In DrylandEcology/rSW2funs: Functions for Derived Variables from SOILWAT2 Simulations

\pagebreak

How to use rSOILWAT2 to calculate SMRs and STRs

Load sufficiently recent versions of the packages rSOILWAT2 and rSW2funs

  stopifnot(
    requireNamespace("rSOILWAT2"),
    requireNamespace("rSW2funs")
  )

Load data and run rSOILWAT2 simulation

  # Load data for an example site: see ?rSOILWAT2::sw_exampleData
  sw_in <- rSOILWAT2::sw_exampleData
  # Run SOILWAT2 for the example site: see ?sw_exec
  sw_out <- rSOILWAT2::sw_exec(inputData = sw_in)

Calculate SMRs and STRs and underlying conditions for the example site

  # For more information, see ?calc_SMTRs
  SMTR <- rSW2funs::calc_SMTRs(sim_in = sw_in, sim_out = sw_out)

  # Check that simulation was successful and regimes could be identified:
  stopifnot(
    as.logical(
      SMTR[c(
        "regimes_done",
        "has_simulated_SoilTemp",
        "has_realistic_SoilTemp"
    )]),
    SMTR[["SMR_normalyears_N"]] > 2
  )

  # Take average across years and select regimes with more than 90% agreement
  crit_agree_frac <- 0.9
  x <- SMTR[["cond_annual"]]

  # --> Soil temperature regime is "Cryic"
  Tregime <- colMeans(SMTR[["STR"]]) >= crit_agree_frac
  print(Tregime)

  # --> Soil moisture regime is "Ustic" / "Typic-Tempustic"
  Sregime <- colMeans(SMTR[["SMR"]]) >= crit_agree_frac
  print(Sregime)

Explore the conditions that define the cryic STR:

  # The STR of the example site is cryic because:
  cryic <-
    #   - there is no permafrost:
    SMTR[["permafrost_yrs"]] == 0 &&

    #   - annual soil temperature at 50-cm depth is between 0 and 8 C:
    mean(x[, "MAT50"] > 0 & x[, "MAT50"] < 8) >= crit_agree_frac &&

    #  - soil is not saturated with water during some part of the summer:
    mean(x[, "CSPartSummer"] == 0) >= crit_agree_frac &&

    #  - soil does not have an O-horizon:
    !SMTR[["has_Ohorizon"]] &&

    #  - summer soil temperature at 50-cm depth is below 15 C:
    mean(x[, "T50jja"] < 15) >= crit_agree_frac

  print(cryic)

Explore the conditions that define the ustic SMR:

  # The SMR of the example site is ustic because:
  ustic <-
    #   - there is no permafrost:
    SMTR[["permafrost_yrs"]] == 0 &&

    #   - moisture control section is not dry for less than 90 cumulative days
    !(mean(x[, "COND3"]) >= crit_agree_frac) &&

    #   - annual soil temperature at 50-cm depth is not more than 22 C
    !(mean(x[, "COND4"]) >= crit_agree_frac) &&

    #   - soils are not completely dry for more than half the days of the year
    #     when soil temperature ato 50-cm depth is more than 5 C
    !(mean(x[, "COND1"]) >= crit_agree_frac) &&

    #   - soils are not moist for more than 45 consecutive days following
    #     the winter soltice
    !(mean(x[, "COND9"]) >= crit_agree_frac)

  print(ustic)

  # The SMR of the example site is typic-tempustic because:
  typic_tempustic <-
    #   - SMR is ustic
    ustic &&

    #   - soils are not moist for more than 45 consecutive days following
    #     the winter soltice
    !(mean(x[, "COND9"]) >= crit_agree_frac)

  print(typic_tempustic)

Determine resilience and resistance (RR) categories:

Note: cryic/ustic conditions have not been included by (Chambers et al. 2014)^[\ref{def:Chambers2014}]^ or (Maestas et al. 2016)^[\ref{def:Maestas2016}]^.

  # Determine resilience & resistance classes (sensu Chambers et al. 2014):
  clim <- rSOILWAT2::calc_SiteClimate(
    weatherList = rSOILWAT2::get_WeatherHistory(sw_in)
  )

  RR <- rSW2funs::calc_RRs_Chambers2014(
    Tregime,
    Sregime,
    MAP_mm = 10 * clim[["MAP_cm"]]
  )
  print(RR)

  # Determine resilience & resistance classes (sensu Maestas et al. 2016):
  RR <- rSW2funs::calc_RRs_Maestas2016(Tregime, Sregime)
  print(RR)

\pagebreak

Notes

• The rest of the vignette explains how rSOILWAT2 has implemented the calculations of soil moisture regime (SMR) and soil temperature regime (STR) and compares the logic with the 'Java Newhall Simulation Model' (jNSM) and with the 'Keys to Soil Taxonomy' (SSS 2014)^[\ref{def:SSS2014}]^.
• Quoted text is directly from SSS (2014)^[\ref{def:SSS2014}]^. So direction of a logic may be opposite of a condition, which will be indicated by ! before the condition.
• jNSM calculations can be found at end of this document. Line numbers refer to file 'BASICSimulationModel.java' (jNSM 2016^[\ref{def:jNSM2016}]^).

Definitions of conditions

Our interpretations of SSS (2014)^[\ref{def:SSS2014}]^ -- language refers to soil layers, not parts

• Dry := soil water potential < -1.5 MPa "the moisture tension is 1500 kPa or more" (p. 29, SSS 2014^[\ref{def:SSS2014}]^)
• Moist/wet := soil water potential >= -1.5 MPa "water is held at a tension of less than 1500 kPa but more than zero" (p. 29, SSS 2014^[\ref{def:SSS2014}]^)

• Saturated := soil water potential >= -0.033 MPa

• \label{def:histic_epipedon} Histic epipedon := a horizon that is periodically saturated with water and that has sufficiently high amounts of organic carbon (O.C. 12 to 18%, by weight, depending on clay content) to be considered organic soil material. Typically, it is at (or near) the surface and is peat or muck at least 20 cm thick." (p.3-10, SSS 2015^[\ref{def:SSS2015}]^)

• \label{def:Ohorizon} O-horizon := "Horizons [...] dominated by organic soil materials. [...] Some O horizons [...] consist of slightly decomposed to highly decomposed litter, such as leaves, needles, twigs, moss, and lichens, that has been deposited on the surface of either mineral or organic soils." (p. 335, SSS 2014^[\ref{def:SSS2014}]^)
• \label{def:OSM} Organic soil material (OSM) := "Soil material that contains more than the amounts of organic carbon described above for mineral soil material is considered organic soil material" (p. 3, SSS 2014^[\ref{def:SSS2014}]^)
• \label{def:MSM} Mineral soil material (MSM) := "(less than 2.0 mm in diameter) either: 1) Is saturated with water for less than 30 days (cumulative) per year in normal years and contains less than 20 percent (by weight) organic carbon; or 2) Is saturated with water for 30 days or more (cumulative) in normal years (or is artificially drained) and, excluding live roots, has an organic carbon content (by weight) of: * Less than 18 percent if the mineral fraction contains 60 percent or more clay; or * Less than 12 percent if the mineral fraction contains no clay; or * Less than 12 + (clay percentage multiplied by 0.1) percent if the mineral fraction contains less than 60 percent clay." (p. 3, SSS 2014^[\ref{def:SSS2014}]^)

Conditions for Soil Moisture Regimes

• \label{def:COND0} COND0: precipitation exceeds AET in all months
• \label{def:COND1} COND1: Dry in ALL layers for more than half of the CUMULATIVE days per year when the soil temperature at a depth of 50cm is above 5C
• \label{def:COND2} COND2: Moist in ANY layer for less than 90 CONSECUTIVE days when the soil temperature at a depth of 50cm is above 8C
• \label{def:COND2_1} COND2_1: Moist in ANY layer for less than 180 CONSECUTIVE days when the soil temperature at a depth of 50cm is above 8C
• \label{def:COND2_2} COND2_2: Moist in ANY layer for less than 270 CONSECUTIVE days when the soil temperature at a depth of 50cm is above 8C
• \label{def:COND2_3} COND2_3: Moist in ANY layer for less or equal than 45 CONSECUTIVE days when the soil temperature at a depth of 50cm is above 8C
• \label{def:COND3} COND3: MCS is dry in ANY layer for < 90 CUMULATIVE days -- sum of days with any dry layer < 90
• \label{def:COND3_1} COND3_1: MCS is dry in ANY layer for < 30 CUMULATIVE days -- sum of days with any dry layer < 30
• \label{def:COND4} COND4: The means annual soil temperature at 50cm is >= 22C
• \label{def:COND5} COND5: The absolute difference between the temperature in winter @ 50cm and the temperature in summer @ 50cm is >= 6C
• \label{def:COND6} COND6: Dry in ALL layers LESS than 45 CONSECUTIVE days in the 4 months following the summer solstice
• \label{def:COND6_1} COND6_1: Dry in ALL layers MORE than 90 CONSECUTIVE days in the 4 months following the summer solstice
• \label{def:COND7} COND7: MCS is moist in ANY layer for more than 180 CUMULATIVE days
• \label{def:COND8} COND8: MCS is moist in ANY layer for more than 90 CONSECUTIVE days
• \label{def:COND9} COND9: Moist in ALL layers MORE than 45 CONSECUTIVE days in the 4 months following the winter solstice
• \label{def:COND10} COND10: Dry in ALL layers for more or equal to 360 days

Conditions for Anhydrous Soils

• \label{def:AnhCOND1} AnhCOND1 : Mean Annual soil temperature at 50 cm depth is less than or equal to 0C
• \label{def:AnhCOND2} AnhCOND2 : Daily soil temperature of all soil layers in 10-70 cm < 5 C
• \label{def:AnhCOND3} AnhCOND3 : In the Lahn Depth, 1/2 of soil dry

  1/2 CUMULATIVE days when Mean Annual ST > 0C

Conditions for Soil Temperature Regimes

• \label{def:st_depth} st_depth : "The control section for soil temperature is either at a depth of 50 cm below the soil surface or at the upper boundary of a root-limiting layer, whichever is shallower." (p. 329, SSS 2014^[\ref{def:SSS2014}]^)
• \label{def:stCOND0} stCOND0 : Annual mean soil temperature of the same layer is less than 0 C for at least two consecutive years for at least one layer
• \label{def:stCOND1} stCOND1 : Mean annual soil temperature at st_depth^[\ref{def:st_depth}]^ is <= 0 C
• \label{def:stCOND2} stCOND2 : Mean annual soil temperature at st_depth^[\ref{def:st_depth}]^ is < 8 C
• \label{def:stCOND3} stCOND3 : Mean annual soil temperature at st_depth^[\ref{def:st_depth}]^ is < 15 C
• \label{def:stCOND4} stCOND4 : Mean annual soil temperature at st_depth^[\ref{def:st_depth}]^ is < 22 C
• \label{def:stCOND5} stCOND5 : Any layer of soil is saturated with water during some part of the summer, e.g., for the northern hemisphere, June 1 (doy 244) - Aug31 (doy 335)
• \label{def:stCOND6} stCOND6 : Mean summer soil temperature at st_depth^[\ref{def:st_depth}]^ is < 13 C
• \label{def:stCOND7} stCOND7 : Mean summer soil temperature at st_depth^[\ref{def:st_depth}]^ is < 6 C
• \label{def:stCOND8} stCOND8 : Mean summer soil temperature at st_depth^[\ref{def:st_depth}]^ is < 15 C
• \label{def:stCOND9} stCOND9 : Mean summer soil temperature at st_depth^[\ref{def:st_depth}]^ is < 8 C

Soil Moisture Regimes

Undefined

• rSOILWAT2
  • not one of {perudic, aridic, xeric, ustic, udic, anhydrous}
• jNSM (2016)^[\ref{def:jNSM2016}]^ (line 3060)
  • not one of {perudic, aridic, xeric, ustic, udic}

Perudic

• Regime characteristic of areas where precipitation exceeds evapotranspiration every month
• rSOILWAT2
  • COND0^[\ref{def:COND0}]^
• jNSM (2016)^[\ref{def:jNSM2016}]^ (lines 2977ff)
  • perudic: [COND0^[\ref{def:COND0}]^] swt != 0
• Characteristics (SSS 2014^[\ref{def:SSS2014}]^)
  • [COND0^[\ref{def:COND0}]^] precipitation exceeds evapotranspiration in all months of normal years
  • the moisture tension rarely reaches 100 kPa in the soil moisture control section
• Generalized Characteristics (SSS 2015^[\ref{def:SSS2015}]^)
  • The soil is almost always moist; soil tension is rarely > 100 kPa (about >1 bar)
  • Precipitation exceeds evapotranspiration by plants in every month.
• Remarks
  • Somewhat unclear if PET or AET should be compared with PPT. "evapotranspiration by plants" sounds like AET, but jNSM uses PET. rSOILWAT2 follows jNSM and uses PET.

Udic

• Regime characteristic of humid regions with seasonally well distributed precipitation
• rSOILWAT2
  • COND3^[\ref{def:COND3}]^ & {{!COND4^[\ref{def:COND4}]^ & COND5^[\ref{def:COND5}]^ & COND6^[\ref{def:COND6}]^} | !{!COND4^[\ref{def:COND4}]^ & COND5^[\ref{def:COND5}]^}}
• jNSM (2016)^[\ref{def:jNSM2016}]^ (lines 3011ff)
  • not one of {perudic, aridic, xeric}
  • udic: [COND3^[\ref{def:COND3}]^] (nd[1] + nd[2]) < 90
  • qualifier:
    • IF ([COND3_1^[\ref{def:COND3_1}]^] (nd[1] + nd[2]) < 30) THEN "typic"
    • ELSEIF ([!COND5^[\ref{def:COND5}]^] dif < 5) THEN "dry-tropudic"
    • ELSE "dry-tempudic"
• Characteristics (SSS 2014^[\ref{def:SSS2014}]^)
  • [COND3^[\ref{def:COND3}]^] "not dry in any part for as long as 90 cumulative days in normal years"
  • AND
  • IF
    • [!COND4^[\ref{def:COND4}]^] "mean annual soil temperature is lower than 22 C"
    • AND
    • [COND5^[\ref{def:COND5}]^] "mean winter and mean summer soil temperatures at a depth of 50 cm below the soil surface differ by 6 C or more"
  • THEN
    • IF [COND6^[\ref{def:COND6}]^] "dry in all parts for less than 45 consecutive days in the 4 months following the summer solstice"
    • THEN UDIC
    • ELSE not UDIC
  • ELSE UDIC
  • AND
    • "except for short periods, a three- phase system, solid-liquid-gas, in part or all of the soil moisture control section when the soil temperature is above 5 C"
• Generalized Characteristics (SSS 2015^[\ref{def:SSS2015}]^)
  • Soil is dry < 90 cumulative days in most years
  • Soil is dry < 45 consecutive days in summer and early fall (except in very warm areas and locations where there is little difference between summer and winter soil temperatures).
• Remarks
  • jNSM ignores COND4^[\ref{def:COND4}]^, COND5^[\ref{def:COND5}]^, and COND6^[\ref{def:COND6}]^
  • rSOILWAT2 and jNSM ignore "except for short periods, a three- phase system, solid-liquid-gas, in part or all of the soil moisture control section when the soil temperature is above 5 C"

Ustic

• Regime characteristic of semiarid climates where moisture is limited but available for portions of the growing season
• rSOILWAT2
  • !permafrost & !COND3^[\ref{def:COND3}]^ & ([(COND4^[\ref{def:COND4}]^ | !COND5^[\ref{def:COND5}]^) & (COND7^[\ref{def:COND7}]^ | COND8^[\ref{def:COND8}]^)] | [(!(COND4^[\ref{def:COND4}]^ | !COND5^[\ref{def:COND5}]^) & !COND1^[\ref{def:COND1}]^ & {COND9^[\ref{def:COND9}]^ & COND6^[\ref{def:COND6}]^ | !COND9^[\ref{def:COND9}]^})])
• jNSM (2016)^[\ref{def:jNSM2016}]^ (lines 3032ff)
  • not one of {perudic, aridic, xeric, udic}
  • ustic: not pergelic && not cryic
  • qualifier:
    • IF ([COND5^[\ref{def:COND5}]^] dif >= 5) {
      • IF ([!COND9^[\ref{def:COND9}]^] nccm <= 45) THEN "typic-tempustic"
      • ELSEIF ([!COND6^[\ref{def:COND6}]^] nccd > 45) THEN "xeric-tempustic"
      • ELSE "wet-tempustic"
    • } ELSE {
      • IF ([COND2_1^[\ref{def:COND2_1}]^] ncpm[2]) < 180) THEN "aridic-tropustic"
      • ELSEIF ([COND2_2^[\ref{def:COND2_2}]^] ncpm[2] < 270) THEN "typic-tropustic"
      • ELSE "udic"
    • }
• Characteristics (SSS 2014^[\ref{def:SSS2014}]^)
  • "not applied to soils that have permafrost" AND
  • IF
    • [COND4^[\ref{def:COND4}]^] "mean annual soil temperature is 22 C or higher"
    • OR
    • [!COND5^[\ref{def:COND5}]^] "mean summer and winter soil temperatures differ by less than 6 C at a depth of 50 cm below the soil surface"
  • THEN
    • [!COND3^[\ref{def:COND3}]^] "dry in some or all parts for 90 or more cumulative days in normal years"
    • AND
    • IF
      • [COND7^[\ref{def:COND7}]^] "moist in some part either for more than 180 cumulative days per year"
      • OR
      • [COND8^[\ref{def:COND8}]^] "moist for 90 or more consecutive days"
    • THEN USTIC
    • ELSE not USTIC
  • ELSE
    • [!COND3^[\ref{def:COND3}]^] "dry in some or all parts for 90 or more cumulative days"
    • AND
    • [!COND1^[\ref{def:COND1}]^] "not dry in all parts for more than half of the cumulative days when the soil temperature at a depth of 50 cm is higher than 5 C"
    • AND
    • IF
      • [COND9^[\ref{def:COND9}]^] "moist in all parts for 45 or more consecutive days in the 4 months following the winter solstice"
      • THEN
      • IF [COND6^[\ref{def:COND6}]^] "dry in all parts for less than 45 consecutive days in the 4 months following the summer solstice"
      • THEN USTIC
      • ELSE not USTIC
    • ELSE USTIC

• Generalized Characteristics (SSS 2015^[\ref{def:SSS2015}]^)

  • In areas that have very warm average annual soil temperature (> 22 C) or that have little difference (< 6 C) between winter and summer soil temperatures
    • The soil is dry for > 90 cumulative days during the year, but
    • The soil is moist during the year for > 90 consecutive days or > 180 cumulative days Or:

  • In other areas with cold to warm soil temperatures (< 22 C):

    • The soil is dry for > 90 cumulative days, but

    • The soil is moist for > 50% of the growing season (when soil temperature > 5 C).

  Or: In other areas where the soil is moist for > 45 consecutive days in winter and early spring, the soil is dry for < 45 consecutive days in summer and early fall. Remarks * jNSM does not explicitly calculate ustic, instead it represents the "other" category (except for the very cold areas)

Xeric

• Regime characteristic of a Mediterranean-type climate with cool, moist winters and warm, dry summers
• rSOILWAT2
  • !COND6^[\ref{def:COND6}]^ & COND9^[\ref{def:COND9}]^ & !COND4^[\ref{def:COND4}]^ & COND5^[\ref{def:COND5}]^
• jNSM (2016)^[\ref{def:jNSM2016}]^ (lines 3000ff)
  • not one of {perudic, aridic}
  • xeric: tma < 22 && dif >= 5 && nccd >= 45 && nccm >= 45
    • equivalent to !COND4^[\ref{def:COND4}]^ && COND5^[\ref{def:COND5}]^ && !COND6^[\ref{def:COND6}]^ && COND9^[\ref{def:COND9}]^
  • qualifier:
    • IF ([COND6_1^[\ref{def:COND6_1}]^] nccd > 90) THEN "dry"
    • ELSE "typic"
• Characteristics (SSS 2014^[\ref{def:SSS2014}]^)
  • [COND9^[\ref{def:COND9}]^] "moist in all parts for 45 or MORE consecutive days in the 4 months following the winter solstice"
  • AND
  • [!COND6^[\ref{def:COND6}]^] "Dry in all parts for 45 or MORE consecutive days in the 4 months following the summer solstice"
• Generalized Characteristics (SSS 2015^[\ref{def:SSS2015}]^)
  • The soil is moist for > 45 consecutive days in winter and early spring and dry for > 45 consecutive days in summer and early fall.
  • The soil is moist is for > 50% of the growing season (when soil temp is > 5 C).
• Remarks
  • SSS (2014)^[\ref{def:SSS2014}]^ does not mention COND4^[\ref{def:COND4}]^ and COND5^[\ref{def:COND5}]^ except maybe indirectly by "Mediterranean-type climate with cool, moist winters and warm, dry summers"

Aridic

• Regime characteristic of arid and semiarid climates that are unsuitable for cultivation without irrigation
• rSOILWAT2
  • COND1^[\ref{def:COND1}]^ & COND2^[\ref{def:COND2}]^
• jNSM (lines 2988ff)
  • not perudic
  • aridic: [COND1^[\ref{def:COND1}]^] nsd[1] > (lt5c / 2) && [COND2^[\ref{def:COND2}]^] ncpm[2] < 90
  • qualifier:
    • IF ([COND10^[\ref{def:COND10}]^] nd[1] == 360) THEN "extreme"
    • ELSEIF ([COND2_3^[\ref{def:COND2_3}]^] ncpm[2] <= 45) THEN "typic"
    • ELSE "weak"
• Characteristics (SSS 2014^[\ref{def:SSS2014}]^)
  • [COND1^[\ref{def:COND1}]^] "Dry in all parts for more than half of the cumulative days per year when the soil temperature at a depth of 50 cm below the soil surface is above 5 C"
  • AND
  • [COND2^[\ref{def:COND2}]^] "Moist in some or all parts for less than 90 consecutive days when the soil temperature at a depth of 50 cm below the soil surface is above 8 C."
• Generalized Characteristics (SSS 2015^[\ref{def:SSS2015}]^)
  • During the growing season:
    • The soil is dry more than half of the total days.
    • The soil is moist < ~90 consecutive days.

Anhydrous

• Very cold and very dry soil conditions
• rSOILWAT2
  • AnhCOND1^[\ref{def:AnhCOND1}]^ & AnhCOND2^[\ref{def:AnhCOND2}]^ & AnhCOND3^[\ref{def:AnhCOND3}]^
• jNSM (2016)^[\ref{def:jNSM2016}]^: not considered
• Characteristics (p. 18-19 in SSS 2014^[\ref{def:SSS2014}]^)
  • [AnhCOND1^[\ref{def:AnhCOND1}]^] "Mean annual soil temperature of 0C or colder"
  • AND
  • At a depth of 10 to 70 cm:
    • [AnhCOND2^[\ref{def:AnhCOND2}]^] "has a soil temperature of less than 5 C throughout the year"
    • AND
    • "Includes no ice-impregnated permafrost"
    • AND
      • [AnhCOND3^[\ref{def:AnhCOND3}]^] "Is dry (water held at 1500 kPa or more) in one-half or more of the soil for one-half or more of the time the layer has a soil temperature above 0 C",
      • OR
      • "Has a rupture-resistance class of loose to slightly hard throughout when the soil temperature is 0 C or colder, except where a cemented pedogenic horizon occurs."
• Generalized Characteristics (SSS 2015^[\ref{def:SSS2015}]^)
  • Mean annual soil temperature is < 0 C
  • At a depth of 10 to 70 cm:
    • Temperature is < 5 C all year, and
    • Soil has no ice-impregnated permafrost, and
    • When temperature is > 0 C (> 1500 kPa tension), soil is very dry, or
    • When temperature is < 0 C, soil is loose to just slightly hard (unless there is pedogenic cementation).
• Remarks
  • rSOILWAT2 ignores "Includes no ice-impregnated permafrost" and "Has a rupture-resistance class of loose to slightly hard throughout when the soil temperature is 0 C or colder, except where a cemented pedogenic horizon occurs."

Soil Temperature Regimes

We currently ignore the 'iso-' prefix, i.e., "the mean summer and mean winter soil temperatures differ by less than 6 C at a depth of 50 cm or at a densic, lithic, or paralithic contact, whichever is shallower", which is applicable to frigid, mesic, thermic, and hyperthermic regimes (SSS 2014^[\ref{def:SSS2014}]^)

Permafrost

• Permanently frozen layers
• "Permafrost may be impregnated by ice or, in the case of insufficient interstitial water, may be dry." (SSS 2014^[\ref{def:SSS2014}]^)
• rSOILWAT2
  • stCOND0^[\ref{def:stCOND0}]^
• jNSM (2016)^[\ref{def:jNSM2016}]^: not considered
• Characteristics (p. 28 in SSS 2014^[\ref{def:SSS2014}]^)
  • [stCOND0^[\ref{def:stCOND0}]^] "a thermal condition in which a material (including soil material) remains below 0 C for 2 or more years in succession"
• Generalized Characteristics (SSS 2015^[\ref{def:SSS2015}]^)
  • p. 3-101: "Layer has temperature of < 0 C for 2 or more consecutive years."

Gelic

• "Gelic materials are mineral (MSM^[\ref{def:MSM}]^) or organic soil materials (OSM^[\ref{def:OSM}]^) that show evidence of cryoturbation (frost churning) and/or ice segregation in the active layer (seasonal thaw layer) and/or the upper part of the permafrost" (SSS 2014^[\ref{def:SSS2014}]^)
• "The gelic soil temperature regime has not been documented in soils of the continental U.S. but occurs in the soils of Alaska." (SSS 2015^[\ref{def:SSS2015}]^)
• rSOILWAT2
  • stCOND1^[\ref{def:stCOND1}]^ | stCOND0^[\ref{def:stCOND0}]^
• jNSM (2016)^[\ref{def:jNSM2016}]^: calls this regime "pergelic"
  • [stCOND1^[\ref{def:stCOND1}]^] tma < 0
• Characteristics (SSS 2014^[\ref{def:SSS2014}]^)
  • [stCOND1^[\ref{def:stCOND1}]^] "mean annual soil temperature at or below 0 C (in Gelic suborders and Gelic great groups) or 1 C or lower (in Gelisols)"
• Generalized Characteristics (SSS 2015^[\ref{def:SSS2015}]^)
  • "Soil is <= 0 C"

Cryic

• Cryic soils are cold but have no permafrost and they are cold also during summer.
• "Too cold for virtually all crops" (SSS 2015^[\ref{def:SSS2015}]^)
• rSOILWAT2
  • !stCOND0^[\ref{def:stCOND0}]^ & !stCOND1^[\ref{def:stCOND1}]^ & stCOND2^[\ref{def:stCOND2}]^ & (![stCOND5^[\ref{def:stCOND5}]^ & {!O-horizon^[\ref{def:Ohorizon}]^ & stCOND8^[\ref{def:stCOND8}]^} | {O-horizon^[\ref{def:Ohorizon}]^ & stCOND9^[\ref{def:stCOND9}]^}] | [stCOND5^[\ref{def:stCOND5}]^ & {!O-horizon^[\ref{def:Ohorizon}]^ & stCOND6^[\ref{def:stCOND6}]^} | {O-horizon^[\ref{def:Ohorizon}]^ & stCOND7^[\ref{def:stCOND7}]^}])
• jNSM (2016)^[\ref{def:jNSM2016}]^:
  • [![stCOND1^[\ref{def:stCOND1}]^]] tma >= 0 && [stCOND2^[\ref{def:stCOND2}]^] tma < 8 && [stCOND8^[\ref{def:stCOND8}]^] ((st - cs) < 15)
• Characteristics (SSS 2014^[\ref{def:SSS2014}]^)
  • [!stCOND0^[\ref{def:stCOND0}]^] "not have permafrost"
  • AND
  • IF "mineral soils^[\ref{def:MSM}]^"
    • IF [!stCOND5^[\ref{def:stCOND5}]^] "not saturated with water during some part of the summer" "(June, July, and August in the Northern Hemisphere and December, January, and February in the Southern Hemisphere)"
      • IF "no O-horizon^[\ref{def:Ohorizon}]^"
      • IF [stCOND8^[\ref{def:stCOND8}]^] mean summer soil temperature "between 0 C to 15 C" THEN cryic
      • ELSE O-horizon^[\ref{def:Ohorizon}]^"
      • IF [stCOND9^[\ref{def:stCOND9}]^] mean summer soil temperature "between 0 C to 8 C" THEN cryic
    • ELSE "soil is saturated with water during some part of the summer"
      • IF "no O-horizon^[\ref{def:Ohorizon}]^"
      • IF [stCOND6^[\ref{def:stCOND6}]^] mean summer soil temperature "between 0 C to 13 C" THEN cryic
      • ELSE O-horizon^[\ref{def:Ohorizon}]^ OR "histic epipedon^[\ref{def:histic_epipedon}]^"
      • IF [stCOND7^[\ref{def:stCOND7}]^] mean summer soil temperature "between 0 C to 6 C" THEN cryic
  • ELSE "[organic soils^[\ref{def:OSM}]^"
    • IF [stCOND7^[\ref{def:stCOND7}]^] mean summer soil temperature "between 0 C to 6 C" THEN cryic
• Generalized Characteristics (SSS 2015^[\ref{def:SSS2015}]^)
  • "Soil is > 0 to < 8 C but has no permafrost and summer temperatures are also cold"
• Remarks
  • jNSM (2016)^[\ref{def:jNSM2016}]^ does not distinguish between "mineral ^[\ref{def:MSM}]^" and "[organic material^[\ref{def:OSM}]^". Thus, it ignores conditions stCOND5^[\ref{def:stCOND5}]^, stCOND6^[\ref{def:stCOND6}]^, stCOND7^[\ref{def:stCOND7}]^, and stCOND9^[\ref{def:stCOND9}]^. It assumes that soils are "not saturated with water during some part of the summer" ([!stCOND5^[\ref{def:stCOND5}]^]) and have "no O-horizon^[\ref{def:Ohorizon}]^", when testing for the cryic regime with [stCOND8^[\ref{def:stCOND8}]^].
  • rSOILWAT2 ignores "organic soils^[\ref{def:OSM}]^", but considers the presence of O-horizons^[\ref{def:Ohorizon}]^.

Frigid

• "Too cold for all but cold weather crops, such as wheat, oats, or barley" (SSS 2015^[\ref{def:SSS2015}]^)
• rSOILWAT2
  • !stCOND0^[\ref{def:stCOND0}]^ & !stCOND1^[\ref{def:stCOND1}]^ & stCOND2^[\ref{def:stCOND2}]^ & !cryic
• jNSM (2016)^[\ref{def:jNSM2016}]^:
  • [stCOND2^[\ref{def:stCOND2}]^] tma < 8 && [!stCOND8^[\ref{def:stCOND8}]^] ((st - cs) >= 15) && [scaled COND5^[\ref{def:COND5}]^?] (dif * fcd) > 5
• Characteristics (SSS 2014^[\ref{def:SSS2014}]^)
  • "A soil with a frigid soil temperature regime is warmer in summer than a soil with a cryic regime, but its mean annual temperature is between 0 and 8 C"
• Generalized Characteristics (SSS 2015^[\ref{def:SSS2015}]^)
  • "Soil is > 0 to < 8 C (but warmer than cryic soils in summer)"
• Remarks
  • Unclear why jNSM (2016)^[\ref{def:jNSM2016}]^ appears to apply a scaled version of COND5^[\ref{def:COND5}]^

Mesic

• "Suited to crops such as corn, wheat, and soybeans" (SSS 2015^[\ref{def:SSS2015}]^)
• rSOILWAT2
  • !stCOND2^[\ref{def:stCOND2}]^ & stCOND3^[\ref{def:stCOND3}]^
• jNSM (2016)^[\ref{def:jNSM2016}]^:
  • [!stCOND2^[\ref{def:stCOND2}]^] tma >= 8 && [stCOND3^[\ref{def:stCOND3}]^] tma < 15
• Characteristics (SSS 2014^[\ref{def:SSS2014}]^)
  • "mean annual soil temperature is 8 C or higher [!stCOND2^[\ref{def:stCOND2}]^] but lower than 15 C [stCOND3^[\ref{def:stCOND3}]^]"
• Generalized Characteristics (SSS 2015^[\ref{def:SSS2015}]^)
  • "Soil is 8 to < 15 C"

Thermic

• "Suited to warm weather crops such as cotton" (SSS 2015^[\ref{def:SSS2015}]^)
• rSOILWAT2
  • !stCOND3^[\ref{def:stCOND3}]^ & stCOND4^[\ref{def:stCOND4}]^
• jNSM (2016)^[\ref{def:jNSM2016}]^:
  • [!stCOND3^[\ref{def:stCOND3}]^] tma >= 15 && [stCOND4^[\ref{def:stCOND4}]^] tma < 22
• Characteristics (SSS 2014^[\ref{def:SSS2014}]^)
  • "mean annual soil temperature is 15 C or higher [!stCOND3^[\ref{def:stCOND3}]^] but lower than 22 C [stCOND4^[\ref{def:stCOND4}]^]"
• Generalized Characteristics (SSS 2015^[\ref{def:SSS2015}]^)
  • "Soil is 15 to < 22 C"

Hyperthermic

• "Suited to citrus and other freeze-intolerant crops" (SSS 2015^[\ref{def:SSS2015}]^)
• rSOILWAT2
  • !stCOND4^[\ref{def:stCOND4}]^
• jNSM (2016)^[\ref{def:jNSM2016}]^:
  • [!stCOND4^[\ref{def:stCOND4}]^] tma >= 22
• Characteristics (SSS 2014^[\ref{def:SSS2014}]^)
  • [!stCOND4^[\ref{def:stCOND4}]^] "mean annual soil temperature is 22 C or higher"
• Generalized Characteristics (SSS 2015^[\ref{def:SSS2015}]^)
  • "Soil is >= 22 C"

jNSM

Code interpretation based on 'BASICSimulationModel.java' and 'NewhallResults.java'.

jNSM variables

• swt = comparison monthly PET vs. PPT
  • [lines 363-369] noMpeGreaterThanPrecip = !all(mpe[1:12] > precip[1:12])
  • [lines 370-373] swt = IF (noMpeGreaterThanPrecip) -1 ELSE 0
• nd with
  • nd[1] = numCumulativeDaysDry = [assumption] MCS is dry in ALL layers (cf. [COND10^[\ref{def:COND10}]^)
  • nd[2] = numCumulativeDaysMoistDry
  • nd[3] = numCumulativeDaysMoist
  • nd[1] + nd[2]: test variable for [COND3^[\ref{def:COND3}]^]
  • [lines ...]
• dif = absolute difference between mean summer and mean winter soil temperature (cf. COND5^[\ref{def:COND5}]^)
  • [lines 199-212]
    • st = mean(temperature[6:8]) + fc
    • wt = mean(temperature[c(1:2, 12)]) + fc
  • IF (southern hemisphere) swap st and wt
  • [lines 241-215] cs = abs(st - wt) * (1 - fcd) / 2
  • [lines 246-248] dif = (st - cs) - (wt + cs)
    • st - cs = mean summer soil temperature
    • wt - cs = mean winter soil temperature
• nccm = moistDaysAfterWinterSolstice = [assumption] CONSECUTIVE days in the 4 months following the winter solstice when MCS is moist in ALL layers (cf. COND9^[\ref{def:COND9}]^)
  • [lines 2147, 2171, 2173, 2209, 2211, 2246, 2247]
  • [line 2252] nccm = max
• nccd = dryDaysAfterSummerSolstice = [assumption] CONSECUTIVE days in the 4 months following the summer solstice when MCS is dry in ALL layers (cf. COND6^[\ref{def:COND6}]^)
  • [lines 2029, 2053, 2055, 2091, 2093, 2128, 2129]
  • [line 2134] nccd = max
• ncpm with
  • ncpm[1] = numConsecutiveDaysMoistInSomeParts
  • ncpm[2] = numConsecutiveDaysMoistInSomePartsOver8C [assumption] CONSECUTIVE days when the soil temperature at a depth of 50cm is above 8C and MCS is moist in ANY layers (cf. COND2^[\ref{def:COND2}]^)
  • [lines ...]
• nsd with
  • nsd[1] = numCumulativeDaysDryOver5C [assumption] cumulative days when MCS is dry in all parts and the soil temperature at a depth of 50cm is above 5C (cf. COND1^[\ref{def:COND1}]^)
  • nsd[2] = numCumulativeDaysMoistDryOver5C
  • nsd[3] = numCumulativeDaysMoistOver5C
  • [lines 1487, 1536, 1563]
• tma = mean annual soil temperature
  • [lines 193-196] sumt = sum(temperature[1:12])
  • [line 198] tma = mean(sumt) + fc
• lt5c = [assumption] cumulative days when the soil temperature at a depth of 50 cm below the soil surface is above 5 C (cf. COND1^[\ref{def:COND1}]^)
  • [lines 1483, 1451, 1565]
• Remarks
  • dif
    • jNSM is using the old limit of 5 C instead of the new limit of 6 C
    • "in 1999 the Iso- definitions were refined from < 5 degrees C to < 6 degrees C" [slide 3 of ' jNSM_Background_Use_Tutorial.pptx']
    • rSOILWAT2 is using new limit of 6 C

jNSM inputs

• precip[1:12] = monthly precipitation in mm
• temperature[1:12] = mean monthly air temperature in C
• mpe[1:12] = monthly potential evaporation in mm based on Thornthwaite 1948
• fc = 2.5 = Degree offset between soil and air temperature in Celsius [Comment: this value is being applied in the code to both monthly and annual data]
• fcd = 0.66 = Soil-Air Relationship Amplitude

References

\label{def:Chambers2014} Chambers, J. C., D. A. Pyke, J. D. Maestas, M. Pellant, C. S. Boyd, S. B. Campbell, S. Espinosa, D. W. Havlina, K. E. Mayer, and A. Wuenschel. 2014. Using Resistance and Resilience Concepts to Reduce Impacts of Invasive Annual Grasses and Altered Fire Regimes on the Sagebrush Ecosystem and Greater Sage-Grouse: A Strategic Multi-Scale Approach. Gen. Tech. Rep. RMRS-GTR-326. U.S. Department of Agriculture, Forest Service, Rocky Mountain Research Station, Fort Collins, CO.

\label{def:Maestas2016} Maestas, J.D., Campbell, S.B., Chambers, J.C., Pellant, M. & Miller, R.F. (2016). Tapping Soil Survey Information for Rapid Assessment of Sagebrush Ecosystem Resilience and Resistance. Rangelands, 38, 120-128.

\label{def:SSS2014} Soil Survey Staff (2014). Keys to soil taxonomy, 12th ed. USDA Natural Resources Conservation Service, Washington, DC.

\label{def:SSS2015} Soil Survey Staff (2015). Illustrated guide to soil taxonomy. USDA Natural Resources Conservation Service, National Soil Survey Center, Lincoln, Nebraska.

\label{def:jNSM2016} jNSM (2016). Java Newhall Simulation Model, version 1.6.1. https://github.com/drww/newhall (accessed Oct 26, 2016).

DrylandEcology/rSW2funs documentation built on June 28, 2023, 2:51 a.m.