From c1660eb7e5cbdbf84f0e8521594ba8a8da0f40bc Mon Sep 17 00:00:00 2001 From: sigmafelix Date: Tue, 19 Nov 2024 14:04:30 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20NIEHS/am?= =?UTF-8?q?adeus@3d7da8d352ade41fc8aee56f713d6e2f80f92e50=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 6 +- LICENSE-text.html | 4 +- LICENSE.html | 4 +- articles/download_functions.html | 8 +- articles/epa_download.html | 6 +- articles/index.html | 4 +- articles/protected_datasets.html | 6 +- articles/workflow.html | 6 +- authors.html | 8 +- deps/data-deps.txt | 4 +- deps/font-awesome-6.5.2/css/all.css | 8028 +++++++++++++++++ deps/font-awesome-6.5.2/css/all.min.css | 9 + deps/font-awesome-6.5.2/css/v4-shims.css | 2194 +++++ deps/font-awesome-6.5.2/css/v4-shims.min.css | 6 + .../webfonts/fa-brands-400.ttf | Bin 0 -> 209128 bytes .../webfonts/fa-brands-400.woff2 | Bin 0 -> 117852 bytes 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| 4 +- reference/calculate_lagged.html | 4 +- reference/calculate_merra2.html | 4 +- reference/calculate_modis.html | 231 + reference/calculate_modis_daily.html | 9 +- reference/calculate_narr.html | 4 +- reference/calculate_nei.html | 4 +- reference/calculate_nlcd.html | 9 +- reference/calculate_sedac_groads.html | 4 +- reference/calculate_sedac_population.html | 4 +- reference/calculate_temporal_dummies.html | 4 +- reference/calculate_terraclimate.html | 4 +- reference/calculate_tri.html | 4 +- reference/check_destfile.html | 4 +- reference/check_for_null_parameters.html | 4 +- reference/check_geom.html | 4 +- reference/check_mysf.html | 4 +- reference/check_mysftime.html | 4 +- reference/check_url_status.html | 4 +- reference/check_urls.html | 4 +- reference/download_aqs.html | 4 +- reference/download_cropscape.html | 4 +- reference/download_data.html | 4 +- reference/download_ecoregion.html | 4 +- reference/download_epa_certificate.html | 4 +- reference/download_geos.html | 4 +- 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reference/process_merra2.html | 4 +- reference/process_merra2_time.html | 4 +- reference/process_modis_merge.html | 4 +- reference/process_modis_sds.html | 6 +- reference/process_modis_swath.html | 4 +- reference/process_modis_warp.html | 4 +- reference/process_narr.html | 4 +- reference/process_nei.html | 4 +- reference/process_nlcd.html | 4 +- reference/process_prism.html | 4 +- reference/process_sedac_codes.html | 4 +- reference/process_sedac_groads.html | 4 +- reference/process_sedac_population.html | 4 +- reference/process_terraclimate.html | 4 +- reference/process_terraclimate_codes.html | 4 +- reference/process_tri.html | 4 +- reference/process_variable_codes.html | 4 +- reference/read_commands.html | 4 +- reference/rename_time.html | 4 +- reference/sf_as_mysftime.html | 4 +- reference/sftime_as_mysftime.html | 4 +- reference/sftime_as_sf.html | 4 +- reference/sftime_as_spatraster.html | 4 +- reference/sftime_as_spatrds.html | 4 +- reference/sftime_as_spatvector.html | 4 +- reference/spatraster_as_sftime.html | 4 +- reference/spatrds_as_sftime.html | 4 +- reference/spatvector_as_sftime.html | 4 +- reference/sum_edc.html | 4 +- reference/test_download_functions.html | 4 +- search.json | 2 +- sitemap.xml | 3 +- 148 files changed, 10815 insertions(+), 288 deletions(-) create mode 100644 deps/font-awesome-6.5.2/css/all.css create mode 100644 deps/font-awesome-6.5.2/css/all.min.css create mode 100644 deps/font-awesome-6.5.2/css/v4-shims.css create mode 100644 deps/font-awesome-6.5.2/css/v4-shims.min.css create mode 100644 deps/font-awesome-6.5.2/webfonts/fa-brands-400.ttf create mode 100644 deps/font-awesome-6.5.2/webfonts/fa-brands-400.woff2 create mode 100644 deps/font-awesome-6.5.2/webfonts/fa-regular-400.ttf create mode 100644 deps/font-awesome-6.5.2/webfonts/fa-regular-400.woff2 create mode 100644 deps/font-awesome-6.5.2/webfonts/fa-solid-900.ttf create mode 100644 deps/font-awesome-6.5.2/webfonts/fa-solid-900.woff2 create mode 100644 deps/font-awesome-6.5.2/webfonts/fa-v4compatibility.ttf create mode 100644 deps/font-awesome-6.5.2/webfonts/fa-v4compatibility.woff2 create mode 100644 news/index.html create mode 100644 reference/calculate_modis.html diff --git a/404.html b/404.html index d7e6944e..aca5e51d 100644 --- a/404.html +++ b/404.html @@ -8,8 +8,8 @@ Page not found (404) • amadeus - - + + @@ -21,7 +21,7 @@ amadeus - 1.1.7 + 1.2.0 + + + + + +
+
+
+

Changelog

+ Source: NEWS.md +
+ +
+ + +
+

Developed by Mitchell Manware, Insang Song, Eva Marques, Mariana Alifa Kassien, Kyle Messier.

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + diff --git a/pkgdown.yml b/pkgdown.yml index 5eef92fe..f3175a4d 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -6,7 +6,7 @@ articles: epa_download: epa_download.html protected_datasets: protected_datasets.html workflow: workflow.html -last_built: 2024-11-15T14:41Z +last_built: 2024-11-19T14:03Z urls: reference: https://niehs.github.io/amadeus/reference article: https://niehs.github.io/amadeus/articles diff --git a/reference/apply_extent.html b/reference/apply_extent.html index 2e9e29c7..548be101 100644 --- a/reference/apply_extent.html +++ b/reference/apply_extent.html @@ -1,5 +1,5 @@ -Apply extent to the processed data — apply_extent • amadeus +Apply extent to the processed data — apply_extent • amadeus Skip to contents @@ -7,7 +7,7 @@ amadeus - 1.1.7 + 1.2.0 + + + + + +
+
+
+

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"
+)
+} # }
+
+
+
+ + +
+

Developed by Mitchell Manware, Insang Song, Eva Marques, Mariana Alifa Kassien, Kyle Messier.

+
+ +
+

Site built with pkgdown 2.1.1.

+
+ +
+ + + + + + + diff --git a/reference/calculate_modis_daily.html b/reference/calculate_modis_daily.html index 5a03e837..6c3d107e 100644 --- a/reference/calculate_modis_daily.html +++ b/reference/calculate_modis_daily.html @@ -1,5 +1,5 @@ -A single-date MODIS worker for parallelization — calculate_modis_daily • amadeusA single-date MODIS worker — calculate_modis_daily • amadeusamadeus - 1.1.7 + 1.2.0