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Create (e.g., init or observation) files for LibBi

Source: R/bi_write.R
bi_write.Rd

This function creates (or appends to) a NetCDF file for LibBi from the given list of vectors and/or data frames. Since any files can be passed to libbi directly via the init, input and obs options, this is mostly used internally, this is mostly used internally.

Usage

bi_write(
  filename,
  variables,
  append = FALSE,
  overwrite = FALSE,
  time_dim,
  coord_dims,
  dim_factors,
  value_column = "value",
  guess_time = FALSE,
  verbose
)

Arguments

filename

a path to a NetCDF file to write the variables into, which will be overwritten if it already exists. If necessary, ".nc" will be added to the file name

variables

a list object, the names of which should be the variable names and values should be either single values or data frames

append

if TRUE, will append variables if file exists; default: FALSE

overwrite

if TRUE, will overwrite variables if file exists; default: FALSE

time_dim

the name of the time dimension, if one exists; default: "time"

coord_dims

the names of the coordinate dimension, if any; should be a named list of character vectors, they are matched to variables names

dim_factors

factors that dimensions have; this corresponds to the dims element of a libbi object

value_column

if any variables are data frames, which column contains the values (default: "value")

guess_time

whether to guess time dimension; this would be a numerical column in the data frame given which is not the value_column; only one such column must exist

verbose

if TRUE, will print variables as they are read

Value

A list of the time and coord dims, and factors in extra dimensions, if any

Details

The list of variables must follow the following rules. Each element of the list must itself be one of:

1) a data frame with a value_column column (see option 'value_column') and any number of other columns indicating one or more dimensions

2) a numeric vector of length one, with no dimensions

The name of the list elements itself is used to create the corresponding variable in the NetCDF file.

Examples

filename <- tempfile(pattern = "dummy", fileext = ".nc")
a <- 3
b <- data.frame(
  dim_a = rep(1:3, time = 2), dim_b = rep(1:2, each = 3), value = 1:6
)
variables <- list(a = a, b = b)
bi_write(filename, variables)
#> $time_dim
#> NULL
#> 
#> $coord_dims
#> $coord_dims$b
#> [1] "dim_a" "dim_b"
#> 
#> 
#> $dims
#> list()
#> 
bi_file_summary(filename)
#> File /tmp/RtmpUFZm4D/dummy373e13a1358f.nc (NC_FORMAT_CLASSIC):
#> 
#>      2 variables (excluding dimension variables):
#>         float a[]   
#>         float b[dim_a,dim_b]   
#> 
#>      2 dimensions:
#>         dim_a  Size:3 
#>             long_name: dim_a
#>         dim_b  Size:2 
#>             long_name: dim_b