cut.default error in heatmap generation R - r

I want to generate a heatmap from a 8*6 dataframe. The last row in the dataframe has the information to annotate the columns. Structure of the dataframe is as follows:
heatmap_try <-structure(list(BGC0000041 = structure(c(1L, 2L, 1L, 1L, 1L, 3L
), .Label = c("0", "0.447458977", "a"), class = "factor"), BGC0000128 = structure(c(1L,
1L, 1L, 3L, 2L, 4L), .Label = c("0", "1.785875195", "4.093659107",
"a"), class = "factor"), BGC0000287 = structure(c(1L, 1L, 1L,
3L, 2L, 4L), .Label = c("0", "1.785875195", "4.456229186", "b"
), class = "factor"), BGC0000294 = structure(c(3L, 1L, 2L, 4L,
1L, 5L), .Label = c("0", "2.035046947", "3.230553742", "3.286304185",
"b"), class = "factor"), BGC0000295 = structure(c(1L, 1L, 1L,
2L, 1L, 3L), .Label = c("0", "2.286304185", "c"), class = "factor"),
BGC0000308 = structure(c(4L, 2L, 3L, 5L, 1L, 6L), .Label = c("6.277728291",
"6.313707588", "6.607936616", "6.622871165", "6.64385619",
"c"), class = "factor"), BGC0000323 = structure(c(1L, 2L,
1L, 1L, 1L, 3L), .Label = c("0", "0.447458977", "c"), class = "factor"),
BGC0000328 = structure(c(1L, 2L, 1L, 1L, 1L, 3L), .Label = c("0",
"0.447458977", "c"), class = "factor")), class = "data.frame", row.names = c("Gut",
"Oral", "Anterior_nares", "Retroauricular_crease", "Vagina",
"AL"))
My code for heatmap generation is as follows (I am using pheatmap library):
library(pheatmap)
heatmap_data1 <- heatmap_try[ c(1:5), c(1:8) ]
anotation_data <- as.data.frame(t(heatmap_try[6, ]))
row.names(anotation_data) <- colnames(heatmap_data1)
pheatmap(heatmap_data1, annotation_col = anotation_data, color = colorRampPalette(c("white","blue"))(n=100),cellwidth = 40,cellheight = 6,fontsize_row = 5,cluster_rows = F,cluster_cols = F)
However, I am getting the following error:
Error in cut.default(x, breaks = breaks, include.lowest = T) :
'x' must be numeric
What I am doing wrong?
Thanks!


This is because the columns of heatmap_data1 are factors, they need to be numeric. One way to convert is with:
heatmap_data1_num <- as.data.frame(lapply(heatmap_data1,
function(x) as.numeric(as.character(x))))
# then as before
pheatmap(heatmap_data1_num, annotation_col = anotation_data, color = colorRampPalette(c("white","blue"))(n=100),cellwidth = 40,cellheight = 6,fontsize_row = 5,cluster_rows = F,cluster_cols = F)

Related

Error using arules - lhs is an unkown item label

I am using Apriori Association rules in R with a database structured as
the following. using the following code:
library(arules)
library(arulesViz)
# Convert data into dataframe with two factors
data3 <- as.data.frame(unclass(morse_code_reasonsv2),
stringsAsFactors = TRUE)
# applying appriori
rules7 <- apriori(data3, parameter = list(support = 0.05,confidence = 0.5,minlen=2, maxlen=3), appearance=list(rhs=c("Firm's.global.reorganization=Yes"),
lhs=c("Delivery.time=Yes",
"Automation.of.production.process=Yes"),default="none"))
Using this formula I get the following error:
error in asMethod(object) :
Delivery.time=Yes is an unknown item label, Automation.of.production.process=Yes is an unknown item label
EDIT: data in dput:
structure(list(Firm.s.global.reorganization = structure(c(1L,
2L, 1L, 2L, 2L), .Label = c("no", "yes"), class = "factor"),
Delivery.time = structure(c(1L, 1L, 1L, 1L, 1L), .Label = c("no",
"yes"), class = "factor"), Automation.of.production.process = structure(c(2L,
1L, 2L, 1L, 1L), .Label = c("no", "yes"), class = "factor"),
Poor.quality.of.offshored.production = structure(c(1L, 1L,
1L, 1L, 1L), .Label = c("no", "yes"), class = "factor"),
Made.in.effect = structure(c(1L, 1L, 1L, 1L, 1L), .Label = c("no",
"yes"), class = "factor"), Proximity.to.customers = structure(c(1L,
1L, 1L, 1L, 1L), .Label = c("no", "yes"), class = "factor")), row.names = c(NA,
5L), class = "data.frame")

R Mlogit Error in replacement rows and impossible to coerce choice variable to logical

I want to run the mlogit function on my discrete choice dataset. Below I have provided the data and the lines of R code utilizing the package mlogit that are producing the errors. I am getting an error when running the full dataset about the dimensions for mlogit.data. When running mlogit, I am getting an error around coercing the "choice" variable to a logical.
Here is a snapshot of the code and the structure to reproduce a subset of it in R.
structure(list(row_id = c("1a", "1b", "1c", "1d", "1e", "1g"), choice = structure(c(2L, 1L, 2L, 1L, 2L, 1L), .Label = c("1", "2"), class = "factor"), alt_var = structure(c(1L, 2L, 1L, 2L, 1L, 2L), .Label = c("1", "2"), class = "factor"), meal_choice = structure(c(1L, 2L, 1L, 1L, 1L, 2L), .Label = c("1", "2"), class = "factor"), transport_choice = structure(c(1L, 2L, 1L, 2L, 2L, 2L), .Label = c("1", "2"), class = "factor"), packaging_source = structure(c(1L, 2L, 1L, 1L, 2L, 2L), .Label = c("1", "2"), class = "factor"), disposal_choice = structure(c(1L, 2L, 1L, 1L, 2L, 2L), .Label = c("1", "2"), class = "factor")), row.names = c(NA, -6L), class = c("data.table", "data.frame"), .internal.selfref = <pointer: 0x7fa6d980f8e0>)
mlogit.data(data = df, choice = "choice", shape = "long", alt.var = "alt_var", id.var = "row_id", drop.index = TRUE)
Error in `$<-.data.frame`(x, name, value) : replacement has 964 rows, data has 965
mlogit(choice ~ meal_choice + transport_choice + packaging_source + disposal_choice, df, reflevel = "car")
`Error in dfidx::dfidx(data = data, dfa$idx, drop.index = dfa$drop.index, :
impossible to coerce the choice variable to a logical`

Melting and converting badly labeled likert Scale R

on my survey I made a mistake for a 5 point likert scale as follows:
dput(head(edu_data))
structure(list(Education.1. = structure(c(1L, 1L, 1L, 1L, 1L,
1L), .Label = c("", "Y"), class = "factor"), Education.2. = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("", "Y"), class = "factor"),
Education.3. = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("",
"Y"), class = "factor"), Education.4. = structure(c(1L, 1L,
1L, 2L, 2L, 1L), .Label = c("", "Y"), class = "factor"),
Education.5. = structure(c(2L, 2L, 2L, 1L, 1L, 1L), .Label = c("",
"Y"), class = "factor")), row.names = c(NA, 6L), class = "data.frame")
I would like to change this into one column with a single value such that
answer_to_ls= 1:5
The output I want to get would be a column with a single number and that means getting rid of the letter. I do off course have a unique respondent's ID
Please tell me if I can somehow be more clear in the style of my question as I want to be a valuable member of the comunity.

I think there are a lot of potential solutions available, try a search of merging or collapsing multiple binary or dichotomous columns into a single column. For example:
R - Convert various dummy/logical variables into a single categorical variable/factor from their name
In your case, you could try something like:
edu_data$answer_to_ls <- apply(edu_data[1:5] == "Y", 1, function(x) { if (any(x)) { as.numeric(gsub(".*(\\d+).", "\\1", names(which(x)))) } else NA })
This will extract the number from the column name for the Likert scale response 1 to 5, make it a numeric value, and include NA if there are no "Y" responses. edu_data[1:5] selects those columns to consider for conversion, in this case columns 1 through 5.
Education.1. Education.2. Education.3. Education.4. Education.5. answer_to_ls
1 Y 5
2 Y 5
3 Y 5
4 Y 4
5 Y 4
6 NA

d <- structure(list(Education.1. = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("", "Y"), class = "factor"),
Education.2. = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("", "Y"), class = "factor"),
Education.3. = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("", "Y"), class = "factor"),
Education.4. = structure(c(1L, 1L, 1L, 2L, 2L, 1L), .Label = c("", "Y"), class = "factor"),
Education.5. = structure(c(2L, 2L, 2L, 1L, 1L, 1L), .Label = c("", "Y"), class = "factor")),
row.names = c(NA, 6L), class = "data.frame")
d$item1 <- 1 * (d$Education.1 == "Y") +
2 * (d$Education.2 == "Y") +
3 * (d$Education.3 == "Y") +
4 * (d$Education.4 == "Y") +
5 * (d$Education.5 == "Y")
print(d)
leads to
> print(d)
Education.1. Education.2. Education.3. Education.4. Education.5. item1
1 Y 5
2 Y 5
3 Y 5
4 Y 4
5 Y 4
6 0

Error in table(data, reference, dnn = dnn, ...) : all arguments must have the same length when run confusionMatrix with caret, in R

I have an issue running a confusionMatrix.
here is what I do:
rf <- caret::train(tested ~.,
data = training_data,
method = "rf",
trControl = ctrlInside,
metric = "ROC",
na.action = na.exclude)
rf
After I get my model this is the next step I take:
evalResult.rf <- predict(rf, testing_data, type = "prob")
predict_rf <- as.factor(ifelse(evalResult.rf <0.5, "positive", "negative"))
And then I am running my confusion matrix.
cm_rf_forest <- confusionMatrix(predict_rf, testing_data$tested, "positive")
And the error comes after I apply the confusionMatrix:
Error in table(data, reference, dnn = dnn, ...) :
all arguments must have the same length
Nevertheless, I give you bits of my data.
train data:
structure(list(tested = structure(c(1L, 1L, 1L, 1L, 1L,
1L), .Label = c("negative", "positive"), class = "factor"), Gender = structure(c(2L,
2L, 1L, 1L, 2L, 2L), .Label = c("Female", "Male", "Other"), class = "factor"),
Age = c(63, 23, 28, 40, 31, 60), number_days_symptoms = c(1,
1, 16, 1, 14, 1), care_home_worker = structure(c(1L, 2L,
1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
health_care_worker = structure(c(1L, 1L, 1L, 1L, 2L, 1L), .Label = c("No",
"Yes"), class = "factor"), how_unwell = c(1, 1, 6, 4, 2,
1), self_diagnosis = structure(c(1L, 1L, 2L, 1L, 2L, 1L), .Label = c("No",
"Yes"), class = "factor"), chills = structure(c(1L, 1L, 2L,
1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
cough = structure(c(1L, 1L, 2L, 2L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), diarrhoea = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
fatigue = structure(c(1L, 2L, 2L, 2L, 2L, 1L), .Label = c("No",
"Yes"), class = "factor"), headache = structure(c(2L, 2L,
3L, 2L, 2L, 2L), .Label = c("Headcahe", "No", "Yes"), class = "factor"),
loss_smell_taste = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), muscle_ache = structure(c(1L,
1L, 2L, 2L, 2L, 2L), .Label = c("No", "Yes"), class = "factor"),
nasal_congestion = structure(c(1L, 1L, 1L, 2L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), nausea_vomiting = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
shortness_breath = structure(c(1L, 1L, 1L, 1L, 2L, 1L), .Label = c("No",
"Yes"), class = "factor"), sore_throat = structure(c(1L,
1L, 1L, 2L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
sputum = structure(c(1L, 1L, 2L, 2L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), temperature = structure(c(4L,
4L, 4L, 4L, 1L, 4L), .Label = c("37.5-38", "38.1-39", "39.1-41",
"No"), class = "factor"), asthma = structure(c(2L, 1L, 1L,
1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
diabetes_type_one = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), diabetes_type_two = structure(c(2L,
1L, 1L, 1L, 1L, 2L), .Label = c("No", "Yes"), class = "factor"),
obesity = structure(c(1L, 2L, 2L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), hypertension = structure(c(1L,
1L, 2L, 1L, 1L, 2L), .Label = c("No", "Yes"), class = "factor"),
heart_disease = structure(c(1L, 1L, 1L, 1L, 1L, 2L), .Label = c("No",
"Yes"), class = "factor"), lung_condition = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
liver_disease = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), kidney_disease = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor")), row.names = c(1L,
3L, 4L, 5L, 6L, 7L), class = "data.frame")
and here is my test_data:
structure(list(tested = structure(c(1L, 1L, 1L, 1L, 1L,
1L), .Label = c("negative", "positive"), class = "factor"), Gender = structure(c(1L,
2L, 1L, 1L, 1L, 2L), .Label = c("Female", "Male", "Other"), class = "factor"),
Age = c(19, 26, 30, 45, 40, 43), number_days_symptoms = c(20,
1, 1, 20, 14, 1), care_home_worker = structure(c(1L, 1L,
1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
health_care_worker = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), how_unwell = c(7, 6, 6, 6, 6,
2), self_diagnosis = structure(c(2L, 1L, 1L, 2L, 2L, 1L), .Label = c("No",
"Yes"), class = "factor"), chills = structure(c(2L, 1L, 1L,
1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
cough = structure(c(2L, 1L, 1L, 2L, 2L, 1L), .Label = c("No",
"Yes"), class = "factor"), diarrhoea = structure(c(2L, 1L,
1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
fatigue = structure(c(2L, 1L, 1L, 2L, 2L, 1L), .Label = c("No",
"Yes"), class = "factor"), headache = structure(c(2L, 2L,
2L, 3L, 2L, 3L), .Label = c("Headcahe", "No", "Yes"), class = "factor"),
loss_smell_taste = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), muscle_ache = structure(c(2L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
nasal_congestion = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), nausea_vomiting = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
shortness_breath = structure(c(2L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), sore_throat = structure(c(1L,
1L, 1L, 2L, 1L, 2L), .Label = c("No", "Yes"), class = "factor"),
sputum = structure(c(2L, 1L, 1L, 2L, 1L, 2L), .Label = c("No",
"Yes"), class = "factor"), temperature = structure(c(4L,
4L, 4L, 1L, 1L, 4L), .Label = c("37.5-38", "38.1-39", "39.1-41",
"No"), class = "factor"), asthma = structure(c(1L, 1L, 1L,
1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
diabetes_type_one = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), diabetes_type_two = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
obesity = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), hypertension = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
heart_disease = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), lung_condition = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
liver_disease = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), kidney_disease = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor")), row.names = c(2L,
8L, 11L, 14L, 20L, 27L), class = "data.frame")
Additionally, I perform a smote balancing class, on a subsample in ctrInside.
This is my smote function:
smotest <- list(name = "SMOTE with more neighbors!",
func = function (x, y) {
115
library(DMwR)
dat <- if (is.data.frame(x)) x else as.data.frame(x)
dat$.y <- y
dat <- SMOTE(.y ~ ., data = dat, k = 3, perc.over = 100, perc.under =
200)
list(x = dat[, !grepl(".y", colnames(dat), fixed = TRUE)],
y = dat$.y) },
first = TRUE)
And ctrlInside is this:
ctrlInside <- trainControl(method = "repeatedcv",
number = 10,
repeats = 5,
summaryFunction = twoClassSummary,
classProbs = TRUE,
savePredictions = TRUE,
search = "grid",
sampling = smotest)
Those function are given just so that you have an idea of what I am doing per whole. Is there a reason why this is happening?

You can use complete.cases to predict only those that have no nas, also you must operate on the matrix, I will show below. Using an example dataset, I make 10 of the variable in a column NAs, and train:
idx = sample(nrow(iris),100)
data = iris
data$Petal.Length[sample(nrow(data),10)] = NA
data$tested = factor(ifelse(data$Species=="versicolor","positive","negative"))
data = data[,-5]
training_data = data[idx,]
testing_data= data[-idx,]
rf <- caret::train(tested ~., data = training_data,
method = "rf",
trControl = ctrlInside,
metric = "ROC",
na.action = na.exclude)
Do the evaluation result and you can see i get the same error:
evalResult.rf <- predict(rf, testing_data, type = "prob")
predict_rf <- as.factor(ifelse(evalResult.rf <0.5, "positive", "negative"))
cm_rf_forest <- confusionMatrix(predict_rf, testing_data$tested, "positive")
Error in table(data, reference, dnn = dnn, ...) :
all arguments must have the same length
So there's two sources of error, 1.. you have NAs and they cannot predict that, and second, evalResult.rf returns a matrix of probabilities, first column is probability being negative class, 2nd being postive:
head(evalResult.rf)
negative positive
3 1.000 0.000
6 1.000 0.000
9 0.948 0.052
12 1.000 0.000
13 0.976 0.024
19 0.998 0.002
To get the classes, you do, get the column with max value for each row, and return the corresponding column name, which is the class:
colnames(evalResult.rf)[max.col(evalResult.rf)]
We do now:
testing_data = testing_data[complete.cases(testing_data),]
evalResult.rf <- predict(rf, testing_data, type = "prob")
predict_rf <- factor(colnames(evalResult.rf)[max.col(evalResult.rf)])
cm_rf_forest <- confusionMatrix(predict_rf, testing_data$tested, "positive")
Confusion Matrix and Statistics
Reference
Prediction negative positive
negative 33 1
positive 0 11
Accuracy : 0.9778
95% CI : (0.8823, 0.9994)
No Information Rate : 0.7333
P-Value [Acc > NIR] : 1.507e-05
Kappa : 0.9416

Error: `data` and `reference` should be factors with the same levels. Confusion matrix for Logistic Regression

I have seen lots of answers with regards to this particular error. I haven't found any answer to it with specifics to my particular issue. Therefore, my problem
This is what I do:
shortness_breath_data <- data_categ_nosev %>%
dplyr::select(shortness_breath, obesity, asthma, diabetes_type_one, diabetes_type_two, obesity, hypertension, heart_disease, lung_condition, liver_disease, kidney_disease, Covid_tested, Gender)
And this is put(head(shortness_breath_data)):
structure(list(shortness_breath = structure(c(1L, 2L, 1L, 1L,
1L, 2L), .Label = c("No", "Yes"), class = "factor"), obesity = structure(c(1L,
1L, 2L, 2L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
asthma = structure(c(2L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), diabetes_type_one = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
diabetes_type_two = structure(c(2L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), hypertension = structure(c(1L,
1L, 1L, 2L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
heart_disease = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), lung_condition = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
liver_disease = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), kidney_disease = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
Covid_tested = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("negative",
"positive"), class = "factor"), Gender = structure(c(2L,
1L, 2L, 1L, 1L, 2L), .Label = c("Female", "Male", "Other"
), class = "factor")), row.names = c(NA, -6L), class = c("tbl_df",
"tbl", "data.frame"), problems = structure(list(row = c(2910L,
35958L), col = c("how_unwell", "how_unwell"), expected = c("a double",
"a double"), actual = c("How Unwell", "How Unwell"), file = c("'/Users/gabrielburcea/Rprojects/data/data_lev_categorical_no_sev.csv'",
"'/Users/gabrielburcea/Rprojects/data/data_lev_categorical_no_sev.csv'"
)), row.names = c(NA, -2L), class = c("tbl_df", "tbl", "data.frame"
)))
And I divide this into training and testing dataset.
shortness_breath_data$shortness_breath <- as.factor(shortness_breath_data$shortness_breath)
n <- nrow(shortness_breath_data)
set.seed(22)
trainingdx <- sample(1:n, 0.7 * n)
train <- shortness_breath_data[trainingdx,]
validate <- shortness_breath_data[-trainingdx,]
train %>% distinct(shortness_breath)
validate %>% distinct(shortness_breath)
And just to do the same in case it will ease you job in finding the issue, I provided dput(head(train)) and dput(head(validate))
train dataset:
structure(list(shortness_breath = structure(c(1L, 1L, 1L, 1L,
1L, 1L), .Label = c("No", "Yes"), class = "factor"), obesity = structure(c(2L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
asthma = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), diabetes_type_one = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
diabetes_type_two = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), hypertension = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
heart_disease = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), lung_condition = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
liver_disease = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), kidney_disease = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
Covid_tested = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("negative",
"positive"), class = "factor"), Gender = structure(c(1L,
1L, 1L, 2L, 1L, 2L), .Label = c("Female", "Male", "Other"
), class = "factor")), row.names = c(NA, -6L), class = c("tbl_df",
"tbl", "data.frame"), problems = structure(list(row = c(2910L,
35958L), col = c("how_unwell", "how_unwell"), expected = c("a double",
"a double"), actual = c("How Unwell", "How Unwell"), file = c("'/Users/gabrielburcea/Rprojects/data/data_lev_categorical_no_sev.csv'",
"'/Users/gabrielburcea/Rprojects/data/data_lev_categorical_no_sev.csv'"
)), row.names = c(NA, -2L), class = c("tbl_df", "tbl", "data.frame"
)))
validate dataset:
structure(list(shortness_breath = structure(c(1L, 2L, 2L, 1L,
1L, 1L), .Label = c("No", "Yes"), class = "factor"), obesity = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
asthma = structure(c(2L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), diabetes_type_one = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
diabetes_type_two = structure(c(2L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), hypertension = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
heart_disease = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), lung_condition = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
liver_disease = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("No",
"Yes"), class = "factor"), kidney_disease = structure(c(1L,
1L, 1L, 1L, 1L, 1L), .Label = c("No", "Yes"), class = "factor"),
Covid_tested = structure(c(1L, 1L, 1L, 1L, 1L, 1L), .Label = c("negative",
"positive"), class = "factor"), Gender = structure(c(2L,
1L, 2L, 2L, 1L, 1L), .Label = c("Female", "Male", "Other"
), class = "factor")), row.names = c(NA, -6L), class = c("tbl_df",
"tbl", "data.frame"), problems = structure(list(row = c(2910L,
35958L), col = c("how_unwell", "how_unwell"), expected = c("a double",
"a double"), actual = c("How Unwell", "How Unwell"), file = c("'/Users/gabrielburcea/Rprojects/data/data_lev_categorical_no_sev.csv'",
"'/Users/gabrielburcea/Rprojects/data/data_lev_categorical_no_sev.csv'"
)), row.names = c(NA, -2L), class = c("tbl_df", "tbl", "data.frame"
)))
And then, I build my logistic regression model with stepwise, forward method.
null_model <- glm(shortness_breath ~ 1, data = train, family = "binomial")
fm_shortness_breath <- glm(shortness_breath ~., data = train, family = "binomial")
stepmodel <- step(null_model, scope = list(lower = null_model, upper = fm_shortness_breath), direction = "forward")
Then I get my summary model and store the predictions in the source data frame.
summary(stepmodel)
validate$pred <- predict(stepmodel, validate, type = "response")
validate$real <- validate$shortness_breath
train$pred <- predict(stepmodel, train, type = "response")
train$real <- train$shortness_breath
Then I plot my ROC curve with no problem:
plot.roc(validate$real, validate$pred, col = "red", main = "ROC Validation Set", percent = TRUE, print.auc = TRUE)
Yet, when I am trying to get my confusion matrix, this is where I get my error. But this is my code:
cm_stepmodel <- confusionMatrix(stepmodel, validate)
And then, the error comes in:
Error: `data` and `reference` should be factors with the same levels.
With Show Traceback:
3.
stop("`data` and `reference` should be factors with the same levels.", call. = FALSE)
2.
confusionMatrix.default(stepmodel, validate)
1.
confusionMatrix(stepmodel, validate)
I simply do not see the problem. And tried several other options but did not work. I have reproduced, step by step the exact approach I am undertaking. And I do not get my answer. Also, I have tag this issue with RMarkdown as well, alongside caret and R, just in case.
Also, libraries used are:
library(tidyverse)
library(conflicted)
library(tidymodels)
library(ggrepel)
library(corrplot)
library(dplyr)
library(corrr)
library(themis)
library(rsample)
library(caret)
library(forcats)
library(rcompanion)
library(MASS)
library(pROC)
library(ROCR)
library(data.table)

Try to convert your predicted probabilities to labels, and then run your confusionMatrix on this:
validate$pred <- predict(stepmodel, validate, type = "response")
validate$pred_label <- as.factor(ifelse(validate$pred >= 0.5, "Yes", "No"))
confusionMatrix(validate$real, validate$pred) # Error
confusionMatrix(validate$real, validate$pred_label) # This will work
Check that you are correctly assigning labels as in your original dataset in the validate$pred_label statement.
I'm not particularly familiar with confusionMatrix, but the general idea is that you make predictions of labels and compare to the actual labels of your data. It threw an error because you were comparing labels with probabilities -- you needed to assign the labels. Please correct me if I made a conceptual error or coding mistake above.

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