From 4f91ff9f0ad3e08b60a95bb697fd61534dd45d03 Mon Sep 17 00:00:00 2001 From: Emma Mendelsohn Date: Tue, 21 Nov 2023 16:46:54 -0500 Subject: [PATCH 01/10] first pass at building augmented dataset. getting error that some (not all) of the forecast anomaly data seems to be invalid ("Couldn't deserialize thrift: TProtocolException: Invalid data") --- R/augment_data.R | 26 + _targets.R | 24 +- _targets/meta/meta | 8082 +++++++++++++++++----------------- data/augmented_data/.gitkeep | 0 renv.lock | 42 +- 5 files changed, 4112 insertions(+), 4062 deletions(-) create mode 100644 R/augment_data.R create mode 100644 data/augmented_data/.gitkeep diff --git a/R/augment_data.R b/R/augment_data.R new file mode 100644 index 0000000..ba2344e --- /dev/null +++ b/R/augment_data.R @@ -0,0 +1,26 @@ + +#' @title +#' @param weather_anomalies +#' @param forecasts_anomalies +#' @param ndvi_anomalies +#' @param augmented_data_directory +#' @return +#' @author Emma Mendelsohn +#' @export +augment_data <- function(weather_anomalies, forecasts_anomalies, + ndvi_anomalies, augmented_data_directory) { + + + weather <- arrow::open_dataset(weather_anomalies) + forecasts <- arrow::open_dataset(forecasts_anomalies) + ndvi <- arrow::open_dataset(ndvi_anomalies) + + left_join(weather, forecasts) |> + left_join(ndvi) |> + group_by(date) |> + write_dataset(augmented_data_directory) + + return(list.files(augmented_data_directory)) + +} + \ No newline at end of file diff --git a/_targets.R b/_targets.R index d4713ae..ad2b2b8 100644 --- a/_targets.R +++ b/_targets.R @@ -313,8 +313,8 @@ data_targets <- tar_plan( lag_intervals, seed = 212) |> filter(select_date) |> pull(date) - ), - + ), + # recorded weather anomalies -------------------------------------------------- tar_target(weather_historical_means_directory, create_data_directory(directory_path = "data/weather_historical_means")), @@ -446,6 +446,26 @@ data_targets <- tar_plan( pattern = ndvi_anomalies, cue = tar_cue("thorough")), # only run this if you need to upload new data + # all anomalies -------------------------------------------------- + tar_target(augmented_data_directory, + create_data_directory(directory_path = "data/augmented_data")), + + tar_target(augmented_data, + augment_data(weather_anomalies, + forecasts_anomalies, + ndvi_anomalies, + augmented_data_directory), + format = "file", + repository = "local", + cue = tar_cue(tar_cue_general)), + + tar_target(augmented_data_upload_aws_s3, + aws_s3_upload(path = augmented_data, + bucket = aws_bucket, + key = augmented_data, + check = TRUE), + pattern = augmented_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 bd0dd64..7ba3691 100644 --- a/_targets/meta/meta +++ b/_targets/meta/meta @@ -1,6 +1,9 @@ name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error -.Random.seed|object|c3d04f83fd4a9f0e||||||||||||||| +.Random.seed|object|b06b34d7ea8c0202||||||||||||||| all_targets|function|2dda5afbd1f92385||||||||||||||| +augment_data|function|c3cec4087a9a7773||||||||||||||| +augmented_data|stem||c36f979deebc5230|4526a19f0a80c88c|-727079193||t19682.8954768503s||0|file|local|vector|||19.393||IOError Could not open Parquet input source Usersemmamendelsohnprojectsopenrvfcastdataforecast_anomaliesforecast_anomaly_20100212.gz.parquet Couldnt deserialize thrift TProtocolException Invalid data +augmented_data_directory|stem|38d377002eafd6cd|24d19f695bf99d43|3d3d9feae01275db|-1705128318|bucket=open-rvfcast-data*region=us-east-1*key=_targets/augmented_data_directory*endpoint=TlVMTA*version=|t19682.8901540582s||51|qs|aws|vector|||0.001|| aws_bucket|object|d9cf2c5ff7cc1be4||||||||||||||| aws_s3_upload_single_type|function|6d277b68ccbb67a2||||||||||||||| cache_aws_branched_target|function|6e2abfa4969de1bf||||||||||||||| @@ -24,7 +27,7 @@ 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|33754be2a31c8b23||||||||||||||| +data_targets|object|6dc9951a9fdb2c33||||||||||||||| 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"CRAN" }, "cachem": { @@ -184,7 +184,7 @@ "classInt": { "Source": "Repository", "Package": "classInt", - "Version": "0.4-9", + "Version": "0.4-10", "Repository": "CRAN" }, "cli": { @@ -333,7 +333,7 @@ "evaluate": { "Source": "Repository", "Package": "evaluate", - "Version": "0.21", + "Version": "0.23", "Repository": "CRAN" }, "fansi": { @@ -374,7 +374,7 @@ "fontawesome": { "Source": "Repository", "Package": "fontawesome", - "Version": "0.5.1", + "Version": "0.5.2", "Repository": "CRAN" }, "forcats": { @@ -386,7 +386,7 @@ "fs": { "Source": "Repository", "Package": "fs", - "Version": "1.6.2", + "Version": "1.6.3", "Repository": "CRAN" }, "furrr": { @@ -446,7 +446,7 @@ "ggplot2": { "Source": "Repository", "Package": "ggplot2", - "Version": "3.4.2", + "Version": "3.4.4", "Repository": "CRAN" }, "ggrepel": { @@ -494,7 +494,7 @@ "gtable": { "Source": "Repository", "Package": "gtable", - "Version": "0.3.3", + "Version": "0.3.4", "Repository": "CRAN" }, "haven": { @@ -524,7 +524,7 @@ "htmltools": { "Source": "Repository", "Package": "htmltools", - "Version": "0.5.5", + "Version": "0.5.7", "Repository": "CRAN" }, "htmlwidgets": { @@ -608,19 +608,19 @@ "knitr": { "Source": "Repository", "Package": "knitr", - "Version": "1.43", + "Version": "1.45", "Repository": "CRAN" }, "labeling": { "Source": "Repository", "Package": "labeling", - "Version": "0.4.2", + "Version": "0.4.3", "Repository": "CRAN" }, "lifecycle": { "Source": "Repository", "Package": "lifecycle", - "Version": "1.0.3", + "Version": "1.0.4", "Repository": "CRAN" }, "listenv": { @@ -920,7 +920,7 @@ "rmarkdown": { "Source": "Repository", "Package": "rmarkdown", - "Version": "2.21", + "Version": "2.25", "Repository": "CRAN" }, "rnaturalearth": { @@ -1020,7 +1020,7 @@ "sp": { "Source": "Repository", "Package": "sp", - "Version": "2.0-0", + "Version": "2.1-1", "Repository": "CRAN" }, "stringfish": { @@ -1074,7 +1074,7 @@ "terra": { "Source": "Repository", "Package": "terra", - "Version": "1.7-39", + "Version": "1.7-55", "Repository": "CRAN" }, "textshaping": { @@ -1127,7 +1127,7 @@ "tinytex": { "Source": "Repository", "Package": "tinytex", - "Version": "0.45", + "Version": "0.48", "Repository": "CRAN" }, "triebeard": { @@ -1151,7 +1151,7 @@ "units": { "Source": "Repository", "Package": "units", - "Version": "0.8-3", + "Version": "0.8-4", "Repository": "CRAN" }, "urltools": { @@ -1178,7 +1178,7 @@ "utf8": { "Source": "Repository", "Package": "utf8", - "Version": "1.2.3", + "Version": "1.2.4", "Repository": "CRAN" }, "uuid": { @@ -1190,7 +1190,7 @@ "vctrs": { "Source": "Repository", "Package": "vctrs", - "Version": "0.6.3", + "Version": "0.6.4", "Repository": "CRAN" }, "viridisLite": { @@ -1226,19 +1226,19 @@ "withr": { "Source": "Repository", "Package": "withr", - "Version": "2.5.1", + "Version": "2.5.2", "Repository": "CRAN" }, "wk": { "Source": "Repository", "Package": "wk", - "Version": "0.7.3", + "Version": "0.9.0", "Repository": "CRAN" }, "xfun": { "Source": "Repository", "Package": "xfun", - "Version": "0.40", + "Version": "0.41", "Repository": "CRAN" }, "xml2": { From bccfd6f1fed59036ff894a2680178415542f5ba0 Mon Sep 17 00:00:00 2001 From: Emma Mendelsohn Date: Mon, 27 Nov 2023 14:44:01 -0500 Subject: [PATCH 02/10] closes #68 but still throws error on join "Last error: IOError: Couldn't deserialize thrift: don't know what type:" --- R/augment_data.R | 9 +- _targets.R | 4 +- _targets/meta/meta | 298 ++++++++++++++++++++++----------------------- 3 files changed, 155 insertions(+), 156 deletions(-) diff --git a/R/augment_data.R b/R/augment_data.R index ba2344e..fad647a 100644 --- a/R/augment_data.R +++ b/R/augment_data.R @@ -8,13 +8,13 @@ #' @author Emma Mendelsohn #' @export augment_data <- function(weather_anomalies, forecasts_anomalies, - ndvi_anomalies, augmented_data_directory) { - - + ndvi_anomalies, augmented_data_directory) { + + weather <- arrow::open_dataset(weather_anomalies) forecasts <- arrow::open_dataset(forecasts_anomalies) ndvi <- arrow::open_dataset(ndvi_anomalies) - + left_join(weather, forecasts) |> left_join(ndvi) |> group_by(date) |> @@ -23,4 +23,3 @@ augment_data <- function(weather_anomalies, forecasts_anomalies, return(list.files(augmented_data_directory)) } - \ No newline at end of file diff --git a/_targets.R b/_targets.R index ad2b2b8..081b423 100644 --- a/_targets.R +++ b/_targets.R @@ -444,7 +444,7 @@ data_targets <- tar_plan( key = ndvi_anomalies, check = TRUE), pattern = ndvi_anomalies, - cue = tar_cue("thorough")), # only run this if you need to upload new data + cue = tar_cue(tar_cue_upload_aws)), # only run this if you need to upload new data # all anomalies -------------------------------------------------- tar_target(augmented_data_directory, @@ -465,7 +465,7 @@ data_targets <- tar_plan( key = augmented_data, check = TRUE), pattern = augmented_data, - cue = tar_cue("thorough")), # only run this if you need to upload new data + cue = tar_cue(tar_cue_upload_aws)), # only run this if you need to upload new data ) diff --git a/_targets/meta/meta b/_targets/meta/meta index 7ba3691..a329c0b 100644 --- a/_targets/meta/meta +++ b/_targets/meta/meta @@ -1,8 +1,8 @@ name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error -.Random.seed|object|b06b34d7ea8c0202||||||||||||||| +.Random.seed|object|2a21dc085439eef7||||||||||||||| all_targets|function|2dda5afbd1f92385||||||||||||||| augment_data|function|c3cec4087a9a7773||||||||||||||| -augmented_data|stem||c36f979deebc5230|4526a19f0a80c88c|-727079193||t19682.8954768503s||0|file|local|vector|||19.393||IOError Could not open Parquet input source Usersemmamendelsohnprojectsopenrvfcastdataforecast_anomaliesforecast_anomaly_20100212.gz.parquet Couldnt deserialize thrift TProtocolException Invalid data +augmented_data|stem||c36f979deebc5230|94e3d8cbe94d0849|-727079193||t19682.8954768503s||0|file|local|vector|||18.399||IOError Couldnt deserialize thrift dont know what type 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forecasts_anomalies_upload_aws_s3_39253fc9|branch|43b491ec43c537e9|c940eb27b789bb5d|5fb3d9814861f33a|1298109257|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_39253fc9*endpoint=TlVMTA*version=|t19667.7629287418s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.285|| forecasts_anomalies_upload_aws_s3_394f0f10|branch|b1342c4cd1f591c5|c940eb27b789bb5d|0dd23e83d2259490|1031426898|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_394f0f10*endpoint=TlVMTA*version=|t19667.7802869061s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.171|| @@ -744,7 +744,7 @@ forecasts_anomalies_upload_aws_s3_6c8ff0bc|branch|4ddeabf5e10e9abd|c940eb27b789b forecasts_anomalies_upload_aws_s3_6cb7492d|branch|cdedc46d8097a76e|c940eb27b789bb5d|0b9366707bf1b092|-1696467692|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_6cb7492d*endpoint=TlVMTA*version=|t19667.7613249183s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.385|| forecasts_anomalies_upload_aws_s3_6cba65c5|branch|f80d74b0ed0ba00c|c940eb27b789bb5d|4eb8ebc1d33beac1|-1258834389|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_6cba65c5*endpoint=TlVMTA*version=|t19667.760626249s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.217|| forecasts_anomalies_upload_aws_s3_6cbe3212|branch|95e237fddef8a3ab|c940eb27b789bb5d|3b957baec4bed0e6|-262103154|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_6cbe3212*endpoint=TlVMTA*version=|t19667.7689693534s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.167|| 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forecasts_anomalies_upload_aws_s3_6e7f6cc3|branch|4c241d357a9cc6ed|c940eb27b789bb5d|9ebede2b5c9f1d34|-1631633742|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_6e7f6cc3*endpoint=TlVMTA*version=|t19667.7731573874s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.195|| forecasts_anomalies_upload_aws_s3_6f02fc7a|branch|c0e3f700365d190a|c940eb27b789bb5d|408cf6979ce7793e|-565395881|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_6f02fc7a*endpoint=TlVMTA*version=|t19667.7597477619s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.508|| @@ -753,7 +753,7 @@ forecasts_anomalies_upload_aws_s3_702ba0af|branch|598ba74fd262475b|c940eb27b789b forecasts_anomalies_upload_aws_s3_70540ab8|branch|a57d6ce1d98bbc41|c940eb27b789bb5d|8ff231375893f0fe|-1009964497|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_70540ab8*endpoint=TlVMTA*version=|t19667.7754838156s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.193|| forecasts_anomalies_upload_aws_s3_70f11590|branch|8974d1573cd0c92b|c940eb27b789bb5d|6d9166efe0f2af9d|-328683233|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_70f11590*endpoint=TlVMTA*version=|t19667.7791035527s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.167|| forecasts_anomalies_upload_aws_s3_71791c87|branch|e43ff3f41bd261c6|c940eb27b789bb5d|aae64ad575cf48a9|-1752500550|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_71791c87*endpoint=TlVMTA*version=|t19667.7654112838s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.173|| 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forecasts_anomalies_upload_aws_s3_7217c05b|branch|4a139903681d415c|c940eb27b789bb5d|3e9506edf8b2beea|-296990220|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_7217c05b*endpoint=TlVMTA*version=|t19667.7703867386s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.189|| forecasts_anomalies_upload_aws_s3_7260e020|branch|1663777c715f01ce|c940eb27b789bb5d|c86d7d3fbb03cf4e|1172611144|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_7260e020*endpoint=TlVMTA*version=|t19667.7627705909s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.236|| @@ -768,7 +768,7 @@ forecasts_anomalies_upload_aws_s3_78f6b7bd|branch|94d177c86c2cff55|c940eb27b789b forecasts_anomalies_upload_aws_s3_79bc257a|branch|2470f85a01c86a80|c940eb27b789bb5d|e22649e65f5eac66|-1191274254|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_79bc257a*endpoint=TlVMTA*version=|t19667.7604109676s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.084|| forecasts_anomalies_upload_aws_s3_79c7bb7e|branch|913391d8247f2d70|c940eb27b789bb5d|b439acf424e3879c|2033175365|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_79c7bb7e*endpoint=TlVMTA*version=|t19667.767458726s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.053|| forecasts_anomalies_upload_aws_s3_7b542c18|branch|eb39b0c65fffccca|c940eb27b789bb5d|a2811e90d47409e5|64737141|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_7b542c18*endpoint=TlVMTA*version=|t19667.7688648609s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.259|| 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forecasts_anomalies_upload_aws_s3_7c701058|branch|57073edee7a74d1f|c940eb27b789bb5d|ecc208590a71b9e2|53196808|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_7c701058*endpoint=TlVMTA*version=|t19667.7789485501s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.21|| forecasts_anomalies_upload_aws_s3_7caeee6e|branch|d82aed68992a7c1b|c940eb27b789bb5d|39e175335c99dee7|-1114170867|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_7caeee6e*endpoint=TlVMTA*version=|t19667.7677135451s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.203|| @@ -807,7 +807,7 @@ forecasts_anomalies_upload_aws_s3_8d77fa98|branch|41494a564e33c9a2|c940eb27b789b forecasts_anomalies_upload_aws_s3_8dea23ca|branch|908201cb6ad4d90b|c940eb27b789bb5d|13235f5b90bdda26|1756013045|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_8dea23ca*endpoint=TlVMTA*version=|t19667.7727908534s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.234|| forecasts_anomalies_upload_aws_s3_8e07166a|branch|ce94bab796c52d5c|c940eb27b789bb5d|bfc9b8b6c154a11a|-1484494412|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_8e07166a*endpoint=TlVMTA*version=|t19667.7683938807s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.195|| forecasts_anomalies_upload_aws_s3_8e1511ca|branch|8a1bc34ec79026f5|c940eb27b789bb5d|aea53ff3d8549c1d|-827485730|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_8e1511ca*endpoint=TlVMTA*version=|t19667.7722619555s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.223|| 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forecasts_anomalies_upload_aws_s3_8f7c0796|branch|e82b9179fd3cca60|c940eb27b789bb5d|57d1ce8e7085335a|-1283440262|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_8f7c0796*endpoint=TlVMTA*version=|t19667.7643023299s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.269|| forecasts_anomalies_upload_aws_s3_8fba46ad|branch|562c2134871202dd|c940eb27b789bb5d|e2091b396db9fbb1|-597643885|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_8fba46ad*endpoint=TlVMTA*version=|t19667.7780132102s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.248|| @@ -890,7 +890,7 @@ forecasts_anomalies_upload_aws_s3_be0f5250|branch|e0fc3152520e16f9|c940eb27b789b forecasts_anomalies_upload_aws_s3_be918458|branch|2006e607f4f25122|c940eb27b789bb5d|d79f14b7983e394e|-1494172777|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_be918458*endpoint=TlVMTA*version=|t19667.7662560667s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.155|| forecasts_anomalies_upload_aws_s3_bff35589|branch|d4bcac8f10168193|c940eb27b789bb5d|92489b6c3b7033c8|73486624|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_bff35589*endpoint=TlVMTA*version=|t19667.7637185237s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.318|| forecasts_anomalies_upload_aws_s3_c015c354|branch|c530c88210e1f2d1|c940eb27b789bb5d|0bdc571ad7086689|-1554652580|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_c015c354*endpoint=TlVMTA*version=|t19667.7655708699s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.294|| 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get_country_bounding_boxes|function|82b21d03b36ce8fe||||||||||||||| get_modis_ndvi_api_parameters|function|c30ed04e0978b176||||||||||||||| From 6bdd25777dea9157bf3f3e3fab2e0d307ef92c1c Mon Sep 17 00:00:00 2001 From: Emma Mendelsohn Date: Tue, 5 Dec 2023 09:45:19 -0500 Subject: [PATCH 03/10] regenerated forecast anomaly files with arrow 14.0.0.2 and seems to be working --- _targets/meta/meta | 909 +++++++++++++++++--------------- renv/settings.json | 19 + scripts/scrap/arrow_debugging.R | 30 ++ 3 files changed, 531 insertions(+), 427 deletions(-) create mode 100644 renv/settings.json create mode 100644 scripts/scrap/arrow_debugging.R diff --git a/_targets/meta/meta b/_targets/meta/meta index a329c0b..3d7b832 100644 --- a/_targets/meta/meta +++ b/_targets/meta/meta @@ -113,434 +113,7 @@ ecmwf_forecasts_transformed_upload_aws_s3_f77cea8f|branch|6e170a6bc685cec2|af110 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diff --git a/renv/settings.json b/renv/settings.json new file mode 100644 index 0000000..f836f3f --- /dev/null +++ b/renv/settings.json @@ -0,0 +1,19 @@ +{ + "bioconductor.version": null, + "external.libraries": [], + "ignored.packages": [], + "package.dependency.fields": [ + "Imports", + "Depends", + "LinkingTo" + ], + "ppm.enabled": null, + "ppm.ignored.urls": [], + "r.version": [], + "snapshot.type": "implicit", + "use.cache": true, + "vcs.ignore.cellar": true, + "vcs.ignore.library": true, + "vcs.ignore.local": true, + "vcs.manage.ignores": true +} diff --git a/scripts/scrap/arrow_debugging.R b/scripts/scrap/arrow_debugging.R new file mode 100644 index 0000000..50e45cb --- /dev/null +++ b/scripts/scrap/arrow_debugging.R @@ -0,0 +1,30 @@ +suppressPackageStartupMessages(source("packages.R")) +for (f in list.files(here::here("R"), full.names = TRUE)) source (f) + +forecasts_anomalies <- list.files("data/forecast_anomalies", full.names = TRUE) + +failed <- map_dfr(forecasts_anomalies, ~{ + result <- tryCatch({ + arrow::read_parquet(.x) + NULL + }, error = function(e) { + cat("Error opening dataset for item:", .x, "\n") + return(data.frame(failed_item = .x)) + }) + + return(result) +}) + +# 1 data/forecast_anomalies/forecast_anomaly_2010-03-27.gz.parquet +# 2 data/forecast_anomalies/forecast_anomaly_2010-08-08.gz.parquet +# 3 data/forecast_anomalies/forecast_anomaly_2010-08-24.gz.parquet +# 4 data/forecast_anomalies/forecast_anomaly_2010-11-17.gz.parquet +# 5 data/forecast_anomalies/forecast_anomaly_2010-11-28.gz.parquet +# 6 data/forecast_anomalies/forecast_anomaly_2011-01-11.gz.parquet +# 7 data/forecast_anomalies/forecast_anomaly_2011-03-14.gz.parquet + +for(f in failed$failed_item) file.remove(f) + +tar_invalidate(forecasts_anomalies) + +tar_make(forecasts_anomalies) From c85a0fd8a3aea1a95bac6b0c737de8a643890ce1 Mon Sep 17 00:00:00 2001 From: Emma Mendelsohn Date: Tue, 5 Dec 2023 09:51:05 -0500 Subject: [PATCH 04/10] tar_prune --- _targets/meta/meta | 168 +++++++++++++++------------------------------ 1 file changed, 55 insertions(+), 113 deletions(-) diff --git a/_targets/meta/meta b/_targets/meta/meta index 3d7b832..5c3465c 100644 --- a/_targets/meta/meta +++ b/_targets/meta/meta @@ -1,46 +1,22 @@ name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error -.Random.seed|object|2a21dc085439eef7||||||||||||||| -all_targets|function|2dda5afbd1f92385||||||||||||||| -augment_data|function|c3cec4087a9a7773||||||||||||||| augmented_data|stem||c36f979deebc5230|94e3d8cbe94d0849|-727079193||t19682.8954768503s||0|file|local|vector|||18.399||IOError Couldnt deserialize thrift dont know what type Deserializing page header failed. augmented_data_directory|stem|38d377002eafd6cd|24d19f695bf99d43|3d3d9feae01275db|-1705128318|bucket=open-rvfcast-data*region=us-east-1*key=_targets/augmented_data_directory*endpoint=TlVMTA*version=|t19682.8901540582s||51|qs|aws|vector|||0.001|| -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|| 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-preprocess_wahis_rvf_outbreaks|function|4762c7a06a997965||||||||||||||| 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||||||||||||||| save_transform_nasa_weather|function|f118a96aaf86e957||||||||||||||| @@ -4800,22 +4757,8 @@ sentinel_ndvi_transformed_upload_aws_s3_fc1a6799|branch|caf6b0d532e56187|03a5755 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"d98c94dacb7e0efcf83b0a133a705504" } } } From f7dd0cd2f7549e942e9b3d61052d526d08dce2c3 Mon Sep 17 00:00:00 2001 From: Emma Mendelsohn Date: Fri, 8 Dec 2023 15:01:31 -0500 Subject: [PATCH 06/10] rerunning forecast anomalies to replace NAs in files --- R/calculate_forecasts_anomalies.R | 6 ++++++ R/utils.R | 5 ++++- 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/R/calculate_forecasts_anomalies.R b/R/calculate_forecasts_anomalies.R index 37d1238..19e1901 100644 --- a/R/calculate_forecasts_anomalies.R +++ b/R/calculate_forecasts_anomalies.R @@ -30,7 +30,13 @@ calculate_forecasts_anomalies <- function(ecmwf_forecasts_transformed, existing_files <- list.files(forecasts_anomalies_directory) if(save_filename %in% existing_files & !overwrite) { message("file already exists, skipping download") + saved <- read_parquet(file.path(forecasts_anomalies_directory, save_filename)) + saved_check <- col_na(saved) + if(!any(saved_check)) { return(file.path(forecasts_anomalies_directory, save_filename)) + }else{ + message("NAs found, regenerating file") + } } # Open dataset to transformed data diff --git a/R/utils.R b/R/utils.R index 929c908..b8a7ea7 100644 --- a/R/utils.R +++ b/R/utils.R @@ -26,4 +26,7 @@ all_targets <- function(env = parent.env(environment()), type = "tar_target") { # # tar_load_s3 <- function(target_name, ...) { # -# } \ No newline at end of file +# } + +#' Get NAs +col_na <- function(df) purrr::map_lgl(df, ~any(is.na(.))) From f252bc57b50a1dcc251661e372d519b1f26fcee2 Mon Sep 17 00:00:00 2001 From: Emma Mendelsohn Date: Mon, 11 Dec 2023 10:25:22 -0500 Subject: [PATCH 07/10] finish forecast anomaly regeneration --- R/augment_data.R | 35 +- R/calculate_forecasts_anomalies.R | 6 - _targets.R | 2 +- _targets/meta/meta | 1191 +++++++++++++++-------------- renv.lock | 6 +- 5 files changed, 628 insertions(+), 612 deletions(-) diff --git a/R/augment_data.R b/R/augment_data.R index fad647a..8feeead 100644 --- a/R/augment_data.R +++ b/R/augment_data.R @@ -1,4 +1,3 @@ - #' @title #' @param weather_anomalies #' @param forecasts_anomalies @@ -10,16 +9,38 @@ augment_data <- function(weather_anomalies, forecasts_anomalies, ndvi_anomalies, augmented_data_directory) { + + message("Load datasets into memory") + weather <- arrow::open_dataset(weather_anomalies) |> dplyr::collect() + forecasts <- arrow::open_dataset(forecasts_anomalies) |> dplyr::collect() + ndvi <- arrow::open_dataset(ndvi_anomalies) |> dplyr::collect() + + message("NA checks") + ## Weather and forecasts + ### NAs are in scaled precip data, due to days with 0 precip + weather_check <- purrr::map_lgl(weather, ~any(is.na(.))) + assertthat::assert_that(all(str_detect(names(weather_check[weather_check]), "scaled"))) - weather <- arrow::open_dataset(weather_anomalies) - forecasts <- arrow::open_dataset(forecasts_anomalies) - ndvi <- arrow::open_dataset(ndvi_anomalies) + forecasts_check <- purrr::map_lgl(forecasts, ~any(is.na(.))) + assertthat::assert_that(all(str_detect(names(forecasts_check[forecasts_check]), "scaled"))) + + ## NDVI + ### Prior to 2018: NAs are due to region missing from Eastern Africa in modis data + ### After 2018: NAs are due to smaller pockets of missing data on a per-cycle basis + ### okay to remove when developing RSA model (issue #72) + ndvi_check <- purrr::map_lgl(ndvi, ~any(is.na(.))) + assertthat::assert_that(!any(ndvi_check[c("date", "x", "y")])) + ndvi <- drop_na(ndvi) + + message("Join into a single object") + augmented_data <- left_join(weather, forecasts, by = join_by(date, x, y)) |> + left_join(ndvi, by = join_by(date, x, y)) - left_join(weather, forecasts) |> - left_join(ndvi) |> + message("Save as parquets using hive partitioning by date") + augmented_data |> group_by(date) |> write_dataset(augmented_data_directory) return(list.files(augmented_data_directory)) -} +} \ No newline at end of file diff --git a/R/calculate_forecasts_anomalies.R b/R/calculate_forecasts_anomalies.R index 19e1901..37d1238 100644 --- a/R/calculate_forecasts_anomalies.R +++ b/R/calculate_forecasts_anomalies.R @@ -30,13 +30,7 @@ calculate_forecasts_anomalies <- function(ecmwf_forecasts_transformed, existing_files <- list.files(forecasts_anomalies_directory) if(save_filename %in% existing_files & !overwrite) { message("file already exists, skipping download") - saved <- read_parquet(file.path(forecasts_anomalies_directory, save_filename)) - saved_check <- col_na(saved) - if(!any(saved_check)) { return(file.path(forecasts_anomalies_directory, save_filename)) - }else{ - message("NAs found, regenerating file") - } } # Open dataset to transformed data diff --git a/_targets.R b/_targets.R index 081b423..59ab0c8 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" # CAUTION changing this to never means targets can miss changes to the code. Use only for developing. +tar_cue_upload_aws = "thorough" # CAUTION changing this to never means targets can miss changes to the code. Use only for developing. # Static Data Download ---------------------------------------------------- static_targets <- tar_plan( diff --git a/_targets/meta/meta b/_targets/meta/meta index 5c3465c..b8db72a 100644 --- a/_targets/meta/meta +++ b/_targets/meta/meta @@ -1,22 +1,47 @@ name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error +.Random.seed|object|fe7861b27a64ff2b||||||||||||||| +all_targets|function|2dda5afbd1f92385||||||||||||||| +augment_data|function|09d9002b654df914||||||||||||||| augmented_data|stem||c36f979deebc5230|94e3d8cbe94d0849|-727079193||t19682.8954768503s||0|file|local|vector|||18.399||IOError Couldnt deserialize thrift dont know what type Deserializing page header failed. augmented_data_directory|stem|38d377002eafd6cd|24d19f695bf99d43|3d3d9feae01275db|-1705128318|bucket=open-rvfcast-data*region=us-east-1*key=_targets/augmented_data_directory*endpoint=TlVMTA*version=|t19682.8901540582s||51|qs|aws|vector|||0.001|| +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||||||||||||||| +col_na|function|81bde41e453c6fa2||||||||||||||| 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|55c14080d770e03f||||||||||||||| 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forecasts_anomalies_upload_aws_s3_c1dd7522|branch|b68e62a17b0725f2|c940eb27b789bb5d|17ab57e20ab39b82|-1404367030|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_c1dd7522*endpoint=TlVMTA*version=|t19667.7724713109s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.273|| forecasts_anomalies_upload_aws_s3_c365f943|branch|5c9d4d00f2bcc015|c940eb27b789bb5d|2000b72f429b862e|-1533562394|bucket=open-rvfcast-data*region=us-east-1*key=_targets/forecasts_anomalies_upload_aws_s3_c365f943*endpoint=TlVMTA*version=|t19667.7596914647s||190|qs|aws|vector|forecasts_anomalies_upload_aws_s3||4.257|| @@ -448,12 +901,12 @@ forecasts_anomalies_upload_aws_s3_c4039b74|branch|446404fa6a7c23f7|c940eb27b789b 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+preprocess_wahis_rvf_outbreaks|function|4762c7a06a997965||||||||||||||| 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||||||||||||||| save_transform_nasa_weather|function|f118a96aaf86e957||||||||||||||| @@ -4757,8 +5226,22 @@ sentinel_ndvi_transformed_upload_aws_s3_fc1a6799|branch|caf6b0d532e56187|03a5755 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diff --git a/renv.lock b/renv.lock index 6aaf219..9691209 100644 --- a/renv.lock +++ b/renv.lock @@ -1,6 +1,6 @@ { "R": { - "Version": "4.3.1", + "Version": "4.3.2", "Repositories": [ { "Name": "RSPM", @@ -1494,7 +1494,7 @@ }, "lattice": { "Package": "lattice", - "Version": "0.22-5", + "Version": "0.21-9", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1505,7 +1505,7 @@ "stats", "utils" ], - "Hash": "7c5e89f04e72d6611c77451f6331a091" + "Hash": "5558c61e0136e247252f5f952cdaad6a" }, "lifecycle": { "Package": "lifecycle", From 3bf2083a0a8ba6d0dd3b94ab468f494293c0f0b4 Mon Sep 17 00:00:00 2001 From: emmamendelsohn Date: Fri, 15 Dec 2023 10:02:25 -0500 Subject: [PATCH 08/10] complete anomaly dataset --- R/augment_data.R | 2 +- _targets.R | 9 +- _targets/meta/meta | 8145 ++++++++++++++------------- scripts/download-aws-s3-anomalies.R | 30 +- 4 files changed, 4121 insertions(+), 4065 deletions(-) diff --git a/R/augment_data.R b/R/augment_data.R index 8feeead..c9f2aeb 100644 --- a/R/augment_data.R +++ b/R/augment_data.R @@ -41,6 +41,6 @@ augment_data <- function(weather_anomalies, forecasts_anomalies, group_by(date) |> write_dataset(augmented_data_directory) - return(list.files(augmented_data_directory)) + return(augmented_data_directory) } \ No newline at end of file diff --git a/_targets.R b/_targets.R index 59ab0c8..455a5be 100644 --- a/_targets.R +++ b/_targets.R @@ -459,13 +459,12 @@ data_targets <- tar_plan( repository = "local", cue = tar_cue(tar_cue_general)), - tar_target(augmented_data_upload_aws_s3, + tar_target(augmented_data_upload_aws_s3, aws_s3_upload(path = augmented_data, bucket = aws_bucket, - key = augmented_data, - check = TRUE), - pattern = augmented_data, - cue = tar_cue(tar_cue_upload_aws)), # only run this if you need to upload new data + key = augmented_data, + check = TRUE), + cue = tar_cue(tar_cue_upload_aws)), # only run this if you need to upload new data ) diff --git a/_targets/meta/meta b/_targets/meta/meta index b8db72a..b7eaf57 100644 --- a/_targets/meta/meta +++ b/_targets/meta/meta @@ -1,8 +1,8 @@ name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error -.Random.seed|object|fe7861b27a64ff2b||||||||||||||| +.Random.seed|object|811190836422d67e||||||||||||||| all_targets|function|2dda5afbd1f92385||||||||||||||| -augment_data|function|09d9002b654df914||||||||||||||| -augmented_data|stem||c36f979deebc5230|94e3d8cbe94d0849|-727079193||t19682.8954768503s||0|file|local|vector|||18.399||IOError Couldnt deserialize thrift dont know what type Deserializing page header failed. +augment_data|function|84f709de1e81df93||||||||||||||| +augmented_data|stem|a2c64eb0ad1ccb98|c36f979deebc5230|b6821dfb08d361d5|-727079193|data/augmented_data|t19705.8672484923s|86cc6efaca9fc8d4|39220431915|file|local|vector||augmented_data_d2fea607|235.427|| 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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|| @@ -5229,7 +5229,7 @@ sentinel_ndvi_transformed_upload_aws_s3_fe57e617|branch|9c54a05570ddc2a7|03a5755 set_ecmwf_api_parameter|function|e3e4962883690ed5||||||||||||||| set_model_dates|function|e64f4ff47f178768||||||||||||||| set_nasa_api_parameter|function|ac1cc420c9c9242c||||||||||||||| 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Please reduce your request rate. weather_historical_means_upload_aws_s3_fee920e3|branch|9408d83b01ed6ca6|b22d4a4a1b5ce653|b2040ddf0024b43f|-1334476359|bucket=open-rvfcast-data*region=NULL*key=_targets/weather_historical_means_upload_aws_s3_fee920e3*endpoint=TlVMTA*version=|t19664.8824982056s||207|qs|aws|vector|weather_historical_means_upload_aws_s3||3.807|| weather_historical_means_upload_aws_s3_ff01b46a|branch|0c3fb2b6149e7b51|b22d4a4a1b5ce653|a9d8236ddd156395|760495033|bucket=open-rvfcast-data*region=NULL*key=_targets/weather_historical_means_upload_aws_s3_ff01b46a*endpoint=TlVMTA*version=|t19664.8682649589s||207|qs|aws|vector|weather_historical_means_upload_aws_s3||4.637|| +col_na|function|81bde41e453c6fa2 +get_wahis_rvf_outbreaks_raw|function|f5ec912c0f3610fb +download_ecmwf_forecasts|function|e38c7849a674aba8 +test_targets|object|1eb1bc8d77111ded +make_africa_outbreak_scale_map|function|1cf69dae8f3f7f78 +set_ecmwf_api_parameter|function|e3e4962883690ed5 +transform_raster|function|47f20ba2b9ef9722 +deploy_targets|object|1eb1bc8d77111ded +aws_bucket|object|d9cf2c5ff7cc1be4 +download_modis_ndvi_delete|function|98fa92fb3d3db8fb +static_targets|object|1a9689b1c83d553e +model_targets|object|1eb1bc8d77111ded +report_targets|object|1eb1bc8d77111ded +download_sentinel_ndvi|function|03e5942d01ac5cc7 +get_sentinel_ndvi_api_parameters|function|ec6ebe60c7637311 +plot_targets|object|1eb1bc8d77111ded +.Random.seed|object|5e8ccec98b11632d +get_modis_ndvi_token|function|f7872f64690bfba2 +calculate_forecasts_anomalies|function|e79c27516696d72f +all_targets|function|2dda5afbd1f92385 +create_country_polygons|function|9917ababa5b4b8f4 +aws_s3_upload_single_type|function|6d277b68ccbb67a2 +calculate_weather_historical_means|function|ac8b9ff61133bd68 +get_country_bounding_boxes|function|82b21d03b36ce8fe +submit_modis_ndvi_task_request|function|a97a6292a38c2323 +augment_data|function|84f709de1e81df93 +dynamic_targets|object|0e0f187df0f1bad4 +calculate_ndvi_historical_means|function|62d8a66e5ef237be +calculate_ndvi_anomalies|function|fa9de87422ce7598 +set_model_dates|function|e64f4ff47f178768 +tar_cue_general|object|5dfd2b49ee8a5f13 +submit_modis_ndvi_bundle_request|function|70d5dcdcf3510fa0 +make_south_africa_outbreaks_timeline|function|bc5fa66f128d8638 +data_targets|object|70f2d819e194046a +rolling_box|function|1195d491d98c697b +download_modis_ndvi|function|104ef42cc2cdbbc6 +preprocess_wahis_rvf_outbreaks|function|4762c7a06a997965 +create_ndvi_date_lookup|function|239a44dd31122aa6 +make_south_africa_outbreak_scale_map|function|6608b5446fc16c9f +create_data_directory|function|5781405b45264703 +get_wahis_rvf_controls_raw|function|1616f0c48da01829 +preprocess_wahis_rvf_controls|function|c2469ccc7d90c840 +preprocess_nasa_weather|function|eab787d86769c2f9 +download_nasa_weather|function|7833150f49a20c75 +calculate_weather_anomalies|function|d0c9f646d334634b +documentation_targets|object|13a110f8518faa3f +submit_modis_ndvi_task_request_continent|function|cd3db23261baafe9 +create_raster_template_plot|function|db738156a3247831 +f|object|9b574eef2d264029 +create_africa_polygon|function|fb2ce70982e38cd3 +tar_cue_upload_aws|object|5dfd2b49ee8a5f13 +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 +augmented_data|stem|a2c64eb0ad1ccb98|c36f979deebc5230|b6821dfb08d361d5|-727079193|data/augmented_data|t19702.879793411s|2c8618a28d6fad70|20480|file|local|vector||augmented_data_d2fea607|235.427|| diff --git a/scripts/download-aws-s3-anomalies.R b/scripts/download-aws-s3-anomalies.R index ec32874..9da4479 100644 --- a/scripts/download-aws-s3-anomalies.R +++ b/scripts/download-aws-s3-anomalies.R @@ -1,21 +1,21 @@ suppressPackageStartupMessages(source("packages.R")) aws_bucket <- Sys.getenv("AWS_BUCKET_ID") -# Weather ------------------------------------------------------------ -message("downloading weather_anomalies_directory") -weather_anomalies_directory <- tar_read(weather_anomalies_directory) -aws_s3_download(path = weather_anomalies_directory, - bucket = aws_bucket , - key = weather_anomalies_directory, - check = TRUE) - -# NDVI ------------------------------------------------------------ -message("downloading ndvi_anomalies_directory") -ndvi_anomalies_directory <- tar_read(ndvi_anomalies_directory) -aws_s3_download(path = ndvi_anomalies_directory, - bucket = aws_bucket , - key = ndvi_anomalies_directory, - check = TRUE) +# # Weather ------------------------------------------------------------ +# message("downloading weather_anomalies_directory") +# weather_anomalies_directory <- tar_read(weather_anomalies_directory) +# aws_s3_download(path = weather_anomalies_directory, +# bucket = aws_bucket , +# key = weather_anomalies_directory, +# check = TRUE) +# +# # NDVI ------------------------------------------------------------ +# message("downloading ndvi_anomalies_directory") +# ndvi_anomalies_directory <- tar_read(ndvi_anomalies_directory) +# aws_s3_download(path = ndvi_anomalies_directory, +# bucket = aws_bucket , +# key = ndvi_anomalies_directory, +# check = TRUE) # Forecasts ------------------------------------------------------------ message("downloading forecasts_anomalies_directory") From 5ad5f45001cb9c0276334f8c33d568ec0028f9a8 Mon Sep 17 00:00:00 2001 From: Emma Mendelsohn Date: Fri, 15 Dec 2023 10:15:31 -0500 Subject: [PATCH 09/10] copy .rprofile from repel --- .Rprofile | 95 ++++++++++++++++++++----------------------------------- 1 file changed, 35 insertions(+), 60 deletions(-) diff --git a/.Rprofile b/.Rprofile index 495daa8..b57f1e8 100644 --- a/.Rprofile +++ b/.Rprofile @@ -1,81 +1,56 @@ -local({ +# Load env vars from any file starting with `.env`. This allows user-specific +# options to be set in `.env_user` (which is .gitignored), and to have both +# encrypted and non-encrypted .env files +load_env <- function(){ for (env_file in list.files(all.files = TRUE, pattern = "^\\.env.*")) { try(readRenviron(env_file), silent = TRUE) } - user_rprof <- Sys.getenv("R_PROFILE_USER", normalizePath("~/.Rprofile", mustWork = FALSE)) - if(interactive() && file.exists(user_rprof)) { - source(user_rprof) +} +load_env() + +# If there is a bucket, cache targets remotely. Otherwise, do so locally. +if(!nzchar(Sys.getenv("TAR_PROJECT"))) { + if(nzchar(Sys.getenv("AWS_BUCKET_ID"))) { + Sys.setenv(TAR_PROJECT = "s3") + } else { + Sys.setenv(TAR_PROJECT = "main") } -}) +} +if(interactive()){ + message(paste("targets project is", Sys.getenv("TAR_PROJECT"))) +} + +# Set options for renv convenience +options( + repos = c(CRAN = "https://cloud.r-project.org", + MILESMCBAIN = "https://milesmcbin.r-universe.dev", + ROPENSCI = "https://ropensci.r-universe.dev"), + renv.config.auto.snapshot = FALSE, ## Attempt to keep renv.lock updated automatically + renv.config.rspm.enabled = TRUE, ## Use RStudio Package manager for pre-built package binaries for linux + renv.config.install.shortcuts = FALSE, ## Use the existing local library to fetch copies of packages for renv + renv.config.cache.enabled = TRUE ## Use the renv build cache to speed up install times +) -# Put the project library *outside* the project -#Sys.setenv(RENV_PATHS_LIBRARY_ROOT = file.path(normalizePath("~/.renv-project-libraries", mustWork = FALSE))) +# Set options for internet timeout +options(timeout = max(300, getOption("timeout"))) +# Use capsule if specified by the user if(Sys.getenv("USE_CAPSULE") %in% c("1", "TRUE", "true")) { if (interactive() && file.exists("renv.lock")) { message("renv library not loaded (found env var USE_CAPSULE=", Sys.getenv("USE_CAPSULE"), "). Use `capsule` functions (see https://github.com/MilesMcBain/capsule)") - if(require(capsule, quietly = TRUE)) { - capsule::whinge() - } else { - message('Install {capsule} with install.packages("capsule", repos = c(mm = "https://milesmcbain.r-universe.dev", getOption("repos")))') - } + capsule::whinge() } } else { source("renv/activate.R") + load_env() # reload project .env files, after renv/activate.R runs renv::load() which reads user's .renviron } -# Use the local user's .Rprofile when interactive. -# Good for keeping local preferences, but not always reproducible. - -if (nzchar( Sys.getenv("TAR_PROJECT"))) { - message(paste0("targets project is '", Sys.getenv("TAR_PROJECT"), "'")) -} else { - message("targets project is default") -} - -options( - repos = c(RSPM = "https://packagemanager.rstudio.com/all/latest", - CRAN = "https://cran.rstudio.com/", - INLA = "https://inla.r-inla-download.org/R/testing"), - - renv.config.auto.snapshot = TRUE, ## Attempt to keep renv.lock updated automatically - renv.config.rspm.enabled = TRUE, ## Use RStudio Package manager for pre-built package binaries - renv.config.install.shortcuts = TRUE, ## Use the existing local library to fetch copies of packages for renv - renv.config.cache.enabled = TRUE, ## Use the renv build cache to speed up install times - renv.config.cache.symlinks = TRUE, ## Keep full copies of packages locally than symlinks to make the project portable in/out of containers - renv.config.install.transactional = FALSE - -) - -# Set maximum allowed total size (in bytes) of global variables for future package. Used to prevent too large exports. -if (Sys.info()[["nodename"]] %in% c("aegypti-reservoir" , "prospero-reservoir")) { - options( - future.globals.maxSize = 4194304000 - ) -} - -# Since RSPM does not provide Mac binaries, always install packages from CRAN -# on mac or windows, even if renv.lock specifies they came from RSPM -if (Sys.info()[["sysname"]] %in% c("Darwin", "Windows")) { - options(renv.config.repos.override = c( - CRAN = "https://cran.rstudio.com/", - INLA = "https://inla.r-inla-download.org/R/testing")) -} else if (Sys.info()[["sysname"]] == "Linux") { - options(renv.config.repos.override = c( - RSPM = "https://packagemanager.rstudio.com/all/latest", - INLA = "https://inla.r-inla-download.org/R/testing")) -} - -# If project packages have conflicts define them here +# If project packages have conflicts define them here so as +# as to manage them across all sessions when building targets if(requireNamespace("conflicted", quietly = TRUE)) { conflicted::conflict_prefer("filter", "dplyr", quiet = TRUE) conflicted::conflict_prefer("count", "dplyr", quiet = TRUE) conflicted::conflict_prefer("select", "dplyr", quiet = TRUE) - conflicted::conflict_prefer("geom_rug", "ggplot2", quiet = TRUE) conflicted::conflict_prefer("set_names", "magrittr", quiet = TRUE) conflicted::conflict_prefer("View", "utils", quiet = TRUE) } - -# Suppress summarize messages -options(dplyr.summarise.inform = FALSE) - From 3e2118b110ee74e72e38d4acd1a1ff0fe68dba74 Mon Sep 17 00:00:00 2001 From: Emma Mendelsohn Date: Fri, 15 Dec 2023 10:18:21 -0500 Subject: [PATCH 10/10] add .Renvignore --- .Renvignore | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 .Renvignore diff --git a/.Renvignore b/.Renvignore new file mode 100644 index 0000000..ac0ae7e --- /dev/null +++ b/.Renvignore @@ -0,0 +1,17 @@ +* +!packages.R +!packages.r +!*.R +!*.r +!R/*.R +!R/*.r +!_targets*.R +!_targets*.r +!vignettes/*.r +!vignettes/*.R +!vignettes/*.Rmd +!vignettes/*.rmd +!reports/*.r +!reports/*.R +!reports/*.Rmd +!reports/*.rmd \ No newline at end of file