I am trying to convert a matrix data frame like this (lowland):
species DT1 DT3 DT6 DT7 DT12 DT13 DT14 DT15 DT28 DT29
1 M_vaccinifolia 0 0 0 0 0 0 1 0 0 1
2 M_vaccinifolia 0 0 0 0 0 0 0 0 0 1
3 M_vaccinifolia 0 0 0 0 0 0 0 0 0 1
4 M_vaccinifolia 0 0 0 0 0 0 0 0 0 1
5 M_vaccinifolia 0 0 0 0 0 0 0 0 0 1
6 M_vaccinifolia 0 0 0 0 0 0 0 0 0 1
7 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
8 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
9 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
10 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
11 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
12 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
13 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
14 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
15 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
16 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
17 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
18 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
19 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
20 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
21 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
22 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
23 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
24 M_vaccinifolia 0 0 0 0 0 0 0 0 0 0
And I want to transform to a list that I can enter the data as the iNEXT data "ciliates" list is used to perform the examples in the rarefaction curves (example in the section "RAW INCIDENCE DATA FUNCTION: incidence_raw" in this link: https://cran.r-project.org/web/packages/iNEXT/vignettes/Introduction.html. Below is how the list is interpreted:
command
str(ciliates$EtoshaPan)
int [1:365, 1:19] 0 0 0 0 0 0 0 0 0 0 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:365] "Acaryophrya.collaris" "Actinobolina.multinucleata.n..sp." "Afroamphisiella.multinucleata.n..sp." "Afrothrix.multinucleata.n..sp." ...
..$ : chr [1:19] "x53" "x54" "x55" "x56" ...
When I convert my data lowland, I just can reach this kind of list
lowland_list <- list(lowland)
str(lowland_list)
List of 1
$ :'data.frame': 24 obs. of 11 variables:
..$ species: chr [1:24] "M_vaccinifolia" "M_vaccinifolia" "M_vaccinifolia" "M_vaccinifolia" ...
..$ DT1 : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
..$ DT3 : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
..$ DT6 : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
..$ DT7 : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
..$ DT12 : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
..$ DT13 : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
..$ DT14 : int [1:24] 1 0 0 0 0 0 0 0 0 0 ...
..$ DT15 : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
..$ DT28 : int [1:24] 0 0 0 0 0 0 0 0 0 0 ...
..$ DT29 : int [1:24] 1 1 1 1 1 1 0 0 0 0 ...
What is not a proper entry data format to iNEXT read as the example. I spent many hours trying to make a list to enter this data but I couldn't figure it out. How can I do this?
Not sure if this helps, but I have 2 data.frames that are in species columns and sites rows (datA and datB). Here's some example code.
make an empty list:
datlist <- list()
datlist$A <- data.frame(t(datA))
datlist$B <- data.frame(t(datB))
then run iNEXT
iNEXT(datlist
, q = c(0, 1, 2)
, "incidence_raw"
, conf = 0.95
, se = TRUE
, knots = 200
, nboot = 200
)