getArgillicBounds(), getCambicBounds(),
mollic.thickness.requirement(),
getSurfaceHorizonDepth() and related functions have been
optimized and now work on SoilProfileCollection objects with length >
1reduceSPC() function for selecting a subset of
minimal plus additional specified columns from a
SoilProfileCollection.NHZ for use with
SoilProfileCollection [ method
object[,,.NHZ] returns a vector with the number of
horizons in each profileplotSPC() gains new arguments for controlling horizon
depth labelsplotSPC() gains horizon depth annotation collision
fixes (https://github.com/ncss-tech/aqp/issues/240)plotSPC() minor bugfix for cases when
n != length(x)plotSPC() important change! y.offset is
now automatically re-ordered by plot.orderbase::aggregate (thanks AGB)depthOf() and related functions: better handling of
NA results from FUNpanel.depth_function() that affected
plotting of grouped data, created by slab()plotSPC() now uses variable (vertical) text alignment
for horizon depth labelsprofileInformationIndex()estimateSoilDepth() now requires a valid horizon
designation (no longer attempts a guess)group_by(),
summarize(), mutate()f.noise() and
resample.twotheta(): use {powdR} package insteadtexture_to_texmod() and
fragvol_to_texmod() c/o @smroeckerslice() implemented as
dice()colorChart() can now show neutral hues in a skinny
panelcolorContrast(),
parseMunsell(), and huePosition() to work
properly with neutral hueshuePosition() gains new arguments and functionality:
origin and directionhuePositionCircle() for helping visualize
differences in Munsell hue on the unit circleplotSPC defaults change:
width = 0.25: slightly wider profile sketchesname = hzdesgnname(x): use metadata if present, no
longer guessing. This may cause your figures to “lose” previously
guessed horizon names, specify with name = 'column name' or
set metadata with hzdesgnname(x) <- 'hzname'checkHzDepthLogic() when
byhz = TRUEsimulateColor() for simulation of
reasonable colorscolorChart() for graphical
depiction of Munsell chip frequency by groupunique method for SoilProfileCollection
objects now returns a SoilProfileCollection by default
SPC = FALSE for previous behavior
(https://github.com/ncss-tech/aqp/issues/159)aggregateColor() now uses mixMunsell for
the estimation of soil color mixturesplotColorMixture() will respect “names” attribute of
colors-to-mix, without erroneous alpha-sortingparseMunsell() now more robust and faster, c/o P.
RoudiermixMunsell:
exact for direct conversion of mixture
spectra to sRGB or closest Munsell chip (via
spec2Munsell())PMS2Munsell() for converting
PMS codes -> closest Munsell chip
(https://github.com/ncss-tech/aqp/issues/124)glom() z1 and z2 arguments
vectorized to allow for profile-specific intervals
z1 and z2 support non-standard evaluation
based on column names in siteNames(p), and also can take
character vector (length 1) with column names in
siteNames(p)depthOf(), minDepthOf(),
maxDepthOf(), getSurfaceHorizonDepth(),
getMineralSoilSurfaceDepth(),
getPlowLayerDepth() can now be applied to multiple
profiles.
SoilProfileCollection has more than one
profile then result is a data.frame containing profile ID,
top or bottom depths, horizon designation and patternSoilProfileCollection methods that conflict
with {dplyr} 1.0+ have been deprecated:
filter, mutate, group_by,
summarizesubset, “mutate”
-> transform, “combine” -> c*SPC syntax: filterSPC,
mutateSPC, groupSPC,
summarizeSPCdplyr::combine (deprecated in {dplyr} 0.7)
still conflictsaqp::union(), previously deprecated, has been removed
from namespace
c() or combine() for
SoilProfileCollection inputcombine() or pbindlist() for
list inputplotSPC() gains vectorized y.offset
support (demonstrated in:
http://ncss-tech.github.io/AQP/aqp/genhz-distance-eval.html)plotSPC() gains argument shrink.thin for
shrinking horizon designation labels when horizons are thinalignTransect() for simplifying relative
positioning of profile sketchesplotMultipleSPC() gains ability to automatically merge
thematic legendscoordinates<- will check formula terms
(unique coordinates) in the @horizons slot, if
needed.spec2Munsell() for converting reflectance
spectra into sRGB coordinates or closest Munsell chipmixMunsell:
mixingMethod argument for selecting several mixing
strategiespanel.depth_function when plotting
grouped step-functions[,j]-index
extraction using {data.table}.LAST, .FIRST and
.HZID SoilProfileCollection “k-keywords”perturb() is the new generalized replacement for
sim() and permute_profile()checkHzDepthLogic() now has a byhz
argument for checking logic by horizon rather than profilefillHzGaps now has to_top and
to_bottom arguments for filling above shallowest top /
deepest bottom by profilefixOverlap() more flexible and will usually settle on a
solution in fewer iterations:
overlapMetrics() instead of findOverlap()
for part of objective functionT0 and
k argumentsalignTransect helper function for computing relative
positions and ordering vector supplied to plotSPCplotSPC() automatically converts logical
data supplied to color argument into
factorglom() is now vectorized over profilesestimateAWC introduced for testing lookup table
estimation of available water capacity (AWC) of fine-earth fractioncorrectAWC introduced for testing corrections of AWC
estimates for rock fragment and saltsfillHzGaps: new function for fixing horizon depth
topological errors and padding top/bottom of profiles with placeholder
(empty) horizonsmixMunsell now relies on suggested package {gower} for
5-10x speed bumpplotColorQuantiles(), now using
{lattice} graphicsequivalent_munsell and method
equivalentMunsellChips for “equivalent” Munsell chips
lookup list based on all pairwise dE00 contrasts for integer “chips” in
{aqp} munsell data setcrit.clay.argillic
rounded to whole numbers per NSSH Part 614, subpart B, sections 614.13
and 614.14mutate_profile uses
data.table::rbindlist(fill=TRUE) to combine site- and
horizon-level transformationshzTopographyCodeToOffset,
hzTopographyCodeToLineType,
hzDistinctnessCodeToOffset)L1_profiles computes multivariate (L1)
medians, compare to marginal medians via slabplotSPC updates:
hz.boundary.lty is a
horizon-level attribute that contains line type codeshz.topography.offset a horizon-level attribute that
contains representative offsets that encode horizon boundary
topographyplotSPC now encodes hz.topography.offset
using a vertical “bump” (chevron)addBracket can now accept multiple bracket annotations
per profilepms.munsell.lut for converting Pantone
spot color codes to (closest) Munsell chipduplicate will makes copies of profiles
within a SoilProfileCollectionus.state.soils: 50 state soils + PR
and VI soilsmixMunsell
plotColorMixture for
visualization of spectra / mixturetextureTriangleSummary:
soiltexture package for visualization
(plotrix implementation dropped)sim = TRUE argument, see
bootstrapSoilTexture for a better approachbootstrapSoilTexture for simulating
realistic sand/silt/clay compositionscombine replaces/expands aqp::union due to
conflicts with base::unionsplit receives some upgrades to the S4 definition to
increase parity with split.defaultfilter is now an alias for new method
subset, which mirrors base::subsetestimateSoilDepth loses
top and bottom arguments, these are
automatically extractedmunsell2SPC, spc2mpsplinereturnData argument to
contrastChartglom(..., invert=TRUE),
glomApply, and better testsglomApply:
aqp::trunc for cases when top and bottom depth interval is
the same for all profiles in a SoilProfileCollectionNULL through $<- and
horizons<- or site<-
(https://github.com/ncss-tech/aqp/issues/163)data.table with character vector
(not formula) interfacespc_in_sync
(https://github.com/ncss-tech/aqp/pull/152)[ subset method and optional use of
data.table (https://github.com/ncss-tech/aqp/pull/155)depths<- has been optimized and minimally validates
input datahzID) is now a
character data typeaqp::union uses depths<- internally;
explicitly enforcing profile ID + top depth order in horizon data is
safer but results in different ordering if union-ing IDs
that “intermingle” (need to be re-sorted).permute_profile; similar to
sim but for boundaries. The interface to this function is
likely to change/be expanded.segment c/o @smroeckerplotSPCplot generic to show aqp::plot in
?plottbl_df and
data.table to SoilProfileCollectionaqp_df_class to determine class name in use
in a SoilProfileCollection objectplotSPC upgrades
(https://github.com/ncss-tech/aqp/pull/146)mollic.thickness.requirement,
hasDarkColorsestimateSoilDepth-like methods for depth to
multiple features via pattern matching: depthOf,
minDepthOf, maxDepthOfssc_to_texcl,
texcl_to_ssc, texmod_to_fragvoltot,
texture_to_taxpartsize)[i,] [,j] subset methods
for data.frame-based slots
(https://github.com/ncss-tech/aqp/issues/135)mutate, mutate_profile
(https://github.com/ncss-tech/aqp/issues/118)getSurfaceHorizonDepth with buried horizons /
non-contiguous instances of matching horizons
(https://github.com/ncss-tech/aqp/issues/132)plotSPC with small number of profiles
((https://github.com/ncss-tech/aqp/issues/128)[ j-index subset
((https://github.com/ncss-tech/aqp/issues/125)slab.structure[2] > max(x)[[ subsetting method; an “ambivalent” accessor
for site- or horizon-level propertiesgrepSPC, filter,
subApply for use in %>%-lineshzDesgn(), get horizon designations from
a SPChzdesgnname()/hzdesgnname()<- and
hztexclname()/hztexclname()<- get/set
column containing horizon designations and texture classesglom()profileApply() enhancement for large
SoilProfileCollection objects
(https://github.com/ncss-tech/aqp/issues/112)profileApply() frameify argument for
data.frame output
(https://github.com/ncss-tech/aqp/issues/111)checkHzDepthLogic() replaces
test_hz_logic()rgb2munsell() and
colorQuantiles() now uses the CIE2000 distance metric for
color comparisoncolorQuantiles until farver
2.0.2 is available on CRANSoilProfileCollection object gains new slot:
@restrictions, fix old objects with
rebuildSPC()evalMissingData() gets new argument for relative
vs. absolute evaluation of missing datahorizonColorIndices(),
harden.rubification(), harden.melanization(),
thompson.bell.darkness() and associated functions in
soilColorIndices.Rrowley2019Hmisc
(hdquantile), loading aqp is now much faster
slab() now uses stats::quantile() as the
default slab functionslab() can be activated via
argument: slab.fun = aqp:::.slab.fun.numeric.HDgeneralize.hz() gets a argument for passing additional
arguments to grep(), e.g. perl=TRUEaddVolumeFraction() can now accept a vector of colors,
as many as number of horizonsjacobs2000, pending documentationaggregateColor() faster and more accurate, using
delta-E00 for quantized colors c/o {farver} (see
https://github.com/ncss-tech/aqp/issues/98)contrastChart() and
soilPalette()plotSPC() gains a new argument for relative
positioning: relative.posfixOverlap(), see
manual page for examplesexplainPlotSPC(), addDiagnosticBracket(),
and addVolumeFraction() updated accordinglyplotSPC() will now attempt to create multi-row legends
when using a factor > n.legend levelsplotSPC() will now generate > 10 colors for legends
associated with a factor
(https://github.com/ncss-tech/aqp/issues/9)munsell2rgb() will now return CIE LAB coordinates if
requested (https://github.com/ncss-tech/aqp/issues/69)aggregateColor() gets a new feature, similar colors can
be grouped via cluster::pam()previewColors(),
colorQuantiles(), plotColorQuantiles()horizonDepths()<-, edit top/bottom
names after SPC initprofile_id()<-, edit profile IDs after
init; be careful!hzID() and hzID()<-,
get/set unique horizon IDshzidname() and
hzidname()<-, get/set column containing unique horizon
IDsrbind.SoilProfileCollection() has been deprecated in
favor of union(), gains new functionality:
https://github.com/ncss-tech/aqp/issues/71horizonNames()<-explainPlotSPC from SPC tutorial to
aqp::explainPlotSPC()plotSPC() is a little better at estimating “extra”
vertical / horizontal space, still needs work
(https://github.com/ncss-tech/aqp/issues/62)plotSPC() gets a new argument, n.legend:
approximate number of classesaggregateColor() for cases when horizon
depths are missing or top/bottom logic flippedaddVolumeFraction() when fragment volume
> 100%addDiagnosticBracket() allowing
for specification of column containing diagnostic feature kindaddBracket() now requires a data.frame with plotting
details, see manual pageshannonEntropy(), confusionIndex(),
and brierScore()get.ml.hz() for horizon names that start
with number or punctuationget.ml.hz() now uses internal aqp functions for Shannon
entropy and Brier scoresmissingDataGrid() relaxing slice() with
strict=FALSEmunsell look-up tableplotSPC() now able to deal with missing horizon data
(thanks Stephen R.)rgb2munsell() now uses CIELAB colorspace for lookup,
results are more accurate as compared to using sRGB
colorspacetexture.triangle.low.rv.high() renamed to
textureTriangleSummary(). The old name still works, but a
message is issuedtextureTriangleSummary()
texture.names: for toggling texture class namestextureTriangleSummary(..., sim=TRUE),
previous simulated compositional data was not correct because the
stats::var() was being used vs. compositions::var.acomp(). the variance
/ covariance values were 2-5x too small.tauW(), added by D.G. Rossiter: see manual
page for referencesrbind-ingsoil_minerals with some common soil mineral
colors source:
http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054286getClosestMunsellChip()sp6) based on
http://www.sciencedirect.com/science/article/pii/S0016706111001972munsell2rgb() can now accommodate neutral hues (N), and
values of “2.5”, see manual page for detailssoilColorSignature(), see manual
pageparseMunsell() for converting strings of
‘10YR 2/2’ into R colors or RGB triplets
munsell2rgb
on parsed strings of full Munsell notationprofile_compare(), getting ready for a
complete overhaul to this functionevalMissingData(), see manual pagegenhzTableToAdjMat,
hzTransitionProbabilitiesrbind.SoilProfileCollection()
related to object re-ordering
profile_id(x) and site(x)[[idname(x)]]) would
not matchgroupedProfilePlot() gains some new arguments and
better documentation (see manual page)plot.SoilProfileCollection gains argument:
default.color (see manual page)munsell2rgb()guessGenHzLevels()aggregateColor() and associated helper
function sharpshootR::aggregateColorPlot()R CMD check --as-cran happyprofileApply()
manual pagedigest::digest is now imported by defaultSoilProfileCollection objectsx.idx.offset: allows for
plotting of multiple SPC objects within the same figure, see
examplesplot.depth.axis: enable /
disable depth axis, useful for multi-collection plotsprofileGroupLabels: simple annotation for
groups of profiles within a profile sketch, see manual page for
examplesplotMultipleSPC: plot several SPC objects
on the same axis, see manual page for examplesaddBrackets(),
panel.depth_function(), and plotSPC()addBrackets() allow for annotation of
bracketslabel, used to set
site-level attribute containing profile labelstexture.triangle.low.rv.high() plots
texture data with low-high range defined by quantilesslab() and
profileApply() via ‘parallel’ packageplotSPC() gets a density argument for
shaded coloring of horizonsslab() re-written from scratch, resulting in reduced
memory footprint and quicker running time ! older code based on slab()
is likely to now broken- sorry, it won’t happen again
sim() for simulation based on a template
soil profile, proper documentation pending…subsetProfiles() for simpler subsetting of
SoilProfileCollection objects via site or horizon-level
attributesget.ml.hz() now returns a ‘confidence’ for each horizon
(as a percent)site(SCP) <- d now tries to merge data from SPC@site
with ‘d’ via left join
strict argument to many functions, to gracefully
account for bad horizon data
SoilProfileCollection
SoilProfileList
classesSoilProfileCollection class
new functions for getting data out of PedonPC (MS Access) databases [windows only for now]
implemented in mix_and_clean_colors()
test_hz_logic() : basic function for testing horizon logic, returns TRUE/FALSE by ID
parallel operations now NON-functional, while we wait for plyr to support doSMP…
new ID plotting style for profile_plot() : handy when plotting large collections and/or long IDs
mapunit_geom_by_ll_bbox() : get map unit geometry by
bounding boxMUKEYS_by_ll_bbox() : get map unit keys by bounding
boxSDA_query() : retrieve soil tabular data via query
written in SQLplotSPCprofile_compare() now calculates slice-wise
dissimilarity matrices in 1/3 the time (thanks llply!)