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| Package: fields | ||
| Version: 12.0 | ||
| Date: 2021-05-06 | ||
| Title: Tools for Spatial Data | ||
| Authors@R: c( person("Douglas", "Nychka", role = c("aut", "cre"), | ||
| email = "douglasnychka@gmail.com"), | ||
| person("Reinhard", "Furrer", role = c("aut"), | ||
| email = "reinhard.furrer@math.uzh.ch"), | ||
| person("John", "Paige", role = c("aut"), | ||
| email = "paigejo@uw.edu"), | ||
| person("Stephan", "Sain", role = "aut", | ||
| email = "sainsr2@gmail.com"), | ||
| person("Florian", "Gerber", role = "aut", | ||
| email = "flora.fauna.gerber@gmail.com"), | ||
| person("Matthew", "Iverson", role = "aut", | ||
| email = "miverson@mymail.mines.edu"), | ||
| person("University Corporation for Atmospheric Research", | ||
| role="cph", email="nychka@ucar.edu") | ||
| ) | ||
| Maintainer: Douglas Nychka <douglasnychka@gmail.com> | ||
| Description: For curve, surface and function fitting with an emphasis | ||
| on splines, spatial data, geostatistics, and spatial statistics. The major methods | ||
| include cubic, and thin plate splines, Kriging, and compactly supported | ||
| covariance functions for large data sets. The splines and Kriging methods are | ||
| supported by functions that can determine the smoothing parameter | ||
| (nugget and sill variance) and other covariance function parameters by cross | ||
| validation and also by restricted maximum likelihood. For Kriging | ||
| there is an easy to use function that also estimates the correlation | ||
| scale (range parameter). A major feature is that any covariance function | ||
| implemented in R and following a simple format can be used for | ||
| spatial prediction. There are also many useful functions for plotting | ||
| and working with spatial data as images. This package also contains | ||
| an implementation of sparse matrix methods for large spatial data | ||
| sets and currently requires the sparse matrix (spam) package. Use | ||
| help(fields) to get started and for an overview. The fields source | ||
| code is deliberately commented and provides useful explanations of | ||
| numerical details as a companion to the manual pages. The commented | ||
| source code can be viewed by expanding the source code version | ||
| and looking in the R subdirectory. The reference for fields can be generated | ||
| by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development | ||
| of this package was supported in part by the National Science Foundation Grant | ||
| 1417857, the National Center for Atmospheric Research, and Colorado School of Mines. | ||
| See the Fields URL | ||
| for a vignette on using this package and some background on spatial statistics. | ||
| License: GPL (>= 2) | ||
| URL: https://github.com/NCAR/Fields | ||
| Depends: R (>= 3.0), methods, spam, viridis | ||
| Imports: maps | ||
| NeedsCompilation: yes | ||
| Repository: CRAN | ||
| Packaged: 2021-05-06 20:45:03 UTC; nychka | ||
| Author: Douglas Nychka [aut, cre], | ||
| Reinhard Furrer [aut], | ||
| John Paige [aut], | ||
| Stephan Sain [aut], | ||
| Florian Gerber [aut], | ||
| Matthew Iverson [aut], | ||
| University Corporation for Atmospheric Research [cph] |
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| All R code and documentation in this package (fields) is licensed | ||
| under the terms of the GPL license. | ||
|
|
||
| NOTE: | ||
|
|
||
| The sparse matrix methods used in fields are supported by the package | ||
| spam. The spam package contains some FORTRAN routines where some | ||
| licensing issues are unclear. Please refer to the spam license | ||
| information for details. Note that many functions in fields e.g. Tps, | ||
| Krig, all the graphical functions, function indepedently of the spam package so much | ||
| of fields will be functional under a GPL license. | ||
|
|
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| exportPattern("^[^\\.]") | ||
|
|
||
| importFrom("grDevices", "chull", "col2rgb", "colors", "palette", "rgb", | ||
| "trans3d") | ||
| importFrom("graphics", "abline", "arrows", "axis", "box", "boxplot", | ||
| "contour", "hist", "lines", "locator", "matlines", | ||
| "matplot", "mtext", "pairs", "par", "persp", "plot", | ||
| "points", "polygon", "rect", "segments", "text", "title") | ||
| importFrom("stats", "D", "approx", "coef", "cor", "dist", "fft", "mad", | ||
| "median", "optim", "optimize", "predict", "quantile", | ||
| "rnorm", "sd", "var","qchisq","pnorm") | ||
| importFrom("utils", "object.size") | ||
| importFrom("maps","map") | ||
| importFrom("viridis","viridis") | ||
| importFrom("stats", "qnorm") | ||
|
|
||
| S3method("[",spatialDesign) | ||
| S3method(coef, Krig) | ||
| S3method(fitted, Krig) | ||
| S3method(image, plot) | ||
| S3method(image, smooth) | ||
| S3method(print, Krig) | ||
| S3method(print, mKrig) | ||
| S3method(print,spatialDesign) | ||
| S3method(print,spatialProcess) | ||
| S3method(print,sreg) | ||
| S3method(print,qsreg) | ||
| S3method(print,summary.Krig) | ||
| S3method(print,summarySpatialDesign) | ||
| S3method(print,mKrigSummary) | ||
| S3method(print,spatialProcessSummary) | ||
| S3method(print,summary.sreg) | ||
| S3method(summary,Krig) | ||
| S3method(summary,sreg) | ||
| S3method(summary,ncdf) | ||
| S3method(summary,qsreg) | ||
| S3method(summary,spatialDesign) | ||
| S3method(summary,spatialProcess) | ||
| S3method(summary,mKrig) | ||
| S3method(plot,Krig) | ||
| S3method(plot,spatialProcess) | ||
| S3method(plot,surface) | ||
| S3method(plot,spatialDesign) | ||
| S3method(plot,sreg) | ||
| S3method(plot,qsreg) | ||
| S3method(plot,vgram.matrix) | ||
| S3method(plot,vgram) | ||
| S3method(surface,Krig) | ||
| S3method(surface,mKrig) | ||
| S3method(surface,default) | ||
| S3method(predict,fastTps) | ||
| S3method(predict,interp.surface) | ||
| S3method(predict,Krig) | ||
| S3method(predict,mKrig) | ||
| S3method(predict,qsreg) | ||
| S3method(predict,sreg) | ||
| S3method(predict,surface) | ||
| S3method(predict,surface.default) | ||
| S3method(predict,Tps) | ||
| S3method(predictSE,Krig) | ||
| S3method(predictSE,mKrig) | ||
| S3method(predictSurface,default) | ||
| S3method(predictSurface,fastTps) | ||
| S3method(predictSurface,Krig) | ||
| S3method(predictSurface,mKrig) | ||
| S3method(predictSurfaceSE,default) | ||
| useDynLib(fields,.registration=TRUE) | ||
|
|
||
| import("spam", "methods") | ||
|
|
||
|
|
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| # fields is a package for analysis of spatial data written for | ||
| # the R software environment . | ||
| # Copyright (C) 2018 | ||
| # University Corporation for Atmospheric Research (UCAR) | ||
| # Contact: Douglas Nychka, nychka@ucar.edu, | ||
| # National Center for Atmospheric Research, PO Box 3000, Boulder, CO 80307-3000 | ||
| # | ||
| # This program is free software; you can redistribute it and/or modify | ||
| # it under the terms of the GNU General Public License as published by | ||
| # the Free Software Foundation; either version 2 of the License, or | ||
| # (at your option) any later version. | ||
| # This program is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with the R software environment if not, write to the Free Software | ||
| # Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA | ||
| # or see http://www.r-project.org/Licenses/GPL-2 | ||
| "BD" <- structure(list(KCl = c(30, 30, 20, 50, 25, | ||
| 10, 40, 15, 50, 10, 20, 45, 50, 35, 40, 35, 30, 15, 40, 30, | ||
| 10, 50, 20, 10, 25, 45, 30, 25, 45, 10, 45, 10, 30, 30, 20, | ||
| 50, 10, 40, 15, 20, 45, 50, 35, 35, 30, 15, 30, 10, 50, 20, | ||
| 25, 45, 30, 25, 45, 10, 45, 10, 30, 30, 25, 50, 10, 40, 40, | ||
| 15, 35, 15, 10, 40, 10, 25, 35, 35, 30, 25, 45, 50, 40, 20, | ||
| 50, 30, 15, 10, 50, 15, 25, 45, 40), MgCl2 = c(5, 5, 4, 7, | ||
| 7, 4, 4, 6, 6, 7, 4, 7, 5, 6, 5, 7, 7, 6, 3, 4, 4, 4, 3, | ||
| 3, 3, 4, 6, 3, 6, 5, 3, 6, 5, 5, 4, 7, 4, 4, 6, 4, 7, 5, | ||
| 6, 7, 7, 6, 4, 4, 4, 3, 3, 4, 6, 3, 6, 5, 3, 6, 5, 5, 7, | ||
| 6, 7, 5, 3, 6, 3, 5, 6, 6, 7, 7, 7, 5, 4, 6, 5, 6, 3, 7, | ||
| 7, 4, 3, 4, 3, 3, 4, 4, 7), KPO4 = c(25, 25, 20, 20, 30, | ||
| 25, 20, 45, 35, 25, 40, 30, 45, 20, 40, 45, 40, 25, 35, 45, | ||
| 30, 40, 30, 20, 45, 30, 30, 35, 20, 40, 40, 35, 25, 25, 20, | ||
| 20, 25, 20, 45, 40, 30, 45, 20, 45, 40, 25, 45, 30, 40, 30, | ||
| 45, 30, 30, 35, 20, 40, 40, 35, 25, 25, 30, 35, 25, 40, 35, | ||
| 40, 25, 20, 45, 25, 20, 35, 40, 30, 35, 40, 35, 30, 45, 40, | ||
| 25, 20, 30, 45, 40, 30, 25, 25, 25), dNTP = c(625, 625, 1500, | ||
| 250, 1500, 1250, 1250, 1250, 1500, 1250, 250, 1250, 1000, | ||
| 1000, 1500, 750, 1000, 250, 250, 1500, 1000, 750, 750, 500, | ||
| 500, 500, 250, 1000, 500, 500, 1250, 750, 625, 625, 1500, | ||
| 250, 1250, 1250, 1250, 250, 1250, 1000, 1000, 750, 1000, | ||
| 250, 1500, 1000, 750, 750, 500, 500, 250, 1000, 500, 500, | ||
| 1250, 750, 625, 625, 1500, 1500, 1250, 1500, 250, 1500, 1500, | ||
| 750, 250, 1500, 750, 1250, 500, 1250, 1250, 1000, 250, 500, | ||
| 1000, 750, 1000, 250, 500, 1250, 750, 1000, 500, 750, 500), | ||
| lnya = c(12.904207, 12.672946, 9.172639, 9.86786, 9.87817, | ||
| 6.423247, 6.131226, 6.011267, 8.44247, 12.072541, 11.252859, | ||
| 9.088173, 10.089967, 13.946539, 8.985946, 9.197255, 9.786954, | ||
| 6.398595, 8.051978, 4.969813, 5.609472, 4.94876, 5.874931, | ||
| 6.50279, 6.811244, 9.69892, 10.348173, 8.101678, 11.703546, | ||
| 13.745088, 8.830543, 11.643954, 13.034624, 12.479909, | ||
| 8.166216, 9.711116, 8.665613, 7.659171, 7.992945, 11.140411, | ||
| 9.588777, 8.074026, 13.478638, 10.410305, 10.817776, | ||
| 7.575585, 7.021084, 7.912057, 6.44254, 6.042633, 7.130899, | ||
| 9.680344, 8.318742, 7.654443, 9.595603, 12.456831, 8.064636, | ||
| 11.060369, 12.128111, 13.191889, 9.268609, 8.273847, | ||
| 12.441145, 8.958025, 8.538955, 7.886081, 8.422883, 8.565983, | ||
| 11.342137, 8.457443, 8.38936, 10.606585, 11.3679, 8.665613, | ||
| 8.773385, 9.384294, 9.78132, 12.25009, 9.510445, 13.311329, | ||
| 11.14331, 9.441452, 9.056023, 8.846497, 8.76873, 9.130214, | ||
| 12.657148, 9.239899, 10.210972)), .Names = c("KCl", "MgCl2", | ||
| "KPO4", "dNTP", "lnya"), class = "data.frame", row.names = c("1", | ||
| "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", | ||
| "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", | ||
| "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", | ||
| "33", "34", "35", "36", "38", "39", "40", "43", "44", "45", | ||
| "46", "48", "49", "50", "52", "53", "54", "55", "57", "58", | ||
| "59", "60", "61", "62", "63", "64", "65", "66", "67", "68", | ||
| "69", "70", "71", "72", "73", "75", "76", "77", "78", "79", | ||
| "80", "81", "82", "83", "84", "85", "86", "87", "88", "89", | ||
| "90", "91", "92", "93", "94", "95", "96")) |
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| # fields is a package for analysis of spatial data written for | ||
| # the R software environment . | ||
| # Copyright (C) 2018 | ||
| # University Corporation for Atmospheric Research (UCAR) | ||
| # Contact: Douglas Nychka, nychka@ucar.edu, | ||
| # National Center for Atmospheric Research, PO Box 3000, Boulder, CO 80307-3000 | ||
| # | ||
| # This program is free software; you can redistribute it and/or modify | ||
| # it under the terms of the GNU General Public License as published by | ||
| # the Free Software Foundation; either version 2 of the License, or | ||
| # (at your option) any later version. | ||
| # This program is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with the R software environment if not, write to the Free Software | ||
| # Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA | ||
| # or see http://www.r-project.org/Licenses/GPL-2 | ||
| "ChicagoO3" <- structure(list(x = structure(c(10.2420950223404, | ||
| 3.80376523711237, 9.10894898014071, 9.62401536295848, -2.42853799498812, | ||
| -12.626852374789, -0.419779101996896, -7.88824165286121, | ||
| 3.54623204570348, -16.9019033521803, -27.2032310085453, -6.18852258956094, | ||
| -5.26140310048807, -12.2147992685346, -25.5550185835271, | ||
| -15.6657440334172, 21.109995699806, 12.9204402129956, 33.8836419936979, | ||
| 28.1148985061338, -8.81404505952784, 6.475624941694, -12.2040623901154, | ||
| -18.5689928883614, 6.8907291046231, -14.9714234763093, -2.03401039835273, | ||
| 10.6958505981398, 12.287083222701, -4.939739538856, 11.4568748968428, | ||
| 20.2432463455088, 35.0486281566463, 28.0610414140067, 23.2873435403219, | ||
| -20.2294095400778, -19.6759373228389, -16.9777602637997, | ||
| -17.5312324810386, -18.4998088612067), .Dim = as.integer(c(20, | ||
| 2)), .Dimnames = list(c("170310032", "170310037", "170310050", | ||
| "170311002", "170311003", "170311601", "170314002", "170314003", | ||
| "170317002", "170436001", "170890005", "170970001", "170971002", | ||
| "170973001", "171110001", "171971008", "180891016", "180892008", | ||
| "181270020", "181270024"), c("East.West", "North.South"))), | ||
| y = c(36.4902936963152, 34.6396930821552, 31.6444005657229, | ||
| 34.4646956838262, 37.7204739668803, 40.1342965426748, | ||
| 37.0181086910068, 38.4001686365134, 44.0485589002946, | ||
| 38.4870329290307, 42.2402282830657, 40.0049235817847, | ||
| 42.1090485712195, 39.6319596353327, 42.8054712629932, | ||
| 44.1097465187358, 35.1186331327201, 46.898470931915, | ||
| 42.9564231070325, 46.6868555984414), lon.lat = structure(c(-87.546, | ||
| -87.671, -87.568, -87.558, -87.792, -87.99, -87.753, | ||
| -87.898, -87.676, -88.073, -88.273, -87.865, -87.847, | ||
| -87.982, -88.241, -88.049, -87.335, -87.494, -87.087, | ||
| -87.199, 41.757, 41.978, 41.708, 41.616, 41.984, 41.668, | ||
| 41.855, 42.039, 42.062, 41.813, 42.05, 42.177, 42.391, | ||
| 42.29, 42.221, 41.592, 41.6, 41.639, 41.631, 41.617), | ||
| .Dim = as.integer(c(20, 2)), .Dimnames = list(c("170310032", | ||
| "170310037", "170310050", "170311002", "170311003", | ||
| "170311601", "170314002", "170314003", "170317002", | ||
| "170436001", "170890005", "170970001", "170971002", | ||
| "170973001", "171110001", "171971008", "180891016", | ||
| "180892008", "181270020", "181270024"), c("lon", | ||
| "lat")))), .Names = c("x", "y", "lon.lat")) |
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|---|---|---|
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| # fields is a package for analysis of spatial data written for | ||
| # the R software environment . | ||
| # Copyright (C) 2018 | ||
| # University Corporation for Atmospheric Research (UCAR) | ||
| # Contact: Douglas Nychka, nychka@ucar.edu, | ||
| # National Center for Atmospheric Research, PO Box 3000, Boulder, CO 80307-3000 | ||
| # | ||
| # This program is free software; you can redistribute it and/or modify | ||
| # it under the terms of the GNU General Public License as published by | ||
| # the Free Software Foundation; either version 2 of the License, or | ||
| # (at your option) any later version. | ||
| # This program is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with the R software environment if not, write to the Free Software | ||
| # Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA | ||
| # or see http://www.r-project.org/Licenses/GPL-2 | ||
| "Exponential" <- function(d, range = 1, alpha = 1/range, phi = 1.0) { | ||
| # | ||
| # Matern covariance function transcribed from Stein's book page 31 | ||
| # nu==smoothness==.5, alpha == 1/range | ||
| # | ||
| # GeoR parameters map to kappa==smoothness and phi == range | ||
| # to make old code from Fuentes and also the package SEHmodel | ||
| # phi is accepted as the marginal variance of the process (see below) | ||
| # within fields this parameter is "sigma" | ||
|
|
||
| # | ||
| # check for negative distances | ||
| if (any(d < 0)) | ||
| stop("distance argument must be nonnegative") | ||
| # | ||
| return(phi*exp(-d * alpha)) | ||
| } |
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|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| # fields is a package for analysis of spatial data written for | ||
| # the R software environment . | ||
| # Copyright (C) 2018 | ||
| # University Corporation for Atmospheric Research (UCAR) | ||
| # Contact: Douglas Nychka, nychka@ucar.edu, | ||
| # National Center for Atmospheric Research, PO Box 3000, Boulder, CO 80307-3000 | ||
| # | ||
| # This program is free software; you can redistribute it and/or modify | ||
| # it under the terms of the GNU General Public License as published by | ||
| # the Free Software Foundation; either version 2 of the License, or | ||
| # (at your option) any later version. | ||
| # This program is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with the R software environment if not, write to the Free Software | ||
| # Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA | ||
| # or see http://www.r-project.org/Licenses/GPL-2 | ||
| ExponentialUpper = function(distMat, range = 1, alpha = 1/range) { | ||
| # Evaluates the exponential covariance function over the upper triangle of the distance matrix | ||
|
|
||
| if(nrow(distMat) != ncol(distMat)) | ||
| stop('distance matrix is non-symmetric. Should not be calling ExponentialUpper.') | ||
|
|
||
| return(.Call("ExponentialUpperC", as.double(distMat), as.integer(nrow(distMat)), as.double(alpha), PACKAGE = "fields")) | ||
|
|
||
| #convert ans to standard matrix | ||
| #ans = ans[[1]] | ||
| #dim(ans) = dim(distMat) | ||
|
|
||
| #return(ans) | ||
| } |
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