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brownag commented on issue ncss-tech/aqp#161

GitHub - Tue, 08/04/2020 - 22:37
brownag commented on issue ncss-tech/aqp#161 Aug 4, 2020 brownag commented Aug 4, 2020

From debug inside of union > o.s [[1]] id soiltaxclasslastupdated mlraoffice series_status family 1 MUSICK 2004-04-20 00:00:00+00 2 established fin…

brownag commented on issue ncss-tech/aqp#161

GitHub - Tue, 08/04/2020 - 22:12
brownag commented on issue ncss-tech/aqp#161 Aug 4, 2020 brownag commented Aug 4, 2020

Yep, this arises from unanticipated and rare? differences in data.table::rbindlist versus plyr::rbind.fill

brownag pushed to master in brownag/CA649

GitHub - Tue, 08/04/2020 - 15:40
brownag pushed to master in brownag/CA649 Aug 4, 2020 1 commit to master

brownag pushed to master in brownag/brownag.github.io

GitHub - Tue, 08/04/2020 - 08:09
brownag pushed to master in brownag/brownag.github.io Aug 4, 2020 1 commit to master
  • a402469 Deploy brownag/brownag.github.io to github.com/brownag/brownag.github…

brownag pushed to master in brownag/brownag.github.io.src

GitHub - Tue, 08/04/2020 - 08:05
brownag pushed to master in brownag/brownag.github.io.src Aug 4, 2020 1 commit to master

Attempts to build a decently-usable, but not quite fetchNASIS-level, gNATSGO SoilProfileCollection for stress testing the S4 methods

Gists - Mon, 08/03/2020 - 19:33
big-SPC-gNATSGO.R library(aqp) library(sf) library(soilDB) library(data.table) library(microbenchmark) # path to gNATSGO Geodatabase dsn <- "~/geodata/gNATSGO/2020/gNATSGO_CONUS.gdb" # This is one of the main bottlenecks (not the only one) to reading out of GDB # chorizon is a pretty large amount of data. Let's save it as a flat file (2.1GB uncompressd) # # in principle, I think all tables could be pre-read out of the GDB and then joined to a # SPC "skeleton" based off of the chorizon data. # # system.time(h <- sf::read_sf(dsn = dsn, layer = "chorizon", # stringsAsFactors = FALSE, as_tibble = FALSE)) # # user system elapsed # # 216.374 5.678 222.533 # # data.table::fwrite(h, file="~/geodata/gNATSGO/2020/horizons.csv") # read the data in from flat file (TODO: consider SQLite storage of all tables and select * from chorizon) starttime <- Sys.time() gnatsgo <- data.table::fread(file = "~/geodata/gNATSGO/2020/horizons.csv") print(Sys.time() - starttime) # Time difference of 9.053402 secs system.time(depths(gnatsgo) <- cokey ~ hzdept_r + hzdepb_r) # user system elapsed # 78.714 1.057 77.307 system.time(l <- get_legend_from_GDB(dsn, "areasymbol != ''")) # user system elapsed # 0.196 0.000 0.195 system.time(m <- get_mapunit_from_GDB(dsn, "muname != ''")) # user system elapsed # 6.555 0.077 6.926 system.time(co <- get_component_from_GDB(dsn = dsn, "compname != ''")) # user system elapsed # 35.453 0.384 36.051 # need chunking # cgd <- soilDB:::.get_cogeomordesc_from_GDB(dsn, co = co) # pmg <- soilDB:::.get_copmgrp_from_GDB(gdb.path, co = co) system.time(site(gnatsgo) <- co) # user system elapsed # 4.334 0.004 3.248 system.time(site(gnatsgo) <- m) # user system elapsed # 3.247 0.000 2.700 system.time(site(gnatsgo) <- l) # user system elapsed # 2.838 0.000 2.499 microbenchmark::microbenchmark({ a <- gnatsgo[round(runif(1, 1, length(gnatsgo))), 1]}, { b <- gnatsgo[round(runif(1, 1, length(gnatsgo))), 1:2]}, { c <- gnatsgo[round(runif(2, 1, length(gnatsgo))), 1]}, { d <- gnatsgo[round(runif(2, 1, length(gnatsgo))), 1:2]}, times = 10) # one or two [random] pedons; one or two horizons [first or first and second] # # Unit: milliseconds # expr min lq mean median uq max neval cld # { a <- gnatsgo[round(runif(1, 1, length(gnatsgo))), 1] } 116.9621 126.7610 131.7065 135.5488 136.5518 139.0037 10 a # { b <- gnatsgo[round(runif(1, 1, length(gnatsgo))), 1:2] } 121.5565 134.4841 135.2277 137.6504 139.2550 141.0407 10 a # { c <- gnatsgo[round(runif(2, 1, length(gnatsgo))), 1] } 117.7989 137.6253 140.2133 138.9760 151.9303 156.8037 10 ab # { d <- gnatsgo[round(runif(2, 1, length(gnatsgo))), 1:2] } 132.5007 135.7209 149.1425 154.1004 155.4409 161.5209 10 b # open-ended j indexing (generally a pretty slow operation) microbenchmark::microbenchmark({foo <- gnatsgo[,1] foo <- NULL}, {foo <- gnatsgo[,2:3] foo <- NULL}, times = 5) # first horizon or second and third horizon, all profiles # Unit: seconds # expr min lq mean median uq max neval cld # { foo <- gnatsgo[, 1] foo <- NULL } 14.97619 15.46312 15.78757 16.09652 16.13384 16.26816 5 a # { foo <- gnatsgo[, 2:3] foo <- NULL } 18.65325 18.68035 18.85315 18.83340 19.03189 19.06688 5 b
Categories: Recent activity

brownag pushed to master in ncss-tech/ncss-tech.github.io

GitHub - Mon, 08/03/2020 - 17:38
brownag pushed to master in ncss-tech/ncss-tech.github.io Aug 3, 2020 1 commit to master
  • 330f85d minor updates to odbc images

brownag commented on issue ncss-tech/aqp#143

GitHub - Sun, 08/02/2020 - 20:22
brownag commented on issue ncss-tech/aqp#143 Aug 2, 2020 brownag commented Aug 2, 2020

aqp Coverage: 64.47% R/aggregateSoilDepth.R: 0.00% R/colorContrastPlot.R: 0.00% R/colorQuantiles.R: 0.00% R/contrastChart.R: 0.00% R/f.noise.R: 0.0…

brownag pushed to master in ncss-tech/aqp

GitHub - Sun, 08/02/2020 - 20:19
brownag pushed to master in ncss-tech/aqp Aug 2, 2020 2 commits to master

brownag pushed to master in brownag/brownag.github.io

GitHub - Sun, 08/02/2020 - 05:01
brownag pushed to master in brownag/brownag.github.io Aug 2, 2020 1 commit to master
  • b3fee23 Deploy brownag/brownag.github.io to github.com/brownag/brownag.github…

brownag pushed to master in brownag/brownag.github.io.src

GitHub - Sun, 08/02/2020 - 04:57
brownag pushed to master in brownag/brownag.github.io.src Aug 2, 2020 1 commit to master

brownag pushed to master in brownag/brownag.github.io

GitHub - Sat, 08/01/2020 - 16:49
brownag pushed to master in brownag/brownag.github.io Aug 1, 2020 1 commit to master
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brownag pushed to master in brownag/brownag.github.io.src

GitHub - Sat, 08/01/2020 - 16:44
brownag pushed to master in brownag/brownag.github.io.src Aug 1, 2020 2 commits to master

brownag pushed to master in ncss-tech/ncss-tech.github.io

GitHub - Fri, 07/31/2020 - 16:48
brownag pushed to master in ncss-tech/ncss-tech.github.io Jul 31, 2020 1 commit to master
  • fb50a49 update driver used for ODBC connection

brownag starred ModelOriented/xspliner

GitHub - Thu, 07/30/2020 - 20:50
brownag starred ModelOriented/xspliner Jul 30, 2020 ModelOriented/xspliner

Explain black box with GLM

R 18 Updated Jul 30

brownag starred r-lib/diffviewer

GitHub - Tue, 07/28/2020 - 21:35
brownag starred r-lib/diffviewer Jul 28, 2020 r-lib/diffviewer

HTML Widget That Shows Differences Between Files

JavaScript 17 Updated Jul 30

brownag starred Robinlovelace/geocompr

GitHub - Tue, 07/28/2020 - 15:33
brownag starred Robinlovelace/geocompr Jul 28, 2020 Robinlovelace/geocompr

Open source book: Geocomputation with R

R 759 1 issue needs help Updated Aug 7

brownag starred dcooley/sfheaders

GitHub - Mon, 07/27/2020 - 17:17
brownag starred dcooley/sfheaders Jul 27, 2020 dcooley/sfheaders

Build sf objects from R and Rcpp

C++ 43 Updated Aug 4

brownag pushed to master in ncss-tech/aqp

GitHub - Mon, 07/27/2020 - 16:11
brownag pushed to master in ncss-tech/aqp Jul 27, 2020 1 commit to master

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