# Farquhar 光合模型的R程序包画光、Ci曲线

Medlyn et al. (2002) PCE. Temperature response of parameters of a biochemically based model of photosynthesis. II. A review of experimental data（见附件）

1. 安装plantecophys

The package is not hosted on CRAN yet, so use the following command to install it. Windows users must have Rtools installed (http://cran.r-project.org/bin/windows/Rtools/)

library(devtools)

install_bitbucket("plantecophys","remkoduursma")

library('plantecophys')  # ok 可以用这个packages了

2. 看一下模型输出结果

Photosyn(VPD = 1.5, Ca = 400, PPFD =1500, Tleaf = 25, Patm = 101,

RH = NULL, gsmodel = c("BBOpti", "BBLeuning", "BallBerry"),

g1 = 4, g0 = 0, gk = 0.5, vpdmin = 0.5, D0 = 5, alpha = 0.24,

theta = 0.85, Jmax = 100, Vcmax = 50, gmeso = NULL, Rd0 = 0.92,

Q10 = 1.92, Rd = NULL, TrefR = 25, Rdayfrac = 1, EaV = 82620.87,

EdVC = 0, delsC = 645.1013, EaJ = 39676.89, EdVJ = 2e+05,

delsJ = 641.3615, Ci =300, Tcorrect = TRUE, returnParsOnly = FALSE,

whichA = c("Ah", "Amin", "Ac", "Aj"))

#      Ci   ALEAF        GS       ELEAF       Ac                Aj        Rd VPD    Tleaf  Ca PPFD

#1 300 11.8059 0.1976779 2.935811 12.73111 15.83267 0.92 1.5     25      400 1500

3. 画出Ci曲线

Ci <- seq(20,1000,by=20)

Pn_Ci <- Photosyn(VPD = 1.5, Ca = 400,PPFD =1500, Tleaf = 25, Patm = 101,

RH = NULL, gsmodel =c("BBOpti", "BBLeuning", "BallBerry"),

g1 = 4, g0 = 0, gk = 0.5,vpdmin = 0.5, D0 = 5, alpha = 0.24,

theta = 0.85, Jmax=100,Vcmax=50, gmeso = NULL, Rd0 = 0.92,

Q10 = 1.92, Rd = NULL,TrefR = 25, Rdayfrac = 1, EaV = 82620.87,

EdVC = 0, delsC =645.1013, EaJ = 39676.89, EdVJ = 2e+05,

delsJ = 641.3615, Ci,Tcorrect = TRUE, returnParsOnly = FALSE,

whichA = c("Ah","Amin", "Ac", "Aj"))

# install.packages('ggplot2')

library(ggplot2)

ggplot(Pn_Ci,aes(Ci)) +

geom_point(aes(y = ALEAF, colour = "ALEAF")) +

geom_point(aes(y = Aj, colour = "Aj")) +

geom_point(aes(y = Ac, colour = "Ac"))

Fig.1.       Ci 响应曲线

4. 画出光曲线

PPFD <- seq(0,2000,by=20)

Pn_PPFD <- Photosyn(VPD = 1.5, Ca = 400,PPFD, Tleaf = 25, Patm = 101,

RH = NULL, gsmodel =c("BBOpti", "BBLeuning", "BallBerry"),

g1 = 4, g0 = 0, gk = 0.5,vpdmin = 0.5, D0 = 5, alpha = 0.24,

theta = 0.85, Jmax=100,Vcmax=50, gmeso = NULL, Rd0 = 0.92,

Q10 = 1.92, Rd = NULL, TrefR= 25, Rdayfrac = 1, EaV = 82620.87,

EdVC = 0, delsC = 645.1013,EaJ = 39676.89, EdVJ = 2e+05,

delsJ = 641.3615, Ci=300,Tcorrect = TRUE, returnParsOnly = FALSE,

whichA = c("Ah","Amin", "Ac", "Aj"))

library(ggplot2)

ggplot(Pn_PPFD,aes(PPFD)) +

geom_point(aes(y = ALEAF, colour = "ALEAF")) +

geom_point(aes(y = Aj, colour = "Aj")) +

geom_point(aes(y = Ac, colour = "Ac"))

Fig.2.   光响应曲线

>Photosyn

F_Photosyn_Model.R

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