From d39f8bd03deda9fa7eb516e77c21fb733223f72c Mon Sep 17 00:00:00 2001 From: emmamendelsohn Date: Mon, 6 Nov 2023 14:28:46 -0500 Subject: [PATCH] complete run --- _targets.R | 4 +- _targets/meta/meta | 6807 ++++++++++++++++++++++++-------------------- renv.lock | 1428 +++++----- 3 files changed, 4467 insertions(+), 3772 deletions(-) diff --git a/_targets.R b/_targets.R index eb4c62f..4a43ad0 100644 --- a/_targets.R +++ b/_targets.R @@ -20,7 +20,7 @@ source("_targets_settings.R") # For development purposes only, it can be helpful to set these targets to have a tar_cue of tar_cue_upload_aws, which means targets will not check the target for changes after it has been built once tar_cue_general = "thorough" # CAUTION changing this to never means targets can miss changes to the code. Use only for developing. -tar_cue_upload_aws = "never" +tar_cue_upload_aws = "never" # CAUTION changing this to never means targets can miss changes to the code. Use only for developing. # Static Data Download ---------------------------------------------------- static_targets <- tar_plan( @@ -440,7 +440,7 @@ data_targets <- tar_plan( key = ndvi_anomalies, check = TRUE), pattern = ndvi_anomalies, - cue = tar_cue(tar_cue_upload_aws)), # only run this if you need to upload new data + cue = tar_cue("thorough")), # only run this if you need to upload new data ) diff --git a/_targets/meta/meta b/_targets/meta/meta index 85b45cd..999a4b5 100644 --- a/_targets/meta/meta +++ b/_targets/meta/meta @@ -1,20 +1,43 @@ name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error +.Random.seed|object|eecaf3e5bc2d0e66||||||||||||||| +all_targets|function|2dda5afbd1f92385||||||||||||||| +aws_bucket|object|d9cf2c5ff7cc1be4||||||||||||||| +aws_s3_upload_single_type|function|6d277b68ccbb67a2||||||||||||||| cache_aws_branched_target|function|6e2abfa4969de1bf||||||||||||||| +calculate_forecasts_anomalies|function|e79c27516696d72f||||||||||||||| +calculate_ndvi_anomalies|function|fa9de87422ce7598||||||||||||||| +calculate_ndvi_historical_means|function|62d8a66e5ef237be||||||||||||||| +calculate_weather_anomalies|function|d0c9f646d334634b||||||||||||||| +calculate_weather_historical_means|function|ac8b9ff61133bd68||||||||||||||| continent_bounding_box|stem|cd4a4ddaa46d634a|bc00ded6218f3e10|d25ebcbef292030f|-1551480776|bucket=open-rvfcast-data*region=NULL*key=_targets/continent_bounding_box*endpoint=TlVMTA*version=|t19517.6854396s||650|qs|aws|vector|||0.001|| continent_polygon|stem|ab9fc6665b7f4674|8fdc308f6950b209|8fda1350e825d6f0|-1018833134|bucket=open-rvfcast-data*region=NULL*key=_targets/continent_polygon*endpoint=TlVMTA*version=|t19517.6854365748s||40351|qs|aws|vector|||0.046|| continent_raster_template|stem|f7447f449dab6127|59215772b6da1296|29b10148e1f5cc06|435814239|bucket=open-rvfcast-data*region=NULL*key=_targets/continent_raster_template*endpoint=TlVMTA*version=|t19625.8040321503s||17991|qs|aws|vector|||0.023|readValues raster has no values| country_bounding_boxes|stem|f3f68e55b6b77d77|30fec9e0e3d1a974|36097b0df0d06db0|1038934427|bucket=open-rvfcast-data*region=NULL*key=_targets/country_bounding_boxes*endpoint=TlVMTA*version=|t19517.695216638s||6273|qs|aws|vector|||0.024|| country_polygons|stem|ece9c72b7e99dba6|cb7eceb109efaff7|a2cdedccfeb044ec|1321015204|bucket=open-rvfcast-data*region=NULL*key=_targets/country_polygons*endpoint=TlVMTA*version=|t19517.6808684524s||17365|qs|aws|vector|||0.901|| +create_africa_polygon|function|fb2ce70982e38cd3||||||||||||||| +create_country_polygons|function|9917ababa5b4b8f4||||||||||||||| +create_data_directory|function|5781405b45264703||||||||||||||| create_ecmwf_forecasts_dataset|function|557bbbb473a2eb1c||||||||||||||| create_example_target|function|df4f421d40047080||||||||||||||| create_modis_ndvi_dataset|function|ed26259cdf3f08e1||||||||||||||| create_nasa_weather_dataset|function|7eb26dcea55b80b9||||||||||||||| +create_ndvi_date_lookup|function|239a44dd31122aa6||||||||||||||| +create_raster_template_plot|function|db738156a3247831||||||||||||||| create_sentinel_ndvi_dataset|function|201d4eaf8c87d0c3||||||||||||||| +data_targets|object|dc50e872042b1ab8||||||||||||||| 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preprocess_ecmwf_forecasts|function|033bd8a3c45b4d46||||||||||||||| +preprocess_nasa_weather|function|eab787d86769c2f9||||||||||||||| preprocess_nasa_weather_dataset|function|dffa4816bb9a77f0||||||||||||||| +preprocess_wahis_rvf_outbreaks|function|1739270cf02b72d6||||||||||||||| process_ndvi_data|function|8a56ce9bd504bbec||||||||||||||| process_weather_data|function|b29a917bff83bf09||||||||||||||| random_select_model_dates|function|75d79de28b5c2e87||||||||||||||| read_transform_raster|function|f7518264efa394ed||||||||||||||| readme|stem|61211399f70244f9|2419a0f44a0792be|4745aa592080ea1d|-165896733|README.md*README.Rmd|t19647.5933814197s|51d2a93de096e351|15409|file|local|vector|||6.498|| +report_targets|object|1eb1bc8d77111ded||||||||||||||| +rolling_box|function|1195d491d98c697b||||||||||||||| save_transform_ecmwf_grib|function|6a76f13bf2e8bad9||||||||||||||| save_transform_grib|function|820e4c12a3d3a749||||||||||||||| 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sentinel_ndvi_transformed_upload_aws_s3_03751119|branch|d88640300db856e0|03a57554ca4bf82e|28d74722a236475c|130488748|bucket=open-rvfcast-data*region=NULL*key=_targets/sentinel_ndvi_transformed_upload_aws_s3_03751119*endpoint=TlVMTA*version=|t19643.0429250803s||220|qs|aws|vector|sentinel_ndvi_transformed_upload_aws_s3||1.533|| sentinel_ndvi_transformed_upload_aws_s3_03e3da2d|branch|b959c8050a7ea5f6|03a57554ca4bf82e|ee2bad62ae10b56d|-1945715166|bucket=open-rvfcast-data*region=NULL*key=_targets/sentinel_ndvi_transformed_upload_aws_s3_03e3da2d*endpoint=TlVMTA*version=|t19643.0425030272s||220|qs|aws|vector|sentinel_ndvi_transformed_upload_aws_s3||1.075|| @@ -4329,11 +5221,26 @@ sentinel_ndvi_transformed_upload_aws_s3_fc1a6799|branch|caf6b0d532e56187|03a5755 sentinel_ndvi_transformed_upload_aws_s3_fcf6e446|branch|43bb7586f53bede5|03a57554ca4bf82e|57b3b186662f48c4|-1460735601|bucket=open-rvfcast-data*region=NULL*key=_targets/sentinel_ndvi_transformed_upload_aws_s3_fcf6e446*endpoint=TlVMTA*version=|t19643.0429629598s||220|qs|aws|vector|sentinel_ndvi_transformed_upload_aws_s3||1.465|| sentinel_ndvi_transformed_upload_aws_s3_fd0f03b2|branch|dc7eaa9f5e3fcdf8|03a57554ca4bf82e|ae89890530dad730|-562017065|bucket=open-rvfcast-data*region=NULL*key=_targets/sentinel_ndvi_transformed_upload_aws_s3_fd0f03b2*endpoint=TlVMTA*version=|t19643.042275691s||220|qs|aws|vector|sentinel_ndvi_transformed_upload_aws_s3||1.16|| sentinel_ndvi_transformed_upload_aws_s3_fe57e617|branch|9c54a05570ddc2a7|03a57554ca4bf82e|b9d77ec2b5e1f1c7|426307785|bucket=open-rvfcast-data*region=NULL*key=_targets/sentinel_ndvi_transformed_upload_aws_s3_fe57e617*endpoint=TlVMTA*version=|t19643.0414296838s||220|qs|aws|vector|sentinel_ndvi_transformed_upload_aws_s3||2.153|| 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-f|object|9b574eef2d264029 -create_africa_polygon|function|fb2ce70982e38cd3 -tar_cue_upload_aws|object|a973f11a0f57f835 -get_wahis_rvf_outbreaks_raw|function|a8564ce9127c9c1d -transform_nasa_weather|function|4ccbd4810fe93074 -transform_ecmwf_forecasts|function|648667cbb23058c3 -transform_modis_ndvi|function|c558b2ceec4076e9 -transform_sentinel_ndvi|function|e34eead242be1095 -get_nasa_weather_coordinates|function|2c23f9e4d93cd8ca diff --git a/renv.lock b/renv.lock index 0e86d2f..7596aa3 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.3.1", + "Version": "4.3.0", "Repositories": [ { "Name": "RSPM", @@ -17,1247 +17,1249 @@ ] }, "Packages": { - "DBI": { + "arrow": { + "Source": "Repository", + "Package": "arrow", + "Version": "13.0.0.1", + "Repository": "RSPM" + }, + "askpass": { + "Source": "Repository", + "Package": "askpass", + "Version": "1.2.0", + "Repository": "RSPM" + }, + "assertthat": { + "Source": "Repository", + "Package": "assertthat", + "Version": "0.2.1", + "Repository": "RSPM" + }, + "atcursor": { + "Source": "GitHub", + "Package": "atcursor", + "Version": "0.0.2", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "milesmcbain", + "RemoteRepo": "atcursor", + "RemoteRef": "main", + "RemoteSha": "52445666e612650cfa787814c3b195eaa1012ab8" + }, + "aws.s3": { + "Source": "Repository", + "Package": "aws.s3", + "Version": "0.3.21", + "Repository": "RSPM" + }, + "aws.signature": { + "Source": "Repository", + "Package": "aws.signature", + "Version": "0.6.0", + "Repository": "RSPM" + }, + "base64url": { + "Source": "Repository", + "Package": "base64url", + "Version": "1.4", + "Repository": "RSPM" + }, + "blastula": { + "Source": "Repository", + "Package": "blastula", + "Version": "0.3.4", + "Repository": "RSPM" + }, + "broom": { + "Source": "Repository", + "Package": "broom", + "Version": "1.0.5", + "Repository": "RSPM" + }, + "bslib": { + "Source": "Repository", + "Package": "bslib", + "Version": "0.5.0", + "Repository": "RSPM" + }, + "capsule": { + "Source": "Repository", + "Package": "capsule", + "Version": "0.4.2", + "Repository": "https://milesmcbain.r-universe.dev", + "RemoteType": "repository", + "RemoteUrl": "https://github.com/milesmcbain/capsule", + "RemoteRef": "master", + "RemoteSha": "401d0c98adc329c17d0bb129069c9ec220a26646" + }, + "containerTemplateUtils": { + "Source": "GitHub", + "Package": "containerTemplateUtils", + "Version": "0.0.0.9006", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "ecohealthalliance", + "RemoteRepo": "containerTemplateUtils", + "RemoteRef": "main", + "RemoteSha": "d707a282139c2b42d929baf96962aa4ce655b82b" + }, + "countrycode": { + "Source": "Repository", + "Package": "countrycode", + "Version": "1.5.0", + "Repository": "RSPM" + }, + "cpp11": { + "Source": "Repository", + "Package": "cpp11", + "Version": "0.4.6", + "Repository": "RSPM" + }, + "credentials": { + "Source": "Repository", + "Package": "credentials", + "Version": "2.0.1", + "Repository": "RSPM" + }, + "crew": { + "Source": "Repository", + "Package": "crew", + "Version": "0.4.0", + "Repository": "RSPM" + }, + "curl": { + "Source": "Repository", + "Package": "curl", + "Version": "5.0.2", + "Repository": "RSPM" + }, + "digest": { + "Source": "Repository", + "Package": "digest", + "Version": "0.6.33", + "Repository": "RSPM" + }, + "dotenv": { + "Source": "Repository", + "Package": "dotenv", + "Version": "1.0.3", + "Repository": "RSPM" + }, + "ecmwfr": { + "Source": "Repository", + "Package": "ecmwfr", + "Version": "1.5.0", + "Repository": "RSPM" + }, + "fansi": { + "Source": "Repository", + "Package": "fansi", + "Version": "1.0.5", + "Repository": "RSPM" + }, + "filelock": { + "Source": "Repository", + "Package": "filelock", + "Version": "1.0.2", + "Repository": "RSPM" + }, + "fnmate": { + "Source": "GitHub", + "Package": "fnmate", + "Version": "0.0.6", + "RemoteType": "github", + "RemoteHost": 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"Repository", + "Package": "googledrive", + "Version": "2.1.1", + "Repository": "RSPM" + }, + "googlesheets4": { + "Source": "Repository", + "Package": "googlesheets4", + "Version": "1.1.1", + "Repository": "RSPM" + }, + "httr": { + "Source": "Repository", + "Package": "httr", + "Version": "1.4.7", + "Repository": "RSPM" + }, + "igraph": { + "Source": "Repository", + "Package": "igraph", + "Version": "1.4.3", + "Repository": "RSPM" + }, + "janitor": { + "Source": "Repository", + "Package": "janitor", + "Version": "2.2.0", + "Repository": "RSPM" + }, + "jsonlite": { + "Source": "Repository", + "Package": "jsonlite", + "Version": "1.8.7", + "Repository": "RSPM" + }, + "kableExtra": { + "Source": "Repository", + "Package": "kableExtra", + "Version": "1.3.4", + "Repository": "RSPM" + }, + "keyring": { + "Source": "Repository", + "Package": "keyring", + "Version": "1.3.1", + "Repository": "RSPM" + }, + "knitr": { + "Source": "Repository", + "Package": "knitr", + "Version": "1.43", + "Repository": "RSPM" + }, + "mirai": { + "Source": "Repository", + "Package": "mirai", + "Version": "0.9.1", + "Repository": "RSPM" + }, + "nanonext": { + "Source": "Repository", + "Package": "nanonext", + "Version": "0.9.1", + "Repository": "RSPM" + }, + "nasapower": { + "Source": "Repository", + "Package": "nasapower", + "Version": "4.0.10", + "Repository": "RSPM" + }, + "openssl": { + "Source": "Repository", + "Package": "openssl", + "Version": "2.1.0", + "Repository": "RSPM" + }, + "parallelly": { + "Source": "Repository", + "Package": "parallelly", + "Version": "1.36.0", + "Repository": "RSPM" + }, + "paws.analytics": { + "Source": "Repository", + "Package": "paws.analytics", + "Version": "0.3.0", + "Repository": "RSPM" + }, + "paws.application.integration": { + "Source": "Repository", + "Package": "paws.application.integration", + "Version": "0.3.1", + "Repository": "RSPM" + }, + "paws.common": { + "Source": "Repository", + "Package": "paws.common", + "Version": "0.5.8", + 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}, + "purrr": { + "Source": "Repository", + "Package": "purrr", + "Version": "1.0.2", + "Repository": "RSPM" + }, + "qs": { + "Source": "Repository", + "Package": "qs", + "Version": "0.25.5", + "Repository": "RSPM" + }, + "RApiSerialize": { + "Source": "Repository", + "Package": "RApiSerialize", + "Version": "0.1.2", + "Repository": "RSPM" + }, + "Rcpp": { + "Source": "Repository", + "Package": "Rcpp", + "Version": "1.0.11", + "Repository": "RSPM" + }, + "remotes": { + "Source": "Repository", + "Package": "remotes", + "Version": "2.4.2.1", + "Repository": "RSPM" + }, + "renv": { + "Source": "Repository", + "Package": "renv", + "Version": "1.0.3", + "Repository": "RSPM" + }, + "rnaturalearth": { + "Source": "Repository", + "Package": "rnaturalearth", + "Version": "0.3.3", + "Repository": "RSPM" + }, + "rnaturalearthhires": { + "Source": "GitHub", + "Package": "rnaturalearthhires", + "Version": "0.2.1", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": 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"Repository": "CRAN" + "Package": "sf", + "Version": "1.0-14", + "Repository": "RSPM" }, - "RColorBrewer": { + "snakecase": { "Source": "Repository", - "Package": "RColorBrewer", - "Version": "1.1-3", - "Repository": "CRAN" + "Package": "snakecase", + "Version": "0.11.0", + "Repository": "RSPM" }, - "Rcpp": { + "sodium": { "Source": "Repository", - "Package": "Rcpp", - "Version": "1.0.11", - "Repository": "CRAN" + "Package": "sodium", + "Version": "1.2.1", + "Repository": "RSPM" }, - "RcppEigen": { + "sp": { "Source": "Repository", - "Package": "RcppEigen", - "Version": "0.3.3.9.3", - "Repository": "CRAN" + "Package": "sp", + "Version": "2.0-0", + "Repository": "RSPM" }, - "RcppParallel": { + "stringfish": { "Source": "Repository", - "Package": "RcppParallel", - "Version": "5.1.7", - "Repository": "CRAN" + "Package": "stringfish", + "Version": "0.15.8", + "Repository": "RSPM" }, - "arrow": { + "sys": { "Source": "Repository", - "Package": "arrow", - "Version": "13.0.0.1", - "Repository": "CRAN" + "Package": "sys", + "Version": "3.4.2", + "Repository": "RSPM" }, - "askpass": { + "tarchetypes": { "Source": "Repository", - "Package": "askpass", - "Version": "1.1", - "Repository": "CRAN" + "Package": "tarchetypes", + "Version": "0.7.6", + "Repository": "RSPM" }, - "assertthat": { + "targets": { "Source": "Repository", - "Package": "assertthat", - "Version": "0.2.1", - "Repository": "CRAN" + "Package": "targets", + "Version": "1.1.3", + "Repository": "RSPM" }, - "atcursor": { + "terra": { + "Source": "Repository", + "Package": "terra", + "Version": "1.7-39", + "Repository": "RSPM" + }, + "tflow": { "Source": "GitHub", - "Package": "atcursor", - "Version": "0.0.2", + "Package": "tflow", + "Version": "0.3.10", "RemoteType": "github", "RemoteHost": "api.github.com", - "RemoteUsername": "milesmcbain", - "RemoteRepo": "atcursor", - "RemoteRef": "main", - "RemoteSha": "52445666e612650cfa787814c3b195eaa1012ab8" + "RemoteUsername": "MilesMcBain", + "RemoteRepo": 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