使用 tapply 将数据帧转换为矩阵将零转换为 NA

Dataframe to matrix conversion using tapply turns zeros to NAs

我需要将数据帧转换为矩阵,我正在使用以下代码:

LoggAbundTGLMSOagg <- tapply(AbundTGLMSOagg$occurrence,list(AbundTGLMSOagg$plot,AbundTGLMSOagg$species),mean)

我得到了所需的矩阵格式,但零变成了 NA。使用 tapply(),如何保留零?

我会写csv文件

write.csv(LoggAbundTGLMSOagg, "LoggAbundTGLMSOagg.csv", na="0", row.names=TRUE)

并将其读回 R 但肯定有更优雅的解决方案。

非常感谢您的任何建议。

这是我的数据:

> dput(AbundTGLMSOagg)
structure(list(plot = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 
6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 8L, 8L, 8L, 
8L, 8L, 8L, 9L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 11L, 11L, 
11L, 11L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L, 12L, 12L, 12L, 
13L, 13L, 13L, 13L, 13L, 13L, 13L, 13L, 14L, 14L, 15L, 15L, 15L, 
15L, 15L, 15L, 15L, 15L, 15L, 16L, 16L, 16L, 16L, 16L, 16L, 16L, 
16L, 16L, 16L, 16L, 16L, 16L, 17L, 17L, 17L, 17L, 18L, 18L, 18L, 
18L, 18L, 18L, 18L, 18L, 18L, 18L, 18L, 19L, 19L, 19L, 19L, 19L, 
19L, 19L, 19L, 19L, 19L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 20L, 
20L, 20L, 20L, 20L, 20L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 21L, 
21L, 21L, 21L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 22L, 23L, 23L, 
23L, 23L, 23L, 23L, 23L, 24L, 24L, 24L, 24L, 24L, 24L, 24L, 25L, 
25L, 25L, 25L, 25L, 25L, 25L, 25L, 26L, 26L, 26L, 26L, 26L, 26L, 
26L, 27L, 27L, 27L, 27L, 27L, 27L, 27L, 27L, 28L, 28L, 28L, 28L, 
28L, 29L, 29L, 29L, 29L, 30L, 30L, 30L, 30L, 31L, 31L, 31L, 31L, 
31L, 31L, 31L, 31L, 32L, 32L, 32L, 32L, 32L, 32L, 32L, 33L, 33L, 
33L, 33L, 33L, 33L, 34L, 34L, 34L, 34L, 34L, 34L, 35L, 35L, 35L, 
35L, 35L, 35L, 35L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 36L, 
37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 37L, 38L, 38L, 38L, 
38L, 38L, 38L, 38L, 38L, 38L, 38L, 38L, 39L, 39L, 39L, 39L, 39L, 
39L, 40L, 40L, 40L, 40L, 40L, 40L, 40L, 40L, 40L, 41L, 41L, 41L, 
41L, 41L, 41L, 42L, 42L, 42L, 42L, 42L, 42L, 42L, 42L, 42L, 42L, 
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55L, 55L, 55L, 55L, 55L, 55L, 55L, 55L, 55L, 55L, 55L, 56L, 56L, 
56L, 56L, 56L, 56L, 56L, 56L, 56L, 57L, 57L, 57L, 57L, 57L, 57L, 
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58L, 58L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 59L, 60L, 
60L, 60L, 60L, 60L, 60L, 60L, 60L, 60L, 61L, 61L, 61L, 61L, 61L, 
61L, 61L, 61L, 61L, 61L, 61L, 61L, 62L, 62L, 62L, 62L, 62L, 62L, 
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64L, 64L, 65L, 65L, 65L, 65L, 65L, 65L, 65L, 65L, 65L, 65L, 66L, 
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67L, 68L, 68L, 68L, 68L, 68L, 68L, 68L, 69L, 69L, 69L, 69L, 69L, 
69L, 69L, 70L, 70L, 70L, 70L, 70L, 70L, 71L, 71L, 71L, 71L, 71L, 
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74L, 74L, 74L, 75L, 75L, 75L, 75L, 75L, 75L, 76L, 76L, 76L, 76L, 
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138L, 138L, 138L, 138L, 139L, 139L, 139L, 139L, 139L, 139L), .Label = c("H01", 
"H02", "H03", "H04", "H05", "H06", "H07", "H08", "H09", "H10", 
"H11", "H12", "H13", "H14", "H15", "H16", "H17", "H18", "H19", 
"H20", "H21", "H22", "H23", "H24", "H25", "H26", "H27", "H28", 
"H29", "H30", "H31", "H32", "H33", "H34", "H35", "H36", "H37", 
"H38", "H39", "H40", "H41", "H42", "H43", "H44", "H45", "H46", 
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"L16", "L17", "L18", "L19", "L20", "L21", "L22", "L23", "L24", 
"L25", "L26", "L27", "L28", "L29", "L30", "L31", "L32", "L33", 
"L34", "L35", "L36", "L37", "L38", "L39", "L40", "L41", "L42", 
"L43", "L44", "L45", "O01", "O02", "O03", "O04", "O05", "O06", 
"O07", "O08", "O09", "O10", "O11", "O12", "O13", "O14", "O15", 
"O16", "O17", "O18", "O19", "O20", "O21", "O22", "O23", "O24", 
"O25", "O26", "O27", "O28", "O29", "O30", "O31", "O32", "O33", 
"O34", "O35", "O36", "O37", "O38", "O39", "O40", "O41", "O42", 
"O43", "O44", "O45"), class = "factor"), species = structure(c(26L, 
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20L, 26L, 34L, 37L, 46L, 50L, 52L, 53L, 56L, 58L, 61L, 62L, 20L, 
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50L, 52L), .Label = c("albleb", "albodo", "antgha", "apovil", 
"artlak", "briret", "buclan", "cansub", "carsph", "catspa", "cropoi", 
"dalcul", "dallan", "dalnig", "daloli", "dilobo", "dioehr", "diomal", 
"dipint", "diptub", "elltom", "erican", "erysuc", "flesoo", "garcow", 
"garobt", "garsoo", "gmearb", "greeri", "halcor", "holpub", "irvoli", 
"lancor", "lopdup", "mancal", "memedu", "memscu", "milleu", "mitrot", 
"morcor", "ochint", "parama", "pavtom", "permem", "phycol", "phyemb", 
"ptemac", "rotwit", "schole", "shoobt", "shorox", "shosia", "sinsia", 
"stegut", "steneu", "strnux", "symrac", "syz001", "terala", "tercal", 
"terche", "xylxyl"), class = "factor"), occurrence = c(1L, 1L, 
1L, 14L, 1L, 10L, 10L, 1L, 1L, 1L, 4L, 1L, 7L, 3L, 3L, 1L, 1L, 
1L, 1L, 9L, 1L, 1L, 1L, 3L, 5L, 1L, 1L, 1L, 5L, 1L, 1L, 4L, 1L, 
1L, 3L, 4L, 1L, 2L, 1L, 9L, 1L, 2L, 6L, 1L, 1L, 10L, 6L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 4L, 1L, 1L, 1L, 3L, 2L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 10L, 21L, 1L, 24L, 5L, 1L, 2L, 3L, 
10L, 10L, 1L, 1L, 2L, 1L, 1L, 1L, 10L, 14L, 31L, 1L, 1L, 1L, 
3L, 1L, 1L, 4L, 1L, 1L, 2L, 4L, 1L, 1L, 2L, 1L, 3L, 2L, 2L, 2L, 
1L, 6L, 13L, 16L, 6L, 1L, 1L, 16L, 3L, 1L, 2L, 3L, 5L, 3L, 2L, 
1L, 28L, 10L, 2L, 1L, 1L, 1L, 1L, 5L, 1L, 1L, 51L, 20L, 1L, 9L, 
5L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 4L, 1L, 12L, 38L, 13L, 3L, 1L, 
1L, 2L, 1L, 1L, 1L, 9L, 10L, 10L, 3L, 1L, 2L, 1L, 1L, 1L, 3L, 
40L, 13L, 1L, 1L, 1L, 16L, 52L, 1L, 6L, 2L, 1L, 1L, 1L, 16L, 
17L, 3L, 1L, 7L, 1L, 8L, 1L, 48L, 8L, 2L, 1L, 5L, 1L, 3L, 1L, 
1L, 1L, 1L, 3L, 3L, 1L, 1L, 4L, 14L, 1L, 1L, 2L, 9L, 10L, 1L, 
6L, 1L, 1L, 26L, 3L, 2L, 20L, 10L, 1L, 1L, 2L, 1L, 1L, 11L, 2L, 
1L, 1L, 1L, 2L, 1L, 28L, 14L, 3L, 1L, 1L, 1L, 16L, 7L, 3L, 3L, 
1L, 1L, 8L, 5L, 3L, 1L, 1L, 2L, 4L, 17L, 5L, 1L, 1L, 5L, 3L, 
1L, 1L, 4L, 17L, 1L, 1L, 2L, 4L, 1L, 1L, 1L, 1L, 3L, 21L, 5L, 
1L, 3L, 1L, 1L, 1L, 1L, 2L, 4L, 1L, 18L, 6L, 4L, 2L, 1L, 1L, 
14L, 13L, 4L, 2L, 2L, 1L, 1L, 1L, 3L, 9L, 2L, 1L, 1L, 1L, 3L, 
28L, 9L, 6L, 1L, 1L, 1L, 3L, 1L, 7L, 9L, 6L, 1L, 4L, 1L, 2L, 
1L, 1L, 1L, 1L, 3L, 2L, 2L, 6L, 2L, 1L, 1L, 1L, 5L, 10L, 1L, 
1L, 5L, 4L, 1L, 1L, 4L, 1L, 4L, 1L, 1L, 1L, 1L, 2L, 3L, 2L, 9L, 
1L, 1L, 1L, 7L, 1L, 1L, 2L, 6L, 1L, 3L, 1L, 5L, 20L, 11L, 2L, 
2L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 2L, 3L, 1L, 1L, 3L, 1L, 1L, 6L, 
18L, 9L, 1L, 1L, 1L, 6L, 16L, 12L, 3L, 4L, 2L, 1L, 1L, 2L, 1L, 
1L, 1L, 8L, 2L, 18L, 27L, 1L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 
1L, 2L, 12L, 21L, 3L, 3L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 
18L, 1L, 5L, 4L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 3L, 
19L, 1L, 12L, 3L, 1L, 1L, 1L, 2L, 3L, 15L, 14L, 2L, 2L, 1L, 1L, 
2L, 1L, 1L, 1L, 5L, 17L, 14L, 2L, 1L, 1L, 1L, 1L, 11L, 2L, 9L, 
15L, 2L, 4L, 5L, 2L, 1L, 2L, 2L, 1L, 6L, 13L, 1L, 1L, 2L, 1L, 
1L, 4L, 7L, 1L, 4L, 2L, 13L, 1L, 3L, 1L, 3L, 2L, 1L, 1L, 3L, 
4L, 9L, 1L, 1L, 2L, 2L, 1L, 2L, 4L, 4L, 27L, 3L, 1L, 1L, 1L, 
1L, 1L, 1L, 5L, 2L, 14L, 1L, 1L, 5L, 5L, 20L, 1L, 1L, 1L, 3L, 
1L, 2L, 15L, 12L, 1L, 1L, 1L, 1L, 1L, 3L, 2L, 3L, 8L, 2L, 1L, 
5L, 1L, 3L, 34L, 7L, 1L, 1L, 2L, 3L, 2L, 23L, 8L, 1L, 2L, 1L, 
1L, 3L, 20L, 8L, 1L, 2L, 1L, 11L, 1L, 9L, 3L, 2L, 2L, 1L, 1L, 
2L, 1L, 12L, 9L, 1L, 5L, 1L, 2L, 1L, 1L, 3L, 15L, 5L, 1L, 2L, 
1L, 1L, 1L, 3L, 35L, 15L, 1L, 1L, 1L, 2L, 1L, 2L, 6L, 7L, 2L, 
3L, 2L, 1L, 20L, 13L, 4L, 1L, 1L, 1L, 14L, 9L, 1L, 2L, 2L, 1L, 
2L, 25L, 10L, 2L, 1L, 1L, 1L, 11L, 14L, 2L, 1L, 1L, 1L, 1L, 2L, 
1L, 12L, 10L, 7L, 1L, 2L, 13L, 23L, 1L, 3L, 3L, 15L, 12L, 2L, 
1L, 1L, 1L, 14L, 8L, 1L, 4L, 1L, 2L, 1L, 1L, 30L, 32L, 1L, 2L, 
1L, 1L, 1L, 3L, 16L, 2L, 1L, 2L, 1L, 2L, 26L, 5L, 3L, 7L, 4L, 
27L, 4L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 29L, 5L, 1L, 1L, 1L, 2L, 
24L, 14L, 3L, 1L, 1L, 1L, 1L, 1L, 4L, 16L, 10L, 1L, 1L, 4L, 2L, 
1L, 1L, 4L, 24L, 9L, 1L, 1L, 1L, 3L, 1L, 8L, 27L, 6L, 2L, 1L, 
1L, 1L, 5L, 18L, 8L, 3L, 1L, 1L, 1L, 1L, 1L, 4L, 24L, 6L, 2L, 
4L, 1L, 6L, 9L, 6L, 4L, 1L, 1L, 4L, 2L, 1L, 3L, 1L, 1L, 3L, 2L, 
1L, 2L, 2L, 6L, 2L, 1L, 6L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
27L, 38L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 29L, 18L, 1L, 1L, 
5L, 1L, 1L, 1L, 1L, 1L, 2L, 17L, 6L, 1L, 1L, 2L, 1L, 3L, 1L, 
1L, 18L, 43L, 1L, 1L, 3L, 3L, 1L, 1L, 4L, 1L, 19L, 16L, 1L, 2L, 
1L, 2L, 1L, 1L, 3L, 19L, 10L, 1L, 1L, 1L, 2L, 1L, 1L, 15L, 20L, 
4L, 1L, 2L, 1L, 5L, 10L, 4L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 41L, 
30L, 7L, 2L, 1L, 1L, 7L, 29L, 1L, 5L, 3L, 2L, 1L, 1L, 1L, 2L, 
2L, 1L, 1L, 1L, 6L, 8L, 16L, 1L, 2L, 2L, 1L, 3L, 2L, 23L, 1L, 
6L, 1L, 1L, 1L, 1L, 2L, 4L, 2L, 7L, 1L, 7L, 7L, 6L, 1L, 3L, 1L, 
1L, 2L, 2L, 2L, 1L, 8L, 5L, 1L, 5L, 1L, 3L, 7L, 3L, 10L, 2L, 
2L, 1L, 1L, 1L, 4L, 2L, 4L, 1L, 1L, 1L, 9L, 8L, 62L, 1L, 1L, 
1L, 1L, 8L, 11L, 2L, 1L, 1L, 1L, 1L, 4L, 7L, 7L, 4L, 3L, 1L, 
1L, 1L, 1L, 1L, 2L, 5L, 26L, 46L, 3L, 1L, 2L, 2L, 1L, 1L, 2L, 
1L, 9L, 15L, 1L, 6L, 1L, 1L, 4L, 7L, 2L, 1L, 14L, 3L, 19L, 12L, 
2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 5L, 23L, 12L, 1L, 1L, 1L, 1L, 
1L, 4L, 1L, 10L, 24L, 8L, 2L, 1L, 1L, 1L, 4L, 20L, 1L, 1L, 4L, 
1L, 2L, 1L, 1L, 34L, 1L, 3L, 5L, 1L, 1L, 4L, 15L, 11L, 1L, 1L, 
1L, 1L, 1L, 2L, 9L, 2L, 1L, 1L, 1L, 1L, 3L, 4L, 4L, 8L, 2L, 5L, 
7L, 1L, 1L, 6L, 8L, 3L, 1L, 1L, 1L, 1L, 16L, 8L, 1L, 1L, 1L, 
1L, 2L, 16L, 3L, 2L, 1L, 1L, 1L, 1L, 25L, 14L, 1L, 1L, 4L, 1L, 
2L, 1L, 1L, 1L, 15L, 7L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 16L, 5L, 
3L, 4L, 1L, 1L, 1L, 28L, 8L, 3L, 2L, 1L, 2L, 28L, 27L, 1L, 3L, 
2L, 3L, 1L, 1L, 2L, 10L, 2L, 10L, 1L, 1L, 1L, 54L, 5L, 5L, 4L, 
1L, 4L, 1L, 1L, 1L, 1L, 1L, 5L, 1L, 6L, 2L, 1L, 6L, 5L, 8L, 1L, 
4L, 1L, 1L, 1L, 1L, 1L, 17L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 8L, 
1L, 1L, 1L, 1L, 1L, 2L, 9L, 2L, 1L, 5L, 2L, 5L, 7L, 28L)), .Names = c("plot", 
"species", "occurrence"), class = c("data.table", "data.frame"
), row.names = c(NA, -1148L), .internal.selfref = <pointer: 0x0000000007b70788>)

default = 0 作为参数添加到您现有的代码中,以便:

LoggAbundTGLMSOagg <- tapply(AbundTGLMSOagg$occurrence,list
                      (AbundTGLMSOagg$plot,AbundTGLMSOagg$species),mean, default = 0)

有关详细信息,请参阅 ?tapply

编辑:或者,将此视为另一种解决方案:How do I replace NA values with zeros in an R dataframe?