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2 changes: 1 addition & 1 deletion 11-start-values.Rmd
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>“迭代法”也称“辗转法”是一种不断用变量的旧值递推新值的过程。
用通俗但不是特别严谨的说法可解释为:每次执行这种算法是,程序都会从原值(也就是我抄的上面迭代法定义的旧值)推出一个新值。
用通俗但不是特别严谨的说法可解释为:每次执行这种算法时,程序都会从原值(也就是我抄的上面迭代法定义的旧值)推出一个新值。

之所以先介绍这个迭代,原因很简单,非线性拟合就是通过迭代的方法,需要对每一个变量**最初的估计值进行不断的迭代,得到一个向一个点收缩或汇聚的值,这个估计值必须在实际值的一定范围内,程序通过不断调整这个值来改善拟合结果**。这就解释了上面的问题,初始值是让程序开始运行的前提,不然没法迭代,必须设定。我下面的内容将以 LI-6800 的光响应曲线的测试数据,使用非直角双曲线模型进行拟合来讲解具体的 R 中的一些实现方法,我们首先导入数据,然后再利用这些数据逐个举例不同的确定初始值的方式。

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32 changes: 16 additions & 16 deletions 12-4-muti-racir.Rmd → 12-4-multiracir.Rmd
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## 利用不同速率的 RACiR 曲线研究植物的光合生理特性 {#multirate-racir}
## 多个速率的 RACiR 曲线研究 {#multi1}

自 RACiR 技术诞生以来,极大的缩短了 Vcmax 以及 Jmax 的测量时间(@stinziano2017),但也引起了一系列争议,作者也对业内的质疑进行了一一的解答 (@stinziano2018),但除了因为时间长短导致酶活性,叶绿体位置等差异外,RACiR 还能说明哪些问题呢?@stinziano2019 最新的研究给出一系列结论:

Expand All @@ -18,11 +18,11 @@

文中利用 R 实现了光呼吸之后模型和气体扩散限制模型,本文内容主要对文献中附录材料的源码进行解释:

### 光呼吸滞后模型 {#photoresp-lag}
### 光呼吸滞后模型 {#multi2}

为测试光呼吸的滞后性,作者使用一系列预先设定的参数,模拟了一条 ACc曲线,假定 Rubisco 激活状态为 100%,并且在整个测量过程中气孔导度是不变的。然后使用这些参数来模拟 RACiRs 曲线,并且假定光呼吸分别需要 0, 15, 30, 60, 120 或 300 s 来对变化的 $CO_2$ 进行响应,在实际效果上,这意味着 Cc 在最初的 0, 15, 30, 60, 120 或 300 内是不变的,最后我们对 $\Gamma^*$ 和 Ci 使用线性回归进行计算。

#### 基础数据 {#base-data}
#### 构造基础数据 {#multi3}

模型第一步,则是对需要使用的参数,根据文献和实际情况进行赋值,具体内容参考代码注释。

Expand Down Expand Up @@ -95,7 +95,7 @@ RateCcmodel <- lm(Cc ~ Counter)
RateCc <- coef(RateCcmodel)[2] * 60
```

### 光呼吸滞后性代码 {code-photoresp}
### 光呼吸滞后性代码 {#code-photoresp}

下面代码的目的是为得到 ACi 响应曲线受光呼吸延迟的影响,尤其是在临近补偿点时。

Expand Down Expand Up @@ -133,7 +133,7 @@ A300 <- vc - 0.5 * vo120 - R
Aapparent300 <- vc - 0.5 * vo300
```

### 数据的构造 {#compi-modu}
### 数据的构造 {#multi4}

下面的代码主要是将上文最终计算的数据构造数据集,并导出。

Expand Down Expand Up @@ -161,7 +161,7 @@ PRdata <- as.data.frame(cbind(Anet, Aapp, Ccfull, Cifull, Delay))
write.csv(PRdata, "./data/PRdata.csv")
```

### 光呼吸滞后性作图 {#photo-resp-graph}
### 光呼吸滞后性作图 {#multi5}

下面的代码是将光呼吸的数据进行作图。

Expand Down Expand Up @@ -266,7 +266,7 @@ AappCi <- ggplot(data, aes(x = Cifull, y = Aapp, colour = Delay)) +
AappCi
```

### 补偿点计算 {#gammastar}
### 补偿点计算 {#multi6}

计算不同的光呼吸时间延迟下的补偿点(基于Ci):

Expand Down Expand Up @@ -486,11 +486,11 @@ summary(lm(ints ~ dels))
plot(ints ~ dels)
```

### 无光呼吸酶失活模块 {#no-phoresp-rubi}
### 无光呼吸酶失活模块 {#multi7}

该部分内容是在测量 ACi 曲线时检测 Rubisco 失活的影响 -- 从激活状态的变化导致了多少的偏移?

#### 数据构造 {#data-pre}
#### 数据构造 {#multi8}

基于文献,假定 $CO_2$ 从 400 ppm 降低至 5 ppm 时,激活率从 100% 降低至 80%。

Expand Down Expand Up @@ -593,7 +593,7 @@ RASdata <-
write.csv(RASdata, "./data/RASdata.csv")
```

### 酶失活作图 {#Graphs-deac}
### 酶失活作图 {#multi9}

```{r, anetdeccc, fig.cap="Rubisco 不同失活程度时 Anet VS Cc", message=FALSE}
data <- read.csv("./data/RASdata.csv")
Expand Down Expand Up @@ -698,7 +698,7 @@ AappCi <-
AappCi
```

### 不同失活程度下补偿点计算{#comp-est-dea}
### 不同失活程度下补偿点计算{#multi10}

此部分内容同未失活状态相似,不在额外介绍,可参考 \@ref(gammastar) 内容。

Expand Down Expand Up @@ -798,7 +798,7 @@ write.csv(RAScomps, "./data/RAScomps.csv")
```


## 时间延迟的扩散限制 {#diffu-limi}
## 时间延迟的扩散限制 {#multi11}

对于扩散限制,下面的内容比较了多速率 RACiR 和标准 ACi 曲线的差别,比较实在有光呼吸和没有光呼吸的两种情况。对于没有扩散限制的表观光合速,采用了已知质量的碱石灰药品,放置于 1.7 ml 的微量离心管内,然后将其置于荧光叶室内部模拟叶片,此时叶室环境控制与其他实验不同,此时不再控制 H2OR。RACiR 测试从 500 到 0 的变化,不同样品的测量是随机的。

Expand Down Expand Up @@ -1212,7 +1212,7 @@ knitr::kable(head(Diffusion))
```


### 扩散限制滞后性 {#difu-limit}
### 扩散限制滞后性 {#multi12}

下面的代码,是根据上面代码的计算结果,结合最初的扩散时间的公式,来计算出各个参数的最大最小值,中间值,构造数据:

Expand Down Expand Up @@ -1391,7 +1391,7 @@ knitr::kable(head(Diffusionplot2))
```


## 扩散限制作图 {#difu-graph}
## 扩散限制作图 {#multi13}

```{r,difuci, fig.cap="不同 Ci 扩散限制下的差异", message=FALSE}
data <- read.csv("./data/DiffusionLimitsACI2.csv")
Expand Down Expand Up @@ -1462,7 +1462,7 @@ red <- 1/data2$TotalRes
plot(ab~red)
```

### 补偿点的计算 {#compen-estimate}
### 补偿点的计算 {#multi14}

计算补偿点,代码同前文类似,只是采用了不同导度下的数值:

Expand Down Expand Up @@ -1499,7 +1499,7 @@ Gamma4 <- -m6$coefficients[1] / m6$coefficients[2]
GammaCi <- c(Gamma0125, Gamma025, Gamma05, Gamma1, Gamma2, Gamma4)
```

### 所有图形代码 {#all-fig}
### 所有图形代码 {#multi15}


```{r, prdataplot, fig.cap="不同时间滞后性的 Anet VS Ci", message=FALSE}
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