if (!require('devtools')) install.packages('devtools') devtools::install_github("aravind-j/augmentedRCBD") # install the developer version of augmentedRCCBD in case of the error where you can't save docx file...
Hello everyone, for correlation, PCA, cluster analysis (ward min variance and k-means) and Multivariate D^2 statistics/Tocher method of clustering do refer the videos which i have already uploaded in the channel
I am facing problems to save my outputs as docx file. when i give command it shows results as ------- Error in read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, : PCDATA invalid Char value 27 [9]..... and it say that ''Removed 2 rows containing missing values (`geom_segment()`). How to solve this?
@The Outlier, I am facing problems to save my outputs as docx file. when i give command it shows results as ------- Error in read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, : PCDATA invalid Char value 27 [9]..... How to solve this? Other graphs are stored in the temporary directory but the docx file is not creating.
please tell me the solution that when I run analysis using augmentedRCBD it says "could not find augmentedRCBD.bulk" function. So, how can I solve this issue?
First check whether you have loaded augmented RCBD package, then check the spelling is exactly right or not. You can also find more info on different function by clicking on augmented RCBD package in packages window.
You might have made a misting while typing name of the variables, please verify the names of "Primary branches Mean","Sec. Branches Mean","Height Mean","Tiller Mean","Fertile grains","STERILE","Total grain number" they have to correspond similar to the name in EXCEL. Or Try changing the names of variables like Primary branches Mean to pbm, it will reduce the error while typing. Remember R is case sensitive.
I tried to follow the step by step but to excute the last command for output is taking very long time I left it over night and no output were produced. What could be a problem. I have 256 accession and three checks.
Sir, could you please give some references about what you said regarding which ANOVA is generally used and how to calculate genotypic and phenotypic correlation and path analysis? Thank you.
Use adjusted means to calculate genotypic correlations. Use the normal data what you used for ANOVA for phenotypic correlation (take average of the checks) Same thing for path analysis also use adjusted means for genotypic path analysis use lavaan package in R or AMOS in SPSS For ANOVA main table you need to take elements from both the tables like this www.indostat.org/moduleslinks/ablinks/aug.pdf Thesis ref Sahoo, P. K., 2018, Genetic analysis for yield,yield components and quality traits in pea. M. Sc (Agri) Thesis., JNKVJabalpur.
Hello sir I was done analysis accordingly in this manner but it showing error like checks can't be inferred as none of treatments replicated across all the blocks ...I tried a lot can't sort out will u suggest me how to solve this error
Firstly thank you for this video sir,but I have a small issue how can we get total number of entries that is genotypes plus check data in ANOVA table as we didn't get total number of entries data in ANOVA
first of all thank you for your nice presentation about augmented block design, saying this after analysis my data "report.augmentedRCBD.bulk(bout, file.path(tempdir(),'' is not working when I doing all analysis finally it says that,,, Error in read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, : PCDATA invalid Char value 27 [9]....so how to report my data result thank you.
Sir ,i want to know how to make aa excel file for two enviroments in augumented design?If any video related with two enviroments analysis please share link
Hello sir, I am also conducting a experimental trial in Augmented Design. The experiment consists of 3 checks 52 genotypes and 4 blocks so the error degree of freedom is 6. I want to ask that whether it is correct or the error df should be more than 10 compulsorily. If that so then I will need to add 2 more checks in my trial in order to make error df equal to 12.
Thank you for the nice presentation, could you please give as a presentation how to assess in r ANOVA and statistics across environments and years for an augmented design. the library augmrntedRCBD is used only for one trial in one environment, i didn't find script to help in order to a,nalyse multi environment trials based on augmented design
Also I wanted to ask how to use this adjusted mean data for path analysis. Under $replication what we have to provide. Since only the checks are replicated
Please do check the names of 205 genotypes once again in Excel sheet and confirm whether they are unique or not one by one. Do the same for checks also
do you have solutions to solve the problem encountered "Error in augmentedRCBD.bulk(data = AON, block = "blk", treatment = "trt", : could not find function "augmentedRCBD.bulk" please?
We can do association studies, in which we look at the correlation between a qualitative trait and trait of our interest (yield), in case if we have molecular data we can do single marker analysis.
while retrieving the results am getting as Error in read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, : PCDATA invalid Char value 27 [9] How to debug this? even following the pinned comment
if (!require('devtools')) install.packages('devtools') devtools::install_github("aravind-j/augmentedRCBD") Use the above lines of code to install developer version. If it's still won't working means try to export the file in excel format using the code report.augmentedRCBD.bulk(aug.bulk = bout, target = file.path(tempdir(), "augmentedRCBD bulk output.xlsx"), file.type = "excel")
@@Guruprasad_A thanks. I have 1 more query. I used augmented block design in my work. And now i want to do d^2 statistics using tocher method, the problem is in my case there are no replications, how can I proceed?
Sir please do read this article especially section "7.1" last part, I did't show the requested part in my video as it consumes lot of time due to more number of genotypes with an outdated processor. aravind-j.github.io/augmentedRCBD/articles/Data_Analysis_with_augmentedRCBD.html
Sir good day. I am a plant breeding student from the Philippines which currently finished conducting my thesis on F3 mungbean genotypes in an Augmented RCBD. My probpem now is how to do the ANOVA in an Augmented RCBD same in this video presented which i find it the same to my study. Can i ask your help sir about my problem? Since i do not know how to do programming like this. If given a chance sir, can i ask your email? Thank you very much.
if (!require('devtools')) install.packages('devtools')
devtools::install_github("aravind-j/augmentedRCBD")
# install the developer version of augmentedRCCBD in case of the error where you can't save docx file...
How to sir?
U channel will surely grow. The lucid way of explaining is just mesmerizing. Hope to see u with more videos
thank you. Best turorial!
Great video. Thank you so much
Hello everyone, for correlation, PCA, cluster analysis (ward min variance and k-means) and Multivariate D^2 statistics/Tocher method of clustering do refer the videos which i have already uploaded in the channel
I really like it & hope you will include others. for the time being, I want cluster & PCA analysis.
Ok I will do a video on PCA.
For cluster, I hope you need tocher method.
Hi sir
Thanks for your videos...
I request you to share the videos on AUGMENTED BLOCK DESIGN FOR MULTI LOCATION
It is not an appropriate design for multi location trail.
thanku for great explaination!
.I am not able to analyze my data. Will you please analyze my data?.
thanku.. this is very useful
How to fix eror : "checks" and "check col" are of unequal length?
you have not considered all the checks across every block, if so please check the names, whether is it same across all the blocks (case sensitive).
I am facing problems to save my outputs as docx file. when i give command it shows results as ------- Error in read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, :
PCDATA invalid Char value 27 [9]..... and it say that ''Removed 2 rows containing missing values (`geom_segment()`).
How to solve this?
First update all packages.
If it won't work try doing it in other computer
Same problem i am facing
Thanks for the video Sir
Really thanks so much for sharing fruitfully work. if possible share for me sign task of augmented designed
What is the solution to this error "Error: unexpected ',' in "bout
Can u send full error report?
options(max.print = 100000)
> str(AUGM)
tibble [88 × 7] (S3: tbl_df/tbl/data.frame)
$ Block : Factor w/ 4 levels "Block1","Block2",..: 1 1 1 1 1 1 1 1 1 1 ...
$ Varaiety: Factor w/ 76 levels "Check1","Check2",..: 1 2 3 4 5 16 27 38 49 60 ...
$ CS : num [1:88] 7 9 9 8 8 10 9 10 8 10 ...
$ TP : num [1:88] 74.3 60.8 63.7 65 63 ...
$ KP : num [1:88] 74 72 77.7 63.7 72 ...
$ TPKP : num [1:88] 7 6 7 8 9 10 8 7 7 8 ...
$ OS : num [1:88] 111 112 111 112 105 108 106 107 106 108 ...
> AUGM$Block AUGM$Varaiety str(AUGM)
tibble [88 × 7] (S3: tbl_df/tbl/data.frame)
$ Block : Factor w/ 4 levels "Block1","Block2",..: 1 1 1 1 1 1 1 1 1 1 ...
$ Varaiety: Factor w/ 76 levels "Check1","Check2",..: 1 2 3 4 5 16 27 38 49 60 ...
$ CS : num [1:88] 7 9 9 8 8 10 9 10 8 10 ...
$ TP : num [1:88] 74.3 60.8 63.7 65 63 ...
$ KP : num [1:88] 74 72 77.7 63.7 72 ...
$ TPKP : num [1:88] 7 6 7 8 9 10 8 7 7 8 ...
$ OS : num [1:88] 111 112 111 112 105 108 106 107 106 108 ...
> bout
@The Outlier, I am facing problems to save my outputs as docx file. when i give command it shows results as ------- Error in read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, :
PCDATA invalid Char value 27 [9]..... How to solve this?
Other graphs are stored in the temporary directory but the docx file is not creating.
Try doing it in another computer.
@The Outlier, i tried on two computers, still getting the same error. help!
@@amitrana734 send screen shot to my mail ID.
@@Guruprasad_A sir i am facing the same problem, please suggest and help
I have raised this issue in Github.
Hello sir it shows data is of type tibble and it also shows test treatments are replicated can you plz help me out
Tibble warning doesn't have any problem with results, but check the replications (checks) name or order correctly in the Excel sheet.
Sir, Can you do a video on how to find genotypic correlation from adjusted means in augmented RCBD and how to find phenotypic correlation also
please tell me the solution that when I run analysis using augmentedRCBD it says "could not find augmentedRCBD.bulk" function. So, how can I solve this issue?
First check whether you have loaded augmented RCBD package, then check the spelling is exactly right or not.
You can also find more info on different function by clicking on augmented RCBD package in packages window.
sir i am getting this error........Error: unexpected string constant in "Primary branches Mean","Sec. Branches Mean","Height Mean","Tiller Mean","Fertile grains","STERILE","Total grain number"),checks = NULL,alpha = 0.05,describe = TRUE,freqdist = TRUE,gva = TRUE,c"
You might have made a misting while typing name of the variables, please verify the names of "Primary branches Mean","Sec. Branches Mean","Height Mean","Tiller Mean","Fertile grains","STERILE","Total grain number" they have to correspond similar to the name in EXCEL.
Or
Try changing the names of variables like Primary branches Mean to pbm, it will reduce the error while typing.
Remember R is case sensitive.
I tried to follow the step by step but to excute the last command for output is taking very long time I left it over night and no output were produced. What could be a problem. I have 256 accession and three checks.
Try this in other computer, or reinstall R and R studio then give it a try.
VERY INFORMATIVE VIDEO SIR, I NEED TO KNOW HOW GET THE BLOCK EFFECT (ELIMINATING TREATMENT) NON SIGNIFICANT
I think what you need is already, there in the anova.
Sir, could you please give some references about what you said regarding which ANOVA is generally used and how to calculate genotypic and phenotypic correlation and path analysis? Thank you.
Use adjusted means to calculate genotypic correlations.
Use the normal data what you used for ANOVA for phenotypic correlation (take average of the checks)
Same thing for path analysis also use adjusted means for genotypic path analysis use lavaan package in R or AMOS in SPSS
For ANOVA main table you need to take elements from both the tables like this
www.indostat.org/moduleslinks/ablinks/aug.pdf
Thesis ref
Sahoo, P. K., 2018, Genetic analysis for yield,yield components and quality traits in pea. M. Sc (Agri) Thesis., JNKVJabalpur.
Hello sir I was done analysis accordingly in this manner but it showing error like checks can't be inferred as none of treatments replicated across all the blocks ...I tried a lot can't sort out will u suggest me how to solve this error
Check the order of checks and their names
Hi i am getting error when i run code output be like this
Error in if (pval > 1) pval
Enter TRUE/False in console, below where you write code.
Firstly thank you for this video sir,but I have a small issue how can we get total number of entries that is genotypes plus check data in ANOVA table as we didn't get total number of entries data in ANOVA
It will be there, please check.
first of all thank you for your nice presentation about augmented block design, saying this after analysis my data "report.augmentedRCBD.bulk(bout, file.path(tempdir(),'' is not working when I doing all analysis finally it says that,,, Error in read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, :
PCDATA invalid Char value 27 [9]....so how to report my data result thank you.
check the pinned comment.
I want to use the method of comparison as lsd, how to do that?
I am getting the following error.
unused argument (method.comp = c("lsd"))
out1
You have to use the argument like above mentioned.
Hello, sir i have data on disease screening of powdery mildew and data are in percentage it is possible to do analysis
Yup,
It will be better if you use scores of an appropriate scale.
Sir ,i want to know how to make aa excel file for two enviroments in augumented design?If any video related with two enviroments analysis please share link
Its not possible to do multi environment analysis in augmented block design.
Sir, Can you give the source of data that you have entered in excel sheet for doing this analysis?
Just I created the data for the video purpose only, its not there with me now.
Good Morning Sir
Is it possible to analyze GCV, PCV, path and D sq in Augmented Block Design without having replicated data.
D square not possible.
Hello sir, I am also conducting a experimental trial in Augmented Design. The experiment consists of 3 checks 52 genotypes and 4 blocks so the error degree of freedom is 6. I want to ask that whether it is correct or the error df should be more than 10 compulsorily. If that so then I will need to add 2 more checks in my trial in order to make error df equal to 12.
Yup error df should be more than 12
Sir...how to do metrology analysis
Thank you for the nice presentation, could you please give as a presentation how to assess in r ANOVA and statistics across environments and years for an augmented design. the library augmrntedRCBD is used only for one trial in one environment, i didn't find script to help in order to a,nalyse multi environment trials based on augmented design
It's not possible to do multi environment analysis using this design, you should have RCBD or Alpha lattice design.
How can we perform pooled analysis of data in augmented design
Check it out in Plant breeding tools.
Thank u sir. But can we save the same thing in notepad instead of word file
Yup.
Also I wanted to ask how to use this adjusted mean data for path analysis. Under $replication what we have to provide. Since only the checks are replicated
@@chaminchimyang4689 You only consider the mean value for path analysis.
Sir. I am having 210 (205 genotypes+5 checks) but while converting into factors it is showing only 208 levels. Please guide me in this regard.
Please do check the names of 205 genotypes once again in Excel sheet and confirm whether they are unique or not one by one.
Do the same for checks also
@@Guruprasad_A ok sir. I will check again
Yes sir. You are right. problem solved. Thank you very much sir for your kind reply.
I want to do path analysis for augmented blockdesign plz help
Use the average data and you can do in amos SPSS software...
m.czcams.com/video/efC81f-Z22Q/video.html&pp=ygUYU3BzcyBhbW9zIHBhdGggYW5hbHlzaXMg
do you have solutions to solve the problem encountered "Error in augmentedRCBD.bulk(data = AON, block = "blk", treatment = "trt", :
could not find function "augmentedRCBD.bulk" please?
You have not loaded the package correctly.
library(augmentedRCBD)
or
you might have done some mistake in spellings please check.
@The Outlier, could you calculate genotype by environment interaction (GxE) using augmented block design across the environments
data.cimmyt.org/dataset.xhtml?persistentId=hdl:11529/10857
Please do check the above software. I hope the manual of the software could help?
Error in if (grepl(gwstring1, x$warnings$GVA)) { :
the condition has length > 1
I am getting this error for some traits. Please guide. 0:29
Please attach the correct timeline
18:17
@@rajithanair4406 please attach the screenshot at gthings1597@gmail.com
Sir, What are the analysis possible for qualitative traits for certain number of accessions?
We can do association studies, in which we look at the correlation between a qualitative trait and trait of our interest (yield), in case if we have molecular data we can do single marker analysis.
@@Guruprasad_A ok sir. Thank you.
Sir, I am not getting word document as an output file ?
Try using developer version of augmentedRCBD.
@@Guruprasad_A Sir, how can i get this version ?
@@binduks4436 Follow the pinned attachment.
while retrieving the results am getting as Error in read_xml.raw(charToRaw(enc2utf8(x)), "UTF-8", ..., as_html = as_html, :
PCDATA invalid Char value 27 [9]
How to debug this? even following the pinned comment
if (!require('devtools')) install.packages('devtools')
devtools::install_github("aravind-j/augmentedRCBD")
Use the above lines of code to install developer version.
If it's still won't working means try to export the file in excel format using the code
report.augmentedRCBD.bulk(aug.bulk = bout,
target = file.path(tempdir(),
"augmentedRCBD bulk output.xlsx"),
file.type = "excel")
I tried doing it in Excel too ...but still it's not working sir.
Did you used Developer version.
Please upload a video of installing R studio.
I have installed R studio but facing some kind of issue
czcams.com/video/NZxSA80lF1I/video.html
How to do analysis if there is 1 incomplete block using augmentedrcbd ??
Same method you can use.
@@Guruprasad_A thanks. I have 1 more query. I used augmented block design in my work. And now i want to do d^2 statistics using tocher method, the problem is in my case there are no replications, how can I proceed?
If you have two season data then you can proceed by considering other has a replication.
@@Guruprasad_A i have data for 1 season only. Is there any other way we can analyse the genetic diversity other than the d^2 statistics?
No you can do hierarchical clustering.
Hello sir. If changes had been made in raw data, the results are not updated. It is giving the same results. Please find me a solution.
Results are mostly dependent on checks .
@@Guruprasad_ASir the basic descriptive statistics also not updated. How can the Max and min value and cv will be the same for all data.
Restart R session and do analysis from start and save the data in Excel before importing.
@@Guruprasad_A Sir how to save the data in Excel. It is generated on temp directory.
Thank you sir. Now I'm getting the new results.
Sir, How can we perform Augmented CRD? Please do a video on augmented CRD
Augmented CRD design is not there, as per my knowledge.
Can you please show the data analysis for RCBD design
Check it out in STAR app, I made a recent video on agriculture statistical tools.
where can I get the augmentedRCBD package
Install.packages(“augmentedRCBD”)
Use the above command to install the package
Hi can you give source of augmented design DMRT analysis..
out1
Sir please do read this article especially section "7.1" last part, I did't show the requested part in my video as it consumes lot of time due to more number of genotypes with an outdated processor.
aravind-j.github.io/augmentedRCBD/articles/Data_Analysis_with_augmentedRCBD.html
need to pass an additional argument using augmentedRCBD() function method.comp="lsd"
Hi sir, How does R calculates adjusted means? and why?
www.reneshbedre.com/blog/ancova.html
@@Guruprasad_A Sir you are saying adjusted means remove the bias of covariate from the model. Is it same for ANOVA also?
No.
@@Guruprasad_A then what is the need of calculating adjusted means?
Adjusted means gives the true (genotypes) value eliminating environmental variations
Sir please do video on PCA and cluster analysis
It's in the pipeline
Minimum population required for augmented block design in vegetable science
Morev then 30, if seeds are more and population is more go with RCBD.
Sir I am using 10 blocks in which 10 F2 population ,3 check, 2 parents and 1 F1 parent in my research, is it correct?
Thanks a lot for the video though you were too fast.
Ya I understand.
Sir good day. I am a plant breeding student from the Philippines which currently finished conducting my thesis on F3 mungbean genotypes in an Augmented RCBD. My probpem now is how to do the ANOVA in an Augmented RCBD same in this video presented which i find it the same to my study. Can i ask your help sir about my problem? Since i do not know how to do programming like this. If given a chance sir, can i ask your email? Thank you very much.
Presently I am not carrying my laptop, I am traveling. I try best to answer you
Thank you very much sir. Keep safe.
Sir i sent you an email. Hopefully you can read it. Thank you.
I’m facing an error can you please share your email??
gthings1597@gmail.com