aqp 1.25

This release of aqp marks a significant step towards major changes planed for version 2.0. Since 1.17, there have been major changes to the internals of the SoilProfileCollection object (thanks to @brownag) and associated methods. We expect some evolution (but less drastic as compared to the previous release) before version 2.0.

See NEWS.md for a complete listing of changes.

Important Changes

• estimateSoilDepth loses top and bottom arguments, these are automatically extracted
• 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
• default horizon ID (hzID) is now a character data type

Enhancements

SoilProfileCollection Internals

• new function duplicate will makes copies of profiles within a SoilProfileCollection
• two new SoilProfileCollection wrapper methods: munsell2SPC, spc2mpspline
• improvements to glom(..., invert=TRUE), glomApply, and better tests
• new wrapper method around glomApply: trunc for cases when top and bottom depth interval is the same for all profiles in a SoilProfileCollection
• enhanced SoilProfileCollection object validity checks via S4; new method spc_in_sync (#152)
• optimization of [ subset method and optional use of data.table (#155)
• depths<- has been optimized and minimally validates input data
• combine 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.
• 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
• optimization of [i,] [,j] subset methods for data.frame-based slots (#135)
• new verbs: mutate, mutate_profile (#118)
• define [[ subsetting method; an "ambivalent" accessor for site- or horizon-level properties
• new subset verbs grepSPC, filter, subApply for use in %>%-lines

Color / Visualization

• 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
• add returnData argument to contrastChart
• plotSPC upgrades (#146)

Everything Else

• 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 c/o @smroecker
• added segment c/o @smroecker

Additions

• new lookup table pms.munsell.lut for converting Pantone spot color codes to (closest) Munsell chip
• new example data us.state.soils: 50 state soils + PR and VI soils
• ROSETTA centroids and water retention by texture class (#131)

Bug Fixes

• fix for routing of NULL through $<- and horizons<- or site<- (#163)
• fix handling of missing metadata in (old) serialized SoilProfileCollection objects
• fix for promotion of data.table with character vector (not formula) interface
• fix for unit-length and zero-length legends in plotSPC
• fix for plot generic to show aqp::plot in ?plot
• fix for getSurfaceHorizonDepth with buried horizons / non-contiguous instances of matching horizons (#132)
• fix for default plotSPC with small number of profiles (#128)
• remove implicit conversion to SpatialPointsDataFrame with unit-length [ j-index subset ((#125)
• fix in slab when slab.structure[2] > max(x)

New Compatibility with Pipe-based Workflows!

The SoilProfileCollection object is now compatible with {magrittr} pipe %>% based workflows. Here is an example using select soil morphologic data from Jacobs (2002) "Redoximorphic Features as Indicators of Seasonal Saturation, Lowndes County, Georgia", a sample dataset available in {aqp} (jacobs2000)

# {aqp} + {magrittr} pipes
library(aqp)
library(magrittr)

# see ?jacobs2000 for details
data("jacobs2000", package = "aqp") 

# create a base plot to inspect full dataset
par(mar=c(0,0,0,2))
plot(jacobs2000, color = "matrix_color", 
     plot.order = order(jacobs2000$time_saturated))

# select 3 profiles along gradient, and truncate 50-150cm interval
jacobs.sub <- jacobs2000 %>% 
                subset(profile_id(.) %in% c("92-2","92-4",'92-7')) %>%
                trunc(50, 150)

# create a base plot
plot(jacobs.sub, color = "matrix_color")

# add redox concentrations
jacobs.sub %>% addVolumeFraction('concentration_pct', 
                     col = .$concentration_color, 
                     pch = 16, cex.max = 1)

# add redox depletions 
jacobs.sub %>% addVolumeFraction('depletion_pct', 
                     col = .$depletion_color, 
                     pch = 16, cex.max = 1)