odds ratio calculation issue in R - r

This is my experimental design which im trying to use taken from this paper code which Im trying to implement it for my dataset which I would like to use.
The code which Im using is here
genomicData = tcgaDesign[,colnames(tcgaDesign)[2:27]]
interactions <- interactionsGenes <- sapply(1:ncol(genomicData), function(i) sapply(1:ncol(genomicData), function(j) {f<- try(fisher.test(genomicData[,i], genomicData[,j]), silent=TRUE); if(class(f)=="try-error") 0 else ifelse(f$estimate>1, -log10(f$p.val),log10(f$p.val))} ))
oddsRatio <- oddsGenes <- sapply(1:ncol(genomicData), function(i) sapply(1:ncol(genomicData), function(j) {f<- try(fisher.test(genomicData[,i] + .5, genomicData[,j] +.5), silent=TRUE); if(class(f)=="try-error") f=NA else f$estimate} ))
w <- p.adjust(tcgaGlm$F.p.value,"BH")<0.05
oddsExpression <- sapply(1:ncol(genomicData), function(i) sapply(1:ncol(genomicData), function(j) {f<- try(fisher.test(abs(testResults[w,i]), abs(testResults[w,j])), silent=TRUE); if(class(f)=="try-error") f=NA else f$estimate} ))
interactionsExpression <- sapply(1:ncol(genomicData), function(i) sapply(1:ncol(genomicData), function(j) {f<- try(fisher.test(abs(testResults[w,i]), abs(testResults[w,j])), silent=TRUE); if(class(f)=="try-error") 0 else ifelse(f$estimate>1, -log10(f$p.val),log10(f$p.val))} ))
oddsRatio[lower.tri(oddsRatio)] <- oddsExpression[lower.tri(oddsExpression)]
interactions[lower.tri(interactions)] <- interactionsExpression[lower.tri(interactions)]
Till that point all fine
Then the next step is adding NA to diagonal
diag(interactions) <- NA
diag(oddsRatio) <- NA
colnames(oddsRatio) <- rownames(oddsRatio) <- colnames(interactions) <- rownames(interactions) <- colnames(genomicData)
The problem occurs here
oddsRatio[10^-abs(interactions) > 0.05] = 1
oddsRatio[oddsRatio<1e-3] = 1e-4
oddsRatio[oddsRatio>1e3] = 1e4
logOdds=log10(oddsRatio)
When i run this
oddsRatio[10^-abs(interactions) > 0.05] = 1
Error in abs(interactions) :
non-numeric argument to mathematical function
What is going wrong here I would like to know im may be I'm not getting the code right?
My data used for this is here
data from tcgaExpr
tcgaExpr <- read.table("data.txt",sep = "\t",strip.white = FALSE,check.names = FALSE,header=TRUE,row.names = 1)
tcgaGlm = lmFit(as.matrix(tcgaExpr), design = tcgaDesign)
tcgaGlm = eBayes(tcgaGlm)
data
dput(tcgaDesign)
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0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0.0598290598290598, 0, 0.0598290598290598, 0,
0, 0, 0.0598290598290598, 0, 0, 0, 0, 0, 1, 0.0598290598290598,
0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0.0512820512820513, 0, 0, 0,
0.0512820512820513, 0, 0, 0, 1, 0, 0.0512820512820513, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0.0512820512820513,
0.0512820512820513, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.0512820512820513,
0, 0.0512820512820513, 0, 0, 0, 0.0512820512820513, 0, 0, 0,
0, 0, 0, 0.0512820512820513, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0), .Dim = c(126L, 27L), .Dimnames = list(c("TCGA-AB-2971",
"TCGA-AB-2930", "TCGA-AB-2891", "TCGA-AB-2851", "TCGA-AB-3011",
"TCGA-AB-2949", "TCGA-AB-2981", "TCGA-AB-2965", "TCGA-AB-2822",
"TCGA-AB-2959", "TCGA-AB-2973", "TCGA-AB-2987", "TCGA-AB-2986",
"TCGA-AB-2921", "TCGA-AB-2863", "TCGA-AB-3009", "TCGA-AB-2812",
"TCGA-AB-2940", "TCGA-AB-2996", "TCGA-AB-2983", "TCGA-AB-2859",
"TCGA-AB-2913", "TCGA-AB-2917", "TCGA-AB-2929", "TCGA-AB-2825",
"TCGA-AB-2900", "TCGA-AB-2846", "TCGA-AB-3002", "TCGA-AB-2871",
"TCGA-AB-2819", "TCGA-AB-2901", "TCGA-AB-2920", "TCGA-AB-2966",
"TCGA-AB-2814", "TCGA-AB-2942", "TCGA-AB-2870", "TCGA-AB-2847",
"TCGA-AB-2844", "TCGA-AB-2806", "TCGA-AB-2980", "TCGA-AB-2861",
"TCGA-AB-2916", "TCGA-AB-2878", "TCGA-AB-2817", "TCGA-AB-2830",
"TCGA-AB-2892", "TCGA-AB-2858", "TCGA-AB-2877", "TCGA-AB-2939",
"TCGA-AB-2890", "TCGA-AB-2811", "TCGA-AB-2918", "TCGA-AB-2898",
"TCGA-AB-2908", "TCGA-AB-2866", "TCGA-AB-2910", "TCGA-AB-2915",
"TCGA-AB-2977", "TCGA-AB-2912", "TCGA-AB-2943", "TCGA-AB-2881",
"TCGA-AB-2988", "TCGA-AB-3000", "TCGA-AB-2948", "TCGA-AB-2895",
"TCGA-AB-2931", "TCGA-AB-2936", "TCGA-AB-2934", "TCGA-AB-2914",
"TCGA-AB-2992", "TCGA-AB-2869", "TCGA-AB-2963", "TCGA-AB-2928",
"TCGA-AB-2924", "TCGA-AB-2818", "TCGA-AB-2975", "TCGA-AB-2874",
"TCGA-AB-2979", "TCGA-AB-2826", "TCGA-AB-2990", "TCGA-AB-2885",
"TCGA-AB-2835", "TCGA-AB-2873", "TCGA-AB-2955", "TCGA-AB-2845",
"TCGA-AB-2836", "TCGA-AB-2925", "TCGA-AB-2884", "TCGA-AB-2820",
"TCGA-AB-2899", "TCGA-AB-3008", "TCGA-AB-2994", "TCGA-AB-2853",
"TCGA-AB-2896", "TCGA-AB-2867", "TCGA-AB-2999", "TCGA-AB-2888",
"TCGA-AB-2839", "TCGA-AB-2865", "TCGA-AB-3007", "TCGA-AB-2932",
"TCGA-AB-2976", "TCGA-AB-2834", "TCGA-AB-2840", "TCGA-AB-2880",
"TCGA-AB-2998", "TCGA-AB-2813", "TCGA-AB-2882", "TCGA-AB-2950",
"TCGA-AB-2810", "TCGA-AB-2935", "TCGA-AB-2821", "TCGA-AB-2952",
"TCGA-AB-2886", "TCGA-AB-2805", "TCGA-AB-2876", "TCGA-AB-2808",
"TCGA-AB-2937", "TCGA-AB-2927", "TCGA-AB-2883", "TCGA-AB-2919",
"TCGA-AB-3012", "TCGA-AB-2875", "TCGA-AB-2984", "TCGA-AB-2970",
"TCGA-AB-2933"), c("Offset", "CEBPA", "DNMT3A", "FLT3_ITD", "FLT3_TKD",
"IDH1", "IDH2", "KIT", "KRAS", "NPM1", "NRAS", "PTPN11", "RUNX1",
"SMC1A", "SMC3", "TET2", "TP53", "U2AF1", "WT1", "complex", "minus5_5q",
"minus7q", "plus8_8q", "plus21", "t_15_17", "t_8_21", "inv16_t16_16"
)))

Related

How to make a correlation matrix of categorical variables showing only frequency of both variables as 1

I have a dataframe with papers and the parameters they reported one-hot encoded:
.
structure(list(CitationKey = c("White2021", "Tunabot2019", "Fujiwara2017",
"Dewar1994a", "Dewar1994b", "Blank2007_BF", "Blank2007_YF", "Katzschmann2018",
"Leftwich2012", "Gibouin2018", "Donley2000_KT", "Donley2000_CM",
"Sepulveda2000_KT", "Sepulveda2000_CM", "Sepulveda2000_YF", "Salumae2013",
"Jezov2012", "Anderson2000", "ShaoXu2019", "Rufo2013", "LauderFlammangAlben2012",
"Low2010", "Chong2009", "Niu2014", "LiuHu2005", "LiuHu2010",
"Tan2006", "Zhang2010", "Zhong2018a", "Zhong2018b", "ZhongDu2016",
"Xie2020", "Struebig2020", "Bainbridge1958_CD", "Bainbridge1958_T",
"Bainbridge1958_G", "Videler1991_PV", "Videler1991_TS", "Videler1991_AF",
"Videler1991_SScom", "Videler1991_GM", "Videler1991_TT", "Videler1991_OM"
), COM = c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0), Duty_Cycle = c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `Re ` = c(1, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Flow_Speed = c(1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
), Drag_Force = c(1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0), Drag_Coefficient = c(1, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0), Head_Amplitude = c(1,
1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
), Tail_Amplitude = c(1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1,
1, 1, 1, 1, 0, 0, 0, 0, 0), Frequency = c(1, 1, 1, 0, 1, 1, 1,
1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), COT = c(1, 1, 1,
1, 0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Stride_Length = c(1,
1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0
), Swimming_Speed = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1), Strouhal_Number = c(1, 1, 0, 0, 0,
0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), WPM = c(1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
), Thrust = c(0, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0), Energy_Consumption = c(0, 0, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Acceleration = c(0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
), Wavelength = c(0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0), Turning_Speed = c(0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Turning_Radius = c(0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
), Lateral_Force = c(0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0), Power = c(0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Efficiency = c(0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
Turning_Diameter = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `Yaw Rate` = c(0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0), Voltage = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Turning_Angle = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0), Froude_Efficiency = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), Speed_Efficiency = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0)), row.names = c(NA, -43L), class = c("tbl_df",
"tbl", "data.frame"))
Using this thread, I was able to make a correlation matrix
reduced_df[,2:ncol(reduced_df)] %>%
cor(use="pairwise.complete.obs", method='spearman') %>%
ggcorrplot(show.diag = F,
type="lower",
lab=TRUE,
lab_size=2)
However, COM and Duty_Cycle, for example have a value of 1.0 because they are both present in the same paper once, and then neither are reported in any other papers - so they correlate exactly. Frequency and COT, however, are co-reported in 8 papers and then vary, so they don't correlate well. I'd like to alter the correlation matrix to show the frequency of both parameters being co-reported in the same papers. COT and Frequency should be 8x higher in value than COM and Duty Cycle.
However, I don't know how to do this. I'd greatly appreciate any advice or ideas.

Counting dummy variable = 1 observations in a dataset for two specific years

I am trying to count how many enterprise zones were designated in two specific years out of 8 total years. I first isolated the years with the following code:
ez <- ezunem %>% select(3,7,8)
Then tried to count the enterprise zones that were in the select columns:
ez %>% count(ez, sort=TRUE)
This didnt work. What is the best way to count dummy variables = 1 out of two columns in R.
Edit: here is the output with dput(ez) command:
structure(list(ez = structure(c(0, 0, 0, 0, 1, 1, 1, 1, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1,
1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0,
0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1,
1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0), format.stata = "%9.0g"),
d84 = structure(c(0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0), format.stata = "%9.0g"),
d85 = structure(c(0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0), format.stata = "%9.0g")), row.names = c(NA,
-198L), class = c("tbl_df", "tbl", "data.frame"))
So, basically I want my output to count the 1's for d84 and d85.

Something like this?
library(dplyr)
ez %>%
group_by(ez) %>%
summarise(across(c(d84, d85), sum, .names="count_{.col}"))
ez count_d84 count_d85
<dbl> <dbl> <dbl>
1 0 16 12
2 1 6 10

Problems with merging two files with yearly binary data for two overlapping subsets of individuals

I work with mark-recaptures of animals, and I have two capture histories I need to merge. Both files look like this:
Both files include subsets of the same group of animals, however, all inividuals are not present in both files. Also, one file contains more YEARS (in columns) than the other. The 0's and 1's indicate whether the animal was observed this year or not.
I need to merge both files, ending up with a file that contains all individuals that are included in these files. Observation data need to be merged for those individuals that are present in both files. If observation status for a given animal is 0 in FILE1 and 0 in FILE2, the observation status in the merged file need to be 0, if 0 in FILE1 and 1 in FILE2, observation status in the merged file should be 1, and if 1 in both files, it still needs to be 1 in the merged file (NOT 2).
Below you'll find samples of both files, FILE1 and FILE2. Any help appreciated.
FILE1:
> dput(FILE1)
structure(list(ID = c("1", "LL-30", "M-300", "NKW-001", "NKW-002",
"NKW-003", "NKW-004", "NKW-006", "NKW-007", "NKW-009", "NKW-010",
"NKW-011", "NKW-012", "NKW-013", "NKW-014", "NKW-015", "NKW-016",
"NKW-017", "NKW-018", "NKW-019", "NKW-021", "NKW-022", "NKW-023",
"NKW-024", "NKW-025", "NKW-026", "NKW-028", "NKW-029", "NKW-030",
"NKW-031", "NKW-032", "NKW-033", "NKW-034", "NKW-035", "NKW-036",
"NKW-037", "NKW-038", "NKW-039", "NKW-040"), `1986` = c(0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1987` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1988` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1989` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1990` = c(0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1991` = c(0,
0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1992` = c(0,
0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1993` = c(0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1994` = c(0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1995` = c(1,
0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1996` = c(0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1997` = c(0,
0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1998` = c(1,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `1999` = c(1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2000` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2001` = c(0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2002` = c(1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2003` = c(1,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2004` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2005` = c(1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0), `2006` = c(0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2007` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2008` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2012` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2013` = c(0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0), `2014` = c(0,
0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0), `2015` = c(0,
0, 0, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), `2016` = c(0,
0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0,
1, 0, 0, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 0), `2017` = c(0,
0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1), `2018` = c(0,
0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 1), `2019` = c(0,
0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0,
0, 1, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 1)), class = "data.frame", row.names = c(NA,
-39L))
FILE2:
> dput(FILE2)
structure(list(ID = c("KI03", "KI05", "KI06", "KI07", "KI08",
"KI10", "NKW-001", "NKW-004", "NKW-005", "NKW-009", "NKW-019",
"NKW-023", "NKW-025", "NKW-027", "NKW-031", "NKW-032", "NKW-040",
"NKW-045", "NKW-424", "NKW-431", "NKW-441", "NKW-443"), `2008` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0
), `2009` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0), `2010` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2011` = c(0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1), `2012` = c(0,
0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1
), `2013` = c(1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0), `2014` = c(0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2015` = c(1, 1, 1, 0, 1, 1,
1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0), `2016` = c(1,
0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0
), `2017` = c(1, 0, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 1, 0, 0, 0), `2018` = c(1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), `2019` = c(0, 0, 0, 1, 1, 1,
0, 1, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 0), `2020` = c(0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
)), class = "data.frame", row.names = c(NA, -22L))

Here is a scalable data.table solution with no merging involved.
If you have got more files, just add them to the list L
library( data.table )
setDT(df1);setDT(df2) #set to data.table format
L <- list( df1, df2 ) #put the data.tables in a list
#melt all data.tables in the list to long format
L.melt <- lapply( L, melt, id.vars = "ID", variable.name = "year", variable.factor = FALSE )
#rowbind to one large data.table
DT <- data.table::rbindlist( L.melt, use.names = TRUE, fill = TRUE )
#summarise, output a logical TRUE (=1) of FALSE = 0 based on the sum of 0's and 1's
ans <- DT[, .( seen = as.numeric( sum(value) > 0 ) ), by = .(ID, year) ]
#cast to wide again, fill in missing observations in years with 0
dcast( ans, ID ~ year, value.var = "seen", fill = 0 )

Lime in R: example is not working Error in glmnet(x[shuffle_order, features]

With the Lime package in R, I want to explain my RF model.
I saw an example on github (scroll a bit down to the section "An Example"): (https://github.com/thomasp85/lime)
I tried to run the exact same code, but with my own data (my data is added below). But, every time I receive the same error. Can anyone help me out here?
I have the understanding that my code is exactly the same as in the example, including the str() of my data. What goes wrong? How can I make this work?
Note that my target variable, is the first column (called target), and that all my data is binary data.
library(caret)
library(lime)
total <- data # the data set is posted below
# Split up the data set
iris_test <- total[2:6,] # I just used the iris name (as in the example)
iris_train <- total[-(2:6),]
iris_lab <- total[[1]][-(2:6)]
iris_lab <- as.factor(iris_lab)
# Create Random Forest model on iris data
model <- train(iris_train, iris_lab, method = 'rf')
First warnings: Warning messages:
1: Setting row names on a tibble is deprecated.
# Create an explainer object
explainer <- lime(iris_train, model)
Second warning:
Warning message:
Data contains numeric columns with zero variance
# Explain new observation
explanation <- explain(iris_test, explainer, n_labels = 1, n_features = 2)
And the error:
Error in glmnet(x[shuffle_order, features], y[[label]][shuffle_order], :
x should be a matrix with 2 or more columns
In addition: There were 12 warnings (use warnings() to see them)
head(explanation) # Did not make it so far...
Edit 1 Removed all the columns with 0 variance (as suggested in the comments). But unfortunately, still the same errors.
My data:
dput(total)
structure(list(target = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), X2 = c(1, 0, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0,
0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0), X3 = c(0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0), X4 = c(0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0), X5 = c(0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), X6 = c(0, 0, 1, 0,
1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0,
0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0),
X7 = c(0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X8 = c(0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X9 = c(0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0),
X10 = c(0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0),
X11 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X12 = c(0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X13 = c(1, 1, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X14 = c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X15 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X16 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X17 = c(0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0,
0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X18 = c(0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0,
1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 1, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0,
0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0),
X19 = c(0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1,
0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0,
0, 0, 1, 1, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1,
0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X20 = c(0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1,
1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1,
1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X21 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0,
1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0,
1, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1,
1, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0,
0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0),
X22 = c(0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1,
1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1),
X23 = c(1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
1, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1,
0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0),
X24 = c(0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 1, 0, 1, 1, 1,
1, 0, 1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0,
0, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 0, 1, 1, 0, 1, 0,
0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0,
0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0,
0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 0, 1,
0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 1, 0, 1,
0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0),
X25 = c(1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 1, 0, 0, 1, 1, 0, 1,
1, 1, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1,
0, 1, 0, 1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 1, 1, 1, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1,
1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, 1, 1, 0, 1, 1,
0, 1, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 1),
X26 = c(0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0,
0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0),
X27 = c(0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1,
1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0),
X28 = c(1, 0, 0, 1, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1,
1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 0, 0, 1, 1, 0, 1,
0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0,
1, 1, 1, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1, 0,
1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 1, 0, 1, 0, 1, 0, 1,
0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0,
0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0,
0, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1),
X29 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X30 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X31 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X32 = c(0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0,
1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0,
1, 0, 1, 0, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1,
0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 0, 1,
0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0,
1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 0, 1, 1,
0, 1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0,
0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 1, 1, 1, 0, 0, 1, 0),
X33 = c(0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1,
1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0),
X34 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X35 = c(0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1,
0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0,
1, 0, 1, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 0,
0, 1, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 1, 1, 0,
0, 1, 1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 1, 0),
X36 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X37 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0),
X38 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X39 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X40 = c(1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 1, 0, 1,
1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0,
1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0,
0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0,
0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0),
X41 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X42 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X43 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X44 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
X45 = c(0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), .Names = c("target",
"X2", "X3", "X4", "X5", "X6", "X7", "X8", "X9", "X10", "X11",
"X12", "X13", "X14", "X15", "X16", "X17", "X18", "X19", "X20",
"X21", "X22", "X23", "X24", "X25", "X26", "X27", "X28", "X29",
"X30", "X31", "X32", "X33", "X34", "X35", "X36", "X37", "X38",
"X39", "X40", "X41", "X42", "X43", "X44", "X45"), row.names = c(NA,
-150L), class = c("tbl_df", "tbl", "data.frame"))

I think the error comes with the tibble data. Here is the working code:
total <- data.frame(total)
total$target <- as.factor(total$target) # intuitive factor coding
Splitting data set:
iris_train <- total[-c(2:6), ]
iris_lab <- total[-c(2:6),1]
iris_test <- total[2:6, ]
The 0 variance columns are handled by the internal function. To avoid messages remove those columns from training sample as:
colNullVarTrain <- as.numeric(which(apply(iris_train, 2, var)==0))
iris_train <- iris_train[ ,-colNullVarTrain]
iris_test <- iris_test[ ,-colNullVarTrain]
Create Random Forest model:
model <- train(iris_train, iris_lab, method = 'rf')
explainer <- lime(iris_train, model)
explanation <- explain(iris_test, explainer, n_labels = 1, n_features = 2)
EDIT:
Removing target variable from the list of explanatory variables.
Object iris_lab can be ommited if the train function is written as:
model <- train(target~., data=iris_train, method = 'rf')
varImp(model) # target is not a predictor

Which of elements come together in different data

I'm trying to write a script to analyze my data. Would be great if you can help me with that.
Let's start with my data:
> dput(tbl_alles[1:100,])
structure(list(`10` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0), `20` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0), `52.5` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0.7306675, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0), `81` = c(0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0.91538769,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0), `110` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0.85441768, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0.61947266, 0, 0, 0), `140.5` = c(0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.5664111,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.6800275, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0.6300494, 0, 0, 0), `189` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0.6234154, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0.987181, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.6194727,
0, 0, 0), `222.5` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0.8632862, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0.3456471, 1, 0, 0), `278` = c(0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0.61502309,
0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0.44036184, 1,
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.42691496, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0.32234716, 0, 0, 0, 0.08890253, 0.67918373,
0, 0), `340` = c(0, 0, 0, 0, 0, 0, 0.583163048, 0, 0, 0, 0, 0,
1, 1, 0, 0, 0, 0, 1, 0.218194067, 0.325932107, 1, 0, 0, 1, 0,
0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.663889907, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0.789927058, 0, 0.44201215,
0, 0, 0, 0, 0.134339392, 0, 0.668372028, 0, 0, 0, 0, 0, 0, 0,
0.387740087, 0, 0, 0, 0, 0, 0, 0), `397` = c(0, 1, 0, 0, 0, 0,
1, 0, 1, 0, 0, 0, 0, 0.63953839, 0, 1, 0, 0, 0, 1, 1, 0.81888525,
0.89884151, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0.51459601, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0.75141988, 0, 0, 0, 0, 0, 0, 0, 0, 0.65763553, 1, 0, 0,
0, 0, 1, 0, 1, 0.67607045, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0,
0, 0.80260185, 0, 0, 0, 0, 0, 0, 1), `453.5` = c(0, 0.66069369,
0, 0, 0, 1, 0.57541627, 1, 1, 0, 0, 0, 1, 0.64615661, 0, 0.45209671,
0, 0, 0, 0.17022498, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0.02056466, 0.08765142, 1, 0, 0, 0, 0, 0, 1, 0.53107365,
0, 0, 1, 0, 0.47454662, 1, 0.58701126, 1, 0.83194495, 0, 0, 1,
0, 0, 0, 0, 0.04550448, 0, 1, 0, 0.65763553, 1, 1, 0.05581525,
0, 0, 0.78992706, 1, 0.80859968, 0.80441503, 1, 1, 0, 0.5866736,
0, 0, 0.75623688, 0.36602167, 0, 0, 1, 0, 0.31053744, 1, 0.52549512,
1, 0, 0, 0, 0, 0.51742419), `529` = c(0, 0.521435654, 0, 0, 1,
0, 0.175996209, 0, 0, 0, 1, 0, 0, 0, 0, 0.886059888, 0, 0, 0,
0.17022498, 0, 0, 0.643526362, 0, 0, 0, 0, 0, 0.438237074, 0.01594858,
0, 0.383182117, 0, 0, 0, 0, 0, 0, 1, 0.101027654, 1, 0, 0, 0,
0, 0, 0, 0.733614607, 0.89648659, 0, 0, 0.703255538, 0, 1, 0.383200069,
0.868653232, 1, 0.065540432, 0, 0, 0.221275397, 0.229618981,
0, 0, 0, 0.14131076, 0, 0.665883882, 0, 0.399096177, 0.570186116,
0.917797708, 0.349222091, 0, 0, 0.872987981, 0, 0, 1, 1, 0.58275186,
0, 0.211497647, 0, 0, 0.929066091, 0.826799766, 0, 0, 0, 0, 0.148043509,
0.802601847, 1, 0.780383116, 0, 0, 0, 0, 0.340224249), `580` = c(0,
0.437291195, 0, 0, 1, 0, 0.20731698, 0, 0, 0, 1, 0, 0, 0, 0,
0.719755907, 0, 0, 0, 0.033248127, 0, 0, 0, 0, 0, 0, 0, 0, 0.443305568,
0, 0, 0.558877749, 0, 0, 0, 0, 0, 0, 1, 0.171621995, 1, 0, 0,
0, 0, 0, 0, 0.28952456, 1, 1, 0, 0.470920245, 0, 0.690299657,
0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0.111377617, 0.740623952, 0,
0, 0.53029633, 0, 0.917797708, 0.395559317, 0, 0, 0.484708125,
0, 0, 0.174273053, 0, 0.693355663, 0, 0.050471201, 1, 0, 0, 1,
0, 0, 0, 0, 0.698359908, 0.298609118, 0.702753583, 0.926794372,
0, 0, 0, 0, 0.320673115), `630.5` = c(0, 0.52204783, 0, 0, 0,
0, 0.48815538, 0, 0, 0, 0, 1, 0, 0, 0, 0.82709638, 0, 0, 0, 0.09539534,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0.45656691,
0.74836669, 0, 0, 0, 0, 0, 0, 0, 0.95701562, 1, 0, 0.67884433,
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0.65763553,
0, 0, 1, 0, 0, 0.77875219, 0, 0, 0.25002477, 0, 1, 0, 0, 0, 0,
0, 0.82679977, 0, 0, 0, 0, 0.84843874, 0.38138487, 0.79820877,
0, 0, 0, 0, 0, 0.51876177), `683.5` = c(0, 0.52429838, 0, 0,
0, 0, 0.59605685, 0, 0, 0, 0, 0, 0, 0, 0, 0.27845748, 0.28224351,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0.94942976, 0, 0, 0, 0, 0, 0.74467188, 0, 0, 0.31501511,
0, 0, 0, 0, 0, 0, 0, 0.73190143, 0, 0, 0, 0, 0, 0.90254266, 0.42921624,
0, 0, 0.56841245, 0, 0, 0.48306937, 0.54177946, 0, 0.70689046,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0.72875619, 0, 0, 0, 0, 1, 0.26676304,
0.77778861, 0, 0, 0, 0, 0, 0.17064527), `735.5` = c(1, 0.3768651,
0, 1, 0, 0, 0.51381348, 0, 0, 0, 0, 0, 0, 0, 0, 0.39914361, 0.22206677,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0.42663351, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.61727598,
0, 0, 0, 0, 0, 0, 0.70045244, 0, 0, 0, 0, 1, 0.62631217, 0, 0,
0, 0, 0, 0, 0.14653411, 1, 1, 0.27513455, 0, 0, 0, 0, 0.75025613,
0, 0, 0, 0, 0, 0.92484335, 0, 1, 0, 1, 0.84843874, 0.12198269,
0.58556836, 0, 0, 0, 0, 0, 0.09714178), `784` = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.45656691, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0.61727598, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 1, 0, 0, 0.84843874, 0, 0, 0, 0, 0, 0, 0, 0
), `832` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0.16189002, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 0, 0.2511846, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0.23427262, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0.45750616,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0.86974453,
1, 0, 0, 0.48180864, 0, 0, 0, 0.93083267, 0, 0, 0, 0), `882.5` = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3111616,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.63931007, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0.73948906, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0), `926.5` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0.63485498, 0, 0, 0, 0, 0, 0, 1, 0,
0.68547559, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.35567368,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0, 0.84973396, 0, 0, 1, 0), `973` = c(0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.86100786, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0.68128251, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0.30811206, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.79599822, 0,
0, 0, 0), `1108` = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0.75365872, 0, 0, 1, 0, 0, 0, 0, 0, 0.52862914,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.20061435, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0.93083267, 0, 0, 0, 0), `1200` = c(0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0.67241551, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0.55638877, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)), .Names = c("10",
"20", "52.5", "81", "110", "140.5", "189", "222.5", "278", "340",
"397", "453.5", "529", "580", "630.5", "683.5", "735.5", "784",
"832", "882.5", "926.5", "973", "1108", "1200"), row.names = c("at1g01050.1",
"at1g01080.1", "at1g01090.1", "at1g01220.1", "at1g01420.1", "at1g01470.1",
"at1g01800.1", "at1g01910.5", "at1g01920.2", "at1g01980.1", "at1g02020.2",
"at1g02100.2", "at1g02130.1", "at1g02140.1", "at1g02150.1", "at1g02500.2",
"at1g02560.1", "at1g02780.1", "at1g02880.3", "at1g02920.1", "at1g02930.2",
"at1g03030.1", "at1g03110.1", "at1g03130.1", "at1g03210.1", "at1g03220.1",
"at1g03230.1", "at1g03310.2", "at1g03330.1", "at1g03475.1", "at1g03630.2",
"at1g03680.1", "at1g03870.1", "at1g03900.1", "at1g04130.1", "at1g04170.1",
"at1g04190.1", "at1g04270.2", "at1g04350.1", "at1g04410.1", "at1g04420.1",
"at1g04530.1", "at1g04640.2", "at1g04690.1", "at1g04750.2", "at1g04810.1",
"at1g04850.1", "at1g04870.2", "at1g05010.1", "at1g05180.1", "at1g05320.3",
"at1g05350.1", "at1g05520.1", "at1g05560.1", "at1g05620.2", "at1g06000.1",
"at1g06110.1", "at1g06130.2", "at1g06290.1", "at1g06410.1", "at1g06550.1",
"at1g06560.1", "at1g06570.1", "at1g06620.1", "at1g06650.2", "at1g06680.2",
"at1g06900.1", "at1g07080.1", "at1g07110.1", "at1g07140.1", "at1g07240.1",
"at1g07250.1", "at1g07440.1", "at1g07750.1", "at1g07780.4", "at1g07890.8",
"at1g07990.1", "at1g08110.3", "at1g08200.1", "at1g08360.1", "at1g08490.1",
"at1g08520.1", "at1g08550.2", "at1g08820.2", "at1g08830.2", "at1g08980.1",
"at1g09010.1", "at1g09020.1", "at1g09130.2", "at1g09210.1", "at1g09300.2",
"at1g09310.1", "at1g09340.1", "at1g09430.1", "at1g09490.2", "at1g09620.1",
"at1g09640.1", "at1g09750.1", "at1g09760.1", "at1g09780.1"), class = "data.frame")
As you can see most of cells contain a number "0".
I would like to create a subsets of my data. Let's call them "clusters". I would like to put in the same cluster "elements" (row.names) which has any value (different than 0) in the same column.
So for example:
row.name Column1 Column2 Column3 Column4
at1g02560.1 0 0.12 0 0
at1g02020.2 1 0 0.55 0.31
at1g14560.2 0.15 0.47 0 0
As you see at1g02560.1 has a value only in column 2, there is one more row which contains any value in the column 2, it's at1g14560.2. That means that they belong to the same cluster (let's say cluster 1).
The problem is that at1g02020.2 and at1g14560.2 has a value different than 0 in the column 1. They should be in the same cluster aswell (cluster 2).
In summary at1g14560.2 belong to two different clusters (cluster 1 and cluster 2).
As a result I would like to add additional column to my data named clusters and fill it with the numbers.
Example:
row.name data data data data Clusters
at1g02560.1 1
at1g14560.2 1,2
at1g02020.2 2
Is it even possible to do with R ?

Yes, it is possible to do with R. Here's one way using apply:
res <- cbind(tbl_alles,
Clusters=apply(tbl_alles, 1, function(x) paste(which(x!=0), collapse=",")))
head(res[, c(1:5, ncol(res))])
# 10 20 52.5 81 110 Clusters
# at1g01050.1 0 0 0 0 0 17
# at1g01080.1 0 0 0 0 0 11,12,13,14,15,16,17
# at1g01090.1 0 0 0 1 0 4
# at1g01220.1 0 0 0 0 0 17
# at1g01420.1 0 0 0 0 0 13,14
# at1g01470.1 0 0 0 0 0 12

You may also try:
indx <- which(!!tbl_alles,arr.ind=T)
tbl_alles$Clusters <- tapply(indx[,2],indx[,1], FUN=paste, collapse=",")
tbl_alles[1:5,c(1:5, ncol(tbl_alles))]
# 10 20 52.5 81 110 Clusters
#at1g01050.1 0 0 0 0 0 17
#at1g01080.1 0 0 0 0 0 11,12,13,14,15,16,17
#at1g01090.1 0 0 0 1 0 4
#at1g01220.1 0 0 0 0 0 17
#at1g01420.1 0 0 0 0 0 13,14

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