https://github.com/cran/aqp
Tip revision: c312f95d9caf634468f33f7790d48270d58148e0 authored by Dylan Beaudette on 07 April 2021, 21:50:02 UTC
version 1.29
version 1.29
Tip revision: c312f95
NEWS.md
# aqp 1.29 (2021-04-05)
* Several `SoilProfileCollection` methods that conflict with {dplyr} 1.0+ have been deprecated:
* `filter`, `mutate`, `group_by`, `summarize`
* New overloaded {base} names:
- {base}-like syntax: "filter" -> `subset`, "mutate" -> `transform`, "combine" -> `c`
* New unique {aqp}/SoilProfileCollection aliases:
- `*SPC` syntax: `filterSPC`, `mutateSPC`, `groupSPC`, `summarizeSPC`
* 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
* Use`combine()` 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.
* `mixMunsell`:
- gains argument for performing mixture estimation via wt. mean of CIELAB coordinates
- 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)
* `estimateSoilDepth` **loses** `top` 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
* `plotSPC` upgrades (https://github.com/ncss-tech/aqp/pull/146)
* new methods related to mollic epipedon: `mollic.thickness.requirement`, `hasDarkColors`
* new `estimateSoilDepth`-like methods for depth to multiple features via pattern matching: `depthOf`, `minDepthOf`, `maxDepthOf`
* soil texture helper functions (`ssc_to_texcl`, `texcl_to_ssc`, `texmod_to_fragvoltot`, `texture_to_taxpartsize`)
* optimization of `[i,]` `[,j]` subset methods for _data.frame_-based slots (https://github.com/ncss-tech/aqp/issues/135)
* new verbs: `mutate`, `mutate_profile` (https://github.com/ncss-tech/aqp/issues/118)
* ROSETTA centroids and water retention by texture class (https://github.com/ncss-tech/aqp/issues/131)
* fix for `getSurfaceHorizonDepth` with buried horizons / non-contiguous instances of matching horizons (https://github.com/ncss-tech/aqp/issues/132)
* fix for default `plotSPC` with small number of profiles ((https://github.com/ncss-tech/aqp/issues/128)
* remove implicit conversion to SpatialPointsDataFrame with unit-length `[` j-index subset ((https://github.com/ncss-tech/aqp/issues/125)
* fix in slab when `slab.structure[2] > max(x)`
# aqp 1.19.01 (2020-02-07)
* proof of concept for tidy SoilProfileCollection subsetting
* define `[[` subsetting method; an "ambivalent" accessor for site- or horizon-level properties
* new subset verbs `grepSPC`, `filter`, `subApply` for use in `%>%`-lines
# aqp 1.19 (2020-01-22)
* CRAN release
* new functions: `hzDesgn()`, get horizon designations from a SPC
* new functions: `hzdesgnname()`/`hzdesgnname()<-` and `hztexclname()`/`hztexclname()<-` get/set column containing horizon designations and texture classes
* better error/logic handling for `glom()`
# aqp 1.18.5 (2020-01-21)
* `profileApply()` enhancement for large `SoilProfileCollection` objects (https://github.com/ncss-tech/aqp/issues/112)
* add `profileApply()` `frameify` argument for `data.frame` output (https://github.com/ncss-tech/aqp/issues/111)
* `checkHzDepthLogic()` replaces `test_hz_logic()`
* thanks to [farver >= 2.0.3](https://CRAN.R-project.org/package=farver), `rgb2munsell()` and `colorQuantiles()` now uses the CIE2000 distance metric for color comparison
# aqp 1.18.4 (2020-01-06)
* bug fix (rare) when setting / replacing horizon attributes (https://github.com/ncss-tech/aqp/issues/105)
* bug fix in `colorQuantiles` until `farver` 2.0.2 is available on CRAN
* `SoilProfileCollection` object gains new slot: `@restrictions`, fix old objects with `rebuildSPC()`
# aqp 1.18.3 (2019-12-19)
* `evalMissingData()` gets new argument for relative vs. absolute evalulation of missing data
* `horizonColorIndices()`, `harden.rubification()`, `harden.melanization()`, `thompson.bell.darkness()` and associated functions in soilColorIndices.R
* fix for https://github.com/ncss-tech/aqp/issues/44
* fix for https://github.com/ncss-tech/aqp/issues/66
* new example data: `rowley2019`
* dropped some dependencies
# aqp 1.17.10 (2019-10-30)
* removing imported functions from `Hmisc` (`hdquantile`), loading `aqp` is now much faster
+ `slab()` now uses `stats::quantile()` as the default slab function
+ details at: https://github.com/ncss-tech/aqp/issues/79
+ 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 \dots 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 Jos? 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 http://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, containin 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
* planning addition of PCA by depth slice
* planning addition of equal-area spline fitting