diff --git a/news/index.html b/news/index.html index 79cb360e..a643a59f 100644 --- a/news/index.html +++ b/news/index.html @@ -83,7 +83,9 @@

aqp 2.1.0
  • 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
    • +
  • 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

    • aqp 2.0.4 (2024-07-30)2024-07-30

    diff --git a/pkgdown.yml b/pkgdown.yml index 8ecf9216..7a4151cd 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -9,4 +9,4 @@ articles: Munsell-color-conversion: Munsell-color-conversion.html NCSP: NCSP.html new-in-aqp-2: new-in-aqp-2.html -last_built: 2024-10-10T21:22Z +last_built: 2024-10-11T14:21Z diff --git a/reference/estimatePSCS.html b/reference/estimatePSCS.html index a049dce5..2d151d34 100644 --- a/reference/estimatePSCS.html +++ b/reference/estimatePSCS.html @@ -1,7 +1,8 @@ -Estimate boundaries of the particle size control section (U.S Soil Taxonomy; 12th edition) — estimatePSCS • aqpEstimate boundaries of the U.S Soil Taxonomy Particle Size Control Section — estimatePSCS • aqp @@ -73,15 +74,16 @@
    -

    Estimate boundaries of the particle size control section (U.S Soil Taxonomy; 12th edition)

    +

    Estimate boundaries of the U.S Soil Taxonomy Particle Size Control Section

    Source: R/estimatePSCS.R

    Estimates the upper and lower boundary of the particle size control section -by applying a programmatic version of the particle size control section key -from the Keys to Soil Taxonomy (12th edition).

    +for Mineral or Organic soilsby applying a programmatic version of the +particle size control section key from the Keys to Soil Taxonomy (13th edition). +See details for assumptions and required data elements.

    @@ -90,8 +92,9 @@

    Estimate boundaries of the particle size control section (U.S Soil Taxonomy; hzdesgn = hzdesgnname(p, required = TRUE), clay.attr = hzmetaname(p, "clay", required = TRUE), texcl.attr = hztexclname(p, required = TRUE), + lieutex = hzmetaname(p, "lieutex"), tax_order_field = "tax_order", - bottom.pattern = "Cr|R|Cd", + bottom.pattern = "Cr|R|Cd|m", simplify = TRUE, ... )

    @@ -107,17 +110,23 @@

    Arguments

    hzdesgn

    Name of the horizon attribute containing the horizon -designation. Default 'hzname'

    +designation. Default hzdesgnname(p, required = TRUE)

    clay.attr

    Name of the horizon attribute containing clay contents. -Default 'clay'

    +Default hzmetaname(p, "clay", required = TRUE)

    texcl.attr

    Name of the horizon attribute containing textural class -(used for finding sandy textures). Default 'texcl'

    +(used for finding sandy textures). Default hztexclname(p, required = TRUE)

    + + +
    lieutex
    +

    Optional data element used in addition to the horizon +designation to identify kinds of organic soil material for soils with organic +surfaces. Default: hzmetaname(p, "lieutex")

    tax_order_field
    @@ -129,12 +138,13 @@

    Arguments

    bottom.pattern

    Regular expression pattern to match a root-restrictive -contact. Default matches Cr, R or Cd. This argument is passed to both -estimateSoilDepth and getArgillicBounds.

    +contact. Default matches Cr, R, Cd or m. This argument is passed to both +minDepthOf() and getArgillicBounds().

    simplify
    -

    Return a length 2 vector with upper and lower boundary when p has length 1? Default TRUE.

    +

    Return a length 2 vector with upper and lower boundary when +p has length 1? Default TRUE.

    ...
    @@ -143,9 +153,11 @@

    Arguments

    Value

    -

    A numeric vector (when simplify=TRUE) containing the top and bottom depth of the particle +

    A numeric vector (when simplify=TRUE) containing the top and bottom +depth of the particle size control section. First value is top, second value is bottom. -If p contains more than one profile, the result is a data.frame with profile ID plus PSCS top and bottom depths.

    +If p contains more than one profile, the result is a data.frame with +profile ID plus PSCS top and bottom depths.

    Details

    @@ -153,7 +165,15 @@

    Details

    designations) with getArgillicBounds() as well as the presence of plow layers and surface organic soil material. Any getArgillicBounds() arguments may be passed to estimatePSCS.

    -

    Requires information on taxonomic order (to handle andisols).

    +

    Also, requires information on taxonomic order to handle Andisols.

    +

    In aqp 2.1, particle size control sections of organic soils Histosols and +Histels are supported. This requires setting the "lieutex" horizon metadata +column using hzmetaname<-() Horizon designations containing "f" or "W" +are recognized as permafrost and water layers, respectively, for application +of the organic soils key to control sections. In lieu textures "SPM" and +"PEAT" are used to identify low density organic materials used for surface +tier thickness. To avoid using the 160 cm surface tier, set the "lieutex" +column to any column that does not contain "SPM" or "PEAT" values.

    WARNING: Soils in arenic or grossarenic subgroups, with fragipans, or with strongly contrasting PSCs may not be classified correctly. The author would welcome a dataset to develop this functionality for.

    @@ -165,7 +185,7 @@

    References

    See also

    -

    getArgillicBounds, getSurfaceHorizonDepth

    +

    getArgillicBounds(), getSurfaceHorizonDepth()

    Author

    @@ -196,6 +216,23 @@

    Examples

    #> 7 P007 25 100 #> 8 P008 27 102 #> 9 P009 28 103 + +# change horizon texture and set inlieu texture column to turn +# first profile into an organic soil +sp1$name[1:6] <- c("Oi1", "Oi2", "Oi3", "Oaf", "Cf1", "Cf2") +sp1$texture <- as.character(sp1$texture) +sp1$texture[1:6] <- c("PEAT", "PEAT", "PEAT", "MUCK", "GRVLS", "GRVLS") +sp1$bottom[6] <- 200 +hzmetaname(sp1, 'lieutex') <- 'texture' + +y <- estimatePSCS(sp1[1, ], simplify = FALSE) + +# 74cm lower boundary is 25cm past the upper boundary of permafrost (49cm) +# but minimum depth is 100cm unless there is a root-limiting layer +y +#> id pscs_top pscs_bottom +#> 1 P001 0 100 +
    diff --git a/reference/index.html b/reference/index.html index 58585bf9..39b3710f 100644 --- a/reference/index.html +++ b/reference/index.html @@ -317,7 +317,7 @@

    All functions

    estimatePSCS()

    -

    Estimate boundaries of the particle size control section (U.S Soil Taxonomy; 12th edition)

    +

    Estimate boundaries of the U.S Soil Taxonomy Particle Size Control Section

    estimateSoilColor()