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Farquhar 光合模型的R程序包画光、Ci曲线
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这是Remko Duursma 用R写的Farquhar 光合模型 The plantecophys R package
见 
https://bitbucket.org/remkoduursma/plantecophys
模型中的主要函数和参数见
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）
http://onlinelibrary.wiley.com/doi/10.1046/j.1365-3040.2002.00891.x/full
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
感兴趣的话，可以看一下Remko Duursma写的Photosyn函数，可以根据自己的需求改一下。
>Photosyn
Medlyn 2002 tempreture photosyn.pdf
这是我根据Remko Duursma写的函数，Kc, Ko ， GammaStar，Vcmax ，Jmax的温度函数采用了Medlyn et al. （2002）中的函数。
https://wap.sciencenet.cn/blog-526092-777410.html
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