Remove ignore and re add files

inst/docs/FF16/FF16-eqns.csv

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+"Variable","Function","Allocation","Growth rate"
+"**(a) Assumed**",,,
+"Height","$H = \alpha_{{\rm l1}} \, \left(A_{\rm l} \, {\rm m^{-2}} \right)^{\alpha_{{\rm l2}}}$","$\frac{{\rm d}H}{{\rm d}A_{\rm l}} = \alpha_{{\rm l2}} \alpha_{{\rm l1}} \left(A_{\rm l} \, {\rm m^{-2}} \right)^{\alpha_{{\rm l2}}-1}$","$\frac{{\rm d}H}{{\rm d}t} = \frac{{\rm d}H}{{\rm d}A_{\rm l}} \, \frac{{\rm d}A_{\rm l}}{{\rm d}t}$"
+"Sapwoood area","$A_{\rm s} = \theta \, A_{\rm l}$","$\frac{{\rm d}A_{\rm s}}{{\rm d} A_{\rm l}} = \theta$","$\frac{{\rm d}A_{\rm s}}{{\rm d}t} = \frac{{\rm d}A_{\rm s}}{{\rm d} A_{\rm l}} \, \frac{{\rm d}A_{\rm l}}{{\rm d}t}$"
+"Bark area","$A_{\rm b} = \alpha_{{\rm b1}} \, \theta \, A_{\rm l}$","$\frac{{\rm d}A_{\rm b}}{{\rm d} A_{\rm l}} = \alpha_{{\rm b1}} \, \theta$","$\frac{{\rm d}A_{\rm b}}{{\rm d}t} = \frac{{\rm d}A_{\rm b}}{{\rm d} A_{\rm l}} \, \frac{{\rm d}A_{\rm l}}{{\rm d}t}$"
+"**(b) Derived**",,,
+"Leaf mass","$M_{\rm l} = \phi \, A_{\rm l}$","$\frac{{\rm d}M_{\rm l}}{{\rm d}A_{\rm l}} = \phi$","$\frac{{\rm d}M_{\rm l}}{{\rm d}t} = \frac{{\rm d}M_{\rm l}}{{\rm d}A_{\rm l}} \, \frac{{\rm d}A_{\rm l}}{{\rm d}t}$"
+"Sapwood mass","$M_{\rm s} = \rho \, \theta \, \eta_{\rm c} \, A_{\rm l} \, H$","$\frac{{\rm d}M_{\rm s}}{{\rm d}A_{\rm l}} = \rho \, \theta \, \eta_{\rm c} \, \big(H + A_{\rm l} \, \frac{{\rm d}H}{{\rm d}A_{\rm l}} \big)$","$\frac{{\rm d}M_{\rm s}}{{\rm d}t} = \frac{{\rm d}M_{\rm s}}{{\rm d}A_{\rm l}} \, \frac{{\rm d}A_{\rm l}}{{\rm d}t}$"
+"Bark mass","$M_{\rm b} = \alpha_{{\rm b1}} \, \rho \, \theta \, \eta_{\rm c} \, A_{\rm l} \, H$","$\frac{{\rm d}M_{\rm b}}{{\rm d}A_{\rm l}} = \alpha_{{\rm b1}} \, \rho \, \theta \, \eta_{\rm c}\big(H + A_{\rm l} \, \frac{{\rm d}H}{{\rm d}A_{\rm l}} \big)$","$\frac{{\rm d}M_{\rm b}}{{\rm d}t} = \frac{{\rm d}M_{\rm b}}{{\rm d}A_{\rm l}} \, \frac{{\rm d}A_{\rm l}}{{\rm d}t}$"
+"Root mass","$M_{\rm r} = \alpha_{{\rm r1}} \, A_{\rm l}$","$\frac{{\rm d}M_{\rm r}}{{\rm d}A_{\rm l}} = \alpha_{{\rm r1}}$","$\frac{{\rm d}M_{\rm r}}{{\rm d}t} = \frac{{\rm d}M_{\rm r}}{{\rm d}A_{\rm l}} \, \frac{{\rm d}A_{\rm l}}{{\rm d}t}$"
+

inst/docs/FF16/FF16-params-core.csv

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+Description,Symbol,Unit,Code
+**Plant construction**,,,
+Crown-shape parameter,$\eta$,,eta
+Leaf mass per area,$\phi$,kg m$^{-2}$,lma
+Wood density,$\rho$,kg m$^{-3}$,rho
+Sapwood area per unit leaf area,$\theta$,,theta
+Height of plant with leaf area of 1m$^2$,$\alpha_{\rm l1}$,m,a_l1
+Exponent of relationship between height and leaf area,$\alpha_{\rm l2}$,,a_l2
+Root mass per unit leaf area,$\alpha_{\rm r1}$,kg m$^{-2}$,a_r1
+Ratio of bark area to sapwood area,$\alpha_{\rm b1}$,,a_b1
+**Production**,,,
+Leaf photosynthesis per area,$\alpha_{\rm p1}$,mol yr$^{-1}$ m$^{-2}$,a_p1
+Saturation of leaf photosynthesis per area,$\alpha_{\rm p2}$,,a_p2
+Yield = fraction of carbon fixed converted into mass,$\alpha_{\rm y}$,,a_y
+Biomass per mol carbon,$\alpha_{\rm bio}$,kg mol$^{-1}$,a_bio
+Leaf respiration per mass,$r_{\rm l}$,mol yr$^{-1}$ kg$^{-1}$,r_l
+Fine-root respiration per mass,$r_{\rm r}$,mol yr$^{-1}$ kg$^{-1}$,r_r
+Sapwood respiration per mass,$r_{\rm s}$,mol yr$^{-1}$ kg$^{-1}$,r_s
+Bark respiration per mass,$r_{\rm b}$,mol yr$^{-1}$ kg$^{-1}$,r_b
+Turnover rate for leaves,$k_{\rm l}$,yr$^{-1}$,k_l
+Turnover rate for sapwood,$k_{\rm s}$,yr$^{-1}$,k_s
+Turnover rate for bark,$k_{\rm b}$,yr$^{-1}$,k_b
+Turnover rate for fine roots,$k_{\rm r}$,yr$^{-1}$,k_r
+**Fecundity**,,,
+Seed mass,$\omega$,kg,omega
+Height at maturation,$H_{{\rm mat}}$,m,hmat
+Maximum allocation to reproduction,$\alpha_{\rm f1}$,,a_f1
+"Parameter determining rate of change in$r(x, m_\textrm{l})$ around$H_{\rm mat}$",$\alpha_{\rm f2}$,,a_f2
+Accessory cost per seed,$\alpha_{\rm f3}$,kg,a_f3
+**Mortality**,,,
+Survival probability during dispersal,$S_{\rm D}$,,S_D
+Parameter influencing survival through germination,$\alpha_{\rm d0}$,kg yr$^{-1}$ m$^{-2}$,a_d0
+Intrinsic or growth-independent mortality,$d_{\rm I}$,yr$^{-1}$,d_I
+Baseline rate for growth-dependent mortality,$\alpha_{\rm dG1}$,yr$^{-1}$,a_dG1
+Risk coefficient for dry-mass production per unit leaf area in growth-dependent mortality,$\alpha_{\rm dG2}$,yr m^${2}$ kg$^{-1}$,a_dG2

inst/docs/FF16/FF16-params-hyper.csv

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+Description,Symbol,Unit,Code
+**Leaf turnover**,,,
+Global average leaf mass per area,$\phi_0$,kg m$^{-2}$,lma_0
+"Rate of leaf turnover at average leaf mass per unit leaf area, $\phi_0$",$\beta_{\rm kl1}$,yr$^{-1}$,B_kl1
+Scaling exponent for $\phi$ in leaf turnover,$\beta_{\rm kl2}$,,B_kl2
+**Sapwood turnover**,,,
+Global average wood density,$\rho_0$,kg m$^{-3}$,rho_0
+"Rate of sapwood turnover at average wood density, $\rho_0$",$\beta_{\rm ks1}$,yr$^{-1}$,B_ks1
+Scaling exponent for $\rho$ in sapwood turnover,$\beta_{\rm ks2}$,,B_ks2
+**Growth-independent mortality**,,,
+"Rate of instantaneous mortality at average wood density, $\rho_0$",$\beta_{\rm dI1}$,yr$^{-1}$,B_dI1
+Scaling exponent for wood density in intrinsic mortality,$\beta_{\rm dI2}$,,B_dI2
+**Photosynthesis**,,,
+Leaf nitrogen per unit leaf area,$\nu$,kg m$^{-2}$,narea
+Global average nitrogen per unit leaf area,$\nu_0$,kg m$^{-2}$,narea_0
+"Potential CO$_2$ photosynthesis at average leaf nitrogen, $\nu_0$",$\beta_{\rm lf1}$,mol d$^{-1}$ m$^{-2}$,B_lf1
+Curvature of light response curve,$\beta_{\rm lf2}$,,B_lf2
+Quantum yield of leaf photosynthesis (CO$_2$ per unit photosynthetically active radiation),$\beta_{\rm lf3}$,,B_lf3
+Scaling exponent for leaf nitrogen in maximum leaf photosynthesis,$\beta_{\rm lf5}$,,B_lf5
+**Respiration**,,,
+CO$_2$ respiration per unit leaf nitrogen,$\beta_{\rm lf4}$,mol yr$^{-1}$ kg$^{-1}$,B_lf4
+CO$_2$ respiration per unit sapwood volume,$\beta_{\rm rs1}$,mol yr$^{-1}$ m$^{-3}$,B_rs1
+CO$_2$respiration per unit bark volume,$\beta_{\rm rb1}$,mol yr$^{-1}$ m$^{-3}$,B_rb1
+**Reproduction**,,,
+Cost of seed accessories per unit seed mass,$\beta_{\rm f1}$,,B_f1

inst/docs/FF16/FF16-vars.csv

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+Symbol,Unit,Description
+**Plant construction**,,
+$x$,,Vector of traits for a species
+$H_0$,m,Height of a seedling after germination
+$H$,m,Height of a plant
+$B$,kg,Biomass originating from parent plant
+$M_i$,kg,Mass of tissue type $i$ retained on plant 
+$A_i$,m$^2$,Surface area or area of cross-section of tissue type $i$
+"$q(z, H)$",m$^{-1}$,Vertical distribution of leaf area across heights $z$ for a plant with height $H$
+"$Q(z, H)$",,Fraction of leaf area above height $z$ for a plant with height $H$Mass production,
+**Mass production**,,
+"$p,\bar{p}$",mol yr$^{-1}$ m$^{-2}$,Photosynthetic rate per unit area 
+$r_i$,mol yr$^{-1}$ kg$^{-1}$ ,Respiration rate per unit mass of tissue type $i$ 
+$k_i$,yr$^{-1}$,Turnover rate for tissue type $i$ 
+**Environment**,,
+$a$,yr,Patch age
+$E_{a}$,,Profile of canopy openness within a patch of age $a$
+$E_{a}(z)$,,Canopy openness at height $z$ within a patch of age $a$
+**Demographic outcomes**,,
+"$g(x, H, E_{a})$",m yr$^{-1}$,Height growth rate of a plant with traits $x$ and height $H$ in the light environment $E_a$ in a patch of age $a$ 
+"$f(x, H, E_{a})$",yr$^{-1}$,Seed production rate of a plant with traits $x$ and height $H$ in the light environment $E_a$ in a patch of age $a$
+"$d(x, H, E_{a})$",yr$^{-1}$,Instantaneous mortality rate of a plant with traits $x$ and height $H$ in the light environment $E_a$ in a patch of age $a$
+"$S_{\rm G} (x, H_0, E_{{\rm a}0})$",,Probability that a seed germinates successfully 

inst/docs/demography-vars.csv

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+Symbol,Unit,Description
+**Patch state variables**,,
+$K$,,Number of species in the metacommunity
+"$a, a^{\prime}$",yr,Patch age (time since disturbance)
+$a_0$,yr,Patch age when plant germinates 
+$E_a$,,Profile of canopy openness within a patch of age $a$
+$E_a(z)$,,Canopy openness at height $z$ within a patch of age $a$
+**Plant state variables**,,
+$x$,,Vector of traits for a species
+$H$,m,Height of a plant
+$H_0(x)$,m,Height of a seedling with traits $x$ after germination
+$z$,m,Height in canopy
+$A_{\rm l}(H)$,m$^2$,Leaf area of a plant with height $H$ 
+"$Q(z, H)$",,Fraction of leaf area above height $z$ for a plant with height $H$
+**Abundance measures**,,
+$P(a)$,yr$^{-1}$,Frequency-density of patches of age $a$ 
+$Y_{x}$,m$^{-2}$ yr$^{-1}$,Global birth rate for a species with traits $x$
+"$N(H, x, a)$",m$^{-1}$ m$^{-2}$,Density of plants at height $H$ per unit ground area for given traits $x$ and patch age $a$
+**Demographic rates**,,
+"$g(x, H, E_a)$",m yr$^{-1}$,Height growth rate of a plant with traits $x$ and height $H$ in the light environment $E_a$ in a patch of age $a$
+"$f(x, H, E_a)$",yr$^{-1}$,Seed production rate of a plant with traits $x$ and height $H$ in the light environment $E_a$ in a patch of age $a$
+"$d(x, H, E_a)$",yr$^{-1}$,Instantaneous mortality rate of a plant with traits $x$ and height $H$ in the light environment $E_a$ in a patch of age $a$
+$d_{\rm P}(a)$,yr$^{-1}$,Instantaneous disturbance rate of a patch of age $a$
+**Demographic outcomes**,,
+"$H(x, a_0, a)$",m,Height of a plant with traits $x$ in a patch of age $a$ having germinated at patch age $a_0$
+$S_{\rm D}$,,Probability a seed survives dispersal 
+"$S_{\rm G} (x, H_0, E_{{\rm a}0})$",,Probability the seed of a plant with traits $x$ germinates successfully at height $H_0$ in the light environment $E_{{\rm a}0}$ in a patch of age $a_0$
+"$S_{\rm I} (x, a_0, a)$",,Probability a plant survives from patch age $a_0$ to patch age $a$
+"$S_{\rm P} ( a_0, a)$",,Probability a patch remains undisturbed from patch age $a_0$ to patch age $a$
+"$\tilde{R}(x, a_0, a)$",,Cumulative seed output for plants with traits $x$ from patch age $a_0$ to patch age $a$ 
+"$R\left(x^\prime, x\right)$",,Basic reproduction ratio for a mutant plant with traits $x^\prime$ growing in a metapopulation of resident plants with traits $x$
+**Miscellaneous constants**,,
+$k_{\rm I}$,,Light extinction coefficient
+$\bar{a}$,yr,Mean interval between patch disturbances