如何在 R 中将多元丰度矩阵转换为出现表？-解网

问：

我有一个多变量丰度矩阵（按地点划分的物种丰度）：

Site<-c("1","2","3","4","5","6")
Long<-c("30.01565","29.99297","29.98867","29.95418","29.96438","29.93963")
Lat<-c("-29.71932","-29.69708","-29.70216","-29.65436","-29.66999","-29.66700")
Sp_A<-c("0","0","3","3","0","8")
Sp_B<-c("3","7","1","0","0","0")
Sp_C<-c("1","0","5","0","3","6")
Sp_D<-c("5","4","3","3","4","4")
data<-cbind(Site,Long,Lat,Sp_A,Sp_B,Sp_C,Sp_D)

     Site Long       Lat         Sp_A Sp_B Sp_C Sp_D
[1,] "1"  "30.01565" "-29.71932" "0"  "3"  "1"  "5" 
[2,] "2"  "29.99297" "-29.69708" "0"  "7"  "0"  "4" 
[3,] "3"  "29.98867" "-29.70216" "3"  "1"  "5"  "3" 
[4,] "4"  "29.95418" "-29.65436" "3"  "0"  "0"  "3" 
[5,] "5"  "29.96438" "-29.66999" "0"  "0"  "3"  "4" 
[6,] "6"  "29.93963" "-29.66700" "8"  "0"  "6"  "4"

我需要使用这个矩阵并创建一个新的表/矩阵。新表应有 4 列，具体为 Species、Long、Lat 和 Presence。对于这张表，我不关心丰度值，而是关心某个位置是否存在特定物种。因此，新表将具有单个物种的多个副本，位于不同位置，在这些位置存在和不存在。该表应如下所示。仅供Sp_A示例：

##    Species   Long        Lat         Presence
## 1  Sp_A      30.01565    -29.71932   0 #Binary meaning absent
## 2  Sp_A      29.99297    -29.69708   0
## 3  Sp_A      29.98867    -29.70216   1 #Binary meaning present
## 4  Sp_A      29.95418    -29.65436   1
## 5  Sp_A      29.96438    -29.66999   0
## 6  Sp_A      29.93963    -29.66700   1

换句话说，对于 die 多元丰度矩阵中的每个物种，我想为每个观测值创建单独的记录。如何使用函数在 R 中自动执行此过程？我的数据格式化技能非常生疏。任何建议将不胜感激。

R 矩阵 Tidyverse 数据操作

library(dplyr)
library(tidyr)

data %>%
  select(-Site) %>%
  pivot_longer(cols = starts_with('Sp'), values_to = 'Presence') %>%
  mutate(Presence = pmin(Presence, 1)) %>%
  arrange(name)

#    Long   Lat name  Presence
#   <dbl> <dbl> <chr>    <dbl>
# 1  30.0 -29.7 Sp_A         0
# 2  30.0 -29.7 Sp_A         0
# 3  30.0 -29.7 Sp_A         1
# 4  30.0 -29.7 Sp_A         1
# 5  30.0 -29.7 Sp_A         0
# 6  29.9 -29.7 Sp_A         1
# 7  30.0 -29.7 Sp_B         1
# 8  30.0 -29.7 Sp_B         1
# 9  30.0 -29.7 Sp_B         1
#10  30.0 -29.7 Sp_B         0
# … with 14 more rows

数据

data<-data.frame(Site,Long,Lat,Sp_A,Sp_B,Sp_C,Sp_D)
data <- type.convert(data)

如何在 R 中将多元丰度矩阵转换为出现表？

How to convert a multivariate abundance matrix into a occurrence table in R?

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