to a "new" column, you can use:
iris$new
thanx for ur ans ..I do already have a column with different values,I wanna replace all values on that column with just 1
So for iris data if you want to change all values for Sepal.Length variable to 1, you can use:
iris$Sepal.Length
scatter Plat and Correlation- 2:04
Thx
Dear Teacher, I can`t install ggbiplot from github, is there other way to install it?
My R version is 3.6.0
you can try this:
library(devtools)
install_github("vqv/ggbiplot")
Thanks, I also found other way to plot the PCA:
library(ggfortify)
autoplot(pc, data = training_set, colour = 'Species',
loadings = TRUE, loadings.colour = 'blue',
loadings.label = TRUE, loadings.label.size = 3)
Thanks for the update!
How to know the exact names of the variables after doing PCA like they are before
Each pc is a combination of all variables and all variables retain their original name.
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.
Do you have a video on PCA for unsupervised learning via clustering and similarity ranking?
not yet.
Sir, can you please suggest how I can perform PCA on my Panel Data? -Regards
What is the difference between using "scale." and "scale"? Is it in order to use z-score vs. min-max?
Here the code requires scale. to be used. It uses z-score.
@@bkrai Okay, thanks! I will try it out! :)
Welcome!
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!
@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
Great video.. What if we want to include factor-like "Control and Heat" for genotypes? Please suggest
It should work fine.
Why do you predict before you build the model? Shouldn't it be the other way around?
If you are referring to 18:34 time point, note that the predict function is using principal component 'model'.
@@bkrai What is it that you are trying to predict there? Compared to what you would predict using the regression model?
Using predict function we are generating principal components. Later, we are using these principal components for developing a classification model. This is a small dataset just to illustrate the process. And will be useful for high dimensional data where one deals with 1000s of variables.
I'm using stata, are there any specific commands for principal component analysis PCA in PANEL DATA Or Just simply run PCA after standardizing variables?
I've not used stata, so difficult to say what command will be correct.
Hello, you put training [5] to reference the column on trg variable....
shouldn't it be training[ , 5]?
It is training[ , 5] in the video.
too good!! plz make more such videos...plz!
Thanks for comments! You may find this useful too:
ruclips.net/p/PL34t5iLfZddu8M0jd7pjSVUjvjBOBdYZ1
Thank you, this video will be really helpful to complete my thesis :)
Good luck!
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.
Thank you for your VDO.
My R version is 3.5.1 and it cannot allow ggbiplot.
Do you have any package instead of ggbiplot ?
Try installing it by running this line:
install_github("ggbiplot", "vqv")
@@bkrai Thank you for your kindly replying
When I ran it, it would shown like this.
Error in install_github("ggbiplot", "vqv") :
could not find function "install_github"
@@safezonesharing914 I'm also getting the same error
@@safezonesharing914 try below command. It worked for me
library(devtools)
install_github("vqv/ggbiplot")
@@ashishsangwan5925 Arf, for few seconds I believed you were my saver ^^. But nope, your alternative didn't work as well
Can u upload a tutorial on boxcox transformation for pca to remove the skewness in the data thanks
thanks for the suggestion! I've added it to my list.
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
how do i get the file
here is the link:
drive.google.com/open?id=0B5W8CO0Gb2GGYTQ2SWxkc2FCVGs
Great lecture. Thanks.
Thanks!
Thank you Sir, I understood so many things. While I was checking with my dataset, I facing little bit problem at nnet library function, the error is coming by saying like that;
trg$Depth
I'm nor sure what type of variable is 'depth'. Note that the response variable should be of factor type.
Thanks Sir. Yes, it might be the reason... I have three different depths (Sur, Mid, Bot) where I am measuring different chemical compounds/parameters. I want to classify the different parameters with respect to different depths and try to check how efficiently PCA is classifying.
you can convert Depth to factor using:
data$Depth
@@bkrai Sir I did it.. thanks a lot for your kind reply. It is much appreciated 🙏🙏🙏
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:
ruclips.net/video/An7nPLJ0fsg/видео.html
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!
Thanks sir .....can u please tell me how start learning on R from beginning?
You can start with this playlist:
ruclips.net/p/PL34t5iLfZddv8tJkZboegN6tmyh2-zr_T
What is the difference between princomp() and prcomp() commands in r
I saw this today. princomp() uses spectral decomposition approach and prcomp() uses singular value decomposition, prcomp() is usually preferred.
Hi Sir,
How can we detect outliers in PCA
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.
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:
ruclips.net/p/PL34t5iLfZddu8M0jd7pjSVUjvjBOBdYZ1
Great work! Thank you
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!