Converting observational data stored in a 2D data frame to a 3D array in R

I am trying to produce a 3D array from a 2D data frame in R and could really use some help. So far, I haven't found a solution to this problem from similar questions that have been posted previously.

My input data are available here: https://www.dropbox.com/s/7f8td34mpzgpvgh/example_data.csv?dl=0, and they resemble the following basic structure: I have 14 sites (i.e. Field) with 6 replicates each (i.e. Replicate) in which a subset of 32 subjects (i.e. columns of species codes: AMGO, BASW, etc.) were counted when present in a survey.

Field

Replicate

AMGO

BASW

A subset of the input data looks like so:

example_data[1:5, 1:5]

Field Replicate AMGO BASW BHCO
1 Brinkman 1 2 0 0
72 Brinkman 2 10 0 0
190 Brinkman 3 6 0 0
283 Brinkman 4 0 0 0
342 Brinkman 5 2 1 0


I'd like to reformat these input data to resemble a 3D array (i.e. 14 sites x 6 replicates x 32 subjects), as exemplified below with the AMGO species:

AMGO

, , = AMGO

1 2 3 4 5 6
Brinkman 0 0 0 0 0 0
Clara 0 0 0 0 0 0
Esckelson 0 0 0 0 0 0
GarnerEast 0 0 0 0 0 0
GarnerWest 0 0 0 0 0 0
KHess 0 0 0 0 0 0
Lounsbury 0 0 0 0 0 0
McCallum 0 0 0 0 0 0
Pomeroy 0 0 0 0 0 0
Sattelberg 0 0 0 0 0 0
THess 0 0 0 0 0 0
Turner 0 0 0 0 0 0
VollmarEast 0 0 0 0 0 0
VollmarWest 0 0 0 0 0 0

...


Note that, in the solution, many of the zeroes above would likely be replaced by non-zero counts when AMGO (and other species) was (were) actually encountered during a survey.

AMGO

Please let me know if there's anything I need to clarify, and thanks in advance!

1 Answer
1

Here's a solution using the reshape() function from base R. I'm applying the function to each of the subject columns and creating a list of reshaped dataframes.

reshape()

df <- read.csv("C:\Users\Shrivatav\Downloads\example_data.csv", encoding = "UTF-8")

# Extract subject columns
list.of.cols <- colnames(df)[3:34]

# Function for reshaping
func.for.reshaping <- function(column)

# Subset the data, keep only Field, replicate and the column input in the
# function
to.keep <- c("Field", "Replicate", column)
subset.df <- df[to.keep]
# reshape from long to wide
reshaped.df <- reshape(subset.df, idvar = "Field", timevar = "Replicate", direction = "wide")
return(reshaped.df)


# Apply the function over all subject columns, reulting
# in a list of dataframes
list.of.reshaped.dfs <- lapply(list.of.cols, func.for.reshaping)

# Name the list for easy access
names(list.of.reshaped.dfs) <- list.of.cols


You can access the elements of the list like: list.of.reshaped.dfs$AMGO and so forth.

list.of.reshaped.dfs$AMGO

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