envirometrix / predictivesoilmapping Goto Github PK

A tertiary source is an index or textual consolidation of primary and secondary sources. Some tertiary sources are not to be used for academic research, unless they can also be used as secondary sources, or to find other sources.

We need to rewrite some sections that represent subjective opinions and try to focus on only summarizing primary / secondary sources. This means that we should avoid using "we" i.e. opinions as much as possible and just review literature, main processing steps and possibilities. In principle, all submitted chapters should also follow closely the five pillars of Wikipedia, especially: Verifiability, Reproducibility, No original research, Neutral point of view, Good faith, No conflict of interest, and no personal attacks.

I am working on SoilGrid and following this procedure,

https://envirometrix.github.io/PredictiveSoilMapping/software.html#Rstudio

session_info()

• Session info ---------------------------------------------------------------------------
  setting value
  version R version 3.5.3 (2019-03-11)
  os Windows >= 8 x64
  system x86_64, mingw32
  ui RStudio
  language (EN)
  collate English_United Kingdom.1252
  ctype English_United Kingdom.1252
  tz Asia/Taipei
  date 2019-04-23

• Packages -------------------------------------------------------------------------------
  ! package * version date lib source
  acepack 1.4.1 2016-10-29 [1] CRAN (R 3.5.2)
  aqp * 1.17 2019-01-03 [1] CRAN (R 3.5.2)
  V assertthat 0.2.0 2019-03-21 [1] CRAN (R 3.5.3)
  automap 1.0-14 2013-08-29 [1] CRAN (R 3.5.3)
  R backports 1.1.3 [1]
  base64enc 0.1-3 2015-07-28 [1] CRAN (R 3.5.0)
  bindr 0.1.1 2018-03-13 [1] CRAN (R 3.5.1)
  bindrcpp 0.2.2 2018-03-29 [1] CRAN (R 3.5.1)
  bitops 1.0-6 2013-08-17 [1] CRAN (R 3.5.0)
  V callr 3.1.1 2019-03-15 [1] CRAN (R 3.5.3)
  caret * 6.0-83 2019-04-18 [1] CRAN (R 3.5.3)
  R caTools 1.17.1.1 [1]
  checkmate 1.9.1 2019-01-15 [1] CRAN (R 3.5.2)
  class * 7.3-15 2019-01-01 [2] CRAN (R 3.5.3)
  classInt 0.3-1 2018-12-18 [1] CRAN (R 3.5.2)
  V cli 1.0.1 2019-03-19 [1] CRAN (R 3.5.3)
  cluster 2.0.7-1 2018-04-13 [2] CRAN (R 3.5.3)
  codetools 0.2-16 2018-12-24 [2] CRAN (R 3.5.3)
  colorRamps 2.3 2012-10-29 [1] CRAN (R 3.5.2)
  R colorspace * 1.4-0 [1]
  crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.1)
  curl 3.3 2019-01-10 [1] CRAN (R 3.5.2)
  R data.table 1.12.0 [1]
  DBI 1.0.0 2018-05-02 [1] CRAN (R 3.5.1)
  desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.2)
  R devtools * 2.0.1 [1]
  digest 0.6.18 2018-10-10 [1] CRAN (R 3.5.1)
  dismo * 1.1-4 2017-01-09 [1] CRAN (R 3.5.2)
  doParallel * 1.0.14 2018-09-24 [1] CRAN (R 3.5.3)
  R dplyr 0.7.8 [1]
  R e1071 1.7-0.1 [1]
  evd 2.3-3 2018-04-25 [1] CRAN (R 3.5.3)
  fasterize * 1.0.0 2018-03-22 [1] CRAN (R 3.5.3)
  FNN 1.1.3 2019-02-15 [1] CRAN (R 3.5.2)
  foreach * 1.4.4 2017-12-12 [1] CRAN (R 3.5.3)
  foreign 0.8-71 2018-07-20 [2] CRAN (R 3.5.3)
  Formula * 1.2-3 2018-05-03 [1] CRAN (R 3.5.2)
  R fs 1.2.6 [1]
  gam * 1.16 2018-07-20 [1] CRAN (R 3.5.3)
  gdata 2.18.0 2017-06-06 [1] CRAN (R 3.5.2)
  generics 0.0.2 2018-11-29 [1] CRAN (R 3.5.2)
  V ggplot2 * 3.1.0 2019-04-07 [1] CRAN (R 3.5.3)
  ggRandomForests * 2.0.1 2016-09-07 [1] CRAN (R 3.5.3)
  glmnet * 2.0-16 2018-04-02 [1] CRAN (R 3.5.3)
  R glue 1.3.0 [1]
  gower 0.2.0 2019-03-07 [1] CRAN (R 3.5.3)
  gplots * 3.0.1.1 2019-01-27 [1] CRAN (R 3.5.3)
  gridExtra 2.3 2017-09-09 [1] CRAN (R 3.5.2)
  GSIF * 0.5-5 2019-01-04 [1] CRAN (R 3.5.2)
  R gstat 1.1-6 [1]
  V gtable 0.2.0 2019-03-25 [1] CRAN (R 3.5.3)
  gtools 3.8.1 2018-06-26 [1] CRAN (R 3.5.2)
  h2o * 3.22.1.1 2019-01-10 [1] CRAN (R 3.5.3)
  h2oEnsemble * 0.2.1 2019-04-23 [1] local
  hexbin * 1.27.2 2018-01-15 [1] CRAN (R 3.5.1)
  Hmisc * 4.2-0 2019-01-26 [1] CRAN (R 3.5.2)
  htmlTable 1.13.1 2019-01-07 [1] CRAN (R 3.5.2)
  htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.5.1)
  htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.5.1)
  intamap * 1.4-9 2018-05-02 [1] CRAN (R 3.5.3)
  intervals 0.15.1 2015-08-27 [1] CRAN (R 3.5.2)
  ipred 0.9-8 2018-11-05 [1] CRAN (R 3.5.3)
  iterators * 1.0.10 2018-07-13 [1] CRAN (R 3.5.3)
  jsonlite 1.6 2018-12-07 [1] CRAN (R 3.5.2)
  KernSmooth 2.23-15 2015-06-29 [2] CRAN (R 3.5.3)
  R knitr 1.21 [1]
  R lattice * 0.20-38 [2]
  latticeExtra 0.6-28 2016-02-09 [1] CRAN (R 3.5.2)
  lava 1.6.5 2019-02-12 [1] CRAN (R 3.5.3)
  R lazyeval 0.2.1 [1]
  lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.5.1)
  magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.2)
  MASS 7.3-51.1 2018-11-01 [2] CRAN (R 3.5.3)
  Matrix * 1.2-15 2018-11-01 [2] CRAN (R 3.5.3)
  matrixStats * 0.54.0 2018-07-23 [1] CRAN (R 3.5.3)
  mda * 0.4-10 2017-11-02 [1] CRAN (R 3.5.3)
  memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.2)
  mnormt 1.5-5 2016-10-15 [1] CRAN (R 3.5.2)
  ModelMetrics 1.2.2 2018-11-03 [1] CRAN (R 3.5.3)
  munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.1)
  R mvtnorm 1.0-8 [1]
  nlme 3.1-137 2018-04-07 [2] CRAN (R 3.5.3)
  nnet * 7.3-12 2016-02-02 [2] CRAN (R 3.5.3)
  nnls * 1.4 2012-03-19 [1] CRAN (R 3.5.2)
  pillar 1.3.1 2018-12-15 [1] CRAN (R 3.5.2)
  pixmap 0.4-11 2011-07-19 [1] CRAN (R 3.5.2)
  V pkgbuild 1.0.2 2019-03-20 [1] CRAN (R 3.5.3)
  pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.5.1)
  pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.2)
  plotKML * 0.5-9 2019-01-09 [1] CRAN (R 3.5.2)
  V plotrix 3.7-4 2019-04-07 [1] CRAN (R 3.5.3)
  plyr * 1.8.4 2016-06-08 [1] CRAN (R 3.5.1)
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  R processx 3.2.1 [1]
  prodlim 2018.04.18 2018-04-18 [1] CRAN (R 3.5.3)
  ps 1.3.0 2018-12-21 [1] CRAN (R 3.5.2)
  psych * 1.8.12 2019-01-12 [1] CRAN (R 3.5.2)
  R purrr 0.3.0 [1]
  quantregForest * 1.3-7 2017-12-19 [1] CRAN (R 3.5.3)
  V R6 2.3.0 2019-02-14 [1] CRAN (R 3.5.3)
  randomForest * 4.6-14 2018-03-25 [1] CRAN (R 3.5.3)
  R randomForestSRC * 2.8.0 [1]
  ranger * 0.11.2 2019-03-07 [1] CRAN (R 3.5.3)
  raster * 2.8-19 2019-01-30 [1] CRAN (R 3.5.2)
  RColorBrewer * 1.1-2 2014-12-07 [1] CRAN (R 3.5.2)
  R Rcpp 1.0.0 [1]
  R RCurl 1.95-4.11 [1]
  recipes 0.1.5 2019-03-21 [1] CRAN (R 3.5.3)
  V remotes 2.0.2 2019-04-10 [1] CRAN (R 3.5.3)
  reshape * 0.8.8 2018-10-23 [1] CRAN (R 3.5.3)
  reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.5.3)
  R rgdal * 1.3-6 [1]
  D rJava * 0.9-11 2019-03-29 [1] CRAN (R 3.5.3)
  R rlang 0.3.1 [1]
  ROCR * 1.0-7 2015-03-26 [1] CRAN (R 3.5.3)
  rpart 4.1-13 2018-02-23 [2] CRAN (R 3.5.3)
  rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.1)
  RSAGA 1.3.0 2018-11-12 [1] CRAN (R 3.5.2)
  V rstudioapi 0.9.0 2019-03-19 [1] CRAN (R 3.5.3)
  scales * 1.0.0 2018-08-09 [1] CRAN (R 3.5.1)
  sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.2)
  shapefiles 0.7 2013-01-26 [1] CRAN (R 3.5.2)
  snow * 0.4-3 2018-09-14 [1] CRAN (R 3.5.2)
  snowfall * 1.84-6.1 2015-10-14 [1] CRAN (R 3.5.2)
  soiltexture * 1.5.1 2018-09-20 [1] CRAN (R 3.5.2)
  sp * 1.3-1 2018-06-05 [1] CRAN (R 3.5.1)
  spacetime 1.2-2 2018-07-17 [1] CRAN (R 3.5.2)
  R stringi 1.2.4 [1]
  V stringr 1.3.1 2019-02-10 [1] CRAN (R 3.5.3)
  SuperLearner * 2.0-24 2018-08-11 [1] CRAN (R 3.5.3)
  survival * 2.43-3 2018-11-26 [2] CRAN (R 3.5.3)
  R tibble 2.0.1 [1]
  R tidyr 0.8.2 [1]
  tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.1)
  timeDate 3043.102 2018-02-21 [1] CRAN (R 3.5.2)
  units 0.6-2 2018-12-05 [1] CRAN (R 3.5.2)
  R usethis * 1.4.0 [1]
  viridis * 0.5.1 2018-03-29 [1] CRAN (R 3.5.1)
  viridisLite * 0.3.0 2018-02-01 [1] CRAN (R 3.5.1)
  withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.1)
  V xfun 0.4 2019-04-02 [1] CRAN (R 3.5.3)
  xgboost * 0.82.1 2019-03-11 [1] CRAN (R 3.5.3)
  R XML 3.98-1.17 [1]
  xts 0.11-2 2018-11-05 [1] CRAN (R 3.5.2)
  R zoo 1.8-4 [1]

[1] D:/UserData/My Documents/R/win-library/3.5
[2] C:/Program Files/R/R-3.5.3/library

V -- Loaded and on-disk version mismatch.
D -- DLL MD5 mismatch, broken installation.
R -- Package was removed from disk.

I got this error,
om.rk
Variable : om
Minium value : 1
Maximum value : 17
Size : 153
Error in plotKML::parse_proj4(p4s = rgdal::CRSargs(CRS(proj4string(object@observed))), :
lazy-load database 'D:/UserData/My Documents/R/win-library/3.5/stringr/R/stringr.rdb' is corrupt
In addition: Warning messages:
1: In plotKML::parse_proj4(p4s = rgdal::CRSargs(CRS(proj4string(object@observed))), :
restarting interrupted promise evaluation
2: In plotKML::parse_proj4(p4s = rgdal::CRSargs(CRS(proj4string(object@observed))), :
internal error -3 in R_decompress1
Error in new("standardGeneric", .Data = function (object) :
object 'prj' not found

plotKML(om.rk)
Error in plotKML::parse_proj4(p4s = rgdal::CRSargs(CRS(proj4string(object@observed))), :
lazy-load database 'D:/UserData/My Documents/R/win-library/3.5/stringr/R/stringr.rdb' is corrupt
In addition: Warning messages:
1: In plotKML::parse_proj4(p4s = rgdal::CRSargs(CRS(proj4string(object@observed))), :
restarting interrupted promise evaluation
2: In plotKML::parse_proj4(p4s = rgdal::CRSargs(CRS(proj4string(object@observed))), :
internal error -3 in R_decompress1
Error in .local(object, ...) : object 'prj' not found

Hi everyone, in this moment i'm working with de GSIF package for calculate soil organic carbon stock, but I had trouble found a function that would allow me to plot the results of the mpspline function. In the ithir package there was a plot_ea_splines function and my question is, is there a similar function in the package GSIF for plot the results of mpspline $var.std?.

It would be good to have a PDF of the book one version in BW and one in color. Is there a programmatic way to convert all color PDFs and PNGs to gray-scale?

Master does not deploy output docs to gh-pages any more hence the HTML version is now out of date. Probably some setting problem in: https://github.com/Envirometrix/PredictiveSoilMapping/blob/master/deploy.sh

It would be very useful to have Travis and all the automated checking functionality as in your Geocomputation for R book. Let me know if I need to make an account or similar.

We need a PDF version of the book following the Lulu specs, that is:

• US Letter, 8.5 x 11in,
• Perfect Bound Paperback,