evanGenHz() now uses stats::cmdscale()
instead of MASS:isoMDS()
migrating a few functions from sharpshootR to aqp:
plotProfileDendrogram()
aggregateColorPlot()
fix for hz_segment() and NCSP() with
data.tableSoilProfileCollection objects
(#320)
fix for generalize.hz() to handle missing depths better
and added na.rm argument (#321)
finally dropping plyr from suggests (#157)
profile_compare() removed, see NCSP()
aqp 2.1.0 (2024-10-16)
CRAN release
added Munsell values of 8.5 and 9.5 to Munsell look up table and
(interpolated) reference spectra (#318)
munsell2rgb() now safely selects the closest Munsell
value and chroma to those available in the package LUT
new function soilTextureColorPal() for suggesting a
color palette suitable for soil texture class
Breaking Change: @sp slot of the
SoilProfileCollection object, and dependency on sp package,
has been removed.
Any SoilProfileCollection objects previously written to
file (.rda, .rds) with aqp <2.1.x will need to be rebuilt using
rebuildSPC() due to changes to S4 object structure
estimatePSCS() gains argument "lieutex"
for in lieu textures which are used in the new routine for
identification of the particle size control section of organic
soils
new function collapseHz() combines and aggregates data
for adjacent horizons matching a pattern or sharing a common ID
new function mutate_profile_raw() for building sets of
dynamic mutate expressions. Also mutate_profile() gains
col_names argument for dynamic naming of columns.
addVolumeFraction() now more robust to very thin
horizons x low volume fractions; also skips horizons without sufficient
or relevant values
aqp 2.0.4 (2024-07-30)
CRAN release
ragged bottom lines in plotSPC() now adjusted as
function of number of profiles and device width
additional metadata from plotSPC() saved to
last_spc_plot in aqp.env
aqp 2.0.3 (2024-04-18)
CRAN release
simulateColor() gains new method mvnorm
for simulating plausible colors
package mvtnorm added to SUGGESTS
performance improvements in profileInformationIndex(),
dice(), slab(), spc2mpspline(),
fillHzGaps(), and flagOverlappingHz()
aesthetic improvements in huePositionCircle()
new function thicknessOf() used for calculating
thickness of horizons within each profile of a
SoilProfileCollection based on horizon-level logical
expressions encoded in a function. Default behavior uses pattern
matching on the horizon designation name.
aqp 2.0.2 (2023-11-18)
CRAN release
bug fix / enhancements in evalMissingData()
new function col2Munsell() generalizes and replaces
rgb2munsell() (thanks Shawn Salley for the suggestion)
rgb2munsell() will be deprecated in aqp 2.1
new function warpHorizons() for warping horizon
thickness (inflate/deflate) (thanks Shawn Salley for idea /
inspiration)
fixed minor bug in plotColorMixture() when final mixed
color does not exist in spectral library
fixed minor namespace collision in
groupedProfilePlot()
major updates to profileInformationIndex() (vignette
pending)
aqp 2.0.1 (2023-09-03)
CRAN release (CRAN check bugfix)
new function flagOverlappingHz() for identifying
horizons with perfect overlap
fillHzGaps(), dice(), slab(),
and several other functions now safely handle horizons with perfect
overlap (#296)
aqp 2.0 (2023-08-28)
This is a major update to aqp that may create some issues for code
depending on specific inputs/outputs in aqp < 1.42, particularly
those relying on slice(), slab(), and
profile_compare(). slice() and
profile_compare() are now deprecated, but will continue to
work for the rest of calendar year 2023. There are no plans to maintain
these functions beyond aqp 2.0. The new version of slab()
is a drop-in replacement for the previous version of the function.
Notable changes include:
deprecation of slice() in favor of the new, faster,
more robust implementation in dice()
complete overhaul of slab(), with new arguments, faster
back-end, and weighted aggregation implemented (finally)
deprecation of profile_compare() in favor of the
NCSP()–a complete overhaul based on Maynard et al., 2020
site level attributes now handled by
compareSites()
variable weights now possible via argument
perturb() and estimatePSCS() are now
vectorized, and optimized for larger collections
mixMunsell() now uses
mixingMethod = 'exact' by default for the simulation of
subtractive mixtures
gower package moved to SUGGESTS
plotColorMixture() now using grid graphics functions to
determine color swatch geometry and setting overlap detection
threshold
removal of PMS2Munsell() and support data
deprecation of coordinates()<- and
proj4string()<- in favor of
initSpatial()<-
removal of rruff.sample example XRD patterns
get.ml.hz() no longer uses the name
argument
Major changes to plotSPC():
The maximum depth range of the figure is now based on
max.depth or max(x). This means that sketches
generated with aqp 2.x will generally have less white space at the
bottom of the figure. Make more room for additional annotation or visual
effect by setting the desired depth range with the
max.depth argument.
now uses electroStatics_1D() for fixing horizon depth
label overlap, solutions are deterministic and almost always better
better depth axis interval heuristics (if not specified), varying
based on figure depth range
depth axis adjustments via new argument depth.axis,
logical or list
deprecation of arguments:
plot.depth.axis: set via
depth.axis = TRUE, depth.axis = FALSE, or
customize depth.axis = list(...)
cex.depth.axis: set via
depth.axis = list(cex = 1)
axis.line.offset: set via
depth.axis = list(line = -2)
New features:
example data, wilson2022
fast prototyping of SPCs via quickSPC() and list /
character templates
re-use arguments to plotSPC() via
options(.aqp.plotSPC.args = list(...))
coarse fragment classification via fragmentSieve() and
fragmentClasses()
S4 as.data.frame(<SPC>) as shorthand for
as(<SPC>, 'data.frame')
plotSPC() now marks truncated profiles with a ragged
bottom
fixOverlap() now has two label-placement solvers, based
on 1) electrostatics and 2) simulated annealing
Incremental changes, should have no effect on previous code:
bug fix in plotSPC() when
fixLabelCollisions = TRUE, adjustments suggested to
fixOverlap() are now scaled correctly
explainPlotSPC() reports label adjustment index when
label collision repair is enabled
aesthetic cleanup in explainPlotSPC()
soilColorSignature() gains arguments and perceptual
color distances (dE00) via farver package
as(<SPC>, "data.frame"): Replace
plyr::join() with merge()
correctAWC(): NA handling - return NA when frags are
NA
mutate_profile(): Faster (data.table-based) evaluation
of profile-level expressions (#255)
profileApply: Add support for custom
lapply()-like function (APPLY.FUN) for
processing chunks (#256)
Add .interpretHorizonColor() outputs to
last_spc_plot in aqp.env for use in custom
legend() (#254)
Add simplify argument to
SoilTextureLevels() and ssc_to_texcl() to
optionally convert to an ordered factor with maximum of 12 levels
(rather than 21). This smaller list of classes excludes sand grain size
variants such as fine sand, loamy coarse sand, and very fine sandy
loam.
aqp 1.42 (2022-04-08)
CRAN release
getArgillicBounds(), getCambicBounds(),
mollic.thickness.requirement(),
getSurfaceHorizonDepth() and related functions have been
optimized and now work on SoilProfileCollection objects with length >
1
Added reduceSPC() function for selecting a subset of
minimal plus additional specified columns from a
SoilProfileCollection
Added new “k-keyword” .NHZ for use with
SoilProfileCollection[ method
object[,,.NHZ] returns a vector with the number of
horizons in each profile
proper identification and conversion of Munsell value == 2.5
interpolated reference spectra for Munsell value == 2.5
neutral color chips in the Munsell look-up table are now based on
direct measurement vs. estimation
aqp 1.41 (2022-02-11)
plotSPC() gains new arguments for controlling horizon
depth labels
plotSPC() minor bugfix for cases when
n != length(x)
plotSPC() important change! y.offset is
now automatically re-ordered by plot.order
bugfix for R 4.2, related to named arguments passed to
base::aggregate (thanks AGB)
depthOf() and related functions: better handling of
NA results from FUN
aqp 1.40 (2022-01-04)
CRAN release
fixed small bug in panel.depth_function() that affected
plotting of grouped data, created by slab()
plotSPC() now uses variable (vertical) text alignment
for horizon depth labels
new function profileInformationIndex()
estimateSoilDepth() now requires a valid horizon
designation (no longer attempts a guess)
{aqp} no longer masks {dplyr} verbs: group_by(),
summarize(), mutate()
removed (deprecated) f.noise() and
resample.twotheta(): use {powdR} package instead
new functions: texture_to_texmod() and
fragvol_to_texmod() c/o @smroecker
faster, more robust version of slice() implemented as
dice()
aqp 1.32 (2021-09-28)
colorChart() can now show neutral hues in a skinny
panel
updates to colorContrast(),
parseMunsell(), and huePosition() to work
properly with neutral hues
huePosition() gains new arguments and functionality:
origin and direction
new function huePositionCircle() for helping visualize
differences in Munsell hue on the unit circle
plotSPC defaults change:
width = 0.25: slightly wider profile sketches
name = 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'
aqp 1.31 (2021-08-19)
CRAN release
bug fix in checkHzDepthLogic() when
byhz = TRUE
new function simulateColor() for simulation of
reasonable colors
unique method for SoilProfileCollection
objects now returns a SoilProfileCollection by default
this may break existing code! use the new argument
SPC = FALSE for previous behavior
(https://github.com/ncss-tech/aqp/issues/159)
aggregateColor() now uses mixMunsell for
the estimation of soil color mixtures
plotColorMixture() will respect “names” attribute of
colors-to-mix, without erroneous alpha-sorting
parseMunsell() now more robust and faster, c/o P.
Roudier
mixMunsell:
new method exact for direct conversion of mixture
spectra to sRGB or closest Munsell chip (via
spec2Munsell())
new convenience function 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.
If the input SoilProfileCollection has more than one
profile then result is a data.frame containing profile ID,
top or bottom depths, horizon designation and pattern
aqp 1.29 (2021-04-05)
CRAN release
Several SoilProfileCollection methods that conflict
with {dplyr} 1.0+ have been deprecated:
Be aware dplyr::combine (deprecated in {dplyr} 0.7)
still conflicts
aqp::union(), previously deprecated, has been removed
from namespace
Use c() or combine() for
SoilProfileCollection input
Usecombine() or pbindlist() for
list input
Methods that used {rlang} for non-standard evaluation now use
{base}
plotSPC() 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 thin
new function alignTransect() for simplifying relative
positioning of profile sketches
plotMultipleSPC() gains ability to automatically merge
thematic legends
coordinates<- will check formula terms
(unique coordinates) in the @horizons slot, if
needed.
new function spec2Munsell() for converting reflectance
spectra into sRGB coordinates or closest Munsell chip
mixMunsell:
new mixingMethod argument for selecting several mixing
strategies
suggestions on interpreting spectral distances, message printed when
greater than reasonable threshold
minor bug-fix in panel.depth_function when plotting
grouped step-functions
aqp 1.28 (2021-03-02)
optimization of SoilProfileCollection [,j]-index
extraction using {data.table}
introduction of .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 profile
fillHzGaps now has to_top and
to_bottom arguments for filling above shallowest top /
deepest bottom by profile
fixOverlap() more flexible and will usually settle on a
solution in fewer iterations:
overlapMetrics() instead of findOverlap()
for part of objective function
cooling schedule is now fully adjustable via T0 and
k arguments
alignTransect helper function for computing relative
positions and ordering vector supplied to plotSPC
plotSPC() automatically converts logical
data supplied to color argument into
factor
glom() is now vectorized over profiles
estimateAWC introduced for testing lookup table
estimation of available water capacity (AWC) of fine-earth fraction
correctAWC introduced for testing corrections of AWC
estimates for rock fragment and salts
aqp 1.27 (2021-01-22)
fillHzGaps: new function for fixing horizon depth
topological errors and padding top/bottom of profiles with placeholder
(empty) horizons
mixMunsell now relies on suggested package {gower} for
5-10x speed bump
{aqp} no longer imports from {reshape} (less one dependency), all
transformations from wide<->long are done via {data.table}
methods from {data.table} are now imported by {aqp} (new
dependency)
Major overhaul of plotColorQuantiles(), now using
{lattice} graphics
New dataset equivalent_munsell and method
equivalentMunsellChips for “equivalent” Munsell chips
lookup list based on all pairwise dE00 contrasts for integer “chips” in
{aqp} munsell data set
Argillic critical clay contents crit.clay.argillic
rounded to whole numbers per NSSH Part 614, subpart B, sections 614.13
and 614.14
aqp 1.26 (2020-11-18)
mutate_profile uses
data.table::rbindlist(fill=TRUE) to combine site- and
horizon-level transformations
updates to horizon boundary encoding functions
(hzTopographyCodeToOffset,
hzTopographyCodeToLineType,
hzDistinctnessCodeToOffset)
new function L1_profiles computes multivariate (L1)
medians, compare to marginal medians via slab
plotSPC updates:
argument named changes: hz.boundary.lty is a
horizon-level attribute that contains line type codes
hz.topography.offset a horizon-level attribute that
contains representative offsets that encode horizon boundary
topography
plotSPC now encodes hz.topography.offset
using a vertical “bump” (chevron)
addBracket can now accept multiple bracket annotations
per profile
aqp 1.25 (2020-10-15)
CRAN release
new lookup table pms.munsell.lut for converting Pantone
spot color codes to (closest) Munsell chip
new function duplicate will makes copies of profiles
within a SoilProfileCollection
new example data us.state.soils: 50 state soils + PR
and VI soils
simulate subtractive mixtures of Munsell colors with
mixMunsell
see companion function plotColorMixture for
visualization of spectra / mixture
complete overhaul of textureTriangleSummary:
uses soiltexture package for visualization
(plotrix implementation dropped)
argument names changes (! may break old code, sorry)
dropped simulation via sim = TRUE argument, see
bootstrapSoilTexture for a better approach
new function bootstrapSoilTexture for simulating
realistic sand/silt/clay compositions
combine replaces/expands aqp::union due to
conflicts with base::union
split receives some upgrades to the S4 definition to
increase parity with split.default
filter is now an alias for new method
subset, which mirrors base::subset
aqp 1.24 (2020-08-31)
estimateSoilDepthlosestop and bottom arguments, these are
automatically extracted
two new SoilProfileCollection wrapper methods:
munsell2SPC, spc2mpspline
add returnData argument to
contrastChart
improvements to glom(..., invert=TRUE),
glomApply, and better tests
new wrapper method around glomApply:
aqp::trunc for cases when top and bottom depth interval is
the same for all profiles in a SoilProfileCollection
fix for routing of NULL through $<- and
horizons<- or site<-
(https://github.com/ncss-tech/aqp/issues/163)
fix handling of missing metadata in (old) serialized
SoilProfileCollection objects
fix for promotion of data.table with character vector
(not formula) interface
aqp 1.23 (2020-07-14)
enhanced SoilProfileCollection object validity checks via
S4; new method spc_in_sync
(https://github.com/ncss-tech/aqp/pull/152)
optimization of [ subset method and optional use of
data.table (https://github.com/ncss-tech/aqp/pull/155)
depths<- has been optimized and minimally validates
input data
default horizon ID (hzID) is now a
character data type
aqp::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).
new experimental method is permute_profile; similar to
sim but for boundaries. The interface to this function is
likely to change/be expanded.
added segment c/o @smroecker
fix for unit-length and zero-length legends in
plotSPC
fix for plot generic to show aqp::plot in
?plot
aqp 1.22 (2020-06-24)
basic support for promotion of tbl_df and
data.table to SoilProfileCollection
new method aqp_df_class to determine class name in use
in a SoilProfileCollection object
previous behavior of slab() can be activated via
argument: slab.fun = aqp:::.slab.fun.numeric.HD
aqp 1.17.08 (2019-10-03)
generalize.hz() gets a argument for passing additional
arguments to grep(), e.g. perl=TRUE
addVolumeFraction() can now accept a vector of colors,
as many as number of horizons
new sample data: jacobs2000, pending documentation
aggregateColor() faster and more accurate, using
delta-E00 for quantized colors c/o {farver} (see
https://github.com/ncss-tech/aqp/issues/98)
new functions contrastChart() and
soilPalette()
aqp 1.18 scheduled for next CRAN release
aqp 1.17.06 (2019-07-15)
plotSPC() gains a new argument for relative
positioning: relative.pos
relative positioning helper function: fixOverlap(), see
manual page for examples
explainPlotSPC(), addDiagnosticBracket(),
and addVolumeFraction() updated accordingly
aqp 1.17.05 (2019-05-18)
new functions colorContrast(), contrastClass(), and
huePosition()
aqp 1.17.02 (2019-03-15)
fixed nasty bug in [-indexing when SPC contains a single profile
(https://github.com/ncss-tech/aqp/issues/85)
new function validSpatialData() to test for place-holder contents of
@sp
rebuildSPC() will now correct invalid, place-holder SpatialPoints in
@sp
aqp 1.17.01 (2019-02-07)
new version number system
plotSPC() will now attempt to create multi-row legends
when using a factor > n.legend levels
plotSPC() 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)
aqp 1.17 (2018-12-28)
CRAN release
aggregateColor() gets a new feature, similar colors can
be grouped via cluster::pam()
new functions: previewColors(),
colorQuantiles(), plotColorQuantiles()
new function: horizonDepths()<-, edit top/bottom
names after SPC init
new function: profile_id()<-, edit profile IDs after
init; be careful!
new functions: hzID() and hzID()<-,
get/set unique horizon IDs
new functions: hzidname() and
hzidname()<-, get/set column containing unique horizon
IDs
rbind.SoilProfileCollection() has been deprecated in
favor of union(), gains new functionality:
https://github.com/ncss-tech/aqp/issues/71
bug fixes in sanity checks within
horizonNames()<-
!!! SoilProfileCollection internal structure has changed:
https://github.com/ncss-tech/aqp/issues/74
see release notes for more:
https://github.com/ncss-tech/aqp/releases/tag/v1.17
aqp 1.16-6 (2018-12-12)
partial bug fix in test_hz_logic() related to missing top AND bottom
depths, needs work: https://github.com/ncss-tech/aqp/issues/65
aqp 1.16-5 (2018-11-21)
moved 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)
aqp 1.16-2 (2018-05-22)
fixing #53 and #54
bug fix for too many decimal places in legend classes (floating
point -> character issue)
plotSPC() gets a new argument, n.legend:
approximate number of classes
aqp 1.15.5 (2018-03-14)
enhancement to aggregateColor() for cases when horizon
depths are missing or top/bottom logic flipped
aqp 1.15.4 (2018-01-29)
bug fix for addVolumeFraction() when fragment volume
> 100%
aqp 1.15.3 (2018-01-24)
added a new argument to addDiagnosticBracket() allowing
for specification of column containing diagnostic feature kind
addBracket() now requires a data.frame with plotting
details, see manual page
aqp 1.15.2 (2017-11-30)
added shannonEntropy(), confusionIndex(),
and brierScore()
bug fix in get.ml.hz() for horizon names that start
with number or punctuation
get.ml.hz() now uses internal aqp functions for Shannon
entropy and Brier scores
aqp 1.15 (2017-11-11)
push to CRAN, getting ready for aqp 2.0
aqp 1.14 (2017-09-19)
missingDataGrid() relaxing slice() with
strict=FALSE
aqp 1.12 (2017-07-05)
CIELAB colors are now in the munsell look-up table
aqp 1.12 (2017-07-05)
plotSPC() now able to deal with missing horizon data
(thanks Stephen R.)
this is likely the last release before aqp 2.0
aqp 1.11 (2017-06-13)
rgb2munsell() now uses CIELAB colorspace for lookup,
results are more accurate as compared to using sRGB
colorspace
aqp 1.10-4 (2017-05-02)
texture.triangle.low.rv.high() renamed to
textureTriangleSummary(). The old name still works, but a
message is issued
new argument to textureTriangleSummary()texture.names: for toggling texture class names
minor bug fix in textureTriangleSummary(..., 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.
new function tauW(), added by D.G. Rossiter: see manual
page for references
aqp 1.10 (2017-01-05)
fixed major bug (https://github.com/ncss-tech/aqp/issues/23) related
to editing horizon-level attributes after rbind-ing
aqp 1.9.13 (2016-10-20)
new dataset soil_minerals with some common soil mineral
colors source:
http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/edu/?cid=nrcs142p2_054286
added clarification to Munsell color conversion: changed “RGB” to
“sRGB”.
aqp 1.9.10 (2016-07-01)
new function for estimating the closest Munsell chip:
getClosestMunsellChip()
new example data set (sp6) based on
http://www.sciencedirect.com/science/article/pii/S0016706111001972
aqp 1.9.8 (2016-03-07)
munsell2rgb() can now accommodate neutral hues (N), and
values of “2.5”, see manual page for details
aqp 1.9.7 (2016-02-25)
new function: soilColorSignature(), see manual
page
new function: parseMunsell() for converting strings of
‘10YR 2/2’ into R colors or RGB triplets
this is a convenience function that calls munsell2rgb
on parsed strings of full Munsell notation
aqp 1.9.6 (2016-02-23)
minor changes to profile_compare(), getting ready for a
complete overhaul to this function
new function: evalMissingData(), see manual page
aqp 1.9.5 (2015-12-28)
documentation for new transition probability functions, see
?hzTransitionProbabilities for details
aqp 1.9.4 (2015-12-22)
better checking for other places where the bug fixed in
rbind.SoilProfileCollection (aqp 1.9.3) could occur
new functions: genhzTableToAdjMat,
hzTransitionProbabilities
aqp 1.9.3 (2015-12-18)
fixed a nasty bug in rbind.SoilProfileCollection()
related to object re-ordering
in aqp < 1.9.3: there was a chance than
profile_id(x) and site(x)[[idname(x)]]) would
not match
bugs like this will no longer be a possibility after aqp 2.0, new
SPC object structure planned
aqp 1.9.1 (2015-11-18)
groupedProfilePlot() gains some new arguments and
better documentation (see manual page)
plot.SoilProfileCollection gains argument:
default.color (see manual page)
aqp 1.9 (2015-08-26)
added neutral colors to munsell2rgb()
new function guessGenHzLevels()
new function aggregateColor() and associated helper
function sharpshootR::aggregateColorPlot()
more code clean-up and fixes in examples to make
R CMD check --as-cran happy
fixed some ancient examples in the profileApply()
manual page
aqp 1.8-5 (2015-04-17)
bug fixes and documentation updates
digest::digest is now imported by default
better documentation for unique-method of
SoilProfileCollection objects
aqp 1.8-3 (2015-03-02)
updated documentation
plotSPC gets a new argument: x.idx.offset: allows for
plotting of multiple SPC objects within the same figure, see
examples
plotSCP gets a new argument: plot.depth.axis: enable /
disable depth axis, useful for multi-collection plots
new function: profileGroupLabels: simple annotation for
groups of profiles within a profile sketch, see manual page for
examples
new function: plotMultipleSPC: plot several SPC objects
on the same axis, see manual page for examples
aqp 1.7-11 (2015-01-30)
fixed bugs in addBrackets(),
panel.depth_function(), and plotSPC()
new arguments to addBrackets() allow for annotation of
brackets
aqp 1.7-10 (2015-01-15)
names() method for SoilProfileCollection objects returns a
concatenated vector of horizon + site names
siteNames() and horizonNames() can now be used to extract from
SoilProfileCollection
siteNames<- and horizonNames<- can now be used to change
names; experimental!
note: internal structure of SoilProfileCollection objects will be
changing soon!!!
aqp 1.7-8 (2014-12-08)
texture.triangle.low.rv.high(): new arguments, likely breaking
previous usage when method=‘closest’, see manual page for details
aqp 1.7-7 (2014-11-06)
bug fix c/o Jose Padarian: SPC objects now understand logical
indexing rules
removed spatial_subset(): this functionality can be
accomplished outside of AQP and removes dependency on rgeos package
aqp 1.7-6 (2014-09-26)
bug fix c/o Jos? Padarian: when promoting coordinates from @site, drop=FALSE is required
to prevent a single remaining attribute from being down-graded to a
vector– thanks!
get.ml.hz() now returns a “pseudo” Brier Score, using the
most-likely horizon label as the “correct” value
new function rgb2munsell()
new function estimateSoilDepth()
new function getSoilDepthClass()
new documentation / tutorials
aqp 1.6-4 (2014-02-14)
When applied to a single categorical variable, the results from
slab() now contain an attribute ‘original.levels’ that contains the
original factor levels. This is important because when casting from
long->wide format, illegal column names are scrubbed by make.names().
This process would convert horizon designations like ‘2Bt’ into ‘X2Bt’.
You can recover the original horizon names via
attr(x, 'original.levels').
aqp 1.6-3 (2014-02-04)
plotSPC() has a new argument: label, used to set
site-level attribute containing profile labels
aqp 1.6-2 (2014-01-10)
plotSPC() now registers plotting parameters in the environment
aqp.env
new function addVolumeFraction() for annotating profile plots with
volumetric information (e.g. rock fragment volume)
aqp 1.6-1 (2013-12-31)
plotSPC() attempts to guess which column contains horizon
designations
plotSPC() can now color horizons based on continuous soil properties
(e.g. clay content)
aqp 1.6 (2013-12-11)
rbind.SoilProfileCollection() now re-orders data according to the
new set of profile IDs
this fixes several problems associated with assumptions in
profile_compare()
profile_compare() will be re-written soon to work natively with SPC
objects
aqp 1.5-6 (2013-11-25)
new function addBracket() for annotating profile sketches with
depth-brackets; useful for plotting diagnostic features
aqp 1.5-6 (2013-11-15)
new function missingDataGrid() for graphically describing the
presence of missing data in an SPC object
aqp 1.5-2 (2013-04-09)
panel.depth_function() now prints “contributing fraction” values in
the same color as corresponding depth-function lines and shaded
areas
panel.depth_function() gains an argument ‘cf.col’ for manually
specifying the CF color
panel.depth_function() gains an argument ‘cf.interval’ for manually
specifying printed CF depths
prepanel.depth_function() now extends x-lim by 5% in either
direction for cleaner-looking plots
added some details to slab() documentation
fixed minor bug in min() and max() methods for SoilProfileCollection
objects in the presence of missing data
min() and max() methods for SoilProfileCollection objects now have a
second argument for checking depth based on the presence of data in that
column
aqp 1.5-1 (2013-03-07)
removed excessive checking in SoilProfileCollection init code, this
may speed things up
previously identified horizonation errors may no longer result in
ERRORS; be sure to test
test_hz_logic() now more useful:
always checks for NA and overlapping horizons
no longer called with initialization of SoilProfileCollection
objects
note that default behavior has changed since version 1.5
moved related documentation to test_hz_logic manual page
new mini-vignette on dealing with bad data
(dealing-with-bad-data.html)
better documentation for slice()
new warnings related to missing data in the grouping variable passed
to slab()
aqp 1.5 (2013-02-24)
profileApply() can now return arbitrary objects = new
subsetting/transformation possibilities
see ?profileApply for examples
panel.depth_function() can now display contributing fraction values
with grouped data
see multi-variate example in ?slab
aqp 1.4-7 (2013-01-24)
HTML version of all documentation (including images) auto-generated
via knitr and available on the r-forge website
new function: texture.triangle.low.rv.high() plots
texture data with low-high range defined by quantiles
aqp 1.4-6 (2013-01-03)
updated documentation and SoilProfileCollection tutorial
plans laid for parallel processing in slab() and
profileApply() via ‘parallel’ package
plotSPC() gets a density argument for
shaded coloring of horizons
aqp 1.4-5 (2012-12-29)
slab() 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
the new code is much slimmer and based on aggregate() rather than
ddply
function arguments have changed so be sure to check the manual
page
user-supplied functions are now much simpler to write and rely on
vectors rather than data.frames (= faster)
the next major release will contain additional examples of how to
use the new features
aqp 1.4 (2012-12-18)
new function sim() for simulation based on a template
soil profile, proper documentation pending…
aqp 1.3-3 (2012-12-06)
new function subsetProfiles() for simpler subsetting of
SoilProfileCollection objects via site or horizon-level
attributes
get.ml.hz() now returns a ‘confidence’ for each horizon
(as a percent)
added experimental ‘filter’ argument to profile_compare()- see
manual page for usage
added new argument to plot.SoilProfileCollection()- alt.label: used
to add secondary labeling via data in @site
plot.SoilProfileCollection() will now do a better job of selecting
the location for profile IDs based on label length, font size, and
figure size
aqp 1.3-2 (2012-11-01)
minor tweaks to plot.SoilProfileCollection() for improved output
with small/large size collections
new function get.ml.hz() attempts to determine the most likely
horizonation after slabbing
fixed bug in profileApply() where further arguments to FUN weren’t
passed on to FUN
missing data report from profile_compare() now only includes
horizons with some data (e.g. Cr and R horizons are skipped)
aqp 1.3-1 (2012-10-17)
speed-bump in profileApply()
splitProfiles() function is no longer defined/used/needed
bug fix in SoilProfileCollection subsetting via []
SoilProfiles with a single horizon confused subsetting in the
presence of spatial data
aqp 1.3 (2012-10-07)
added rbind.SoilProfileCollection() for concatenating SPC objects
this function performs basic sanity checks, but cannot combine
unlike objects
aqp 1.2-10 (2012-09-05)
fixed minor bug in prepanel.depth_function() where an error would
occur when input data was all NA
aqp 1.2-9 (2012-08-31)
new ‘unique’ method for SoilProfileCollection objects, returns
indices of unique profiles
fixed bug in NAMESPACE that caused an error when ‘sp’ library wasn’t
loaded
added another sanity check to ‘site<-’ for cases where duplicates
occur in the source data set
added some new documentation to package help page see ‘help(aqp)’
for details
aqp 1.2-8 (2012-08-28)
the names() method for SoilProfileCollection objects now returns a
named list of horizon and site column names
improved examples: see ?sp4 and ?ca630
fixed minor bug related to subsetting a SoilProfileCollection
object, followed by coercion to SpatialPointsDataFrame
aqp 1.2-7 (2012-08-23)
plot() method for SoilProfileCollection object no longer sets page
margins, this will cause some figures to change
added demo ‘slope_effect_hz_thickness’
aqp 1.2-6 (2012-06-26)
fixed minor bug in panel.depth_function(): grouping + paneling
ignored full suite of colors
fixed minor bug in NAMESPACE
minor bug fix in unroll(), was not previously respecting the max
depth argument
minor speed-bump and simplification of profile_compare()
documentation updates
added helper message related to profile_compare() stopping when any
profile contains insufficient data
profile_compare() now issues a notice when some data are
missing, leading to biased results
slice() now computes the fraction of variables within a slice that
are missing data ! bug introduced into slab() when use.wts=TRUE [should
have a fix soon]
aqp 1.1 (2012-04-18)
merged documentation for soil.slot() and slab()
slab() should be used in all places where soil.slot() was used
soil.slot() will disappear from the package NAMESPACE eventually, so
don’t use it directly!
minor bug fix in panel.depth_function()
cleanup of documentation and examples
added horizon boundary distinctness code conversions and plotting
functionality
see ?sp1 and ?random_profile for new examples
aqp 1.0-2 (2012-03-29)
More NAMESPACE cleaning
aqp 1.0-1 (2012-03-28)
Cleaned NAMESPACE and DESCRIPTION
removed un-necessary dependencies
join added to the plyr imports
added scales to the Imports as well, and removed rescaler() in the
code, repaced by scales::rescale
hack in munsell2rgb to avoid the ‘no visible binding for global
variable ’munsell’ at package R CMD check and make the whole thing more
robust (using load and system.file rather than data(…)
Dylan is now the only maintainer, as per Uwe request
when using plyr **ply function, switched from using the .(foo)
interface to “foo” - seems more foolproof
aqp 1.0 (2012-03-26)
1.0 release, still missing condensed vignettes- should be ready
soon
see https://casoilresource.lawr.ucdavis.edu/drupal/taxonomy/term/56
for samples
A small bug in profile_compare() was fixed, where slices were
evaluated as ‘soil’ based on the bottom depth of the profile, and NOT on
the presence of actual data. See ?profile_compare for details. This
change will have a minor affect on profile comparisons in cases where Cr
or R horizons (usually missing most characterization data) have been
extended down to some arbitrary depth (usually 150 or 200 cm) AND a
maximum depth of evaluation (max_d) was set beyond the actual depth of
most profiles in the collection.
aqp 0.99-9.8 (2012-03-02)
profile_compare() will now use site-level attributes if input is a
SoilProfileCollection
horizon / site level data currently weighted equally
NOTE: this feature is new, test-first!
minor bug fixes in profile_compare() to remove spurious
warnings
better error check in slice()
removed old code and documentation: format_slices() and
plot_slices()
aqp 0.99-9.6 (2012-02-21)
spurious warnings from profile_compare() caused by daisy() now
suppressed
warnings were generated when calling daisy() on a matrix of all NA
which typically occurred when using too-large a lower depth for
evaluation of D
preliminary support for diagnostic horizons via diagnostic_hz()
new examples
error and warnings messages cleaned-up
aqp 0.99-9.52 (2012-01-31)
converting all messages passed to the user from cat() to message()
and warning()
profile_compare() and slab() now default to no progress
bars, see ‘progress’ argument to adjust
profileApply() now provides access to all aspects of the
SoilProfileCollection object
that means that: profileApply(SPC, function(x) … ) operates on x,
which is a soilProfileCollection containing only profile_i note that
this may break functionality based on aqp 0.99-9.3
aqp 0.99-9.4 (2012-01-09)
site(SCP) <- d now tries to merge data from SPC@site
with ‘d’ via left join
this means that all new SPC objects will have a single column of
@site data, containing
profile IDs
plot-SoilProfileCollection now tries to guess the best orientation
of IDs
override with id.style=‘top’ or id.style=‘side’
slice-SoilProfileCollection now accepts ‘.’ to define all columns
should be returned at requested slices
slice(SPC, 1:50 ~ . ) # this means all vars. ID, top, bottom are
automatically removed
aqp 0.99-9.1 (2011-12-27)
pedonPC, NASIS, and SDA functions moved out of aqp, and
into new package: soilDB
removed associated, suggested packages from aqp
soilDB will be on CRAN shortly
new argument to plot(SoilProfileCollection, …, divide.hz=TRUE|FALSE)
that can optionally suppress plotting of dividing lines between horizons
(suggested by Ludwig Hilger)
new function profileApply() for applying functions by profile
aqp 0.99-9 (2011-12-22)
almost ready for AQP 1.0, vignettes are the last missing piece
:)
slice(SPC, …) is now 10-100x faster, scales linearly
slice(SPC, …) can simultaneously slice categorical and continuous
variables
converted ID column in sample data to character class
fixed a bug in slice() where NA would be returned when IDs were
factors
added test to depths()<- such that factor IDs are converted into
character IDs and a warning is issued
added join conditions for most functions using plyr::join(),
resulting in less chatter on the console
aqp 0.99-8.58 (2011-12-21)
WARNING: soil.slot.multiple() renamed to slab()
fixed minor bug in slice(), when numerical IDs are used: ddply() and
cast() implicitly re-order data…
added strict argument to many functions, to gracefully
account for bad horizon data
enforce quality control with strict=TRUE
munsell2rgb() is now 100x faster thanks to plyr::join()
note that factors cannot be used in the conversion, see:
https://github.com/hadley/plyr/issues/43
there is a check and conversion within the function that should
prevent segfaults
documentation updates, demo(aqp) updates, more examples
bug fix in slice(), now works with numeric OR categorical vars, but
NOT both…
matrix-style subsetting functional:
s[i, j] —> i is the profile index, and j is the horizon/slice
index
s[i, ] returns a SoilProfileCollection
s[, j] returns a SpatialPointsDataFrame when a single slice is
used
spatial_subset() can be used to extract members of a
SoilProfileCollection with a geometry (uses rgeos)
smarter $<- methods so that site/horizon data slots are
auto-selected
aqp 0.99-8.50 (2011-11-29)
added “site(SoilProfileCollection) <-” method for data.frame
started VERY basic AQP Introduction vignette… still
experimental
adding coercion methods for common objects and sp-class objects
matrix-style subsetting almost works:
s[i, j] —> i is the profile index, and j is the horizon/slice
index
added a ‘slice’ method for SoilProfileCollection objects
returns selected variables along depth slice(s) (i.e. no
aggregation)
added NAMESPACE file for R >= 2.14 compatibility
stabilized S4 class, working on S4-izing all related functions
preliminary documentation on the new S4 classes/methods
logistic power peak (LPP) can now be used to generate synthetic
depth functions
added contributing fraction annotation in
panel.depth_function()
aqp 0.99-8.4 (2011-10-04)
minor bug fixes and enhancements in PedonPC function
S4 interface to soil.slot.multiple()
aqp 0.99-8.2 (2011-09-21)
added S4 class/methods for SoilProfileCollection
this supersedes the (now removed) S3 SoilProfileList
classes
basic accessors/setters are in place, subject to change
profile_plot() now uses the SoilProfileCollection class
initSoilProfileList() is no longer supported; see depths() for
similar functionality
expect some tumultuous times ahead in the API… should be ironed
out by 1.0 release
aqp 0.99-8 (2011-09-14)
soil.slot() will now accept boundaries defining a ‘slab’ over which
aggregates are computed
soil.slot.multiple() now cleanly wraps soil.slot(), accepting all
arguments
these two changes make it possible to ask: “what is the wt. mean
value of some property within this slab, and among these groups?”
soil.slot.multiple() now uses a formula interface: NOTE that this
will break existing scripts (sorry)
aqp 0.99-7 (2011-09-01)
new functions for getting data out of PedonPC (MS Access)
databases [windows only for now]
get_site_data_from_pedon_db() : site and pedon aggregate data
get_hz_data_from_pedon_db() : horizon level data
get_colors_from_pedon_db() : formats and mixes multiple colors /
horizon
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
aqp 0.99-4 (2011-08-15)
code and documentation clean-up
Soil Sata Access (SDA) query functions have been added
mapunit_geom_by_ll_bbox() : get map unit geometry by
bounding box
MUKEYS_by_ll_bbox() : get map unit keys by bounding
box
SDA_query() : retrieve soil tabular data via query
written in SQL
additional customization added to plotSPC
two new sample data sets + examples
aqp 0.99-1 (2011-01-26)
soil.slot() and profile_compare() now have support for parallel
computation thanks to bug-fixes in plyr 1.4
plyr >= 1.4, foreach, and doMC packages are required
specific examples are not yet documented, but should be soon
this feature is still experimental! testing is advised
profile_compare() now calculates slice-wise
dissimilarity matrices in 1/3 the time (thanks llply!)
aqp 0.98-4 (2010-12-15)
fixed minor bug in soil.slot() when computing probabilities from
profiles that had missing horizons and that had only a single class
within the variable to be aggregated
aqp 0.98-1 (2010-11-23)
added basic demo: demo(aqp)
soil.slot() now computes aggregate probabilities over user-defined
segments
re-write of weighted profile aggregation functions
aqp package now requires Hmisc package
using Hmisc::wtd.{mean,var,quantile} to compute values
better adjustment of weights when computing weighted SD
fixes long-standing bugs with wt. mean/SD when NA present in x_i and
not in wt_i
weighted quantiles now computed
addition of new (experimental) S4 classes and methods
these are now in the aqp_S4 branch
added n.depth.ticks option to profile_plot()
profile_compare() algorithm stabilized, new default settings
removed code in profile_compare() that is now obsolete
note that this will cause changes to numerical classification of
soil profiles
aqp 0.97-1 (2010-10-06)
verified that weighted standard deviations are correct when seg_size
> 1
removed notices about possible problems with sd calculations
aqp 0.97 (2010-09-22)
soil.slot() streamlined and functionality restored to pre-0.95
condition
aqp 0.96-1 (2010-09-21)
fixed weighted mean / SD calculation when using 1 unit segments in
soil.slot()
wt. mean / SD still disabled for user-defined segment sizes
aqp 0.96 (2010-09-20)
temporarily disabled parallel computation, will be re-added in next
release
bug fixes in panel.depth_function where ‘groups’ was not
defined
bug fixes and major re-factoring of soil.slot() when called with
user-defined segment size, or segmenting vector:
SD values are probably too low due to an inflated ‘n’ in the
calculation
calculation of weighted mean and sd is currently disabled
aqp 0.95 (2010-09-15)
added VERY experimental support for parallel processing based on the
latest versions of plyr, doMC, and foreach packages
updated vignette with technical details on aggregation and
dissimilarity computation
new options to profile_plot()
aqp 0.94 (2010-08-11)
fixed bug in soil.slot() when aggregating a categorical variable,
with a user-supplied segmenting vector
soil.slot() now requires that categorical variables be encoded as
factors
aqp 0.93 (2010-08-07)
bug fixes, new documentation + examples
AQP now requires R >= 2.9.0
aqp 0.92 (2010-08-03)
including a new column in the results from soil.slot(), denoting
number of profiles used in slice-wise aggregation
added note to soil.slot() manual page highlighting possible problems
with SD calculation
aqp 0.90 (2010-07-13)
better error checking on profile aggregation and classification
functions
most functions now require that horizon depths are integers
aqp 0.89 (2010-07-10)
added plot_distance_graph() function for visualizing between-profile
dissimilarity
updated documentation: extended manual is now accessible as a
vignette
major improvements in profile_compare() when add_soil_flag=TRUE and
replace_na=TRUE
appears to create much more realistic groupings when there are both
shallow and deep soils in the collection
new functionality requires further testing
plotting under dendrograms generated by ape::plot.phylo() may need
some manual adjustments
aqp 0.88 (2010-07-06)
new version of plyr (1.0) should speed up most functions in aqp
package
added support for user-defined aggregate functions in soil.slot and
soil.slot.multiple