Error in `[.data.frame`(data.frame(x), i, j, drop = FALSE) : undefined columns selected

[bc-anaisabel]

I added new soil variables (C and N) to table amptk.mapping_file.csv. When doing the soil analysis in 4_models.R script I got an error message when trying to do a subset based on a vector I created with all the names of the soil variables (using now the new ones):

#subset 
soil <- subset_samples(texcoco.binary.models, Type %in% "soil") # phyloseq object subset with only soil samples
soil

binary_table <- otu_table(soil) #just otu table
binary_table

meta_table <- sample_data(soil) #only sample data and only from soil samples
meta_table

env <- c("pH","Pdis","Ca","Mg","K","Na","H","Al", "SoilM","C","N") 

#Transform columns to numeric values, each column separately 

env_table <- subset(meta_table, select = env)

Error message was:

> env_table <- subset(meta_table, select = env)
Error in `[.data.frame`(data.frame(x), i, j, drop = FALSE) : 
  undefined columns selected

[bc-anaisabel]

Trying out solutions I remembered the "Al" column has some empty cells because that's how the data came, there were missing values for Aluminum in some of the samples. So I removed the "Al" from the c vector but still it does not work

[bc-anaisabel]

It was an incorrect column name. SoilM was named SoilMoisture in csv data so it was not defining this column name because it could not find it. Changed .csv file.