From 5d08a3657edb7dede4d36e3950034babf4260c5f Mon Sep 17 00:00:00 2001 From: thengl Date: Sun, 17 Mar 2019 17:35:09 +0100 Subject: [PATCH] refs fix --- 01-Introduction.Rmd | 2 +- 03-Soil_variables.Rmd | 2 +- 04-Soil_covariates.Rmd | 8 +++-- index.Rmd | 2 +- refs.bib | 72 ++++-------------------------------------- 5 files changed, 15 insertions(+), 71 deletions(-) diff --git a/01-Introduction.Rmd b/01-Introduction.Rmd index c13a170..9139bb4 100755 --- a/01-Introduction.Rmd +++ b/01-Introduction.Rmd @@ -370,7 +370,7 @@ $o$ for organisms (including humans), $r$ is relief, $p$ is parent material or geology and $t$ is time. The Eq. \@ref(eq:clorpt) is the CLORPT model originally presented by Jenny [-@jenny1994factors]. -@MCBRATNEY20033 re-conceptualized and extended the CLORPT model via the +@McBratney2003Geoderma re-conceptualized and extended the CLORPT model via the *“scorpan”* model in which soil properties are modeled as a function of: - (auxiliary) **s**oil classes or properties, diff --git a/03-Soil_variables.Rmd b/03-Soil_variables.Rmd index bb5f401..5a06943 100755 --- a/03-Soil_variables.Rmd +++ b/03-Soil_variables.Rmd @@ -1792,7 +1792,7 @@ TT.plot(class.sys = "USDA.TT", tri.data = tdf, This shows that not all positions in the triangle have the same prior probability. So probably a more sensitive way to estimate uncertainty of converting soil texture classes to fractions would be to run simulations using a density image showing the actual distribution of classes and then, by using the `rpoint` function in the [spatstat package](http://spatstat.org), we could also derive even more realistic conversions from texture-by-hand classes to texture fractions. -## Converting Munsell color codes to other color systems +### Converting Munsell color codes to other color systems In the next example we look at the Munsell color codes and conversion algorithms from a code to RGB and other color spaces. Munsell color codes can be matched with RGB values via the [Munsell color codes conversion table](http://www.cis.rit.edu/mcsl/online/munsell.php). You can load a table with 2350 entries from the book repository: diff --git a/04-Soil_covariates.Rmd b/04-Soil_covariates.Rmd index 71d3f07..36d2794 100755 --- a/04-Soil_covariates.Rmd +++ b/04-Soil_covariates.Rmd @@ -6,8 +6,12 @@ ### Types of soil covariates -Soils (and vegetation + ecosystems) form under complex interactions between climate, living organism and anthropogenic influences, modified by relief and hydrological processes and operating over long periods of time. -This has been clearly identified first by @jenny1994factors with his CLORPT factors of soil formation and subsequently extended by @MCBRATNEY20033 with the SCORPAN formulation (see section \@ref(soil-mapping-theory)). +Soils (and vegetation + ecosystems) form under complex interactions between +climate, living organism and anthropogenic influences, modified by relief and +hydrological processes and operating over long periods of time. +This has been clearly identified first by @jenny1994factors with his CLORPT +factors of soil formation and subsequently extended by @McBratney2003Geoderma +with the SCORPAN formulation (see section \@ref(soil-mapping-theory)). The following groups of covariates are commonly considered for use in Predictive Soil Mapping: diff --git a/index.Rmd b/index.Rmd index cb49327..4826b9f 100755 --- a/index.Rmd +++ b/index.Rmd @@ -93,7 +93,7 @@ learning techniques to fit models for the purpose of producing spatial and/or spatiotemporal predictions of soil variables, i.e. maps of soil properties and classes at different resolutions. It is a multidisciplinary field combining statistics, data science, soil science, physical geography, remote sensing, -geoinformation science and a number of other sciences [@Scul01; @MCBRATNEY20033; @Henderson2004Geoderma; @Boettinger2010Springer; @Zhu2015PSM]. *Predictive Soil Mapping with R* +geoinformation science and a number of other sciences [@Scul01; @McBratney2003Geoderma; @Henderson2004Geoderma; @Boettinger2010Springer; @Zhu2015PSM]. *Predictive Soil Mapping with R* is about understanding the main concepts behind soil mapping, mastering R packages that can be used to produce high quality soil maps, and about optimizing all processes involved so that production costs can also be reduced. diff --git a/refs.bib b/refs.bib index 3b58a23..d518f01 100755 --- a/refs.bib +++ b/refs.bib @@ -122,7 +122,6 @@ @Book{Adhikari2013 Author = {Adhikari, Kabindra and Kheir, Rania Bou and Greve, Mette B. and B{\o}cher, Peder K. and Malone, Brendan P. and Minasny, Budiman and McBratney, Alex B. and Greve, Mogens H.}, Year = {2013}, Volume = {in press}, - Doi = {10.2136/sssaj2012.0275}, Journal = {Soil Sci. Soc. Am. J.}, Pages = {--} @@ -136,7 +135,6 @@ @Article{Adhikari2014101 Number = {0}, Pages = {101 - 113}, Volume = {214/215}, - Doi = {10.1016/j.geoderma.2013.09.023}, ISSN = {0016-7061} } @@ -149,7 +147,6 @@ @Article{agarwal2002zero Number = {4}, Pages = {341--355}, Volume = {9}, - Publisher = {Springer} } @@ -159,7 +156,6 @@ @Book{central2014world Publisher = {Claitors Pub Division}, Year = {2014}, Series = {World Factbook}, - ISBN = {9781598047424} } @@ -180,7 +176,6 @@ @Article{ahmad2010estimating Number = {1}, Pages = {69--80}, Volume = {33}, - Publisher = {Elsevier} } @@ -198,12 +193,10 @@ @Article{Aksoy2016 Author = {Aksoy, Ece and Yigini, Yusuf and Montanarella, Luca}, Journal = {PLoS ONE}, Year = {2016}, - Month = {03}, Number = {3}, Pages = {1-17}, Volume = {11}, - Doi = {10.1371/journal.pone.0152098}, Publisher = {Public Library of Science} } @@ -222,7 +215,6 @@ @Article{DailyNews2014Tanzania Author = {{AllAfrica Global Media}}, Journal = {AllAfrica.com}, Year = {2014}, - Month = {Sept}, Pages = {2} } @@ -242,7 +234,6 @@ @Book{AGRA2014 Author = {{Alliance for a Green Revolution in Africa (AGRA)}}, Publisher = {Alliance for a Green Revolution in Africa (AGRA)}, Year = {2014}, - Address = {Nairobi, Kenya}, Series = {Africa agriculture status reports} } @@ -266,7 +257,6 @@ @InProceedings{AmengualToral2004 Pages = {203-212}, Series = {Presented at the Society of Photo-Optical Instrumentation Engineers (SPIE) Conference}, Volume = {5471}, - Doi = {10.1117/12.556419} } @@ -286,7 +276,6 @@ @Article{antonic2003spatial Number = {2}, Pages = {363--371}, Volume = {170}, - Publisher = {Elsevier} } @@ -312,11 +301,11 @@ @InCollection{Arro01 } @book{arrouays2014globalsoilmap, - title={{GlobalSoilMap: basis of the global spatial soil information system}}, - author={Arrouays, Dominique and McKenzie, Neil and {de Forges}, Anne Richer and Hempel, Jon and McBratney, Alex B}, - year={2014}, - publisher={CRC press}, - address={Boca Raton, USA} + Title={{GlobalSoilMap: basis of the global spatial soil information system}}, + Author={Arrouays, D. and McKenzie, N. and {de Forges}, A.R. and Hempel, J. and McBratney, A.B.}, + Year={2014}, + Publisher={CRC press}, + Address={Boca Raton, USA} } @InCollection{Arrouays201493, @@ -329,7 +318,6 @@ @InCollection{Arrouays201493 Pages = {93 - 134}, Series = {Advances in Agronomy}, Volume = {125}, - Doi = {10.1016/B978-0-12-800137-0.00003-0}, ISSN = {0065-2113} } @@ -370,7 +358,6 @@ @Article{bardossy2013interpolation Number = {8}, Pages = {4545--4565}, Volume = {49}, - Publisher = {Wiley Online Library} } @@ -389,7 +376,6 @@ @InProceedings{Baade2014IEE Year = {2014}, Month = {July}, Pages = {4327-4330}, - Doi = {10.1109/IGARSS.2014.6947447} } @@ -408,7 +394,6 @@ @InProceedings{Balabio2014 Author = {Cristiano Ballabio and Luca Montanarella and Panos Panagos}, Booktitle = {ASA, CSSA, \& SSSA International Annual Meeting}, Year = {2014}, - Address = {Long Beach, CA}, Month = {November}, Publisher = {ASA, CSSA, \& SSSA}, @@ -422,7 +407,6 @@ @Article{Ballabio2016110 Year = {2016}, Pages = {110 - 123}, Volume = {261}, - Doi = {10.1016/j.geoderma.2015.07.006}, ISSN = {0016-7061} } @@ -449,11 +433,9 @@ @Article{Rainer2010 Author = {Baritz, Rainer and Seufert, Guenther and Montanarella, Luca and {Van Ranst}, Eric}, Journal = {Forest Ecology and Management}, Year = {2010}, - Month = {06/2010}, Pages = {262 - 277}, Volume = {260}, - Doi = {10.1016/j.foreco.2010.03.025}, ISSN = {03781127} } @@ -463,12 +445,10 @@ @Article{Barre2008 Author = {Barr\'{e}, H.M.J. and Duesmann, B. and Kerr, Y.H.}, Journal = {Geoscience and Remote Sensing, IEEE Transactions on}, Year = {2008}, - Month = {march}, Number = {3}, Pages = {587-593}, Volume = {46}, - Doi = {10.1109/TGRS.2008.916264}, ISSN = {0196-2892} } @@ -552,7 +532,6 @@ @Article{batjes1997possibilities Number = {2}, Pages = {161--173}, Volume = {3}, - Publisher = {Wiley Online Library} } @@ -563,7 +542,6 @@ @Article{BauerMarschallinger201484 Year = {2014}, Pages = {84 - 93}, Volume = {72}, - Doi = {10.1016/j.cageo.2014.07.005}, ISSN = {0098-3004} } @@ -595,7 +573,6 @@ @Article{Beaudette2013CompGeo Number = {0}, Pages = {258 - 268}, Volume = {52}, - Doi = {10.1016/j.cageo.2012.10.020}, ISSN = {0098-3004} } @@ -693,7 +670,6 @@ @Article{ben2009using Year = {2009}, Pages = {S38--S55}, Volume = {113}, - Publisher = {Elsevier} } @@ -704,7 +680,6 @@ @Article{berhongaray2013ipcc Year = {2013}, Pages = {241--245}, Volume = {181}, - Publisher = {Elsevier} } @@ -722,12 +697,10 @@ @Article{Biau2016 Author = {Biau, G{\'e}rard and Scornet, Erwan}, Journal = {TEST}, Year = {2016}, - Month = {Jun}, Number = {2}, Pages = {197--227}, Volume = {25}, - Day = {01}, Doi = {10.1007/s11749-016-0481-7}, ISSN = {1863-8260}, @@ -887,11 +860,9 @@ @InCollection{Bouma1989S Author = {Bouma, J.}, Booktitle = {{Proceedings of a symposium organized by the International Society of Soil Science}}, Year = {1989}, - Address = {Wageningen}, Editor = {Bouma, J. and Bregt, A.K.}, Pages = {3-13}, - Publisher = {Wageningen University} } @@ -903,7 +874,6 @@ @Article{bouma1998exploring Number = {1}, Pages = {43--59}, Volume = {86}, - Publisher = {Elsevier} } @@ -915,7 +885,6 @@ @Article{breiman2001random Number = {1}, Pages = {5--32}, Volume = {45}, - Publisher = {Springer} } @@ -927,7 +896,6 @@ @Article{Brei02 Number = {2}, Pages = {123--140}, Volume = {24}, - Publisher = {Springer} } @@ -946,7 +914,6 @@ @Article{breiman2001statistical Number = {3}, Pages = {199--231}, Volume = {16}, - Publisher = {Institute of Mathematical Statistics} } @@ -958,7 +925,6 @@ @Article{Brennan1998 Number = {17-18}, Pages = {2683-2689}, Volume = {29}, - Doi = {10.1080/00103629809370143}, Publisher = {Taylor \& Francis} } @@ -968,7 +934,6 @@ @InProceedings{Brenning2008SAGA2 Author = {Brenning, A.}, Booktitle = {SAGA --- Seconds Out}, Year = {2008}, - Address = {Hamburg}, Editor = {B\"{o}hner, J. and Blaschke, T. and Montanarella, L.}, Pages = {23--32}, @@ -983,7 +948,6 @@ @InProceedings{Brenning2012 Year = {2012}, Month = {July}, Pages = {5372-5375}, - Doi = {10.1109/IGARSS.2012.6352393}, ISSN = {2153-6996} } @@ -995,7 +959,6 @@ @Article{brevik2016soil Year = {2016}, Pages = {256--274}, Volume = {264}, - Publisher = {Elsevier} } @@ -1013,11 +976,9 @@ @Article{Brown2007DUE Author = {Brown, James D. and Heuvelink, Gerard B. M.}, Journal = {Comput. Geosci.}, Year = {2007}, - Month = {February}, Pages = {172--190}, Volume = {33}, - Doi = {10.1016/j.cageo.2006.06.015}, Issue = {2}, Numpages = {19} @@ -1029,8 +990,6 @@ @InCollection{Brow01 Booktitle = {Encyclopedia of Hydrological Sciences}, Publisher = {John Wiley \& Sons, Ltd}, Year = {2006}, - - Keywords = {uncertainty analysis soil hydrology model uncertainty input uncertainty Monte Carlo simulation} } @Article{Brown2014JSS, @@ -4368,7 +4327,7 @@ @InProceedings{McBratney2006WCSS Publisher = {IUSS} } -@Article{MCBRATNEY20033, +@Article{McBratney2003Geoderma, Title = {On digital soil mapping}, Author = {McBratney, A.B and Mendon\c{c}a Santos, M.L and Minasny, B}, Journal = {Geoderma}, @@ -4389,16 +4348,6 @@ @Article{McBratney1998 Volume = {50} } -@Article{McBratney2003Geoderma, - Title = {{On digital soil mapping}}, - Author = {McBratney, A.~B. and Mendo\c{c}a Santos, M.~L. and Minasny, B.}, - Journal = {Geoderma}, - Year = {2003}, - Number = {1-2}, - Pages = {3-52}, - Volume = {117} -} - @Article{McBratney2002Geoderma, Title = {From pedotransfer functions to soil inference systems}, Author = {McBratney, A.~B. and Minasny, B. and Cattle, S.R. and Vervoort, R.W.}, @@ -6888,7 +6837,6 @@ @Article{verburg2011challenges Number = {2}, Pages = {974--989}, Volume = {17}, - Publisher = {Wiley Online Library} } @@ -6909,7 +6857,6 @@ @Article{Veronesi2012STR Year = {2012}, Pages = {111-118}, Volume = {124}, - Doi = {10.1016/j.still.2012.05.009} } @@ -6919,7 +6866,6 @@ @Article{ViscarraRossel2014GCB Journal = {Global Change Biology}, Year = {2014}, Pages = {n/a--n/a}, - Doi = {10.1111/gcb.12569}, ISSN = {1365-2486} } @@ -6929,10 +6875,8 @@ @Book{TERN2014 Author = {Viscarra Rossel, Raphael and Chen, Charlie and Grundy, Mike and Searle, Ross and Clifford, David and Odgers, Nathan and Holmes, Karen and Griffin, Ted and Liddicoat, Craig and Kidd, Darren}, Publisher = {CSIRO}, Year = {2014}, - Address = {Canberra, Australia}, Series = {Data Collection}, - Doi = {10.4225/08/547523BB0801A} } @@ -6941,12 +6885,10 @@ @Article{Visser2015 Author = {Visser, Marco D. and McMahon, Sean M. and Merow, Cory and Dixon, Philip M. and Record, Sydne and Jongejans, Eelke}, Journal = {PLoS Comput Biol}, Year = {2015}, - Month = {03}, Number = {3}, Pages = {e1004140}, Volume = {11}, - Doi = {10.1371/journal.pcbi.1004140}, Publisher = {Public Library of Science} } @@ -6965,7 +6907,6 @@ @Article{Voosen2009NYT Author = {Voosen, P.}, Journal = {New York Times}, Year = {2009}, - Month = {August}, Pages = {2} } @@ -7032,7 +6973,6 @@ @Article{wosten2013soil Year = {2013}, Pages = {79--86}, Volume = {195}, - Doi = {10.1016/j.geoderma.2012.11.021}, Publisher = {Elsevier} }