In ashiklom/fortebaseline: Forest Resilience and Threshold Experiment (FoRTE) ED2 baseline runs source code and manuscript

fig <- function(...) {
  knitr::include_graphics(here::here("analysis", "figures", ...))
}
knitr::opts_chunk$set(
  collapse = TRUE,
  warning = FALSE,
  message = FALSE,
  echo = FALSE,
  comment = "#>",
  out.width = "\\linewidth"
)

### Figure S1
umbs_map_cap <- paste(
  "Location of University of Michigan Biological Station (UMBS; black dot)",
  "in the US Upper Midwest."
)
fig("umbs-map.png")

\clearpage

### Figure S2
structure_default_light_cap <- paste(
  "Radiation profiles of cohorts from ED2 runs with",
  "default parameters, across different configurations.",
  "Each point represents a single cohort of the given PFT,",
  "position on the y-axis represents the height of that cohort,",
  "and position on the x-axis represents the relative light level",
  "received by that cohort."
)
fig("default-light-levels.png")

\clearpage

### Figure S3
pft_histogram_cap <- paste(
  "ED-2.2 ensemble predictions of PFT aboveground biomass fractions."
)
fig("pft-histogram.png")

\clearpage

### Figure S4
fitobs_pie_cap <- paste(
  "NPP predictions from best-fit parameters."
)

fig("pie-fitobs.png")

\clearpage

### Figure S5
params_fit_observed_cap <- paste(
  "PFT parameters resulting in runs that fit observed NPP and LAI."
)

fig("params-fit-observed.png")

\clearpage

### Figure S6
diversity_pie_cap <- paste(
  "NPP predictions from most diverse parameters."
)

fig("pie-diversity.png")

\clearpage

### Figure S7
params_high_diversity_cap <- paste(
  "PFT parameters resulting in runs that produce NPFT > 2 and total LAI > 1."
)

fig("params-high-diversity.png")

\clearpage

Table: ED-2.2 default parameter values

| Parameter | Unit | Plant functional type | Value | |--------------------------|---------------------------------------|---------------------------|----------------------| | Specific leaf area (SLA) | m$^2$ kgC$^{-1}$ | Early hardwood | 14.4 | | | | Mid hardwood | 11.616 | | | | Late hardwood | 28.8 | | | | Pine | 2.88 | | V$_{c,\max}$ | $\mu$mol m$^{-2}$ s$^{-1}$ | Early hardwood | 28.9 | | | | Mid hardwood | 24.7 | | | | Late hardwood | 9.90 | | | | Pine | 16.1 | | C:N leaf | Unitless | Early hardwood | 13.5 | | | | Mid hardwood | 19.3 | | | | Late hardwood | 18.1 | | | | Pine | 78.0 | | Clumping factor | Unitless (0 - 1) | Early, Mid, Late hardwood | 0.84 | | | | Pine | 0.735 | | Leaf orientation factor | Unitless (-1 - 1) | All | 0 | | Refl. (VIS) | Unitless (0 - 1) | All | 0.11 | | Refl. (NIR) | Unitless (0 - 1) | All | 0.11 | | Trans. (VIS) | Unitless (0 - 1) | All | 0.11 | | Trans. (NIR) | Unitless (0 - 1) | All | 0.11 | | Quant. eff. | mol CO$_2$ (mol photons)$^{-1}$ | All | 0.08 | | Stomatal slope | Unitless | All | 7.20 | | Water cond. | m$^2$ a$^{-1}$ (kgC root)$^{-1}$ | All | $1.9 \times 10^{-5}$ | | Growth resp. | Unitless (0 - 1) | Early, Mid, Late hardwood | 0 | | | | Pine | 0.45 | | Leaf turnover | year$^{-1}$ | Pine | 0.333 | | Root turnover | year$^{-1}$ | Early hardwood | 5.77 | | | | Mid hardwood | 5.08 | | | | Late hardwood | 5.07 | | | | Pine | 3.93 | | F. labile | Unitless (0 - 1) | All | 0.79 | | Mort. C rate | year$^{-1}$ | All | 1 | | Mort. C bal. | Unitless | All | 20 | | Mort. bg. rate. | year$^{-1}$ | Early hardwood | 0.00614 | | | | Mid hardwood | 0.00381 | | | | Late hardwood | 0.00428 | | | | Pine | 0.00339 | | Mort. seedling | Unitless (0 - 1) | All | 0.95 | | Repro. C frac. | Unitless | All | 0.3 | | Dispersal | Unitless (0 - 1) | Early hardwood | 1 | | | | Mid hardwood | 0.325 | | | | Late hardwood | 0.074 | | | | Pine | 0.766 | | Min. height | m | All | 18 | | Root:leaf | Unitless | Early, Mid, Late hardwood | 1.13 | | | | Pine | 0.346 | | Leaf resp. | $\mu$mol m$^2$ s$^{-1}$ | Early hardwood | 0.419 | | | | Mid hardwood | 0.359 | | | | Late hardwood | 0.144 | | | | Pine | 0.233 | | Root resp. | $\mu$mol CO$_2$ (kg fine root)$^{-1}$ | All | 0.794 |

\clearpage

Table: Prior distributions for trait meta-analysis. Trait descriptions and units are given in Table 2 (main text).

| Parameter | Plant Functional Type | Distribution | |--------------------|---------------------------|----------------------| | Specific leaf area | Early, Mid, Late hardwood | Gamma(5.13, 0.234) | | '' | Pine | Gamma(2, 0.2) | | Vcmax | All | Weibull(1.7, 80) | | C:N leaf | Early, Mid, Late hardwood | Gamma(15.53, 0.87) | | '' | Pine | Uniform(3, 300) | | Clumping | All | Beta(3, 1.5) | | F. labile | All | Beta(1.5, 1.5) | | Root:leaf | Early, Mid, Late hardwood | LogNormal(0.21, 0.6) | | '' | Pine | LogNormal(-0.25, 1) | | Growth resp. | Early, Mid, Late hardwood | Beta(4.06, 7.2) | | '' | Pine | Beta(3, 3.6) | | Refl. (NIR) | Early hardwood | Beta(561.2, 776.7) | | '' | Mid hardwood | Beta(34.8, 56.0) | | | Late hardwood | Beta(393.2, 595.0) | | | Pine | Beta(35.0, 34.6) | | Refl. (VIS) | Early hardwood | Beta(258.9, 4463.9) | | '' | Mid hardwood | Beta(10.1, 157.5) | | | Late hardwood | Beta(72.4, 1282.6) | | | Pine | Beta(5.5, 53.0) | | Leaf resp. | All | Gamma(1.5, 0.4) | | Trans. (NIR) | Early hardwood | Beta(173.2, 199.2) | | '' | Mid hardwood | Beta(16.5, 17.3) | | | Late hardwood | Beta(95.6, 85.6) | | | Pine | Beta(5.52, 13.8) | | Trans. (VIS) | Early hardwood | Beta(15.4, 561.1) | | '' | Mid hardwood | Beta(2.1, 37.9) | | | Late hardwood | Beta(8.8, 189.0) | | | Pine | Beta(1.1, 73.8) | | Leaf turnover | Pine | Gamma(4, 8) | | Mort. C rate | All | Gamma(1, 0.05) | | Mort. C bal. | All | Gamma(1.47, 0.0578) | | Mort. bg. rate | All | Uniform(0, 0.02) | | Dispersal | All | Beta(1.1, 1.5) | | Leaf orient. | All | Uniform(-0.5, 0.5) | | Quant. eff. | Early, Mid hardwood, Pine | Weibull(3.32, 0.08) | | '' | Late hardwood | Gamma(2, 22) | | Repro. C frac. | All | Beta(2, 4) | | Min. height | All | Gamma(1.5, 0.2) | | Root resp. | All | Weibull(2, 10) | | Root turnover | Early, Mid hardwood, Pine | Weibull(1.55, 1.5) | | '' | Late hardwood | Weibull(1.55, 0.862) | | Mort. seedlng | All | Beta(3.61, 0.433) | | Stomatal slope | All | LogNormal(2.3, 1) | | Water cond. | All | LogNormal(2e-5, 3.5) |

ashiklom/fortebaseline documentation built on May 9, 2020, 1:56 a.m.