reinstall r

zhujiedong · Apr 30, 2019 · c984be7 · c984be7
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diff --git a/01-batch-data.Rmd b/01-batch-data.Rmd
@@ -6,7 +6,7 @@
 
 暂时只有我的 github repo 中的版本：
 
-```{r}
+```{r,eval=FALSE}
 devtools::install_github("zhujiedong/readphoto")
 ```
 

diff --git a/02-fvcb.Rmd b/02-fvcb.Rmd
@@ -400,14 +400,6 @@ fits <- fitacis(manyacidat2, group = "Curve", fitmethod="bilinear", quiet = TRUE
 # 拟合结果为list，我们可以只提取第一个的拟合结果
 fits[[1]]
 
-# 所有参数均可传递到 plot.acifit，例如：
-# 将所有的数据点作图，并将数据点标记为蓝色
-par(mar = c(4.5, 4.5, 2, 2))
-par(mfrow = c(1, 2))
-plot(fits, how="oneplot", what="data", col="blue", addlegend = FALSE)
-# 在上图的基础上增加模型拟合的线
-plot(fits, how="oneplot", what="data", col="blue", addlegend = FALSE)
-plot(fits, how="oneplot", add=TRUE, what="model", lwd=c(1,1), addlegend = FALSE)
 # 使用sapply提取拟合结果的RMSE(均方根误差)
 rmses <- sapply(fits, "[[", "RMSE")
 plot(rmses, type='h', ylab="RMSE", xlab="Curve nr")

diff --git a/03-stomatal.Rmd b/03-stomatal.Rmd
@@ -71,7 +71,8 @@ library(plantecophys)
 
 aci <- read.csv("./data/aci.csv")
 aci <- subset(aci, Obs > 0)
-fitBB(aci, gsmodel = "BBOpti", fitg0 = TRUE)
+fitBB(aci, varnames = list(ALEAF = "Photo", GS = "Cond", VPD = "VpdL",
+  Ca = "CO2S", RH = "RH_S"), gsmodel = "BBOpti", fitg0 = TRUE)
 ```
 
 ## `fitBBs` 函数 {#fitbbs}

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diff --git a/_bookdown_files/bookdown_files/figure-latex/2dim-1.pdf b/_bookdown_files/bookdown_files/figure-latex/2dim-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/acplot-1.pdf b/_bookdown_files/bookdown_files/figure-latex/acplot-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/alpf-1.pdf b/_bookdown_files/bookdown_files/figure-latex/alpf-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/alpp-1.pdf b/_bookdown_files/bookdown_files/figure-latex/alpp-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/dcplot-1.pdf b/_bookdown_files/bookdown_files/figure-latex/dcplot-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/fitaci6400-1.pdf b/_bookdown_files/bookdown_files/figure-latex/fitaci6400-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/fitacisr-1.pdf b/_bookdown_files/bookdown_files/figure-latex/fitacisr-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/fitacisr-2.pdf b/_bookdown_files/bookdown_files/figure-latex/fitacisr-2.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/loadingpca-1.pdf b/_bookdown_files/bookdown_files/figure-latex/loadingpca-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/malp-1.pdf b/_bookdown_files/bookdown_files/figure-latex/malp-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/maxvar-1.pdf b/_bookdown_files/bookdown_files/figure-latex/maxvar-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/mcomp-1.pdf b/_bookdown_files/bookdown_files/figure-latex/mcomp-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/mrecr-1.pdf b/_bookdown_files/bookdown_files/figure-latex/mrecr-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/nexpr-1.pdf b/_bookdown_files/bookdown_files/figure-latex/nexpr-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/nrecr-1.pdf b/_bookdown_files/bookdown_files/figure-latex/nrecr-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/pomp-1.pdf b/_bookdown_files/bookdown_files/figure-latex/pomp-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/ppfd-1.pdf b/_bookdown_files/bookdown_files/figure-latex/ppfd-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/ppfd-2.pdf b/_bookdown_files/bookdown_files/figure-latex/ppfd-2.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/racircheck-1.pdf b/_bookdown_files/bookdown_files/figure-latex/racircheck-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/racircor-1.pdf b/_bookdown_files/bookdown_files/figure-latex/racircor-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/racircorpkg-1.pdf b/_bookdown_files/bookdown_files/figure-latex/racircorpkg-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/recr-1.pdf b/_bookdown_files/bookdown_files/figure-latex/recr-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/scorepca-1.pdf b/_bookdown_files/bookdown_files/figure-latex/scorepca-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/scree-1.pdf b/_bookdown_files/bookdown_files/figure-latex/scree-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/supply-1.pdf b/_bookdown_files/bookdown_files/figure-latex/supply-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/unnamed-chunk-17-1.pdf b/_bookdown_files/bookdown_files/figure-latex/unnamed-chunk-17-1.pdf
diff --git a/_bookdown_files/bookdown_files/figure-latex/vpd-1.pdf b/_bookdown_files/bookdown_files/figure-latex/vpd-1.pdf
diff --git a/bookdown.aux b/bookdown.aux
diff --git a/bookdown.lof b/bookdown.lof
@@ -25,19 +25,19 @@
 \contentsline {figure}{\numberline {9.2}{\ignorespaces 初修正后断 alpha 的初始值\relax }}{80}{figure.caption.30}% 
 \contentsline {figure}{\numberline {9.3}{\ignorespaces 检验作图法的初始值判断\relax }}{82}{figure.caption.31}% 
 \contentsline {figure}{\numberline {9.4}{\ignorespaces 多个 alpha 取值的差异\relax }}{83}{figure.caption.32}% 
-\contentsline {figure}{\numberline {9.5}{\ignorespaces 两种方法结果的对比展示\relax }}{86}{figure.caption.33}% 
-\addvspace {10\p@ }
-\contentsline {figure}{\numberline {10.1}{\ignorespaces 找出最合理的校准曲线数据范围\relax }}{91}{figure.caption.34}% 
-\contentsline {figure}{\numberline {10.2}{\ignorespaces 校准曲线查看\relax }}{91}{figure.caption.35}% 
-\contentsline {figure}{\numberline {10.3}{\ignorespaces RACiR 方法与常规结果的比较\relax }}{99}{figure.caption.36}% 
-\contentsline {figure}{\numberline {10.4}{\ignorespaces 调制式测量的 ojip 曲线的快速预览\relax }}{104}{figure.caption.39}% 
-\contentsline {figure}{\numberline {10.5}{\ignorespaces 连续式测量的 ojip 曲线的快速预览\relax }}{104}{figure.caption.40}% 
-\addvspace {10\p@ }
-\contentsline {figure}{\numberline {11.1}{\ignorespaces 数据的中心化\relax }}{107}{figure.caption.41}% 
-\contentsline {figure}{\numberline {11.2}{\ignorespaces PC1 的诞生\relax }}{107}{figure.caption.42}% 
-\contentsline {figure}{\numberline {11.3}{\ignorespaces 变异最大的极端情况\relax }}{108}{figure.caption.43}% 
-\contentsline {figure}{\numberline {11.4}{\ignorespaces PC2 的诞生\relax }}{108}{figure.caption.44}% 
-\contentsline {figure}{\numberline {11.5}{\ignorespaces iris 碎石图\relax }}{110}{figure.caption.45}% 
-\contentsline {figure}{\numberline {11.6}{\ignorespaces iris 载荷图\relax }}{110}{figure.caption.46}% 
-\contentsline {figure}{\numberline {11.7}{\ignorespaces iris 得分图\relax }}{111}{figure.caption.47}% 
+\contentsline {figure}{\numberline {9.5}{\ignorespaces 两种方法结果的对比展示\relax }}{87}{figure.caption.33}% 
+\addvspace {10\p@ }
+\contentsline {figure}{\numberline {10.1}{\ignorespaces 找出最合理的校准曲线数据范围\relax }}{93}{figure.caption.34}% 
+\contentsline {figure}{\numberline {10.2}{\ignorespaces 校准曲线查看\relax }}{93}{figure.caption.35}% 
+\contentsline {figure}{\numberline {10.3}{\ignorespaces RACiR 方法与常规结果的比较\relax }}{101}{figure.caption.36}% 
+\contentsline {figure}{\numberline {10.4}{\ignorespaces 调制式测量的 ojip 曲线的快速预览\relax }}{106}{figure.caption.39}% 
+\contentsline {figure}{\numberline {10.5}{\ignorespaces 连续式测量的 ojip 曲线的快速预览\relax }}{106}{figure.caption.40}% 
+\addvspace {10\p@ }
+\contentsline {figure}{\numberline {11.1}{\ignorespaces 数据的中心化\relax }}{109}{figure.caption.41}% 
+\contentsline {figure}{\numberline {11.2}{\ignorespaces PC1 的诞生\relax }}{109}{figure.caption.42}% 
+\contentsline {figure}{\numberline {11.3}{\ignorespaces 变异最大的极端情况\relax }}{110}{figure.caption.43}% 
+\contentsline {figure}{\numberline {11.4}{\ignorespaces PC2 的诞生\relax }}{110}{figure.caption.44}% 
+\contentsline {figure}{\numberline {11.5}{\ignorespaces iris 碎石图\relax }}{112}{figure.caption.45}% 
+\contentsline {figure}{\numberline {11.6}{\ignorespaces iris 载荷图\relax }}{112}{figure.caption.46}% 
+\contentsline {figure}{\numberline {11.7}{\ignorespaces iris 得分图\relax }}{113}{figure.caption.47}% 
 \addvspace {10\p@ }
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,7 +6,7 @@ @@
     暂时只有我的 github repo 中的版本：
-    ```{r}
+    ```{r,eval=FALSE}
     devtools::install_github("zhujiedong/readphoto")
     ```
@@ Expand Down @@