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Calculate MODIS product covariates in multiple CPU threads

Source: R/calculate_covariates.R
calculate_modis.Rd

calculate_modis essentially runs calculate_modis_daily function in each thread (subprocess). Based on daily resolution, each day's workload will be distributed to each thread. With product argument, the files are processed by a customized function where the unique structure and/or characteristics of the products are considered.

Usage

calculate_modis(
  from = NULL,
  locs = NULL,
  locs_id = "site_id",
  radius = c(0L, 1000L, 10000L, 50000L),
  preprocess = process_modis_merge,
  name_covariates = NULL,
  subdataset = NULL,
  fun_summary = "mean",
  package_list_add = NULL,
  export_list_add = NULL,
  max_cells = 3e+07,
  geom = FALSE,
  ...
)

Arguments

from

character. List of paths to MODIS/VIIRS files.

locs

sf/SpatVector object. Unique locs where covariates will be calculated.

locs_id

character(1). Site identifier. Default is "site_id"

radius

numeric. Radii to calculate covariates. Default is c(0, 1000, 10000, 50000).

preprocess

function. Function to handle HDF files.

name_covariates

character. Name header of covariates. e.g., "MOD_NDVIF_0_". The calculated covariate names will have a form of "{name_covariates}{zero-padded buffer radius in meters}", e.g., 'MOD_NDVIF_0_50000' where 50 km radius circular buffer was used to calculate mean NDVI value.

subdataset

Indices, names, or search patterns for subdatasets. Find detail usage of the argument in notes.

fun_summary

character or function. Function to summarize extracted raster values.

package_list_add

character. A vector with package names to load these in each thread. Note that sf, terra, exactextractr, doParallel, parallelly and dplyr are the default packages to be loaded.

export_list_add

character. A vector with object names to export to each thread. It should be minimized to spare memory.

max_cells

integer(1). Maximum number of cells to be read at once. Higher values will expedite processing, but will increase memory usage. Maximum possible value is 2^31 - 1. See exactextractr::exact_extract for details.

geom

FALSE/"sf"/"terra".. Should the function return with geometry? Default is FALSE, options with geometry are "sf" or "terra". The coordinate reference system of the sf or SpatVector is that of from.

...

Arguments passed to preprocess.

Value

A data.frame or SpatVector with an attribute:

  • attr(., "dates_dropped"): Dates with insufficient tiles. Note that the dates mean the dates with insufficient tiles, not the dates without available tiles.

Note

Overall, this function and dependent routines assume that the file system can handle concurrent access to the (network) disk by multiple processes. File system characteristics, package versions, and hardware settings and specification can affect the processing efficiency. locs is expected to be convertible to sf object. sf, SpatVector, and other class objects that could be converted to sf can be used. Common arguments in preprocess functions such as date and path are automatically detected and passed to the function. Please note that locs here and path in preprocess functions are assumed to have a standard naming convention of raw files from NASA. The argument subdataset should be in a proper format depending on preprocess function:

  • process_modis_merge(): Regular expression pattern. e.g., "^LST_"

  • process_modis_swath(): Subdataset names. e.g., c("Cloud_Fraction_Day", "Cloud_Fraction_Night")

  • process_blackmarble(): Subdataset number. e.g., for VNP46A2 product, 3L. Dates with less than 80 percent of the expected number of tiles, which are determined by the mode of the number of tiles, are removed. Users will be informed of the dates with insufficient tiles. The result data.frame will have an attribute with the dates with insufficient tiles.

See also

This function leverages the calculation of single-day MODIS covariates:

Also, for preprocessing, please refer to:

Examples

## NOTE: Example is wrapped in `\dontrun{}` as function requires a large
##       amount of data which is not included in the package.
if (FALSE) { # \dontrun{
locs <- data.frame(lon = -78.8277, lat = 35.95013, id = "001")
locs <- terra::vect(locs, geom = c("lon", "lat"), crs = "EPSG:4326")
calculate_modis(
  from =
    list.files("./data", pattern = "VNP46A2.", full.names = TRUE),
  locs = locs,
  locs_id = "site_id",
  radius = c(0L, 1000L),
  preprocess = process_modis_merge,
  name_covariates = "cloud_fraction_0",
  subdataset = "Cloud_Fraction",
  fun_summary = "mean"
)
} # }