cor_bakers_gamma error - Githubissues

I'm following your tutorial and am running into an error when I try to reproduce the 95% confidence interval of cor_bakers_gamma() results.

Specifically, I'm using this code chunk with my two own small dendrograms:

dend1 <- dend15
dend2 <- dend51

set.seed(23801)

R <- 100
dend1_labels <- labels(dend1)
dend2_labels <- labels(dend2)
cor_bakers_gamma_results <- numeric(R)
for(i in 1:R) {
   sampled_labels <- sample(dend1_labels, replace = TRUE)
   dend_mixed1 <- sample.dendrogram(dend1, 
                                    dend_labels=dend1_labels,
                                    fix_members=TRUE,fix_order=TRUE,fix_midpoint=FALSE,
                                    replace = TRUE, sampled_labels=sampled_labels
                                      )
   dend_mixed2 <- sample.dendrogram(dend2, dend_labels=dend2_labels,
                                    fix_members=TRUE,fix_order=TRUE,fix_midpoint=FALSE,
                                    replace = TRUE, sampled_labels=sampled_labels
                                      )                                    
   cor_bakers_gamma_results[i] <- cor_bakers_gamma(dend_mixed1, dend_mixed2, warn = FALSE)
}

I am getting the following warning: It is impossible to produce a one-to-one cut for the k/h you specidied. 0's have been introduced. Note that this result would be different from R's default cutree output.It is impossible to produce a one-to-one cut for the k/h you specidied. 0's have been introduced. Note that this result would be different from R's default cutree output

I was hoping I could get some help with this warning and some information to solve it. Calculating cor_bakers_gamma() works with the original dendrograms and I'm also able to calculate a bootstrap p-value. However, I'm interested in calculating the 95% CI.

Thanks! Caitlin

Hey Caitlin, Sorry - but I won't get to review this issue in the coming weeks. Just wanted to let you know. If you happen to solve it, please let me know.

On Mon, Feb 1, 2021 at 10:43 PM Caitlin Simopoulos notifications@github.com wrote:

I'm following your tutorial https://cran.r-project.org/web/packages/dendextend/vignettes/dendextend.html and am running into an error when I try to reproduce the 95% confidence interval of cor_bakers_gamma() results.

Specifically, I'm using this code chunk with my two own small dendrograms:

dend1 <- dend15dend2 <- dend51

set.seed(23801) R <- 100dend1_labels <- labels(dend1)dend2_labels <- labels(dend2)cor_bakers_gamma_results <- numeric(R)for(i in 1:R) { sampled_labels <- sample(dend1_labels, replace = TRUE) dend_mixed1 <- sample.dendrogram(dend1, dend_labels=dend1_labels, fix_members=TRUE,fix_order=TRUE,fix_midpoint=FALSE, replace = TRUE, sampled_labels=sampled_labels ) dend_mixed2 <- sample.dendrogram(dend2, dend_labels=dend2_labels, fix_members=TRUE,fix_order=TRUE,fix_midpoint=FALSE, replace = TRUE, sampled_labels=sampled_labels ) cor_bakers_gamma_results[i] <- cor_bakers_gamma(dend_mixed1, dend_mixed2, warn = FALSE) }

I am getting the following warning: It is impossible to produce a one-to-one cut for the k/h you specidied. 0's have been introduced. Note that this result would be different from R's default cutree output.It is impossible to produce a one-to-one cut for the k/h you specidied. 0's have been introduced. Note that this result would be different from R's default cutree output

I was hoping I could get some help with this warning and some information to solve it. Calculating cor_bakers_gamma() works with the original dendrograms and I'm also able to calculate a bootstrap p-value. However, I'm interested in calculating the 95% CI.

Thanks! Caitlin

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talgalili / dendextend

cor_bakers_gamma error #103