A B C D E F G H I J L M N O P R S T U V X misc
aqp-package | Algorithms for Quantitative Pedology |
accumulateDepths | Accumulate horizon depths, and reflect reversed depths, relative to new datum |
addBracket | Add Depth Brackets |
addDiagnosticBracket | Annotate Diagnostic Features |
addVolumeFraction | Symbolize Volume Fraction on a Soil Profile Collection Plot |
aggregateColor | Summarize Soil Colors |
aggregateSoilDepth | Probabalistic Estimation of Soil Depth within Groups |
alignTransect | Calculate Relative Positions from Transect Data |
allocate | Allocate soil properties within various classification systems. |
aqp | Algorithms for Quantitative Pedology |
aqp.env | Algorithms for Quantitative Pedology |
aqp_df_class | Get aqp_df_class entry from metadata or return a safe value. |
aqp_df_class-method | Get aqp_df_class entry from metadata or return a safe value. |
aqp_df_class<- | Get aqp_df_class entry from metadata or return a safe value. |
aqp_df_class<--method | Get aqp_df_class entry from metadata or return a safe value. |
argillic.clay.increase.depth | Return upper boundary of argillic horizon |
as | Coerce SoilProfileCollection with 'as()' |
as-method | Coerce SoilProfileCollection with 'as()' |
barron.torrent.redness.LAB | Barron & Torrent (1986) Redness Index in LAB color space |
bootstrapSoilTexture | Bootstrap Soil Texture Data |
brierScore | Multinominal Brier Score |
buntley.westin.index | Buntley-Westin (1965) Index |
c | Combine SoilProfileCollection objects |
c-method | Combine SoilProfileCollection objects |
ca630 | Soil Data from the Central Sierra Nevada Region of California |
checkHzDepthLogic | Check a SoilProfileCollection object for errors in horizon depths. |
checkSPC | Test for a valid SoilProfileCollection |
colorChart | Visualize soil colors in Munsell notation according to within-group frequency. |
colorContrast | Metrics of Contrast Suitable for Comparing Soil Colors |
colorContrastPlot | Color Contrast Plot |
colorQuantiles | Soil Color Range via Quantiles |
combine | Combine SoilProfileCollection objects |
combine-method | Combine SoilProfileCollection objects |
compositeSPC | Return a list representation of site and horizon level data |
compositeSPC-method | Return a list representation of site and horizon level data |
confusionIndex | Confusion Index |
contrastChart | Color Contrast Chart |
contrastClass | Soil Color Contrast |
coordinates | Get coordinates from spatial slot |
coordinates-method | Get coordinates from spatial slot |
coordinates<--method | Get coordinates from spatial slot |
correctAWC | Apply rock fragment or salt correction to available water content |
crit.clay.argillic | Determines threshold (minimum) clay content for argillic upper bound |
denormalize | Create a (redundant) horizon-level attribute from a site-level attribute |
depthOf | Get top or bottom depths of horizons matching a regular expression pattern |
depths<- | Initialize a SoilProfileCollection from a data.frame object |
depths<--method | Initialize a SoilProfileCollection from a data.frame object |
depthWeights | Return a vector of contributing fractions over a depth interval |
depthWeights-method | Return a vector of contributing fractions over a depth interval |
depth_units | Get depth units from metadata |
depth_units-method | Get depth units from metadata |
depth_units<- | Get depth units from metadata |
depth_units<--method | Get depth units from metadata |
diagnostic_hz | Retrieve diagnostic data from SoilProfileCollection |
diagnostic_hz-method | Retrieve diagnostic data from SoilProfileCollection |
diagnostic_hz<- | Add data to the diagnostic slot |
diagnostic_hz<--method | Add data to the diagnostic slot |
dice | Efficient Slicing of 'SoilProfileCollection' Objects |
duplicate | Duplicte Profiles of a SoilProfileCollection |
equivalentMunsellChips | Identify "equivalent" (whole number value/chroma) Munsell chips |
equivalent_munsell | Indices of "equivalent" Munsell chips in the 'munsell' data set |
estimateAWC | Estimate available water capacity for fine-earth fraction |
estimatePSCS | Estimate boundaries of the particle size control section (U.S Soil Taxonomy; 12th edition) |
estimateSoilDepth | Estimate Soil Depth |
evalGenHZ | Evaluate Generalized Horizon Labels |
evalMissingData | Evaluate Missing Data |
explainPlotSPC | Visual Explanation for 'plotSPC' |
fillHzGaps | Find and Fill Horizon Gaps |
findOverlap | Find Overlap within a Sequence |
fixOverlap | Fix Overlap within a Sequence via Simulated Annealing |
fragvol_to_texmod | Textural conversions |
generalize.hz | Generalize Horizon Names |
genhzTableToAdjMat | Horizon Transition Probabilities |
genSlabLabels | Slab-Wise Aggregation of SoilProfileCollection Objects |
get.increase.depths | Return the horizon top depths from a call to get.increase.matrix() |
get.increase.matrix | compute pair-wise distances to determine where an attribute increases within a vertical distance specified |
get.ml.hz | Determine ML Horizon Boundaries |
get.slice | Slicing of SoilProfileCollection Objects |
getArgillicBounds | Estimate upper and lower boundary of argillic diagnostic subsurface horizon |
getCambicBounds | Find all intervals that are potentially part of a Cambic horizon |
getClosestMunsellChip | Get Approximate Munsell Chip |
getLastHorizonID | Get IDs of Deepest Horizons by Profile |
getMineralSoilSurfaceDepth | Determine thickness of horizons (continuous from surface) matching a pattern |
getPlowLayerDepth | Determine thickness of horizons (continuous from surface) matching a pattern |
getSoilDepthClass | Generate Soil Depth Class Matrix |
getSurfaceHorizonDepth | Determine thickness of horizons (continuous from surface) matching a pattern |
glom | Subset soil horizon data using a depth or depth interval |
glom-method | Subset soil horizon data using a depth or depth interval |
glomApply | Subset an SPC by applying glom to each profile |
glomApply-method | Subset an SPC by applying glom to each profile |
grepSPC | Subset SPC with pattern-matching for text-based attributes |
grepSPC-method | Subset SPC with pattern-matching for text-based attributes |
groupedProfilePlot | Grouped Soil Profile Plot |
groupSPC | (EXPERIMENTAL) Store groupings within a profile collection. |
group_by | (EXPERIMENTAL) Store groupings within a profile collection. |
guessGenHzLevels | Guess Appropriate Ordering for Generalized Horizon Labels |
guessHzAttrName | Guess Horizon Slot Column Names |
guessHzDesgnName | Guess Horizon Slot Column Names |
guessHzTexClName | Guess Horizon Slot Column Names |
harden.melanization | Harden (1982) Melanization |
harden.rubification | Harden (1982) Rubification |
harmonize | Harmonize a property by profile-level denormalization for convenient visualization or analysis of ranges |
harmonize-method | Harmonize a property by profile-level denormalization for convenient visualization or analysis of ranges |
hasDarkColors | Find horizons with colors darker than a Munsell hue, value, chroma threshold |
horizonColorIndices | Horizon Color Indices |
horizonDepths | Set horizon depth column names |
horizonDepths-method | Set horizon depth column names |
horizonDepths<- | Set horizon depth column names |
horizonDepths<--method | Set horizon depth column names |
horizonNames | Set horizon column names |
horizonNames-method | Set horizon column names |
horizonNames<- | Set horizon column names |
horizonNames<--method | Set horizon column names |
horizons | Retrieve horizon data from SoilProfileCollection |
horizons-method | Retrieve horizon data from SoilProfileCollection |
horizons<- | Retrieve horizon data from SoilProfileCollection |
horizons<--method | Retrieve horizon data from SoilProfileCollection |
huePosition | Munsell Hue Reference and Position Searching |
huePositionCircle | Visual Description of Munsell Hue Ordering |
hurst.redness | Hurst (1977) Redness Index |
hzAbove | Horizons Above or Below |
hzBelow | Horizons Above or Below |
HzDepthLogicSubset | Subset 'SoilProfileCollection' Objects or Horizons via 'checkHzDepthLogic' |
hzDepthTests | Tests of horizon depth logic |
hzDesgn | Get horizon designation column name |
hzDesgn-method | Get horizon designation column name |
hzdesgnname | Get or Set Horizon Designation Column Name |
hzdesgnname-method | Get or Set Horizon Designation Column Name |
hzdesgnname<- | Get or Set Horizon Designation Column Name |
hzdesgnname<--method | Get or Set Horizon Designation Column Name |
hzDistinctnessCodeToOffset | Convert Horizon Boundary Distinctness to Vertical Offset |
hzID | Set horizon IDs |
hzID-method | Set horizon IDs |
hzID<- | Set horizon IDs |
hzID<--method | Set horizon IDs |
hzidname | Set horizon ID column name |
hzidname-method | Set horizon ID column name |
hzidname<- | Set horizon ID column name |
hzidname<--method | Set horizon ID column name |
hzOffset | Horizons Above or Below |
hztexclname | Get or Set Horizon Texture Class Column Name |
hztexclname-method | Get or Set Horizon Texture Class Column Name |
hztexclname<- | Get or Set Horizon Texture Class Column Name |
hztexclname<--method | Get or Set Horizon Texture Class Column Name |
hzTopographyCodeToLineType | Convert Horizon Boundary Topography to Line Type |
hzTopographyCodeToOffset | Convert Horizon Boundary Topography to Vertical Offset |
hzTransitionProbabilities | Horizon Transition Probabilities |
idname | Get profile ID column name |
idname-method | Get profile ID column name |
invertLabelColor | Make High Contrast Label Colors |
jacobs2000 | Soil Morphologic Data from Jacobs et al. 2002. |
L1_profiles | Create Representative Soil Profiles via L1 Estimator |
length | Get the number of profiles in a SoilProfileCollection |
length-method | Get the number of profiles in a SoilProfileCollection |
lunique | Eliminate duplicate instances of profile IDs in a list of SoilProfileCollections |
max | Get the maximum bottom depth in a SoilProfileCollection |
max-method | Get the maximum bottom depth in a SoilProfileCollection |
maxDepthOf | Get top or bottom depths of horizons matching a regular expression pattern |
metadata | Retrieve metadata from SoilProfileCollection |
metadata-method | Retrieve metadata from SoilProfileCollection |
metadata<- | Retrieve metadata from SoilProfileCollection |
metadata<--method | Retrieve metadata from SoilProfileCollection |
min | Get the minimum bottom depth in a SoilProfileCollection |
min-method | Get the minimum bottom depth in a SoilProfileCollection |
minDepthOf | Get top or bottom depths of horizons matching a regular expression pattern |
missingDataGrid | Missing Data Grid |
mixMunsell | Mix Munsell Colors via Spectral Library |
mollic.thickness.requirement | Calculate the minimum thickness requirement for Mollic epipedon |
mostLikelyHzSequence | Horizon Transition Probabilities |
munsell | Munsell to sRGB Lookup Table for Common Soil Colors |
munsell.spectra | Spectral Library of Munsell Colors |
munsell.spectra.wide | Spectral Library of Munsell Colors |
munsell2rgb | Convert Munsell Color Notation to other Color Space Coordinates (sRGB and CIELAB) |
munsell2spc | Merge Munsell Hue, Value, Chroma converted to sRGB & CIELAB into a SoilProfileCollection |
munsell2spc-method | Merge Munsell Hue, Value, Chroma converted to sRGB & CIELAB into a SoilProfileCollection |
munsellHuePosition | Munsell Hue Position Reference |
mutate | Transform a SPC with expressions based on site or horizon level attributes |
mutate-method | Transform a SPC with expressions based on site or horizon level attributes |
mutate_profile | Transform a SPC (by profile) with a set of expressions |
mutate_profile-method | Transform a SPC (by profile) with a set of expressions |
names | Get names of columns in site and horizons table |
names-method | Get names of columns in site and horizons table |
nrow | Get the number of horizons in a SoilProfileCollection |
nrow-method | Get the number of horizons in a SoilProfileCollection |
overlapMetrics | Find and Quantify Overlap within a 1D Sequence |
panel.depth_function | Lattice Panel Function for Soil Profiles |
parseMunsell | Parse Munsell Color Notation |
pbindlist | Combine a list of SoilProfileCollection objects |
pc | Numerical Soil Profile Comparison |
pc.SPC | Numerical Soil Profile Comparison |
permute_profile | Perturb soil horizon depths using boundary distinctness |
perturb | Perturb soil horizon depths using boundary distinctness |
plot | Create Soil Profile Sketches |
plot,SoilProfileCollection,ANY-method,plot.SoilProfileCollection | Create Soil Profile Sketches |
plot-method | Create Soil Profile Sketches |
plotColorMixture | Visualize Spectral Mixing of Munsell Colors |
plotColorQuantiles | Visualize Color Quantiles |
plotMultipleSPC | Plot Multiple 'SoilProfileCollection' Objects |
plotSPC | Create Soil Profile Sketches |
plot_distance_graph | Between Individual Distance Plot |
pms.munsell.lut | Pantone Colors / Munsell Lookup Table |
PMS2Munsell | Convert Pantone PMS codes to Munsell notation |
prepanel.depth_function | Lattice Panel Function for Soil Profiles |
previewColors | Preview Colors |
profileApply | Iterate over profiles in a SoilProfileCollection |
profileApply-method | Iterate over profiles in a SoilProfileCollection |
profileGroupLabels | Soil Profile Group Labels |
profileInformationIndex | Soil Profile Information Index |
profile_compare | Numerical Soil Profile Comparison |
profile_compare-method | Numerical Soil Profile Comparison |
profile_id | Set profile IDs |
profile_id-method | Set profile IDs |
profile_id<- | Set profile IDs |
profile_id<--method | Set profile IDs |
proj4string-method | Set PROJ4 string for the SoilProfileCollection |
proj4string<--method | Set PROJ4 string for the SoilProfileCollection |
random_profile | Random Profile |
rebuildSPC | Rebuild a SoilProfileCollection object |
reduceSPC | Select a subset of columns from a SoilProfileCollection |
reorderHorizons | Re-order corrupted horizon data |
reorderHorizons-method | Re-order corrupted horizon data |
repairMissingHzDepths | Repair Problematic Lower Horizon Depths |
replaceHorizons<- | Replace data in the horizon slot |
replaceHorizons<--method | Replace data in the horizon slot |
restrictions | Retrieve restriction data from SoilProfileCollection |
restrictions-method | Retrieve restriction data from SoilProfileCollection |
restrictions<- | Add data to the restrictions slot |
restrictions<--method | Add data to the restrictions slot |
rgb2munsell | sRGB to Munsell Color Conversion |
ROSETTA.centroids | Average Hydraulic Parameters from the ROSETTA Model by USDA Soil Texture Class |
rowley2019 | Soil Morphologic, Geochemical, and Mineralogy Data from Rowley et al. 2019. |
rruff.sample | Sample XRD Patterns |
segment | Segmenting of Soil Horizon Data by Depth Interval |
shannonEntropy | Shannon Entropy |
sierraTransect | Soil Physical and Chemical Data Related to Studies in the Sierra Nevada Mountains, CA, USA. |
sim | DEPRECATED Simulate Soil Profiles |
simulateColor | Simulate Soil Colors |
site | Retrieve site data from SoilProfileCollection |
site-method | Retrieve site data from SoilProfileCollection |
site<- | Retrieve site data from SoilProfileCollection |
site<--method | Retrieve site data from SoilProfileCollection |
siteNames | Set site column names |
siteNames-method | Set site column names |
siteNames<- | Set site column names |
siteNames<--method | Set site column names |
slab | Slab-Wise Aggregation of SoilProfileCollection Objects |
slab-method | Slab-Wise Aggregation of SoilProfileCollection Objects |
slab-methods | Slab-Wise Aggregation of SoilProfileCollection Objects |
slab2 | Slab-Wise Aggregation of SoilProfileCollection Objects |
slice | Slicing of SoilProfileCollection Objects |
slice-method | Slicing of SoilProfileCollection Objects |
slice-methods | Slicing of SoilProfileCollection Objects |
slice.fast | Slicing of SoilProfileCollection Objects |
slicedHSD | Tukey's HSD Over Slices |
soilColorSignature | Soil Profile Color Signatures |
soilPalette | Soil Color Palette |
SoilProfileCollection | An S4 object representation of a group of soil profiles. |
SoilProfileCollection-class | An S4 object representation of a group of soil profiles. |
soiltexture | Lookup tables for sand, silt, clay, texture class, and textural modifiers. |
SoilTextureLevels | Ranking Systems for USDS Soil Texture Classes |
soil_minerals | Munsell Colors of Common Soil Minerals |
sp1 | Soil Profile Data Example 1 |
sp2 | Honcut Creek Soil Profile Data |
sp3 | Soil Profile Data Example 3 |
sp4 | Soil Chemical Data from Serpentinitic Soils of California |
sp5 | Sample Soil Database #5 |
sp6 | Soil Physical and Chemical Data from Manganiferous Soils |
spc2mpspline | Missing-data-safe, SPC-wide wrapper around mpspline2::mpspline "continuous" 1cm output |
spc2mpspline-method | Missing-data-safe, SPC-wide wrapper around mpspline2::mpspline "continuous" 1cm output |
spc_in_sync | Quickly assess relative state of site and horizon slots |
spec2Munsell | Convert reflectance spectra to closest Munsell chip |
spectral.reference | Standard Illuminants and Observers |
split-method | Split a SoilProfileCollection object into a list of SoilProfileCollection objects. |
splitLogicErrors | Split a SoilProfileCollection into a list based on types of horizon logic errors |
ssc_to_texcl | Textural conversions |
subApply | Subset SPC based on result of performing function on each profile |
subApply-method | Subset SPC based on result of performing function on each profile |
subset | Subset a SoilProfileCollection with logical expressions |
subset-method | Subset a SoilProfileCollection with logical expressions |
subsetHz | Subset the horizons in a SoilProfileCollection using logical criteria |
subsetHz-method | Subset the horizons in a SoilProfileCollection using logical criteria |
subsetProfiles | DEPRECATED use subset |
subsetProfiles-method | DEPRECATED use subset |
summarize | Perform summaries on groups (from 'group_by') and create new site or horizon level attributes |
summarizeSPC | Perform summaries on groups (from 'group_by') and create new site or horizon level attributes |
summarizeSPC,SoilProfileCollection-method, | Perform summaries on groups (from 'group_by') and create new site or horizon level attributes |
summaryTauW | Compute weighted naive and _tau_ statistics for a cross-classification matrix |
tauW | Compute weighted naive and _tau_ statistics for a cross-classification matrix |
texcl_to_ssc | Textural conversions |
texmod_to_fragvoltot | Textural conversions |
textureTriangleSummary | Soil Texture Low-RV-High as Defined by Quantiles |
texture_to_taxpartsize | Textural conversions |
texture_to_texmod | Textural conversions |
thompson.bell.darkness | Thompson-Bell (1996) Index |
traditionalColorNames | Traditional Soil Color Names |
transform-method | Transform a SPC with expressions based on site or horizon level attributes |
trunc | Truncate a SoilProfileCollection to specified top and bottom depth |
trunc-method | Truncate a SoilProfileCollection to specified top and bottom depth |
unique | Uniqueness within a 'SoilProfileCollection' via MD5 Hash |
unique-method | Uniqueness within a 'SoilProfileCollection' via MD5 Hash |
unroll | Unroll Genetic Horizons |
us.state.soils | US State Soils |
validSpatialData | Get names of columns in site table |
validSpatialData-method | Get names of columns in site table |
xtableTauW | Format a LaTeX table with results |
$ | Get data from column of horizon or site data in a SoilProfileCollection |
$-method | Get data from column of horizon or site data in a SoilProfileCollection |
$<- | Set data in column of horizon or site data in a SoilProfileCollection |
$<--method | Set data in column of horizon or site data in a SoilProfileCollection |
.as.data.frame.aqp | Wrapper method for data.frame subclass conversion |
.data_dots | Make a data.frame from non-standard expressions evaluated in a data environment |
.lpp | Random Profile |
[-method | Matrix/data.frame-like access to profiles and horizons in a SoilProfileCollection |
[[ | Get column of horizon or site data in a SoilProfileCollection |
[[,SoilProfileCollection,ANY-method, | Get column of horizon or site data in a SoilProfileCollection |
[[-method | Get column of horizon or site data in a SoilProfileCollection |
[[<- | Add or change column of horizon or site data in a SoilProfileCollection |
[[<--method | Add or change column of horizon or site data in a SoilProfileCollection |