MCA error in CA(Ztot, ncp = min(ncp, ncol(Z) - length(act)), row.sup = ind.sup, : length of vector row.w should be the number of active rows

[Hugo Fernández Mena]

Dear FactoMineR community,
I already checked everything I could, updated R to 4.3.3 version and updated all Facto packages. I verified the categories of my columns and explore the dataset to identify possible NA values, but 0. I still get an error message in my code, as you can see below.
Any ideas?
Thank you all,
Hugo FM










> #MCA Factominer > library(FactoMineR) > update.packages("FactoMineR") 

> library(factoextra) Loading required package: ggplot2 Keep up to date with changes at https://tidyverse.org/blog/ Welcome! Want to learn more? See two factoextra-related books at https://goo.gl/ve3WBa 

> library(Factoshiny) Loading required package: shiny Loading required package: FactoInvestigate 

> library(FactoInvestigate)

> str(data_simplified) 

'data.frame': 3507 obs. of 5 variables: 

 $ Yield : num 200 183 180 180 180 ... 

 $ Plantation_density: num 6536 4444 4000 4000 4545 ... 

 $ Label : Factor w/ 3 levels "PDO","PGI","Unlabeled_wine": 3 2 2 2 2 2 3 3 3 2 ... 

 $ Organic : Factor w/ 2 levels "NO","YES": 1 1 1 1 1 1 1 1 1 1 ... 

 $ Irrigation : Factor w/ 3 levels "NO","Unknown",..: 2 2 2 2 2 2 1 2 1 2 ... 

> colSums(is.na(data_simplified)) 

Yield Plantation_density Label Organic Irrigation 0 0 0 0 0 

> res.mca <- MCA(data_simplified, 

                 + quanti.sup = c(1, 2), # Yield and Plantation_density 

                 + quali.sup = c(3,4,5)) # year_of_survey, Variety, Label, Organic, Irrigation 

Error in CA(Ztot, ncp = min(ncp, ncol(Z) - length(act)), row.sup = ind.sup, : length of vector row.w should be the number of active rows 

 Warning message: In CA(Ztot, ncp = min(ncp, ncol(Z) - length(act)), row.sup = ind.sup, : The rows 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, [... truncated]

[Francois HUSSON]

Hi,

It seems that you have no active variables. So there in no data to perform MCA. If you want to perfrom MCA on the 3 categorical variables, do:

res.mca <- MCA(data_simplified, quanti.sup = c(1, 2))

FH

---

De: "Hugo Fernández Mena" <hugob...@gmail.com>
À: "FactoMineR users" <factomin...@googlegroups.com>
Envoyé: Jeudi 6 Juin 2024 11:04:49
Objet: [SOCIAL]MCA error in CA(Ztot, ncp = min(ncp, ncol(Z) - length(act)), row.sup = ind.sup, : length of vector row.w should be the number of active rows

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[Hugo Fernández Mena]

Hi François, 

Thanks! It works for your example, but if I want to perform the MCA on Yield (2nd quantitative variable) I still get an error:

#MCA Yield as active

> res.mca <- MCA(data_simplified,

+ quanti.sup = 2, # Plantation_density

+ quali.sup = c(3,4,5)) # Label, Organic, Irrigation

Error in CA(Ztot, ncp = min(ncp, ncol(Z) - length(act)), row.sup = ind.sup, : length of vector row.w should be the number of active rows In addition: Warning message: In CA(Ztot, ncp = min(ncp, ncol(Z) - length(act)), row.sup = ind.sup, : The rows 3502, 3503, 3504, 3505, 3506, 3507 sum at 0. They were suppressed from the analysis

El viernes, 7 de junio de 2024 a las 15:13:29 UTC+2, Hugo Fernández Mena escribió:

Hi François, 

Thanks! It works for your example, but if I want to perform the MCA on Yield (2nd quantitative variable) I still get an error:
#MCA Yield as active > res.mca <- MCA(data_simplified, + quanti.sup = 2, # Plantation_density + quali.sup = c(3,4,5)) # Label, Organic, Irrigation Error in CA(Ztot, ncp = min(ncp, ncol(Z) - length(act)), row.sup = ind.sup, : length of vector row.w should be the number of active rows In addition: Warning message: In CA(Ztot, ncp = min(ncp, ncol(Z) - length(act)), row.sup = ind.sup, : The rows 3502, 3503, 3504, 3505, 3506, 3507 sum at 0. They were suppressed from the analysis

[Hugo Fernández Mena]

any ideas why ?

[Emmanuel Detrinidad]

In my humble opinion, It is an error of syntax, 

Try this one:

res.mca <- MCA(data_simplified, quanti.sup = 2, quali.sup = 3,4,5) # Label, Organic, Irrigation

The "c (3,4,5)" is not required, only the number of columns (= 3,4,5) 

 
good luck, 

Emmanuel

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[François Husson]

You only have 1 active variable!

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--
François Husson
Department Statistics & Computer Science
L'Institut Agro
65 rue de St-Brieuc - 35042 Rennes
Tel: +33 2 23 48 58 86
https://husson.github.io/
https://www.youtube.com/@HussonFrancois/videos

[Hugo Fernández Mena]

Ok, rigth with only one active variable it was a very bad exemple to try with, but other active / supplementary variables I tried did not work either. 
For instance, in this case I used all the following variables as active, except Yield and Label, and still get an error. Any ideas why ?

> str(data_simplified)

'data.frame': 3507 obs. of 8 variables:

$ Variety : Factor w/ 59 levels "ALICANTE BOUSCHET NOIR",..: 1 1 1 1 1 1 1 1 1 1 ...

$ Yield : num 133 30 100 83 30 ...

$ Vine_age : int 33 21 38 37 31 36 27 4 29 45 ...

$ Plantation_density: num 4167 5000 3704 3333 3333 ...

$ Label : Factor w/ 3 levels "PDO","PGI","Unlabeled_wine": 3 3 2 2 3 3 3 2 3 2 ...

$ Organic : Factor w/ 2 levels "NO","YES": 1 1 1 1 1 1 1 1 1 1 ... $ Irrigation : Factor w/ 3 levels "NO","Unknown",..: 1 1 3 1 1 2 2 2 1 2 ...

$ Rootstock : Factor w/ 14 levels "1103P","110R",..: 9 14 9 9 6 9 9 9 9 8 ...

> res.mca <- MCA(data_simplified,

+ quanti.sup = 2, # Yield

+ quali.sup = 5) # Label

Error in aggregate.data.frame(as.data.frame(x), ...) :

arguments must have same length

In addition: Warning message:

In sqrt(Nj * ((N - 1)/(N - Nj))) : NaNs produced

El jueves, 13 de junio de 2024 a las 12:35:10 UTC+2, Hugo Fernández Mena escribió:

Ok, rigth with only one active variable it was a very bad exemple to try with, but other active / supplementary variables I tried did not work either. 
For instance, in this case I used all the following variables as active, except Yield and Label, and still get an error. Any ideas why ?

> str(data_simplified) 'data.frame': 3507 obs. of 8 variables: $ Variety : Factor w/ 59 levels "ALICANTE BOUSCHET NOIR",..: 1 1 1 1 1 1 1 1 1 1 ... $ Yield : num 133 30 100 83 30 ... $ Vine_age : int 33 21 38 37 31 36 27 4 29 45 ... $ Plantation_density: num 4167 5000 3704 3333 3333 ... $ Label : Factor w/ 3 levels "PDO","PGI","Unlabeled_wine": 3 3 2 2 3 3 3 2 3 2 ... $ Organic : Factor w/ 2 levels "NO","YES": 1 1 1 1 1 1 1 1 1 1 ... $ Irrigation : Factor w/ 3 levels "NO","Unknown",..: 1 1 3 1 1 2 2 2 1 2 ... $ Rootstock : Factor w/ 14 levels "1103P","110R",..: 9 14 9 9 6 9 9 9 9 8 ... > #MCA Yield as active > res.mca <- MCA(data_simplified, + quanti.sup = 2, # Yield + quali.sup = 5) # Label Error in aggregate.data.frame(as.data.frame(x), ...) : arguments must have same length In addition: Warning message: In sqrt(Nj * ((N - 1)/(N - Nj))) : NaNs produced

[Hugo Fernández Mena]

The problem might be that I have 59 levels for my variable called "Variety", too many levels...

[François Husson]

There is a quantitaive variable as active, which is not possible in MCA.
FH

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[Hugo Fernández Mena]

ah OK now I understand, this might be the most important thing I should know about it..
Then, if I want to have both categorical and quantitative variables I have to swith to something else, like a MFA ?

[francois.husson]

You can use FAMD for mixed data

-------- Message d'origine --------

De : Hugo Fernández Mena <hugob...@gmail.com>

Date : 13/06/2024 15:33 (GMT+01:00)

À : FactoMineR users <factomin...@googlegroups.com>

Objet : [SOCIAL]Re: [SOCIAL]Re: [SOCIAL]Re: [SOCIAL]MCA error in CA(Ztot, ncp = min(ncp, ncol(Z) - length(act)), row.sup = ind.sup, : length of vector row.w should be the number of active rows

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