Scripts for review #2
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R/Sharis/Ameriflux_functions.R
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| # Initialize data frame | ||
| table <- data.frame(attributeName = rep("NA", n), |
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There is a function in the base R package called table that creates table objects. You generally want to avoid naming variables after functions (although the table function is a bit obscure).
You could change this something like att_table
R/Sharis/Ameriflux_functions.R
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| for (i in seq_len(n)) { | ||
| # add attribute name | ||
| table$attributeName[i] = colnames(data)[i] |
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You can move colnames(data) outside the for loop so it only runs once rather than n times.
Something like col_names <- colnames(data). Then you can reference col_names[i] in the for loop.
R/Sharis/Ameriflux_functions.R
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| table$attributeName[i] = colnames(data)[i] | ||
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| ## check if the name has a qualifier at the end | ||
| if (any(endsWith(colnames(data)[i], suffix = qualifiers))) { |
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same comment here about moving colnames(data) outside the for loop.
R/Sharis/Ameriflux_functions.R
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| main_label<- substr(colnames(data)[i], 1, nchar(colnames(data)[i])-len) | ||
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| # get definition for main label | ||
| main_def <- attributes$uniqueAttributeDefinition[attributes$uniqueAttributeLabel == main_label] |
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at the beginning of your function you could specify colnames(attributes) <- ("category", "label", "definition", "unit", "SI_unit") and get rid "uniqueAttribute" everywhere in your code.
The benefit is making your code more readable - also not your fault, the column names from that csv aren't great.
R/Sharis/Ameriflux_functions.R
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| # case if there is no qualifier | ||
| } else { | ||
| table$attributeDefinition[i] = attributes$uniqueAttributeDefinition[attributes$uniqueAttributeLabel == colnames(data)[i]] |
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remove extra spaces by the ==
R/Sharis/Ameriflux_functions.R
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| } else { | ||
| table$measurementScale[i] = "ratio" | ||
| table$domain[i] = "numericDomain" | ||
| table$numberType[i] <- "real" |
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Most style guides advocate using <- as the assignment operator, and using = only inside function calls.
If you're interested in reading more this blog post is pretty good https://renkun.me/2014/01/28/difference-between-assignment-operators-in-r/ .
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| generate_attributes_table <- function(csv_file_path, | |||
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If you'd like you can document what this function does. Check out the multiline comments (#' is the multiline comment symbol in R) at the top of this function: https://github.com/NCEAS/datamgmt/blob/master/R/guess_member_node.R
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| ## Data Objects | ||
| ### Adding data tables for a whole folder of files with the same attributes |
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This section is so awesome! I just had to do this but forgot you wrote it up until I mostly finished. In any case, interesting to see slightly different ways of doing the same thing!
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