如何将 Dataframe (或向量)转换为矩阵,以便将R基线包用于所提供的示例数据以外的数据?

btxsgosb  于 2022-12-25  发布在  其他
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我有一个x和y值的数据框形式的数据,绘制时看起来像这样:

(The以绿色突出显示的部分对应于下面的dput()数据)。
我想使用基线包来试验“Liland,K. H.,Almøy,T.,& Mevik,B.-H.(2010).光谱多元校准的基线校正的最佳选择.应用光谱学,64(9),1007- 1016.doi:10.1366/000370210792434350”中描述的不同基线校正算法.
该包规定“数据必须组织为矩阵或data.frame中的行向量”,然而,简单地将y值转换为矩阵是行不通的:

> baseline(as.matrix(y, byrow=T))
Error in rep(3, p - 4) : invalid 'times' argument

随包提供的示例数据具有一种结构,我无法解释或弄清楚如何使用自己的数据进行模拟。

> library(baseline)
> data(milk)
> str(milk)
'data.frame':   45 obs. of  2 variables:
 $ cow    : num  0 0.25 0.375 0.875 0.5 0.75 0.5 0.125 0 0.125 ...
 $ spectra: num [1:45, 1:21451] 1029 371 606 368 554 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : NULL
  .. ..$ : chr [1:21451] "4999.94078628963" "5001.55954267662" "5003.17856106153" "5004.79784144435" ...
 - attr(*, "terms")=Classes 'terms', 'formula'  language cow ~ spectra
  .. ..- attr(*, "variables")= language list(cow, spectra)
  .. ..- attr(*, "factors")= int [1:2, 1] 0 1
  .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. ..$ : chr [1:2] "cow" "spectra"
  .. .. .. ..$ : chr "spectra"
  .. ..- attr(*, "term.labels")= chr "spectra"
  .. ..- attr(*, "order")= int 1
  .. ..- attr(*, "intercept")= int 1
  .. ..- attr(*, "response")= int 1
  .. ..- attr(*, ".Environment")=<environment: R_GlobalEnv> 
  .. ..- attr(*, "predvars")= language list(cow, spectra)
  .. ..- attr(*, "dataClasses")= Named chr [1:2] "numeric" "nmatrix.21451"
  .. .. ..- attr(*, "names")= chr [1:2] "cow" "spectra"

如果有人能告诉我如何对自己的数据调用baseline(),我将非常感激。
下面是我正在处理的数据的一个子部分,对应于上图中绿色突出显示的部分:

> dput(fid_df[fid_df$rt>12.5&fid_df$rt<12.8,])
structure(list(rt = c(12.5002866914485, 12.5011200182712, 12.5019533450939, 
12.5027866719166, 12.5036199987393, 12.5044533255619, 12.5052866523846, 
12.5061199792073, 12.50695330603, 12.5077866328527, 12.5086199596754, 
12.5094532864981, 12.5102866133207, 12.5111199401434, 12.5119532669661, 
12.5127865937888, 12.5136199206115, 12.5144532474342, 12.5152865742568, 
12.5161199010795, 12.5169532279022, 12.5177865547249, 12.5186198815476, 
12.5194532083703, 12.5202865351929, 12.5211198620156, 12.5219531888383, 
12.522786515661, 12.5236198424837, 12.5244531693064, 12.5252864961291, 
12.5261198229517, 12.5269531497744, 12.5277864765971, 12.5286198034198, 
12.5294531302425, 12.5302864570652, 12.5311197838878, 12.5319531107105, 
12.5327864375332, 12.5336197643559, 12.5344530911786, 12.5352864180013, 
12.536119744824, 12.5369530716466, 12.5377863984693, 12.538619725292, 
12.5394530521147, 12.5402863789374, 12.5411197057601, 12.5419530325827, 
12.5427863594054, 12.5436196862281, 12.5444530130508, 12.5452863398735, 
12.5461196666962, 12.5469529935189, 12.5477863203415, 12.5486196471642, 
12.5494529739869, 12.5502863008096, 12.5511196276323, 12.551952954455, 
12.5527862812776, 12.5536196081003, 12.554452934923, 12.5552862617457, 
12.5561195885684, 12.5569529153911, 12.5577862422138, 12.5586195690364, 
12.5594528958591, 12.5602862226818, 12.5611195495045, 12.5619528763272, 
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12.5727861250221, 12.5736194518448, 12.5744527786674, 12.5752861054901, 
12.5761194323128, 12.5769527591355, 12.5777860859582, 12.5786194127809, 
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12.7961177135015, 12.7969510403242, 12.7977843671469, 12.7986176939696, 
12.7994510207923), value = c(17.3893229166667, 17.394140625, 
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17.3888020833333, 17.3864583333333, 17.3825520833333, 17.3834635416667, 
17.386328125, 17.3854166666667, 17.384375, 17.3852864583333, 
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17.3901041666667, 17.3950520833333, 17.3963541666667, 17.3970052083333, 
17.3907552083333, 17.3846354166667, 17.3760416666667, 17.3743489583333
)), row.names = 15002:15361, class = "data.frame")

(p.s这里的问题是:R-package(baseline) application to sample dataset似乎也有类似的问题,但没有解决如何将简单的x,y数据转换为基线包所需的格式)。

w8ntj3qf

w8ntj3qf1#

基线包希望光谱显示在行中,但您的代码创建了一个矩阵,光谱显示在单列中。如果您将从data.frame到矩阵的转换更改为以下内容,它应该可以工作:

baseline(matrix(y, nrow=1))

这个问题是由两个因素引起的:使用as.matrix(),它不接受您需要的参数;使用byrow=T而不是nrow=1byrow控制填充矩阵的方向(按行或按列),但对输出维数没有影响。
milk数据中的额外模糊在这里没有帮助,所以我将在下一个包更新中删除它,我还将研究允许以矢量格式处理单个光谱而不是显式强制矩阵输入的可能性。
P.S.我能够用一点额外的努力复制出你的数据,但怀疑你需要原始数据直接从这个页面复制粘贴,因为dput行包含som子集。

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