重新排序因子会给出不同的结果，具体取决于加载的包

Question

我想创建一个条形图，其中条形按高度而不是按字母顺序按类别排序。当我加载的唯一包是 ggplot2 时，这很好用。但是，当我加载更多包并运行创建、排序和绘制数据框的相同代码时，条形图又恢复为按字母顺序排序。

我每次都使用str() 检查数据框，结果发现数据框的属性现在不同了，即使我每次都运行相同的代码。

我的代码和输出如下所示。谁能解释不同的行为？为什么加载一些明显不相关的包（在某种意义上说我正在使用的函数似乎都没有被新加载的包掩盖）会改变运行transform() 函数的结果？

案例 1：只加载了 ggplot2

library(ggplot2)

group = c("C","F","D","B","A","E")
num = c(12,11,7,7,2,1)
data = data.frame(group,num)
data1 = transform(data, group=reorder(group,-num))

> str(data1)
'data.frame':   6 obs. of  2 variables:
 $ group: Factor w/ 6 levels "C","F","B","D",..: 1 2 4 3 5 6
  ..- attr(*, "scores")= num [1:6(1d)] -2 -7 -12 -7 -1 -11
  .. ..- attr(*, "dimnames")=List of 1
  .. .. ..$ : chr  "A" "B" "C" "D" ...
 $ num  : num  12 11 7 7 2 1

案例 2：加载多个包，然后再次运行相同的代码

library(plyr)
library(xtable)
library(Hmisc)
library(gmodels)
library(reshape2)
library(vcd)
library(lattice)

group = c("C","F","D","B","A","E")
num = c(12,11,7,7,2,1)
data = data.frame(group,num)
data1 = transform(data, group=reorder(group,-num))

> str(data1)
'data.frame':   6 obs. of  2 variables:
 $ group: Factor w/ 6 levels "A","B","C","D",..: 3 6 4 2 1 5
 $ num  : num  12 11 7 7 2 1

更新：SessionInfo()

案例1：加载ggplot2后运行sessionInfo()

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
  [1] C/en_US.UTF-8/C/C/C/C

attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
  [1] ggplot2_0.9.1

loaded via a namespace (and not attached):
  [1] MASS_7.3-18        RColorBrewer_1.0-5 colorspace_1.1-1   dichromat_1.2-4    digest_0.5.2       grid_2.15.0       
[7] labeling_0.1       memoise_0.1        munsell_0.3        plyr_1.7.1         proto_0.3-9.2      reshape2_1.2.1    
[13] scales_0.2.1       stringr_0.6        tools_2.15.0

案例 2：加载附加包后运行 sessionInfo()

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
  [1] C/en_US.UTF-8/C/C/C/C

attached base packages:
  [1] grid      splines   stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
  [1] lattice_0.20-6   vcd_1.2-13       colorspace_1.1-1 MASS_7.3-18      reshape2_1.2.1   gmodels_2.15.2  
[7] Hmisc_3.9-3      survival_2.36-14 xtable_1.7-0     plyr_1.7.1       ggplot2_0.9.1   

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.0-5 cluster_1.14.2     dichromat_1.2-4    digest_0.5.2       gdata_2.8.2        gtools_2.6.2      
[7] labeling_0.1       memoise_0.1        munsell_0.3        proto_0.3-9.2      scales_0.2.1       stringr_0.6       
[13] tools_2.15.0

Answer 1

发生这种情况是因为：

1. gmodels 进口 gdata
2. gdata 为 reorder.factor 创建一个新方法

开始一个干净的会话。那么：

methods("reorder")
[1] reorder.default*    reorder.dendrogram*

现在加载gdata（或者加载gmodels，效果一样）：

library(gdata)
methods("reorder")
[1] reorder.default*    reorder.dendrogram* reorder.factor 

注意没有掩码，因为reorder.factor 不存在于基础中

重新创建问题，但这次显式调用不同的包：

group = c("C","F","D","B","A","E")
num = c(12,11,7,7,2,1)
data = data.frame(group,num)

基础 R 版本（使用 reorder.default）：

str(transform(data, group=stats:::reorder.default(group,-num)))
'data.frame':   6 obs. of  2 variables:
 $ group: Factor w/ 6 levels "C","F","B","D",..: 1 2 4 3 5 6
  ..- attr(*, "scores")= num [1:6(1d)] -2 -7 -12 -7 -1 -11
  .. ..- attr(*, "dimnames")=List of 1
  .. .. ..$ : chr  "A" "B" "C" "D" ...
 $ num  : num  12 11 7 7 2 1

gdata 版本（使用reorder.factor）：

str(transform(data, group=gdata:::reorder.factor(group,-num)))
'data.frame':   6 obs. of  2 variables:
 $ group: Factor w/ 6 levels "A","B","C","D",..: 3 6 4 2 1 5
 $ num  : num  12 11 7 7 2 1