A Inbuilt parameter estimation

A.1 Introduction

Package medfate has been designed to allow simulations requiring a minimum set of vegetation functional parameters. This entails that several other parameters have to be estimated automatically (via inbuilt procedures) before starting simulations. Inbuilt parameter estimation is done in functions spwbInput(), growthInput(), forest2spwbInput() and forest2growthInput(), with the user controlling the process through the species parameter table input (e.g., SpParamsMED) and the object control (see default control values in defaultControl()).

A.2 Strict, scaled and imputable parameters

Different kinds of vegetation functional parameters can be distinguished according to whether inbuilt parameter estimation is possible and how it is conducted:

  • Strictly-required parameters are those for which there are no inbuilt estimation procedures implemented in the initialization functions. Hence, either values in the species parameter table input are non-missing or suitable values need to be specified before running simulation models. Since medfate ver. 2.3, only plant/leaf classification parameters and plant size parameters are strict. The remaining ones can be estimated from other parameters. This facilitates having a functional species parameter table, because only a set of parameters have to be strictly filled, from either soft trait databases or forest inventory data.
  • Scaled parameters are functional parameters that cannot be defined at the species level, because they need to be estimated taking into account the size and structure of the plant cohort. These are not normally defined at the level of species parameter table. Specific control parameters are used to determine how scaling is performed.
  • Imputable parameters parameters are those for which the initialization routines can provide default values or estimations derived from relationships with other parameters. Parameter imputation is conducted if control parameter fillMissingSpParams = TRUE. Sometimes, default parameter values are also specified in the control object.

The following tables describe how the different functional parameters are dealt with, grouped by function. Links are given to the chapter subsections where scaling and/or imputation procedures are described.

Plant/leaf classification

Symbol R Description Strict Scaled Imputable
\(GF\) GrowthForm Growth form, defined depending on the treatment in forest inventory plots (Tree, Shrub or Tree/Shrub) Yes No No
\(LF\) LifeForm Raunkiaer life form Yes No No
\(L_{shape}\) LeafShape Leaf type (Linear, Needle, Broad, Scale, Spines or Succulent) Yes No No
\(L_{size}\) LeafSize Leaf size (Small, Medium, Large) Yes No No
\(L_{pheno}\) PhenologyType Leaf phenology type Yes No No

Plant size

Symbol R Description Strict Scaled Imputable
\(H_{max}\) Hmed Maximum plant height Yes No No
\(H_{med}\) Hmed Median plant height Yes No No
\(f_{HD,min}\) fHDmin Minimum height-to-diameter ratio Yes No No
\(f_{HD,max}\) fHDmax Maximum height-to-diameter ratio Yes No No

Allometric coefficients

Symbol R Description Strict Scaled Imputable
\(a_{ash}\), \(b_{ash}\) a_ash, b_ash Coefficients relating the square of shrub height with shrub area No No A.3.1
\(a_{bsh}\), \(b_{bsh}\) a_bsh, b_bsh Coefficients relating crown volume with dry weight of shrub individuals No No A.3.1
\(cr\) cr Ratio between crown length and total height for shrubs No No A.3.1
\(a_{fbt}\), \(b_{fbt}\), \(c_{fbt}\) a_fbt, b_fbt, c_fbt Coefficients to calculate foliar biomass of an individual tree No No A.3.2
\(a_{cr}\), \(b_{1cr}\), \(b_{2cr}\), \(b_{3cr}\), \(c_{1cr}\), \(c_{2cr}\) a_cr, b_1cr, b_2cr, b_3cr, c_1cr, c_2cr Coefficients to calculate crown ratio of trees No No A.3.2
\(a_{cw}\), \(b_{cw}\) a_cw, b_cw Regression coefficients used to calculate the crown width of trees No No A.3.2

Leaf phenology

Symbol R Description Strict Scaled Imputable
\(LD\) LeafDuration Average duration of leaves No No A.3.8
\(t_{0,eco}\) t0gdd Degree days corresponding to leaf budburst No No A.3.8
\(S^*_{eco}\) Sgdd Degree days corresponding to leaf budburst No No A.3.8
\(T_{eco}\) Tbgdd Base temperature for the calculation of degree days to leaf budburst No No A.3.8
\(S^*_{sen}\) Ssen Degree days corresponding to leaf senescence No No A.3.8
\(Ph_{sen}\) Phsen Photoperiod corresponding to start counting senescence degree-days No No A.3.8
\(T_{sen}\) Tbsen Base temperature for the calculation of degree days to leaf senescence No No A.3.8
\(x_{sen}\) xsen Discrete values, to allow for any absent/proportional/more than proportional effects of temperature on senescence No No A.3.8
\(y_{sen}\) ysen Discrete values, to allow for any absent/proportional/more than proportional effects of photoperiod on senescence No No A.3.8

Plant anatomy

Symbol R Description Strict Scaled Imputable
\(1/H_{v}\) Al2As Ratio of leaf area to sapwood area No No A.3.6
\(RLR\) Ar2Al Fine root area to leaf area ratio No No A.3.7
\(LW\) LeafWidth Leaf width No No A.3.3
\(SLA\) SLA Specific leaf area No No A.3.3
\(\rho_{leaf}\) LeafDensity Leaf tissue density No No A.3.4
\(\rho_{wood}\) WoodDensity Wood tissue density No No A.3.4
\(\rho_{fineroot}\) FineRootDensity Fine root tissue density No No A.3.4
\(f_{conduits}\) conduit2sapwood Proportion of sapwood corresponding to xylem conduits No No A.3.6
\(SRL\) SRL Specific fine root length No No A.3.5
\(RLD\) RLD Fine root length density No No A.3.5
\(r_{6.35}\) r635 Ratio between the weight of leaves plus branches and the weight of leaves alone for branches of 6.35 mm No No A.3.3

Radiation balance and water interception

Symbol R Description Strict Scaled Imputable
\(k_{b}\) kDIR Direct light extinction coefficient No No A.3.10
\(k_{PAR}\) kPAR PAR extinction coefficient No No A.3.10
\(\alpha_{SWR}\) alphaSWR Short-wave radiation leaf absorbance coefficient No No A.3.10
\(\gamma_{SWR}\) gammaSWR Short-wave radiation leaf reflectance (albedo) No No A.3.10
\(s_{water}\) g Crown water storage capacity No No A.3.10

Hydraulics, transpiration, photosynthesis

Symbol R Description Strict Scaled Imputable
\(T_{max, LAI}\) Tmax_LAI Empirical coefficient relating LAI with the ratio of maximum transpiration over potential evapotranspiration No No A.3.9
\(T_{max, sqLAI}\) Tmax_LAIsq Empirical coefficient relating squared LAI with the ratio of maximum transpiration over potential evapotranspiration No No A.3.9
\(WUE_{\max}\) WUE Water use efficiency at VPD = 1kPa and without light or CO2 limitations No No A.3.9
\(WUE_{PAR}\) WUE_par Coefficient describing the progressive decay of WUE with lower light levels No No A.3.9
\(WUE_{CO2}\) WUE_co2 Coefficient for WUE dependency on atmospheric CO2 concentration No No A.3.9
\(WUE_{VPD}\) WUE_vpd Coefficient for WUE dependency on vapor pressure deficit No No A.3.9
\(\Psi_{extract}\) Psi_Extract The water potential at which plant transpiration is 50% of its maximum No No A.3.9
\(\Psi_{critic}\) Psi_Critic The water potential corresponding to 50% of stem xylem cavitation No No A.3.15
\(g_{swmin}\) Gwmin Minimum stomatal conductance to water vapour No No A.3.11
\(g_{swmax}\) Gwmax Maximum stomatal conductance to water vapour No No A.3.11
\(J_{max, 298}\) Jmax298 Maximum rate of electron transport at 298K No No A.3.16
\(V_{max, 298}\) Vmax298 Rubisco’s maximum carboxylation rate at 298K No No A.3.16
\(K_{stem,max,ref}\) Kmax_stemxylem Maximum stem sapwood reference conductivity per leaf area unit No No A.3.13
\(K_{root,max,ref}\) Kmax_rootxylem Maximum root sapwood reference conductivity per leaf area unit No No A.3.13
\(k_{leaf, \max}\) VCleaf_kmax Maximum leaf hydraulic conductance No A.4.2 A.3.14
\(k_{stem, \max}\) VCstem_kmax Maximum stem hydraulic conductance No A.4.1 No
\(k_{root, \max,s}\) VCroot_kmax Maximum root hydraulic conductance for each soil layer No A.4.3 No
\(k_{rhizo,\max, s}\) VGrhizo_kmax Maximum hydraulic conductance of the rhizosphere for each soil layer No A.4.4 No
\(c_{leaf}\), \(d_{leaf}\) VCleaf_c, VCleaf_d Parameters of the vulnerability curve for leaves No No A.3.15
\(c_{stem}\), \(d_{stem}\) VCstem_c, VCstem_d Parameters of the vulnerability curve for stem xylem No No A.3.15
\(c_{root}\), \(d_{root}\) VCroot_c, VCroot_d Parameters of the vulnerability curve for root xylem No No A.3.15

Plant water storage

Symbol R Description Strict Scaled Imputable
\(\epsilon_{leaf}\) LeafEPS Modulus of elasticity of leaves No No A.3.12
\(\epsilon_{stem}\) StemEPS Modulus of elasticity of symplastic xylem tissue No No A.3.12
\(\pi_{0,leaf}\) LeafPI0 Osmotic potential at full turgor of leaves No No A.3.12
\(\pi_{0,stem}\) StemPI0 Osmotic potential at full turgor of symplastic xylem tissue No No A.3.12
\(f_{apo,leaf}\) LeafAF Apoplastic fraction in leaf tissues No No A.3.12
\(f_{apo,stem}\) StemAF Apoplastic fraction in stem tissues No No A.3.12
\(V_{leaf}\) Vleaf Leaf water capacity per leaf area unit No A.4.5 No
\(V_{sapwood}\) Vsapwood Sapwood water capacity per leaf area unit No A.4.5 No

Growth and mortality

Symbol R Description Strict Scaled Imputable
\(N_{leaf}\) Nleaf Leaf nitrogen concentration per dry mass No No A.3.17
\(N_{sapwood}\) Nsapwood Sapwood nitrogen concentration per dry mass No No A.3.17
\(N_{fineroot}\) Nfineroot Fine root nitrogen concentration per dry mass No No A.3.17
\(MR_{leaf}\) RERleaf Leaf respiration rate at 20 ºC No No A.3.17
\(MR_{sapwood}\) RERsapwood Living sapwood (parenchymatic tissue) respiration rate at 20 ºC No No A.3.17
\(MR_{fineroot}\) RERfineroot Fine root respiration rate at 20 ºC No No A.3.17
\(RGR_{leaf, max}\) RGRleafmax Maximum leaf area daily growth rate, relative to sapwood area No No A.3.18
\(RGR_{cambium, max}\) RGRsapwoodmax Maximum tree daily sapwood growth rate relative to cambium perimeter length No No A.3.18
\(RGR_{sapwood, max}\) RGRsapwoodmax Maximum shrub daily sapwood growth rate relative to sapwood area No No A.3.18
\(RGR_{fineroot, max}\) RGRfinerootmax Maximum daily fine root relative growth rate No No A.3.18
\(SR_{sapwood}\) SRsapwood Daily sapwood senescence rate No No A.3.19
\(SR_{fineroot}\) SRfineroot Daily fine root senescence rate No No A.3.19
\(RSSG\) RSSG Minimum relative starch for sapwood growth No No A.3.20
\(C_{wood}\) WoodC Wood carbon content per dry weight No No A.3.21
\(P_{mort,base}\) MortalityBaselineRate Default deterministic proportion or probability specifying the baseline reduction of cohort’s density occurring in a year No No A.3.22

Recruitment

Symbol R Description Strict Scaled Imputable
\(H_{seed}\) SeedProductionHeight Minimum height for seed production No No A.3.23
\(TCM_{recr}\) MinTempRecr Minimum average temperature (Celsius) of the coldest month for successful recruitment No No A.3.23
\(MI_{recr}\) MinMoistureRecr Minimum value of the moisture index for successful recruitment No No A.3.23
\(FPAR_{recr}\) MinFPARRecr Minimum percentage of PAR at the ground level for successful recruitment No No A.3.23
\(DBH_{recr}\) RecrTreeDBH Recruitment DBH for trees No No A.3.23
\(H_{tree, recr}\) RecrTreeHeight Recruitment height for trees No No A.3.23
\(N_{tree, recr}\) RecrTreeDensity Recruitment density for trees No No A.3.23
\(Cover_{shrub, recr}\) RecrShrubCover Recruitment cover for shrubs No No A.3.23
\(H_{shrub, recr}\) RecrShrubHeight Recruitment height for shrubs No No A.3.23
\(Z50_{recr}\) RecrZ50 Soil depth corresponding to 50% of fine roots for recruitment No No A.3.23
\(Z95_{recr}\) RecrZ95 Soil depth corresponding to 95% of fine roots for recruitment No No A.3.23

Flammability

Symbol R Description Strict Scaled Imputable
\(\rho_{p}\) PD Density of fuel particles No No A.3.24
\(\sigma\) SAV Surface-area-to-volume ratio of the small fuel (1h) fraction (leaves and branches < 6.35mm) No No A.3.24
\(h\) HeatContent High fuel heat content. No No A.3.24
\(LI\) PercentLignin Percentage of lignin in leaves No No A.3.24

A.3 Imputation of missing values

The following figure summarizes the percentage of missing values in SpParamsMED for different model parameters and the other model parameters used for the imputation of missing values:

Representation of imputation relationships between model parameters. The percentage of missing parameter values increases from left to right. Left-most parameters are strict.

Figure A.1: Representation of imputation relationships between model parameters. The percentage of missing parameter values increases from left to right. Left-most parameters are strict.

A.3.1 Shrub allometric coefficients

Missing shrub allometric coefficients are filled using information from Raunkiaer’s life form and maximum plant height (\(H_{max}\)).

Life form \(H_{max}\) \(a_{ash}\) \(b_{ash}\) \(a_{bsh}\) \(b_{bsh}\) \(cr\)
Chamaephyte [any] 24.5888 1.1662 0.7963 0.3762 0.8076
Phanerophyte < 300 cm 1.0083 1.8700 0.7900 0.6942 0.6630
Phanerophyte > 300 cm 5.8458 1.4944 0.3596 0.7138 0.7190
(Hemi)cryptophyte [any] 24.5888 1.1662 0.7963 0.3762 0.9500

Allometric coefficients were taken from De Cáceres et al. (2019).

A.3.2 Tree allometric coefficients

Missing tree allometric coefficients are replaced with values depending on whether the plant species is a gymnosperm or an angiosperm:

Parameter Gymnosperm Angiosperm
\(a_{fbt}\) 0.1300 0.0527
\(b_{fbt}\) 1.2285 1.5782
\(c_{fbt}\) -0.0147 -0.0066
\(a_{cw}\) 0.747 0.839
\(b_{cw}\) 0.672 0.735
\(a_{cr}\) 1.995 1.506
\(b_{1cr}\) -0.649 -0.706
\(b_{2cr}\) -0.020 -0.078
\(b_{3cr}\) -0.00012 0.00018
\(c_{1cr}\) -0.004 -0.007
\(c_{2cr}\) -0.159 0.000

A.3.3 Leaf width, specific leaf area and fine foliar ratio

Leaf width (\(LW\)), specific leaf area (\(SLA\)) and the ratio between the weight of leaves plus branches and the weight of leaves alone for branches of 6.35 mm (\(r_{6.35}\)) are key anatomical parameters. When missing from species parameter table, default estimates for these parameters are obtained from combinations of leaf shape and leaf size:

Leaf shape Leaf size \(SLA\) \(LW\) \(r_{6.35}\)
Broad Large 16.039 6.898 2.278
Broad Medium 11.499 3.054 2.359
Broad Small 9.540 0.644 3.026
Linear Large 5.522 0.639 3.261
Linear Medium 4.144 0.639 3.261
Linear Small 13.189 0.639 3.261
Needle [any] 9.024 0.379 1.716
Scale [any] 4.544 0.101 1.483

These estimates have been obtained by averaging species-level values across combinations of the categorical variables.

A.3.4 Tissue density

Default values for the dry weight density of leaves and wood (in \(g \cdot cm^{-3}\)) are determined from taxonomic family using an internal data set (medfate:::trait_family_means):

Table A.1: Default leaf density and wood density values by taxonomic family.
LeafDensity WoodDensity
Acanthaceae 0.2959003 0.5684693
Achariaceae 0.2552495 0.6052036
Acoraceae 0.1000000 NA
Actinidiaceae 0.4439776 0.4092320
Adoxaceae 0.3916194 0.5157416
Aextoxicaceae NA 0.5666667
Aizoaceae 0.0824125 NA
Akaniaceae NA 0.5547825
Alismataceae 0.1914208 NA
Altingiaceae 0.6833971 0.6010948
Amaranthaceae 0.2045831 0.6315739
Amaryllidaceae 0.1220704 NA
Amphorogynaceae NA 0.6097400
Anacardiaceae 0.4568088 0.5685583
Anisophylleaceae NA 0.6734780
Annonaceae 0.3757811 0.5642062
Aphloiaceae 0.4627060 0.6205200
Apiaceae 0.2874756 0.2561785
Apocynaceae 0.2981148 0.5683635
Aptandraceae 0.3318492 0.7076756
Aquifoliaceae 0.4812626 0.5579305
Araceae 0.1659746 NA
Araliaceae 0.3118821 0.4142687
Araucariaceae 0.3447902 0.4641456
Arecaceae 0.4393589 0.5913967
Aristolochiaceae 0.2681434 0.2900000
Asparagaceae 0.1425099 0.4254258
Asphodelaceae 0.5512472 0.3951990
Aspleniaceae 0.2644557 NA
Asteraceae 0.2511093 0.4822337
Asteropeiaceae NA 0.7554862
Atherospermataceae 0.2451357 0.4767621
Athyriaceae 0.2270615 NA
Austrobaileyaceae 0.2620992 NA
Balanopaceae NA 0.7348976
Balsaminaceae 0.3948094 NA
Begoniaceae 0.1626789 NA
Berberidaceae 0.3599453 0.7028850
Betulaceae 0.4446528 0.5381493
Bignoniaceae 0.3572590 0.6256030
Bixaceae 0.4400000 0.3546357
Blechnaceae 0.3147993 NA
Bonnetiaceae 0.2797829 0.8400000
Boraginaceae 0.2850462 0.4987559
Brassicaceae 0.2267605 0.4516377
Bromeliaceae 0.1677139 NA
Brunelliaceae NA 0.3112500
Bruniaceae NA 0.5636500
Burseraceae 0.4226787 0.5205008
Buxaceae 0.2706294 0.7314511
Cactaceae 0.1819372 0.6187500
Calophyllaceae 0.4065092 0.6067855
Calycanthaceae 0.3204073 0.6500550
Calyceraceae 0.1689366 NA
Campanulaceae 0.2396318 NA
Canellaceae NA 0.6808255
Cannabaceae 0.3529720 0.5502170
Capparaceae 0.3632941 0.6338137
Caprifoliaceae 0.3282343 0.4186392
Cardiopteridaceae 0.3136349 0.6210142
Caricaceae 0.2145354 0.1925092
Caryocaraceae 0.4728080 0.6758165
Caryophyllaceae 0.2175001 0.4356813
Casuarinaceae 0.6581279 0.8237662
Celastraceae 0.4299601 0.6414639
Centroplacaceae NA 0.6550000
Cephalotaxaceae NA 0.5317845
Cercidiphyllaceae 0.2896931 0.4509256
Cervantesiaceae NA 0.6151433
Chloranthaceae 0.2125841 0.3912405
Chrysobalanaceae 0.4203120 0.7862446
Cistaceae 0.3085107 0.4830942
Cleomaceae NA 0.6126000
Clethraceae 0.5042730 0.5336779
Clusiaceae 0.3408792 0.6987069
Cochlospermaceae 0.4378883 0.2521050
Comandraceae 0.2630059 NA
Combretaceae 0.3763244 0.6564542
Commelinaceae 0.1837240 NA
Connaraceae 0.3994071 0.5589860
Convolvulaceae 0.2614034 0.5267363
Cordiaceae 0.3528759 0.5565679
Cornaceae 0.3834263 0.6195792
Corynocarpaceae 0.2498751 0.6665337
Coulaceae 0.4529368 0.8115261
Crypteroniaceae NA 0.4976753
Ctenolophonaceae NA 0.7691998
Cucurbitaceae 0.2327745 0.3557651
Cunoniaceae 0.3642028 0.5754400
Cupressaceae 0.3130010 0.4938816
Curtisiaceae NA 0.7302190
Cyatheaceae 0.1297339 0.7355404
Cycadaceae 0.6448750 NA
Cyperaceae 0.3216514 0.2346031
Cyrillaceae NA 0.5998411
Cystopteridaceae 0.2800436 NA
Daphniphyllaceae NA 0.5062947
Degeneriaceae NA 0.3425000
Dennstaedtiaceae 0.2658944 NA
Dichapetalaceae 0.3522732 0.6249660
Dicksoniaceae 0.4697549 NA
Didiereaceae NA 0.3829183
Dilleniaceae 0.3224518 0.5886310
Dioscoreaceae 0.1793296 NA
Dipentodontaceae 0.2965124 NA
Dipterocarpaceae 0.4738273 0.6409882
Droseraceae 0.1342673 NA
Dryopteridaceae 0.2796327 NA
Ebenaceae 0.4250532 0.6863834
Ehretiaceae 0.3819970 0.5687138
Elaeagnaceae 0.3121046 0.5644408
Elaeocarpaceae 0.4251434 0.5453120
Ephedraceae NA 0.7800000
Equisetaceae 0.2590369 0.2031353
Ericaceae 0.4544895 0.6055498
Erythropalaceae 0.4039757 0.7154823
Erythroxylaceae 0.3420025 0.7799333
Escalloniaceae 0.2204192 0.5585952
Eucommiaceae NA 0.7620000
Euphorbiaceae 0.3391137 0.4889655
Euphroniaceae NA 0.6200000
Eupomatiaceae 0.2445709 0.5779000
Eupteleaceae NA 0.5425200
Fabaceae 0.3851583 0.6822180
Fagaceae 0.5090006 0.6683896
Fouquieriaceae 0.2453718 NA
Frankeniaceae NA 0.5000000
Garryaceae 0.3579628 0.6870722
Gentianaceae 0.2977642 0.6877612
Geraniaceae 0.2641399 0.1644500
Gesneriaceae 0.1013848 NA
Ginkgoaceae 0.2238538 0.4618849
Gleicheniaceae 0.4916560 NA
Gnetaceae NA 0.6100000
Goodeniaceae 0.2051090 NA
Goupiaceae 0.4660717 0.7255032
Griseliniaceae NA 0.6035000
Grossulariaceae 0.3485915 0.5977569
Gyrostemonaceae NA 0.3646622
Haematococcaceae 0.2933351 NA
Haloragaceae 0.1312446 NA
Hamamelidaceae 0.3884526 0.6424968
Heliotropiaceae NA 0.5090196
Hernandiaceae 0.4152598 0.2911796
Himantandraceae NA 0.5126388
Humiriaceae 0.4953617 0.7700458
Hydrangeaceae 0.1690825 0.8300000
Hydrocharitaceae 0.4004979 NA
Hydrophyllaceae 0.1879433 NA
Hymenophyllaceae 0.3299410 NA
Hypericaceae 0.2990752 0.5892664
Hypoxidaceae 0.1299171 NA
Icacinaceae NA 0.6500000
Iridaceae 0.2546647 0.3087906
Irvingiaceae NA 0.8841681
Ixerbaceae 0.4306632 NA
Ixonanthaceae 0.3649649 0.6799304
Juglandaceae 0.5200369 0.5183733
Juncaceae 0.2014423 0.2399980
Kirkiaceae NA 0.5079900
Lacistemataceae 0.2515838 0.4832675
Lamiaceae 0.2869862 0.5072119
Lauraceae 0.4352734 0.5415881
Lecythidaceae 0.4223276 0.6769009
Lepidobotryaceae NA 0.4836652
Liliaceae 0.1000000 NA
Linaceae 0.2893664 0.7008226
Loasaceae 0.2700000 NA
Loganiaceae 0.4213886 0.6304908
Loranthaceae 0.3770995 0.6322000
Lycopodiaceae 0.4802434 NA
Lygodiaceae 0.5066007 NA
Lythraceae 0.3848205 0.6020073
Magnoliaceae 0.3486896 0.4707890
Malpighiaceae 0.3387076 0.6262188
Malvaceae 0.3336333 0.4855630
Marcgraviaceae 0.1698113 NA
Melanthiaceae 0.1811793 NA
Melastomataceae 0.3293654 0.6442241
Meliaceae 0.3738590 0.5899613
Melianthaceae 0.2942168 0.6210538
Menispermaceae 0.2978386 0.5205924
Menyanthaceae 0.1224487 NA
Metteniusaceae 0.5448075 0.5446187
Molluginaceae 0.1400000 NA
Monimiaceae 0.2778594 0.5179823
Montiaceae 0.0859106 NA
Moraceae 0.3518887 0.5014756
Moringaceae NA 0.2617440
Muntingiaceae 0.3376553 0.3000000
Myodocarpaceae NA 0.6344000
Myricaceae 0.4691690 0.5578848
Myristicaceae 0.4033709 0.4976416
Myrtaceae 0.4379521 0.7656349
Namaceae 0.5166315 0.5400000
Nothofagaceae 0.3869412 0.5955200
Nyctaginaceae 0.2497878 0.5346327
Nyssaceae 0.5290780 0.4782400
Ochnaceae 0.4787112 0.7208319
Octoknemaceae NA 0.6880101
Olacaceae 0.3487339 0.6607729
Oleaceae 0.4051166 0.6754889
Onagraceae 0.2783621 0.4502300
Onocleaceae 0.2663707 NA
Ophioglossaceae 0.2084852 NA
Opiliaceae 0.3161129 0.6480673
Orchidaceae 0.1930601 NA
Orobanchaceae 0.2426225 0.4122466
Osmundaceae 0.2679487 NA
Oxalidaceae 0.1876039 0.5741802
Paeoniaceae 0.2851982 NA
Pandaceae NA 0.6180903
Pandanaceae NA 0.3309000
Papaveraceae 0.3526680 NA
Paracryphiaceae 0.4686036 0.5192721
Parnassiaceae NA 0.3211286
Passifloraceae 0.1951307 0.5966667
Paulowniaceae NA 0.2597687
Penaeaceae NA 0.6994190
Pennantiaceae NA 0.4950750
Pentaphylacaceae 0.3707627 0.5633463
Penthoraceae 0.1942110 NA
Peraceae 0.3692442 0.6620175
Peridiscaceae NA 0.6945082
Phrymaceae 0.1098008 0.6440000
Phyllanthaceae 0.2922610 0.6160133
Phyllocladaceae 0.5787037 0.5924191
Phytolaccaceae 0.2547709 0.4116385
Picramniaceae 0.4159664 0.6208382
Picrodendraceae 0.8566338 0.8414544
Pinaceae 0.3436503 0.4480469
Piperaceae 0.2438998 0.3891992
Pittosporaceae 0.3517531 0.6168509
Plantaginaceae 0.2346642 0.2571076
Platanaceae 0.4819040 0.5298601
Plumbaginaceae 0.2603992 0.2500000
Poaceae 0.3774014 0.2860215
Podocarpaceae 0.5048204 0.5063839
Polemoniaceae 0.2775675 0.3382400
Polygalaceae 0.2708272 0.6965020
Polygonaceae 0.3254643 0.5853623
Polypodiaceae 0.2460060 NA
Pontederiaceae 0.1500000 0.4876272
Portulacaceae 0.3800000 NA
Potamogetonaceae 0.1588772 NA
Primulaceae 0.3083310 0.6369957
Proteaceae 0.4633521 0.6563858
Pteleocarpaceae NA 0.6350000
Pteridaceae 0.2198842 0.6304250
Putranjivaceae 0.3849495 0.6921646
Quiinaceae 0.4274606 0.8260544
Ranunculaceae 0.2466518 0.3342750
Resedaceae 0.1507363 NA
Rhabdodendraceae 0.2511215 0.8000000
Rhamnaceae 0.4167308 0.6552146
Rhizophoraceae 0.3339246 0.7225795
Rosaceae 0.3956651 0.6180205
Rousseaceae NA 0.6170000
Rubiaceae 0.3151996 0.6213798
Rutaceae 0.3406166 0.6337629
Sabiaceae 0.2269258 0.4766550
Salicaceae 0.4176502 0.5537335
Salvadoraceae NA 0.5940900
Santalaceae 0.2638240 0.7741829
Sapindaceae 0.4055140 0.6701493
Sapotaceae 0.4524219 0.6748673
Sarcolaenaceae NA 0.8988205
Saxifragaceae 0.1446601 NA
Schisandraceae NA 0.5792130
Schoepfiaceae 0.3474414 0.7157100
Sciadopityaceae NA 0.6320000
Scrophulariaceae 0.3540547 0.6839313
Selaginellaceae 0.2176000 NA
Simaroubaceae 0.3298179 0.4155088
Siparunaceae 0.2955010 0.6271829
Sladeniaceae NA 0.5700000
Smilacaceae 0.2017709 0.7343021
Solanaceae 0.2560480 0.4931198
Staphyleaceae 0.2801318 0.4132592
Stemonuraceae 0.3123012 0.5123802
Stilbaceae 0.4577089 0.6787550
Stixaceae NA 0.8400000
Strombosiaceae NA 0.7027465
Styracaceae 0.3357136 0.4604059
Surianaceae 0.2843963 0.9240450
Symplocaceae 0.4826660 0.5170835
Talinaceae 0.2671358 NA
Tamaricaceae NA 0.6636284
Tapisciaceae NA 0.3885924
Taxaceae 0.4541759 0.5533938
Tetramelaceae NA 0.3042230
Tetrameristaceae NA 0.6350000
Theaceae 0.4039158 0.5640233
Thymelaeaceae 0.3129399 0.5328326
Torricelliaceae 0.3383541 NA
Trigoniaceae NA 0.6966667
Trochodendraceae NA 0.3366510
Turneraceae NA 0.6265213
Typhaceae 0.1688785 NA
Ulmaceae 0.4534660 0.5979531
Urticaceae 0.3193102 0.3727392
Verbenaceae 0.3037701 0.5782080
Violaceae 0.3195701 0.6266302
Vitaceae 0.2737953 0.4965250
Vochysiaceae 0.4017484 0.5536239
Winteraceae 0.3228721 0.5236569
Ximeniaceae 0.8709687 0.8323008
Zamiaceae 0.3920216 NA
Zygophyllaceae 0.4229786 0.8554052

If the family is not any of those in the table, default values are \(\rho_{leaf} = 0.7\) and \(\rho_{wood} = 0.652\). The default value for fine root density is always \(\rho_{fineroot} = 0.165\).

A.3.5 Specific root length and root length density

Default values for specific fine root length and fine root length density are \(3870\, cm \cdot g^{-1}\) and \(10\, cm \cdot cm^{-3}\), respectively. [JUSTIFICATION MISSING]

A.3.6 Huber value and ratio of conduits to sapwood

Missing values for Al2As, the inverse of the Huber value (\(1/Hv\)) are determined from taxonomic family using an internal data set (medfate:::trait_family_means):

Table A.2: Default leaf area to sapwood area (m2/m2) / Huber value (cm2/m2) and fraction of sapwood corresponding to conduits by taxonomic family.
Al2As Hv conduit2sapwood
Acanthaceae 3070.43202 3.2568707 0.6300000
Adoxaceae 4889.57295 2.0451684 NA
Altingiaceae 5129.90090 1.9493554 0.8226667
Amaranthaceae 973.13500 10.2760665 NA
Amborellaceae 4255.31915 2.3500000 NA
Anacardiaceae 19581.70525 0.5106808 0.7155889
Annonaceae 10266.65654 0.9740269 0.5685000
Apiaceae 81.15013 123.2283950 NA
Apocynaceae 19766.80134 0.5058987 0.7112500
Aquifoliaceae 4886.36183 2.0465124 0.6528500
Araliaceae 3928.39877 2.5455664 0.7785000
Araucariaceae 3846.15385 2.6000000 0.9375000
Arecaceae 5492.53731 1.8206522 NA
Asteraceae 2421.76507 4.1292197 0.7219423
Atherospermataceae 2435.95630 4.1051640 0.7560000
Austrobaileyaceae 15384.61538 0.6500000 NA
Berberidaceae 570.06271 17.5419298 NA
Betulaceae 6158.73417 1.6237103 0.8444000
Bignoniaceae 12439.80827 0.8038709 0.6360476
Bixaceae 12274.01424 0.8147294 NA
Burseraceae 12218.54705 0.8184279 0.8204286
Buxaceae NA NA 0.8330000
Cactaceae 2554.61304 3.9144872 0.3636905
Calophyllaceae 2662.52127 3.7558385 0.7335000
Calycanthaceae NA NA 0.6535500
Cannabaceae 29406.04715 0.3400661 0.7598125
Capparaceae 37525.87992 0.2664828 0.7005000
Caprifoliaceae 7568.54261 1.3212583 NA
Cardiopteridaceae NA NA 0.6300000
Caryocaraceae 5183.13611 1.9293339 NA
Casuarinaceae 3647.15784 2.7418610 NA
Celastraceae 8199.20056 1.2196311 NA
Chrysobalanaceae 10531.83851 0.9495018 0.5876000
Cistaceae 2129.37624 4.6962109 NA
Clusiaceae 6707.44573 1.4908805 0.5005000
Cochlospermaceae 1757.46925 5.6900000 0.7070000
Combretaceae 23650.62103 0.4228219 0.6416667
Cordiaceae 10754.86431 0.9298118 0.6300000
Cornaceae 7478.58356 1.3371516 0.6740000
Coulaceae 10676.38668 0.9366465 0.6520000
Cunoniaceae 4781.22975 2.0915121 0.7110000
Cupressaceae 1793.78915 5.5747912 0.9242857
Dichapetalaceae 7505.55229 1.3323470 NA
Dilleniaceae 7707.14493 1.2974973 0.5432500
Dipterocarpaceae NA NA 0.7043750
Ebenaceae 5746.58263 1.7401647 0.6300000
Ehretiaceae 3401.36054 2.9400000 NA
Elaeagnaceae NA NA 0.5641000
Elaeocarpaceae 8949.89085 1.1173321 0.6970000
Ericaceae 2717.89086 3.6793236 0.7423400
Erythropalaceae 11359.73085 0.8803025 NA
Erythroxylaceae 16409.39633 0.6094069 NA
Escalloniaceae NA NA 0.5755000
Euphorbiaceae 9648.31966 1.0364499 0.6630417
Eupomatiaceae 12833.11560 0.7792340 0.6010000
Fabaceae 13004.75675 0.7689494 0.6096376
Fagaceae 5426.21990 1.8429036 0.5965700
Garryaceae 3187.80223 3.1369575 NA
Gnetaceae 10683.76068 0.9360000 NA
Goupiaceae NA NA 0.6360000
Grossulariaceae 5478.25000 1.8254004 NA
Hernandiaceae NA NA 0.6350000
Humiriaceae 6548.42050 1.5270858 0.7283333
Juglandaceae 19643.00000 0.5090872 0.7247857
Lacistemataceae 15122.28822 0.6612756 NA
Lamiaceae 6104.68000 1.6380875 0.6817381
Lauraceae 9015.94422 1.1091462 0.6868438
Lecythidaceae 9281.45093 1.0774178 0.6052857
Linaceae 8947.01119 1.1176917 0.7125000
Loranthaceae 1657.46812 6.0332985 NA
Lythraceae 8169.26722 1.2241000 0.6600000
Magnoliaceae NA NA 0.8122000
Malpighiaceae 8433.60354 1.1857328 NA
Malvaceae 13911.40409 0.7188347 0.5338667
Melastomataceae 9869.59558 1.0132127 NA
Meliaceae 19432.70158 0.5145965 0.6400476
Metteniusaceae 5891.68760 1.6973066 NA
Moraceae 9851.68927 1.0150543 0.5142727
Myristicaceae 7469.72436 1.3387375 0.6990000
Myrtaceae 5657.59469 1.7675356 0.6921435
Namaceae 5314.00000 1.8818216 NA
Nothofagaceae 1642.23662 6.0892565 NA
Nyctaginaceae 43532.77978 0.2297120 0.5990000
Nyssaceae 6434.40511 1.5541452 0.7885000
Ochnaceae 10152.77493 0.9849524 0.7070000
Oleaceae 6884.98407 1.4524362 0.7367889
Pandaceae 8942.22690 1.1182897 NA
Passifloraceae NA NA 0.3352381
Peraceae NA NA 0.6800000
Phrymaceae 2450.00000 4.0816327 0.5515000
Phyllanthaceae 5535.64829 1.8064731 0.6230000
Phyllocladaceae 3344.48161 2.9900000 NA
Phytolaccaceae 88495.57522 0.1130000 NA
Picramniaceae 18326.74493 0.5456506 0.6370000
Picrodendraceae 4179.29865 2.3927460 0.5635000
Pinaceae 2648.66805 3.7754825 0.9235957
Piperaceae 17361.11111 0.5760000 NA
Platanaceae NA NA 0.6000000
Podocarpaceae 3147.27895 3.1773478 0.9086667
Polygalaceae 14013.36411 0.7136045 NA
Polygonaceae 8927.24402 1.1201665 0.8932000
Primulaceae 4722.91675 2.1173356 0.5600000
Proteaceae 3201.08553 3.1239403 0.5774167
Putranjivaceae 12724.49969 0.7858855 NA
Ranunculaceae 23795.00000 0.4202564 0.8130000
Rhamnaceae 3931.36135 2.5436481 0.8017273
Rhizophoraceae 4314.38201 2.3178291 0.7810000
Rosaceae 7878.01050 1.2693560 0.7084800
Rubiaceae 18589.27280 0.5379447 0.6721167
Rutaceae 11439.50207 0.8741639 0.7012857
Sabiaceae 5863.83253 1.7053693 NA
Salicaceae 12890.58086 0.7757602 0.7726667
Santalaceae 2626.05148 3.8079985 0.6450000
Sapindaceae 7991.30943 1.2513594 0.7544318
Sapotaceae 7934.19459 1.2603674 0.5657500
Scrophulariaceae 1341.78411 7.4527638 NA
Simaroubaceae 10548.49222 0.9480028 0.5160000
Siparunaceae 4727.72947 2.1151802 NA
Solanaceae 34232.00295 0.2921243 0.7681667
Staphyleaceae 7311.44239 1.3677192 NA
Stemonuraceae NA NA 0.4470000
Styracaceae 2782.75060 3.5935667 NA
Symplocaceae 4458.13562 2.2430901 NA
Tapisciaceae 13677.69753 0.7311172 NA
Taxaceae NA NA 0.8600000
Theaceae 6942.20609 1.4404643 NA
Thymelaeaceae 2285.01060 4.3763473 0.8295333
Ulmaceae 18867.92453 0.5300000 0.7870000
Urticaceae 14813.36776 0.6750659 0.6653750
Verbenaceae 8196.72131 1.2200000 0.7923500
Violaceae 7385.96177 1.3539198 0.4460000
Vitaceae 1444.04332 6.9250000 0.5700000
Vochysiaceae 5382.75239 1.8577856 0.6060000
Winteraceae 2239.03703 4.4662057 NA
Ximeniaceae NA NA 0.8682000
Zygophyllaceae NA NA 0.7712000

If there is no information derived from taxonomic family for Al2As, a default value is given depending on leaf shape and leaf size:

Leaf shape Leaf size Al2As
Broad Large 4768.7
Broad Medium 2446.1
Broad Small 2284.9
Linear Large 2156.0
Linear Medium 2156.0
Linear Small 2156.0
Needle [any] 2751.7
Scale [any] 1696.6

Missing values for \(f_{conduits}\), the fraction of sapwood corresponding to conduits are derived from taxonomic family (see table above). If information from taxonomic family is missing, default values are \(f_{conduits} = 0.7\) (i.e. 30% of parenchyma) for angiosperms, and \(f_{conduits} = 0.925\) (i.e. 7.5% of parenchyma) for gymnosperms (Plavcová & Jansen 2015).

A.3.7 Fine root to leaf area ratio

When missing, the fine root area to leaf area ratio is given a default value of \(RLR = 1\; m^2\cdot m^{-2}\).

A.3.8 Leaf phenology

When missing, leaf duration is assigned a value of 1 year for winter-deciduous species and 2.41 years for the remaining leaf phenology types.

Default values for leaf phenological parameters are the same regardless of the leaf phenology type:

Phenology type t0gdd Sgdd Tbgdd Ssen Phsen Tbsen xsen ysen
One-flush evergreen 50 200 0 8268 12.5 28.5 2 2
Winter deciduous 50 200 0 8268 12.5 28.5 2 2
Winter semi-deciduous 50 200 0 8268 12.5 28.5 2 2
Drought deciduous 50 200 0 8268 12.5 28.5 2 2

Leaf senescence values were derived for deciduous broad-leaved forests by Delpierre et al. (2009).

A.3.9 Basic transpiration and water-use efficiency

When the basic soil water balance model is used, \(T_{max,LAI}\) and \(T_{max,sqLAI}\) are species-specific parameters that regulate the maximum transpiration of plant cohorts (see 6.1.1). When these parameters are missing from SpParams table, they are given default values \(T_{max,LAI} = 0.134\) and \(T_{max,sqLAI} = -0.006\), according to Granier et al. (1999).

When maximum water use efficiency (\(WUE_{\max}\)) is missing, it is given a value of \(WUE_{\max} = 7.55\). By default, the coefficient describing the decay of water use efficiency with lower light levels is given a default value of \(WUE_{PAR} = 0.2812\), and the coefficient regulating the relationship between gross photosynthesis and CO2 concentration is given a default \(WUE_{CO2} = 0.0028\).

When missing, the water potential corresponding to 50% of transpiration (\(\Psi_{extract}\)) is estimated by calculating the water potential corresponding to the loss leaf turgor (\(\Psi_{tlp}\)), using equation (10.4) from Bartlett et al. (2012). The parameters of the leaf pressure-volume curve needed for applying equation (10.4) may be themselves estimated (see A.3.12). Note that \(\Psi_{tlp}\) has been found to be highly correlated to \(\Psi_{gs50}\), the water potential corresponding to 50% of stomatal conductance (Bartlett et al. 2016).

A.3.10 Radiation balance and water interception

Default value for direct light extinction is \(k_b = 0.8\). Default values for diffuse radiation extinction, absorbance, reflectance and water interception parameters depend on the leaf shape:

Leaf shape \(k_{PAR}\) \(\alpha_{SWR}\) \(\gamma_{SWR}\) \(s_{water}\)
Broad 0.55 0.70 0.18 0.5
Linear 0.45 0.70 0.15 0.8
Needle/Scale 0.50 0.70 0.14 1.0

where \(k_{PAR}\) is the diffuse PAR extinction coefficient, \(\alpha_{SWR}\) is the short-wave radiation leaf absorbance coefficient, \(\gamma_{SWR}\) is the short-wave radiation leaf reflectance (albedo) and \(s_{water}\) is the crown water storage capacity per LAI unit.

A.3.11 Stomatal conductance

Default values for minimum and maximum conductance to water vapour (\(g_{swmin}\) and \(g_{swmax}\); in \(mol\, H_2O \cdot s^{-1} \cdot m^{-2}\)) were defined depending on taxonomic family, from Duursma et al. (2018) and Hoshika et al. (2018), and stored in an internal data set (medfate:::trait_family_means):

Table A.3: Default minimum and maximum conductance to water vapour by taxonomic family.
Gswmin Gswmax
Acanthaceae NA 0.2500000
Altingiaceae NA 0.5000000
Amaranthaceae NA 0.0750000
Amaryllidaceae 0.0180400 NA
Anacardiaceae 0.0122299 0.3148333
Apiaceae 0.0015873 NA
Aquifoliaceae 0.0005740 0.2600000
Araliaceae 0.0003902 NA
Araucariaceae 0.0018786 NA
Arecaceae 0.0004500 NA
Aristolochiaceae 0.0035896 NA
Aspleniaceae 0.0082000 NA
Asteraceae 0.0105288 0.1275000
Balsaminaceae 0.0126573 NA
Berberidaceae 0.0016500 NA
Betulaceae 0.0029731 0.3965000
Boraginaceae 0.0057402 NA
Brassicaceae 0.0106600 NA
Cactaceae 0.0000243 NA
Calophyllaceae NA 0.1350000
Cannabaceae NA 0.3300000
Caryophyllaceae 0.0018519 NA
Cephalotaxaceae 0.0022700 NA
Cercidiphyllaceae NA 0.4000000
Chrysobalanaceae NA 0.1740000
Cistaceae 0.0082820 NA
Clethraceae NA 0.2500000
Combretaceae 0.0131200 NA
Convolvulaceae 0.0041967 NA
Cordiaceae 0.0065600 NA
Cornaceae NA 0.3000000
Crassulaceae 0.0022751 NA
Cupressaceae 0.0063192 0.0840000
Cyperaceae 0.0190600 NA
Dipterocarpaceae NA 0.3874722
Ehretiaceae NA 0.2900000
Elaeagnaceae NA 0.1700000
Ericaceae 0.0041455 0.1723333
Euphorbiaceae 0.0026500 0.2616667
Fabaceae 0.0085178 0.3066667
Fagaceae 0.0060137 0.3127601
Geraniaceae 0.0043050 NA
Hamamelidaceae NA 0.2600000
Juglandaceae 0.0039355 0.4900000
Krameriaceae NA 0.1600000
Lamiaceae 0.0052377 0.7300000
Lauraceae NA 0.2212500
Magnoliaceae 0.0038800 0.3075000
Malvaceae 0.0064056 0.5532500
Meliaceae NA 0.1600000
Moraceae 0.0064020 0.3835000
Myristicaceae NA 0.0880000
Myrtaceae 0.0078149 0.2310769
Oleaceae 0.0046740 NA
Onagraceae 0.0169506 NA
Oxalidaceae 0.0022524 NA
Paeoniaceae 0.0082000 NA
Pentaphylacaceae NA 0.1200000
Phyllanthaceae 0.0077900 NA
Phyllocladaceae 0.0050406 NA
Pinaceae 0.0036139 0.1776737
Plantaginaceae 0.0061086 NA
Platanaceae 0.0066100 0.4250000
Poaceae 0.0160657 0.4691495
Podocarpaceae 0.0076971 NA
Polygalaceae NA 0.0870000
Polygonaceae 0.0139237 NA
Pontederiaceae NA 0.2400000
Proteaceae 0.0075187 NA
Ranunculaceae 0.0096204 NA
Rosaceae 0.0092820 0.5316667
Rubiaceae 0.0061500 NA
Rutaceae 0.0090200 NA
Salicaceae 0.0086680 0.3373333
Sapindaceae 0.0035583 0.2119630
Sapotaceae NA 0.1870000
Sciadopityaceae 0.0066554 NA
Simaroubaceae NA 0.6320000
Solanaceae NA 0.6000000
Taxaceae 0.0037033 NA
Theaceae 0.0068781 0.4600000
Ulmaceae NA 0.4425000
Urticaceae NA 0.6075000
Verbenaceae 0.0120000 NA
Vitaceae 0.0056426 NA
Zygophyllaceae NA 0.1580769

If there is no information derived from taxonomic family, \(g_{swmin} = 0.0049\) and \(g_{swmax} = 0.200\).

A.3.12 Pressure-volume curves

Parameters of the pressure-volume curve (i.e. \(\pi_{0,stem}\) and \(\epsilon_{stem}\)) for leaf and stem symplastic tissue are required for each species.

When parameters for stem tissue are missing, medfate estimates them from wood density following Christoffersen et al. (2016): \[\begin{equation} \pi_{0,stem} = 0.52 - 4.16 \cdot \rho_{wood} \end{equation}\]

\[\begin{equation} \epsilon_{stem} = \sqrt{1.02 \cdot e^{8.5\cdot \rho_{wood}}-2.89} \end{equation}\] while the apoplastic fraction of stem is assumed \(f_{apo,stem} = f_{conduits}\) (see A.3.6).

Default values for leaf pressure-volume parameters, i.e. \(\pi_{0,leaf}\), \(\epsilon_{leaf}\) and \(f_{apo,leaf}\), are determined from taxonomic family using an internal data set (medfate:::trait_family_means):

Table A.4: Default leaf pressure-volume parameters by taxonomic family.
LeafPI0 LeafEPS LeafAF
Acanthaceae -3.395000 23.230000 0.1270000
Adoxaceae -1.560000 12.790000 NA
Amaranthaceae -2.250000 NA NA
Anacardiaceae -1.700000 12.760000 NA
Annonaceae -2.160000 23.710000 NA
Apocynaceae -2.390000 20.940000 NA
Aquifoliaceae -2.300000 20.700000 0.4000000
Araliaceae -1.528503 11.231462 0.4065000
Arecaceae -3.400000 73.400000 0.2000000
Aspleniaceae -1.240000 35.300000 NA
Asteraceae -1.471389 14.491429 0.2435000
Atherospermataceae -1.340000 8.380000 NA
Betulaceae -1.246984 5.498667 NA
Bignoniaceae -1.990000 17.610000 0.1770000
Boraginaceae -1.140000 NA NA
Brassicaceae -1.485000 7.710000 0.2320000
Burseraceae -1.435000 14.980000 NA
Cactaceae NA 8.700000 NA
Cannabaceae -1.580000 5.180000 NA
Capparaceae -2.840000 14.750000 0.1723333
Caryocaraceae -1.710000 11.340000 NA
Celastraceae -2.600000 19.060000 NA
Combretaceae -2.110000 6.830000 NA
Connaraceae -2.250000 18.010000 NA
Convolvulaceae -1.320000 NA NA
Cordiaceae -1.647500 11.295938 NA
Cucurbitaceae -0.980000 NA NA
Cupressaceae -1.480000 12.600000 0.2720000
Dipterocarpaceae -1.131429 23.630000 0.4634286
Dryopteridaceae -1.425000 48.950000 NA
Ebenaceae -2.110000 14.650000 NA
Ericaceae -1.670000 14.382000 0.4660000
Erythroxylaceae -1.916667 16.993333 NA
Euphorbiaceae -1.260000 17.570000 0.4745000
Fabaceae -1.641724 13.577917 0.2609091
Fagaceae -1.994080 18.132800 0.2206667
Geraniaceae -0.730000 3.740000 NA
Goodeniaceae -1.500000 NA NA
Grossulariaceae -1.845000 NA NA
Hydrophyllaceae -1.260000 NA NA
Irvingiaceae -1.690000 38.380000 0.4760000
Lamiaceae -1.184000 6.120000 0.2200000
Lauraceae -2.074728 16.763373 0.1760000
Lindsaeaceae -1.970000 7.340000 0.1700000
Lythraceae -1.535000 6.055000 NA
Magnoliaceae -1.430000 9.140000 0.1560000
Malpighiaceae -1.540000 9.450000 NA
Malvaceae -2.110000 17.730000 NA
Melastomataceae -1.754000 12.306667 NA
Moraceae -1.353563 13.575000 NA
Myrtaceae -1.852385 14.462948 0.4006000
Nothofagaceae -1.480000 8.380000 NA
Nyctaginaceae -1.280000 NA NA
Oleaceae -2.060557 14.205556 NA
Onagraceae -1.200000 NA NA
Orchidaceae -0.530000 14.766667 0.2366667
Paeoniaceae -1.860000 NA NA
Papaveraceae -1.610000 NA NA
Pentaphylacaceae -1.550000 9.270000 NA
Phyllanthaceae -1.263333 13.966667 0.3036667
Pinaceae -1.771562 17.837500 0.2587500
Pittosporaceae -1.946262 9.759533 0.3610000
Platanaceae -1.390000 8.810000 0.3600000
Poaceae -1.137143 4.856667 NA
Polygalaceae -1.590000 26.760000 0.4140000
Polygonaceae -1.600000 5.030000 NA
Polypodiaceae -1.158333 34.250000 0.2100000
Primulaceae -1.700000 15.320000 NA
Proteaceae -2.114345 15.525000 NA
Rhamnaceae -2.041667 6.200000 0.0770000
Rhizophoraceae -2.320000 9.650000 NA
Rosaceae -1.766687 10.812958 0.4820000
Rubiaceae -1.681563 12.938015 0.4500000
Salicaceae -1.891667 15.555000 NA
Sapindaceae -1.357544 7.156992 0.1000000
Sapotaceae -1.785000 17.835000 0.3830000
Scrophulariaceae -1.210000 NA NA
Simmondsiaceae -2.420000 NA NA
Solanaceae -1.072000 9.465000 NA
Styracaceae -2.280000 24.565000 NA
Symplocaceae -1.485000 NA NA
Tetrameristaceae -2.970000 NA NA
Urticaceae -1.040250 9.126500 NA
Verbenaceae -1.100000 4.850000 0.2270000
Violaceae -1.390000 17.840000 0.3720000
Vitaceae -1.292900 6.647000 NA
Vochysiaceae -2.135000 19.995000 NA
Winteraceae -1.480000 11.620000 NA
Zygophyllaceae -2.780000 NA NA

If family-level values are missing, following Bartlett et al. (2012) average values for Mediterranean climate leaves are taken as defaults, i.e. \(\pi_{0,leaf} = -2\) MPa, \(\epsilon_{leaf} = 17\), whereas a 29% leaf apoplastic fraction is assumed (i.e. \(f_{apo,leaf} = 0.29\)).

A.3.13 Stem and root maximum hydraulic conductivity

Tissue-level maximum conductivity parameters (i.e. \(K_{stem,max,ref}\) and \(K_{root,max,ref}\)) are not direct parameters to simulation functions. Instead, theay are scaled to estimate stem- and root-level hydraulic conductances (i.e. \(k_{stem, \max}\) and \(k_{root, \max}\)) using plant size (see A.4.1 and A.4.3 for details). \(K_{stem,max,ref}\) and \(K_{root,max,ref}\) are supplied via species parameter table and missing values can therefore occur.

Default values for \(K_{stem,max,ref}\) are determined from taxonomic family using an internal data set (medfate:::trait_family_means):

Table A.5: Default maximum stem hydraulic conductivity by taxonomic family.
Kmax_stemxylem
Adoxaceae 4.0535575
Altingiaceae 0.5050000
Amaranthaceae 0.0819000
Amborellaceae 0.5400000
Anacardiaceae 4.0772016
Annonaceae 5.2706667
Apiaceae 0.5150000
Apocynaceae 2.5651667
Aquifoliaceae 0.2255757
Araliaceae 1.6809011
Araucariaceae 0.7322500
Asteraceae 0.4986571
Austrobaileyaceae 2.3000000
Berberidaceae 0.0873333
Betulaceae 2.8733374
Bignoniaceae 2.1014900
Bruniaceae 0.2515000
Burseraceae 3.4050000
Cactaceae 1.8688095
Calophyllaceae 0.8982857
Cannabaceae 4.3396105
Capparaceae 0.5572667
Caprifoliaceae 0.2521010
Caryocaraceae 1.7587273
Casuarinaceae 1.8954048
Cistaceae 0.3958482
Clusiaceae 0.5950000
Cochlospermaceae 7.7500000
Combretaceae 5.7436667
Convolvulaceae 2.2000000
Cordiaceae 4.4607389
Cornaceae 2.3439777
Cupressaceae 0.9325131
Daphniphyllaceae 0.4600000
Dennstaedtiaceae 21.9800000
Dilleniaceae 1.2500000
Dipterocarpaceae 8.8857143
Ebenaceae 1.5527759
Ehretiaceae 0.4100000
Ericaceae 0.6151806
Erythroxylaceae 0.5352000
Euphorbiaceae 3.3816717
Eupomatiaceae 1.1239700
Fabaceae 2.9075403
Fagaceae 2.5306061
Garryaceae 1.9333333
Gnetaceae 1.2900000
Iteaceae 0.4500000
Juglandaceae 4.2050000
Lamiaceae 4.8686077
Lauraceae 1.1201255
Lecythidaceae 6.5443450
Loranthaceae 0.2817696
Lythraceae 6.1800000
Malpighiaceae 11.0500000
Malvaceae 5.0140647
Melastomataceae 3.2448243
Meliaceae 3.5074214
Moraceae 4.2635627
Myricaceae 2.0300000
Myrothamnaceae 0.8700000
Myrtaceae 3.0899244
Nothofagaceae 0.7973333
Nyctaginaceae 3.4236667
Nyssaceae 0.1800000
Ochnaceae 0.9111500
Oleaceae 0.8444824
Onagraceae 1.0800000
Pandaceae 1.1963139
Phyllanthaceae 2.5362078
Phyllocladaceae 0.6930000
Phytolaccaceae 2.0410000
Picrodendraceae 3.9400000
Pinaceae 0.7547927
Piperaceae 4.4389250
Pittosporaceae 1.7800000
Poaceae 4.5583333
Podocarpaceae 0.4627272
Polygalaceae 0.1615533
Polygonaceae 2.4000000
Primulaceae 1.4938311
Proteaceae 1.6704393
Putranjivaceae 0.6000000
Rhamnaceae 1.9312597
Rhizophoraceae 1.1050000
Rosaceae 5.6895709
Rubiaceae 2.1240290
Rutaceae 1.5498517
Salicaceae 3.0508423
Santalaceae 1.8595493
Sapindaceae 2.5607242
Sapotaceae 0.5590170
Sciadopityaceae 0.4400000
Scrophulariaceae 0.2350000
Simaroubaceae 2.4300000
Solanaceae 3.6970125
Stachyuraceae 0.5500000
Staphyleaceae 2.6500000
Styracaceae 2.3407222
Symplocaceae 3.2000000
Tamaricaceae 2.6600000
Taxaceae 0.3200000
Theaceae 2.8179558
Thymelaeaceae 0.5627650
Ulmaceae 0.6210000
Urticaceae 4.9860000
Verbenaceae 1.7200000
Vochysiaceae 1.4756667
Winteraceae 0.4133333

If family-level values are missing, suitable \(K_{stem,max,ref}\) values are decided according to combinations of taxon group (either Angiosperm or Gymnosperm), growth form (either tree or shrub) and leaf phenology (Maherali et al. 2004):

Group Growth form Leaf phenology \(K_{stem,max,ref}\)
Angiosperm Tree Winter-(semi)deciduous 1.58
Angiosperm Shrub Winter-(semi)deciduous 1.55
Angiosperm Tree/Shrub Evergreen 2.43
Gymnosperm Tree any 0.48
Gymnosperm Shrub any 0.24

Following Oliveras et al. (2003), missing values for \(K_{root,max,ref}\) are assumed to be four-times the values given or estimated for \(K_{stem,max,ref}\).

A.3.14 Leaf maximum hydraulic conductance

Leaf maximum hydraulic conductance (\(k_{l, max}\), in \(mmol \cdot m^{-2} \cdot s^{-1} \cdot MPa^{-1}\)) is an input parameter that should be provided for each species. When missing, leaf maximum hydraulic conductance can be estimated from maximum stomatal conductance (\(g_{swmax}\)), following Franks (2006) (original coefficients were modified for better fit): \[\begin{equation} k_{l, max} = (g_{swmax}/0.015)^{1/1.3} \end{equation}\] Note that values for \(g_{swmax}\) may also be imputed (see A.3.11).

A.3.15 Xylem vulnerability

Default values for \(\Psi_{50,stem}\) are determined from taxonomic family using an internal data set (medfate:::trait_family_means):

Table A.6: Default stem P50 values by taxonomic family.
P50
Adoxaceae -3.0384833
Altingiaceae -2.0370147
Amaranthaceae -2.4252402
Amborellaceae -3.0000000
Anacardiaceae -2.6535235
Annonaceae -2.5276068
Apiaceae -5.7000000
Apocynaceae -2.4864334
Aquifoliaceae -3.6437782
Araliaceae -1.6530859
Araucariaceae -2.6183226
Arecaceae -1.8100000
Asparagaceae -1.6960000
Asteraceae -3.2565860
Atherospermataceae -3.0063333
Austrobaileyaceae -0.4990000
Berberidaceae -4.5000000
Betulaceae -2.1017591
Bignoniaceae -0.8616667
Boraginaceae -3.5677066
Bruniaceae -3.3883558
Burseraceae -1.3054970
Buxaceae -8.0000000
Cactaceae -1.2875000
Calophyllaceae -1.5400000
Calycanthaceae -1.2808475
Canellaceae -0.2320000
Cannabaceae -1.5325304
Capparaceae -2.3615234
Caprifoliaceae -5.5144833
Caryocaraceae -1.6766667
Casuarinaceae -2.1750000
Celastraceae -3.4679167
Chloranthaceae -1.7228571
Chrysobalanaceae -2.2000000
Cistaceae -7.1951892
Cleomaceae -2.1842678
Clusiaceae -1.3172327
Cochlospermaceae -1.4400000
Combretaceae -1.8483333
Convolvulaceae -1.5987102
Cordiaceae -2.3307795
Cornaceae -4.1378833
Cunoniaceae -1.1500000
Cupressaceae -8.3049767
Daphniphyllaceae -0.5985705
Dennstaedtiaceae -1.9900000
Dilleniaceae -1.4112676
Dipterocarpaceae -0.3628571
Dryopteridaceae -2.5797602
Ebenaceae -1.5093287
Ehretiaceae -3.8200000
Ericaceae -2.8142685
Euphorbiaceae -1.4638127
Eupomatiaceae -0.3950000
Fabaceae -2.3909838
Fagaceae -2.5878534
Fouquieriaceae -1.3452785
Garryaceae -6.2691850
Ginkgoaceae -4.3306349
Gnetaceae -3.8601667
Grossulariaceae -3.5658333
Haematococcaceae -1.0161048
Himantandraceae -1.3000000
Iteaceae -2.4945237
Juglandaceae -1.5701852
Lamiaceae -4.1494102
Lauraceae -2.1528796
Lecythidaceae -1.3583333
Lomariopsidaceae -1.1192688
Lythraceae -1.1835117
Magnoliaceae -1.6162070
Malpighiaceae -1.2600000
Malvaceae -1.5443759
Melastomataceae -2.2465000
Meliaceae -1.6824730
Menispermaceae -0.6400000
Moraceae -1.0012407
Myricaceae -1.6301207
Myrtaceae -2.1681342
Nothofagaceae -2.5384687
Nyctaginaceae -3.3618225
Nyssaceae -1.7354355
Ochnaceae -1.6475300
Oleaceae -3.3224338
Onagraceae -1.6250000
Pandaceae -2.6000000
Pentaphylacaceae -1.2000000
Phyllanthaceae -1.9312493
Phyllocladaceae -6.9215266
Phytolaccaceae -2.9000000
Pinaceae -3.9399344
Pittosporaceae -1.9328674
Platanaceae -1.5447656
Poaceae -2.5980959
Podocarpaceae -3.6786525
Polygalaceae -1.5000000
Polygonaceae -1.8324549
Polypodiaceae -1.4328381
Primulaceae -2.4159524
Proteaceae -3.0023208
Pteridaceae -1.6296520
Putranjivaceae -2.2150279
Ranunculaceae -1.6100000
Rhamnaceae -5.0583305
Rhizophoraceae -5.1853958
Rosaceae -4.2920879
Rubiaceae -2.7428916
Rutaceae -1.4957143
Salicaceae -1.9309521
Sapindaceae -2.3003821
Sapotaceae -1.9824490
Sarcobataceae -2.1745285
Schisandraceae -2.6653333
Sciadopityaceae -2.4279818
Simaroubaceae -1.5043567
Solanaceae -1.6191103
Stachyuraceae -4.0791455
Staphyleaceae -1.9981312
Stemonuraceae -0.1800000
Styracaceae -2.6750000
Symplocaceae -2.1074074
Tamaricaceae -1.2780403
Taxaceae -6.9838493
Tectariaceae -1.2443660
Theaceae -3.3275000
Thelypteridaceae -1.1367341
Thymelaeaceae -4.3968716
Trimeniaceae -0.8180000
Trochodendraceae -1.8850000
Urticaceae -0.7786495
Verbenaceae -1.7193146
Violaceae -2.5751935
Vitaceae -0.3520000
Vochysiaceae -1.4583013
Winteraceae -3.4099667
Zygophyllaceae -3.8233368

If family-level values is missing, a suitable estimate of \(\Psi_{50,stem}\) the water potential corresponding to 50% of conductance loss, can be obtained from Maherali et al. (2004) according to combinations of taxon group (either Angiosperm or Gymnosperm), growth form (either tree or shrub) and leaf phenology:

Group Growth form Leaf phenology \(\Psi_{50,stem}\)
Angiosperm Tree/Shrub Winter-(semi)deciduous -2.34
Angiosperm Tree Evergreen -1.51
Angiosperm Shrub Evergreen -5.09
Gymnosperm Tree any -4.17
Gymnosperm Shrub any -8.95

\(\Psi_{50,stem}\) estimates are taken for parameter \(\Psi_{critic}\), in the case of the basic water balance model.

Vulnerability curves in the advanced model need to be specified for leaves, stem and root segments via the two parameters of the Weibull function (see 10.2). When any of the parameters of the stem vulnerability curve is missing, a regression equation using data from Choat et al. (2012) can be used to estimate \(\Psi_{88,stem}\) from \(\Psi_{50,stem}\): \[\begin{equation} \Psi_{88,stem} = -1.4264 + 1.2593 \cdot \Psi_{50,stem} \end{equation}\]

Finally, estimates for \(c_{stem}\) and \(d_{stem}\) are obtained from \(\Psi_{50,stem}\) and \(\Psi_{88,stem}\) via function hydraulics_psi2Weibull().

Vulnerability curves for root xylem are less common than for stem xylem. If these values are missing, \(\Psi_{50,stem}\) is first estimated according to its definition and the stem vulnerability curve parameters, \(c_{stem}\) and \(d_{stem}\). Then, a relationship from Bartlett et al. (2016) is used to estimate \(\Psi_{50, root}\) from \(\Psi_{50,stem}\): \[\begin{equation} \Psi_{50, root} = 0.4892 + 0.742 \cdot \Psi_{50,stem} \end{equation}\] Finally, \(\Psi_{88,stem}\) and the Weibull vulnerability parameters are obtained as explained for stems.

Vulnerability curves for leaf xylem are also less common than for stem xylem. If these values are missing, the water potential at turgor los point \(\Psi_{tlp}\) is first estimated from \(\pi_{leaf}\) and \(\epsilon_{leaf}\) according to eq. (10.4). Then, a relationship calibrated with data from Bartlett et al. (2016) is used to estimate \(\Psi_{50, leaf}\) from \(\Psi_{tlp}\): \[\begin{equation} \Psi_{50, leaf} = 0.2486 + 0.9944 \cdot \Psi_{tlp} \end{equation}\] Finally, \(\Psi_{88,leaf}\) and the Weibull vulnerability parameters are obtained as explained for stems.

A.3.16 Photosynthesis rates

Rubisco’s maximum carboxylation rate at 25ºC (\(V_{max, 298}\), in \(\mu mol CO_2 \cdot s^{-1} \cdot m^{-2}\)) is a required input parameter for each species (Vmax298). When missing, the work by Walker et al. (2014) suggests that suitable estimates can be derived from \(SLA\) and \(N_{area}\), the latter being the nitrogen concentration per leaf area: \[\begin{equation} V_{max, 298} = e^{1.993 + 2.555\cdot \log(N_{area}) - 0.372 \cdot \log(SLA) + 0.422 \cdot \log(N_{area})\cdot \log(SLA) } \end{equation}\]

In turn, imputation for \(SLA\) is explained in A.3.3, whereas values for \(N_{area}\) are determined from \(N_{leaf}\) and \(SLA\), being \(N_{leaf}\) estimated as indicated in A.3.17. Would \(N_{leaf}\) and \(SLA\) values be both unavailable, a default value of 100 \(\mu mol CO_2 \cdot s^{-1} \cdot m^{-2}\) is used for \(V_{max, 298}\) imputation.

When the maximum rate of electron transport at the same temperature (\(J_{max, 298}\)) is not provided by the user, it can be estimated from \(V_{max, 298}\) using (Walker et al. 2014):

\[\begin{equation} J_{max, 298} = e^{1.197 + 0.847\cdot \log(V_{max,298})} \end{equation}\]

A.3.17 Maintenance respiration rates

When missing at the species parameter table, maintenance respiration rates for leaves, sapwood and fine roots (\(RER_{leaf}\), \(RER_{sapwood}\) and \(RER_{fineroot}\); all in \(g\,gluc\cdot g\,dry^{-1}\cdot day^{-1}\)) are estimated from corresponding tissue nitrogen concentrations (\(N_{leaf}\), \(N_{sapwood}\) and \(N_{fineroot}\); all in \(mg\,N \cdot g\,dry^{-1}\)) following the equations given by Reich et al. (2008) (after appropriate unit conversion): \[\begin{eqnarray} RER_{leaf} &=& e^{0.691+ 1.639 \cdot \log(N_{leaf}))} \\ RER_{sapwood} &=& e^{1.024 + 1.344 \cdot \log(N_{sapwood}))} \\ RER_{fineroot} &=& e^{0.980 + 1.352 \cdot \log(N_{fineroot}))} \end{eqnarray}\] where in the previous equations nitrogen concentrations are in \(mmol\,N\cdot g\,dry^{-1}\) and respiration rates in \(nmol\,CO2\cdot g\,dry^{-1}\cdot s^{-1}\).

In turn, when tissue nitrogen concentrations are missing they are estimated from taxonomic family using an internal data set (medfate:::trait_family_means):

Table A.7: Default nitrogen concentration per dry mass in different tissues by taxonomic family.
Nleaf Nsapwood Nfineroot
Acanthaceae 27.122403 NA 5.580000
Achariaceae 22.162815 NA NA
Acoraceae 18.000000 NA NA
Actinidiaceae 20.183321 NA NA
Adoxaceae 20.566364 NA 11.013750
Aextoxicaceae 9.621429 NA NA
Aizoaceae 14.800000 NA NA
Alismataceae 27.287834 NA NA
Alstroemeriaceae 19.402857 NA NA
Altingiaceae 15.462547 NA 7.550000
Amaranthaceae 23.740694 NA 12.411441
Amaryllidaceae 28.734076 NA 11.440000
Amphorogynaceae 25.236766 NA NA
Anacardiaceae 17.914439 NA 10.539737
Annonaceae 23.593695 NA 23.830391
Apiaceae 24.746891 NA 10.787434
Apocynaceae 21.754119 NA 16.845575
Aptandraceae 28.435524 NA NA
Aquifoliaceae 14.645818 NA 14.324450
Araceae 22.255347 NA NA
Araliaceae 18.093569 NA 20.500000
Araucariaceae 12.622035 NA 13.000000
Arecaceae 18.349681 NA 13.216667
Aristolochiaceae 31.726525 NA NA
Asparagaceae 22.875870 NA NA
Asphodelaceae 12.352222 NA NA
Aspleniaceae 28.260000 NA NA
Asteraceae 22.036543 NA 9.346061
Atherospermataceae 17.869722 NA 23.200000
Athyriaceae 26.901037 NA NA
Aulacomniaceae 8.000000 NA NA
Balsaminaceae 36.003950 NA NA
Begoniaceae 34.200000 NA NA
Berberidaceae 17.997372 NA 21.087500
Betulaceae 24.194029 14.505149 13.430951
Bignoniaceae 23.830902 6.575973 19.915047
Bixaceae 25.531043 NA NA
Blechnaceae 11.749050 NA NA
Bonnetiaceae 9.800000 NA NA
Boraginaceae 23.032555 NA NA
Brassicaceae 34.316821 NA 18.501306
Bromeliaceae 9.559591 NA NA
Brunelliaceae 21.006960 NA NA
Bruniaceae 7.781667 NA NA
Burseraceae 19.028712 NA 10.964427
Butomaceae 42.600000 NA NA
Buxaceae 22.691830 NA NA
Cabombaceae 19.500000 NA NA
Cactaceae 16.988641 NA NA
Calophyllaceae 12.424790 NA NA
Calycanthaceae 17.400000 NA NA
Calyceraceae 43.000000 NA NA
Campanulaceae 27.682767 NA 5.721013
Cannabaceae 28.941055 NA NA
Cannaceae 39.700000 NA NA
Capparaceae 30.523096 9.456375 NA
Caprifoliaceae 19.333331 NA 12.382333
Cardiopteridaceae 19.882555 NA NA
Caricaceae 36.177864 NA NA
Caryocaraceae 18.085982 NA NA
Caryophyllaceae 22.682234 NA 12.024146
Casuarinaceae 13.167778 NA NA
Celastraceae 18.486005 NA 16.244311
Centroplacaceae 15.890000 NA NA
Cephalotaxaceae 19.300000 NA NA
Chloranthaceae 18.710157 NA NA
Chrysobalanaceae 16.190293 NA NA
Cibotiaceae 17.187976 NA NA
Cistaceae 17.353120 NA 10.170000
Cleomaceae 40.580000 NA NA
Clethraceae 14.113977 NA NA
Clusiaceae 15.111239 NA NA
Cochlospermaceae 18.036146 NA NA
Codonaceae 46.700000 NA NA
Colchicaceae 24.100437 NA NA
Comandraceae 20.452929 NA NA
Combretaceae 18.537698 3.045745 8.040984
Commelinaceae 22.817426 NA NA
Connaraceae 18.671267 NA NA
Convolvulaceae 27.043628 NA 20.610000
Corallinaceae 24.600000 NA NA
Cordiaceae 26.773979 NA 22.222748
Coriariaceae 23.145656 NA NA
Cornaceae 19.015650 NA 7.812801
Corynocarpaceae 30.000000 NA 34.200000
Costaceae 20.694025 NA NA
Coulaceae 18.024187 NA NA
Crassulaceae 20.890131 NA 9.510000
Crypteroniaceae 11.190000 NA NA
Cucurbitaceae 34.184894 NA NA
Cunoniaceae 11.596341 NA 13.000000
Cupressaceae 11.557371 5.200000 10.299874
Curtisiaceae 14.750000 NA NA
Cyatheaceae 20.146356 NA 9.750000
Cycadaceae 22.709697 NA NA
Cyclanthaceae 19.600000 NA NA
Cyperaceae 19.578327 NA 7.069177
Cyrillaceae 11.676042 NA NA
Cystopteridaceae 26.087701 NA NA
Daphniphyllaceae 16.697078 NA NA
Dennstaedtiaceae 21.009091 NA NA
Diapensiaceae 11.225000 NA NA
Dichapetalaceae 16.234979 NA NA
Dicksoniaceae 14.845833 NA 13.200000
Dicranaceae 6.960000 NA NA
Didiereaceae 13.800000 NA NA
Dilleniaceae 13.395289 NA 4.090000
Dioscoreaceae 21.481420 NA NA
Dipterocarpaceae 16.617894 NA 11.000000
Droseraceae 13.592376 NA NA
Dryopteridaceae 21.617072 NA NA
Ebenaceae 17.540189 NA 14.088678
Ehretiaceae 24.178348 NA NA
Elaeagnaceae 34.198757 NA 28.100000
Elaeocarpaceae 15.733059 NA 13.850000
Ephedraceae 14.259159 NA NA
Equisetaceae 18.233321 NA 10.919654
Ericaceae 11.965271 2.780000 9.215721
Eriocaulaceae 21.633333 NA NA
Erythropalaceae 21.326093 NA NA
Erythroxylaceae 21.484533 NA NA
Escalloniaceae 18.094942 NA NA
Euphorbiaceae 25.053831 4.319765 7.033673
Eupteleaceae 21.400000 NA NA
Fabaceae 28.117544 7.428306 17.968186
Fagaceae 17.363505 7.268250 11.620330
Fissidentaceae 15.100000 NA NA
Flagellariaceae 24.324811 NA NA
Fouquieriaceae 13.857143 NA NA
Garryaceae 13.408563 NA NA
Gentianaceae 20.818110 NA NA
Geraniaceae 21.715382 NA 8.446347
Gesneriaceae 21.044023 NA NA
Ginkgoaceae 19.375000 NA NA
Gleicheniaceae 12.503416 NA NA
Gnetaceae 23.623621 NA NA
Goodeniaceae 12.770560 NA NA
Goupiaceae 17.470304 NA NA
Griseliniaceae 9.968742 NA 30.200000
Grossulariaceae 21.745764 NA 12.475793
Gunneraceae 22.700000 NA NA
Gyrostemonaceae 16.700000 NA NA
Haematococcaceae 26.810000 NA NA
Haemodoraceae 35.460000 NA NA
Haloragaceae 13.066600 NA NA
Hamamelidaceae 13.017588 NA 11.917021
Heliconiaceae 23.191582 NA NA
Heliotropiaceae 26.496602 NA NA
Hemidictyaceae 24.343333 NA NA
Hernandiaceae 28.683333 NA NA
Hookeriaceae 11.550000 NA NA
Humiriaceae 13.643659 NA NA
Hydrangeaceae 24.405094 NA NA
Hydrocharitaceae 26.033333 NA NA
Hydrophyllaceae 34.211537 NA NA
Hylocomiaceae 8.000000 NA NA
Hypericaceae 19.973686 NA NA
Hypoxidaceae 20.550000 NA NA
Icacinaceae 26.315503 NA NA
Iridaceae 17.467285 NA NA
Irvingiaceae 27.566667 NA NA
Iteaceae 19.533741 NA NA
Ixerbaceae 7.300000 NA NA
Ixonanthaceae 18.222880 NA NA
Juglandaceae 20.948555 NA NA
Juncaceae 19.689440 NA 8.612483
Juncaginaceae 27.705506 NA NA
Krameriaceae 19.533354 NA NA
Lacistemataceae 21.106849 NA NA
Lamiaceae 22.628692 7.238641 13.011714
Lardizabalaceae 14.882698 NA 12.200000
Lauraceae 19.918654 8.450000 17.581342
Lecythidaceae 21.725974 NA NA
Lentibulariaceae 19.585904 NA NA
Lepidobotryaceae 16.734855 NA NA
Liliaceae 27.279029 NA NA
Linaceae 19.989866 NA NA
Lindsaeaceae 30.491111 NA NA
Loasaceae 13.160000 NA NA
Loganiaceae 18.399957 NA NA
Loranthaceae 17.936468 NA NA
Lycopodiaceae 8.880979 NA 11.162034
Lygodiaceae 35.050000 NA NA
Lythraceae 16.257492 NA NA
Magnoliaceae 20.262715 NA 13.491060
Malpighiaceae 22.741160 2.900607 18.996699
Malvaceae 23.035658 7.246698 14.587437
Marantaceae 22.009839 NA NA
Marattiaceae 25.368000 NA NA
Marcgraviaceae 12.700000 NA NA
Mazaceae 25.876667 NA NA
Melanthiaceae 30.511836 NA NA
Melastomataceae 18.901019 NA NA
Meliaceae 25.025835 2.849435 18.080098
Melianthaceae 22.290319 NA NA
Menispermaceae 20.320352 NA NA
Menyanthaceae 35.361370 NA 7.084952
Metteniusaceae 13.976361 NA NA
Molluginaceae 25.736364 NA NA
Monimiaceae 23.291032 NA 29.500000
Montiaceae 24.054583 NA NA
Moraceae 21.530594 NA 8.931110
Musaceae 34.583333 NA NA
Myodocarpaceae 9.800000 NA NA
Myricaceae 20.594828 NA 13.895174
Myristicaceae 20.059672 NA NA
Myrtaceae 13.833610 NA 11.460063
Namaceae 29.637748 NA NA
Nartheciaceae 24.700000 NA NA
Nelumbonaceae 26.200000 NA NA
Nephrolepidaceae 16.740417 NA NA
Nitrariaceae 33.503973 NA 21.340000
Nothofagaceae 14.163151 NA 12.909500
Nyctaginaceae 37.234569 NA NA
Nymphaeaceae 32.458333 NA NA
Nyssaceae 14.463636 NA NA
Ochnaceae 14.940688 NA NA
Olacaceae 30.456560 NA NA
Oleaceae 18.699032 2.780000 14.568902
Oleandraceae 16.600000 NA NA
Onagraceae 23.152644 NA 10.018291
Onocleaceae 25.498562 NA NA
Ophioglossaceae 32.783960 NA NA
Opiliaceae 42.403480 NA NA
Orchidaceae 17.957874 NA NA
Orobanchaceae 25.757066 NA NA
Orthotrichaceae 6.080000 NA NA
Osmundaceae 26.414177 NA NA
Oxalidaceae 30.182499 NA NA
Paeoniaceae 19.423601 NA NA
Pandaceae 34.392599 NA NA
Pandanaceae 16.656945 NA NA
Papaveraceae 32.656816 NA NA
Paracryphiaceae 10.386259 NA 16.200000
Parnassiaceae 17.298686 NA NA
Passifloraceae 30.295379 NA NA
Paulowniaceae 15.004442 NA NA
Pedaliaceae 22.850000 NA NA
Penaeaceae 18.045000 NA NA
Pentaphylacaceae 12.533642 NA NA
Penthoraceae 40.820000 NA NA
Peraceae 16.848913 NA NA
Peridiscaceae 13.921055 NA NA
Phrymaceae 18.115084 NA NA
Phyllanthaceae 20.024243 NA NA
Phyllocladaceae 9.113553 NA 14.350000
Phytolaccaceae 36.682157 NA NA
Picramniaceae 25.729169 NA NA
Picrodendraceae 15.085556 NA NA
Pinaceae 12.942295 1.978810 11.012076
Piperaceae 30.478808 NA NA
Pittosporaceae 12.747401 NA 13.192372
Plagiogyriaceae 23.332250 NA NA
Plantaginaceae 20.813263 NA 10.781608
Platanaceae 23.238229 NA NA
Plumbaginaceae 22.717457 NA 7.400000
Poaceae 18.316675 NA 9.301720
Podocarpaceae 11.271467 NA 14.250000
Polemoniaceae 20.570795 NA NA
Polygalaceae 20.319486 NA NA
Polygonaceae 28.319115 NA 11.440555
Polypodiaceae 12.511738 NA NA
Polytrichaceae 11.378150 NA NA
Pontederiaceae 33.306667 NA NA
Portulacaceae 20.621667 NA NA
Potamogetonaceae 38.299866 NA 14.518003
Pottiaceae 15.300000 NA NA
Primulaceae 16.739662 NA 13.625000
Proteaceae 7.704847 NA 12.426033
Pteridaceae 17.948399 NA NA
Putranjivaceae 22.615313 NA 7.600000
Quiinaceae 16.384609 NA NA
Quillajaceae 10.333333 NA NA
Ranunculaceae 24.728950 NA 12.308324
Resedaceae 35.625000 NA NA
Restionaceae 8.000000 NA NA
Rhamnaceae 21.278492 NA 16.700000
Rhizogoniaceae 6.280000 NA NA
Rhizophoraceae 17.008370 NA 6.400000
Rosaceae 20.490021 NA 11.643586
Rubiaceae 21.408919 NA 14.758185
Rutaceae 24.805269 NA 21.805537
Sabiaceae 14.937467 NA NA
Salicaceae 23.130763 2.830072 11.972095
Salvadoraceae 26.152886 NA NA
Santalaceae 10.792099 NA NA
Sapindaceae 21.286530 4.139490 13.702663
Sapotaceae 19.108913 7.281857 14.795813
Sarcobataceae 16.902834 NA NA
Sarraceniaceae 9.705030 NA NA
Saxifragaceae 19.018039 NA NA
Schisandraceae 15.268439 NA NA
Schlegeliaceae 8.200000 NA NA
Schoepfiaceae 28.046620 NA NA
Scrophulariaceae 18.090465 NA 20.600000
Sematophyllaceae 6.900000 NA NA
Simaroubaceae 24.803286 NA 11.600000
Simmondsiaceae 16.913670 NA NA
Siparunaceae 27.322658 NA NA
Smilacaceae 17.314717 NA NA
Solanaceae 35.779496 NA 16.605000
Sphagnaceae 8.866667 NA NA
Staphyleaceae 17.921574 NA NA
Stemonuraceae 17.489870 NA NA
Stixaceae 23.666667 NA NA
Strasburgeriaceae 7.700000 NA NA
Strombosiaceae 29.209762 NA NA
Stylidiaceae 12.808803 NA NA
Styracaceae 16.376992 NA NA
Symplocaceae 15.478410 NA NA
Tamaricaceae 21.012878 NA 13.095000
Tapisciaceae 21.542615 NA NA
Taxaceae 16.422887 NA NA
Tectariaceae 25.618889 NA NA
Tetradiclidaceae 19.294690 NA NA
Theaceae 13.292438 NA 6.300000
Thelypteridaceae 26.939679 NA NA
Thymelaeaceae 22.203805 NA NA
Tofieldiaceae 13.727586 NA NA
Trigoniaceae 25.450000 NA NA
Typhaceae 23.837149 NA NA
Ulmaceae 22.750298 NA 23.700000
Urticaceae 25.005457 NA NA
Velloziaceae 21.096491 NA NA
Verbenaceae 21.378480 NA NA
Violaceae 26.430388 NA 18.342843
Viscaceae 26.300000 NA NA
Vitaceae 23.425993 NA NA
Vivianiaceae 24.000000 NA NA
Vochysiaceae 16.407386 NA NA
Winteraceae 11.822776 NA 13.900000
Ximeniaceae 17.667625 NA NA
Zamiaceae 18.337149 NA NA
Zingiberaceae 19.486452 NA NA
Zygophyllaceae 23.141902 NA 15.277484

When family values are also missing, default tissue-averaged nitrogen concentrations are given: \(N_{leaf} = 20.088\), \(N_{sapwood} = 3.9791\) and \(N_{fineroot} = 12.207\).

Default control values (\(MR_{leaf} = 0.00260274\)), sapwood (\(MR_{sapwood} = 6.849315e-05\)) and fine roots (\(MR_{fineroot} 0.002054795\)) were used in previous model versions, derived from Ogle & Pacala (2009), but these are no longer used because of easier parameterization using tissue nitrogen concentration.

A.3.18 Relative growth rates

When missing at the species parameter table, maximum relative growth rates for leaves, sapwood and fine roots are taken from control parameters. Default values are provided in 15.5.3.

A.3.19 Senescence rates

When missing at the species parameter table, senescence rates for sapwood and fine roots are taken from control parameters.

A.3.20 Relative starch for sapwood growth

When missing at the species parameter table, the minimum relative starch for sapwood growth is taken from control parameters. Default value is provided in 15.5.3.

A.3.21 Wood carbon

Default values for \(C_{wood}\) are determined from taxonomic family using an internal data set (medfate:::trait_family_means):

Table A.8: Default wood carbon content by taxonomic family.
WoodC
Acanthaceae 0.4242167
Altingiaceae 0.4435000
Amaranthaceae 0.4197662
Amaryllidaceae 0.4508400
Anacardiaceae 0.4566867
Annonaceae 0.4726000
Apiaceae 0.4413076
Apocynaceae 0.4924750
Aquifoliaceae 0.4400000
Araliaceae 0.4540667
Arecaceae 0.4556000
Asparagaceae 0.4631000
Asteraceae 0.4375956
Betulaceae 0.4721962
Bignoniaceae 0.4618077
Boraginaceae 0.4153500
Brassicaceae 0.4274775
Burseraceae 0.4548544
Calophyllaceae 0.4663000
Campanulaceae 0.4498475
Cannabaceae 0.4683583
Caprifoliaceae 0.4475552
Caryophyllaceae 0.4147683
Casuarinaceae 0.4200000
Celastraceae 0.4900000
Chrysobalanaceae 0.4886000
Cistaceae 0.4698925
Clethraceae 0.4400000
Combretaceae 0.4678282
Convolvulaceae 0.4200000
Cordiaceae 0.4652500
Corynocarpaceae 0.4520000
Cupressaceae 0.5006151
Cyperaceae 0.4639737
Dipterocarpaceae 0.4744750
Ebenaceae 0.4828000
Ehretiaceae 0.4500000
Elaeocarpaceae 0.4350000
Ericaceae 0.4865107
Euphorbiaceae 0.4715052
Fabaceae 0.4559793
Fagaceae 0.4642838
Gentianaceae 0.4654867
Geraniaceae 0.4381400
Haematococcaceae 0.4400000
Hypericaceae 0.4547167
Juglandaceae 0.4898900
Juncaceae 0.4238725
Juncaginaceae 0.4056355
Lamiaceae 0.4650444
Lauraceae 0.4677907
Lecythidaceae 0.4618750
Lentibulariaceae 0.4450200
Loganiaceae 0.4943000
Lythraceae 0.4219000
Magnoliaceae 0.4500000
Malpighiaceae 0.4765989
Malvaceae 0.4671722
Melastomataceae 0.4801500
Meliaceae 0.4667281
Moraceae 0.4638776
Muntingiaceae 0.4200000
Myristicaceae 0.4884667
Myrtaceae 0.4270234
Namaceae 0.4700000
Nothofagaceae 0.5225000
Ochnaceae 0.4840000
Oleaceae 0.4748772
Orobanchaceae 0.4437020
Pentaphylacaceae 0.5000000
Phyllanthaceae 0.4668417
Pinaceae 0.4955591
Pittosporaceae 0.4630000
Plantaginaceae 0.4240841
Platanaceae 0.4813333
Plumbaginaceae 0.4353996
Poaceae 0.4362235
Podocarpaceae 0.4700000
Polygalaceae 0.4819000
Polygonaceae 0.4477000
Primulaceae 0.4223568
Quillajaceae 0.4900000
Ranunculaceae 0.4408600
Rhamnaceae 0.4745500
Rhizophoraceae 0.4293500
Rosaceae 0.4407549
Rubiaceae 0.4631136
Rutaceae 0.4718524
Salicaceae 0.4787565
Sapindaceae 0.4755988
Sapotaceae 0.4575714
Schisandraceae 0.4550000
Scrophulariaceae 0.4400000
Simaroubaceae 0.4649167
Solanaceae 0.4325000
Staphyleaceae 0.4490000
Styracaceae 0.4750000
Theaceae 0.4760500
Ulmaceae 0.4859000
Urticaceae 0.4555722
Violaceae 0.4471733
Vochysiaceae 0.4759417

If family-level values are missing, default value of \(C_{wood} = 0.5\,g\,C\cdot g\,dry^{-1}\) is used.

A.3.22 Mortality baseline rate

When missing at the species parameter table, the mortality baseline rate is taken from control parameters. Default value is provided in 15.5.3.

A.3.23 Recruitment

Imputation of missing values for recruitment is specified via control parameters. Default values are provided in 18.4.3.

A.3.24 Flammability

Default values for the surface-area-to-volume ratio (\(\sigma\)), fuel heat content (\(h\)) and lignin percent (\(LI\)) are defined from leaf size and leaf shape as follows:

Leaf shape Leaf size \(\sigma\) \(h\) \(LI\)
Broad Large 5740 19740 15.50
Broad Medium 4039 19825 20.21
Broad Small 4386 20062 22.32
Linear/Needle Large 3620 18250 24.52
Linear/Needle Medium 4758 21182 24.52
Linear/Needle Small 6697 21888 18.55
Spines [any] 6750 20433 14.55
Scale [any] 1120 20504 14.55

Default value for the density of fuel particles (\(\rho_p\)) is 400 \(kg\cdot m^{-3}\).

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