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Farquhar 光合模型的R程序包画光、Ci曲线

已有 9447 次阅读 2014-3-19 17:10 |个人分类:学习资料分享|系统分类:科研笔记| Farqhuar, 光合模型, 光响应曲线, 响应曲线

这是Remko Duursma 用R写的Farquhar 光合模型 The plantecophys R package

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 



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


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


F_Photosyn_Model.R

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。




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