In gregmacfarlane/omxr: Read and Write Open Matrix Files

set.seed(10)

library(omxr)

Create and write

.omx files are HDF5 containers storing many different matrices and their attributes. You can create a new container with the create_omx command.

zones <- 1:10
rhdf5::H5close()
omxfile <- tempfile(fileext = ".omx")
create_omx(omxfile, numrows = length(zones), numcols = length(zones))

Let's start with a 10-zone system with random trips and costs.

trips <- matrix(rnorm(n = length(zones)^2, 200, 50),  
                nrow = length(zones), ncol = length(zones))
cost <- matrix(rlnorm(n = length(zones)^2, 1, 1),
               nrow = length(zones), ncol = length(zones))

We can store these in the omx container.

write_omx(file = omxfile, matrix = trips, "trips", 
          description = "Total Trips")

write_omx(file = omxfile, matrix = cost, "cost", 
          description = "Generalized Cost")

Read

Now that the matrices are in the file, we can try reading them.

read_omx(omxfile, "trips")
read_omx(omxfile, "cost")

You can transform a matrix to long format, which is more tidyverse friendly.

library(tidyverse)
read_omx(omxfile, "trips") %>%
  gather_matrix("trips")

You can also read subsets of matrices.

read_omx(omxfile, "trips", row_index = 2:4, col_index = 2:5)

There are also functions to get the attributes of an OMX file. A call to list_omx() will show the names of the matrices inside the file.

get_omx_attr(omxfile)
list_omx(omxfile)

Lookups

Perhaps a better way to read a subset of a matrix is with a defined "lookup." These can be stored in the omx container in addition to the matrices. You specify the lookup with a vector of the appropriate length, where TRUE means the row or column should be included, and FALSE means otherwise.

lookup <- zones %in% c(1, 2:5, 9)
lookup
write_lookup(omxfile, lookup_v = lookup, 
             name = "trial", description = "test lookup", replace = TRUE)

Now we can get the selected rows and columns from either matrix automatically.

read_selected_omx(omxfile, "trips", 
                  row_selection = "trial", col_selection = "trial")

gregmacfarlane/omxr documentation built on May 7, 2022, 11:42 a.m.