Functions to generate and process data files for the SCRC data pipeline.
To install:
library(devtools)
install_github("ScottishCovidResponse/SCRCdataAPI")
In the following example, we will populate "array.h5" with array type data downloaded from https://github.com/ScottishCovidResponse/simple_network_sim/blob/master/sample_output_files/sample-1591198608.csv. The component path is input via the
component argument, e.g. group dz, subgroup total.
download.file("https://github.com/ScottishCovidResponse/simple_network_sim/raw/master/sample_output_files/sample-1591198608.csv", "sample.csv")
sample <- read.csv("sample.csv")
To add this data to table.h5:
create_table(filename = "table.h5", component = "dz/total", df = sample)
Note that the filename argument can take the name of a file you want to create,
or an existing *.h5 file.
To check contents:
file.h5 <- H5File$new(filename)
file.h5$ls(recursive = TRUE)
file.h5[["dz/total/table"]][]
file.h5$close_all()
In the following example, we will populate "array.h5" with array type data.
To create an array:
filename <- "array.h5"
component <- "dz/total"
array <- matrix(1:10, 5)
colnames(array) <- paste0("age", 1:2)
rownames(array) <- paste0("dz", 1:5)
dimension_names <- list(`area names` = rownames(array),
`age classes` = colnames(array))
# demonstrating column values with missing row values
dimension_values <- list(NA, data.frame(a = 1:2, b = 3:4))
dimension_units <- list("10km", "5years")
create_array(filename, component, array, dimension_names, dimension_values, dimension_units)
To check contents:
file.h5 <- H5File$new(filename)
file.h5$ls(recursive = TRUE)
file.h5[["dz/total/Dimension_1_names"]][]
file.h5[["dz/total/Dimension_1_title"]][]
file.h5[["dz/total/Dimension_2_names"]][]
file.h5[["dz/total/Dimension_2_title"]][]
file.h5[["dz/total/Dimension_2_units"]][]
file.h5[["dz/total/Dimension_2_values"]][]
file.h5$close_all()