I'm having some issues running iNEXT with this new dataset
I'm trying to get species estimates as well as sample-coverage based accumulation curve from camera trapping efforts. But am having issues with loading the dataset into iNEXT.
I've followed the format of the incidence_raw data example given in the iNEXT manual (ciliates) but to no avail.
Here's the data and how I tried to convert the data into a species incidence matrix (row = species; every column = sampling unit):
#load packages
library(iNEXT)
#data here
ct <-structure(list(Station = structure(c(3L, 3L, 3L, 3L, 3L, 3L,
3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("CT01",
"CT02", "CT03"), class = "factor"), Date = structure(c(10L, 11L,
12L, 12L, 13L, 14L, 16L, 16L, 17L, 17L, 1L, 1L, 15L, 15L, 15L,
15L, 15L, 18L, 19L, 2L), .Label = c("1/11/19", "13/11/19", "14/11/19",
"15/11/19", "17/11/19", "18/11/19", "22/11/19", "23/11/19", "25/10/19",
"26/10/19", "27/10/10", "27/10/19", "28/10/19", "29/10/19", "3/11/19",
"30/10/19", "31/10/19", "6/11/19", "7/11/19"), class = "factor"),
Time = structure(c(23L, 22L, 25L, 28L, 24L, 15L, 31L, 20L,
18L, 19L, 2L, 8L, 3L, 7L, 6L, 16L, 17L, 21L, 9L, 14L), .Label = c("0:34:24",
"0:43:46", "13:07:10", "16:49:34", "17:26:28", "19:06:56",
"19:11:56", "19:13:28", "19:34:58", "19:53:00", "19:56:42",
"2:33:36", "2:34:40", "20:21:42", "20:27:00", "20:31:42",
"20:32:08", "22:25:22", "23:19:00", "23:50:24", "23:50:44",
"3:19:00", "4:26:00", "4:28:00", "4:46:00", "4:56:04", "5:13:32",
"5:18:00", "5:19:00", "5:56:00", "6:31:00"), class = "factor"),
DateTimeOriginal = structure(c(18L, 18L, 18L, 18L, 19L, 20L,
20L, 17L, 22L, 23L, 1L, 2L, 11L, 13L, 12L, 14L, 15L, 24L,
25L, 3L), .Label = c("1/11/19 0:43", "1/11/19 19:13", "13/11/19 20:21",
"14/11/19 17:26", "15/11/19 19:56", "17/11/19 0:34", "18/11/19 4:56",
"22/11/19 5:13", "23/11/19 2:33", "23/11/19 2:34", "3/11/19 13:07",
"3/11/19 19:06", "3/11/19 19:11", "3/11/19 20:31", "3/11/19 20:32",
"30/10/19 23:22", "30/10/19 23:50", "30/10/19 23:58", "30/10/19 23:59",
"31/10/19 0:00", "31/10/19 16:49", "31/10/19 22:25", "31/10/19 23:19",
"6/11/19 23:50", "7/11/19 19:34"), class = "factor"), Scientific_name_1 = structure(c(2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L,
2L, 2L, 2L, 2L), .Label = c("Callosciurus_notatus", "Rattus_tiomanicus"
), class = "factor"), Abundance_1 = c(2L, 1L, 4L, 3L, 4L,
3L, 1L, 2L, 1L, 3L, 2L, 2L, 2L, 3L, 2L, 3L, 3L, 1L, 1L, 4L
)), row.names = c(NA, 20L), class = "data.frame")
ct$trapnights <- paste(ct$Station, ct$Date, sep="_")
#create contingency table
ct.matrix <- xtabs(Abundance_1~Scientific_name_1+trapnights, data=ct)
#create species incidence matrix
ct.df1 <- ifelse(ct.matrix>0,1,0)
#run iNEXT
ct.inext <- iNEXT(ct.df2, datatype="incidence_raw")
At this point, I'll run into this error:
Error in arr[1, , ] <- t(as.matrix(ChaoSpecies(x, datatype, conf))) :
incorrect number of subscripts
I'm almost positive it's something wrong with my formatting but I'm just not sure where the problem lies.
Any help would be greatly appreciated! Thank you
I am not familiar with iNEXT. However, I could see that when datatype="incidence_raw", x should be a list. I converted the ct.df1 to list and tried. Here's the output.
> ct.df1 <- ifelse(ct.matrix>0,1,0)
> ct.df2<- list(ct.df1)
> ct.inext <- iNEXT(ct.df2, datatype="incidence_raw")
> ct.inext
Compare 1 assemblages with Hill number order q = .
$class: iNEXT
$DataInfo: basic data information
site T U S.obs SC Q1 Q2 Q3 Q4 Q5 Q6 Q7 Q8 Q9 Q10
1 site.1 14 15 2 1 1 0 0 0 0 0 0 0 0 0
$iNextEst: diversity estimates with rarefied and extrapolated samples.
[[1]]
t method order qD qD.LCL qD.UCL SC SC.LCL SC.UCL
1 1 interpolated 0 1.071 0.922 1.221 0.933 0.828 1.000
2 1 interpolated 0 1.071 0.922 1.221 0.933 0.828 1.000
10 7 interpolated 0 1.500 0.839 2.161 0.933 0.878 0.989
11 7 interpolated 0 1.500 0.839 2.161 0.933 0.878 0.989
20 14 observed 0 2.000 1.111 2.889 1.000 1.000 1.000
30 21 extrapolated 0 2.000 1.111 2.889 1.000 1.000 1.000
31 21 extrapolated 0 2.000 1.111 2.889 1.000 1.000 1.000
40 28 extrapolated 0 2.000 1.111 2.889 1.000 1.000 1.000
$AsyEst: asymptotic diversity estimates along with related statistics.
Site Diversity Observed Estimator s.e. LCL UCL
1 A Species richness 2.000 2.000 0.472 2.000 3.585
2 A Shannon diversity 1.278 1.324 0.218 1.278 1.751
3 A Simpson diversity 1.142 1.143 0.129 1.142 1.396
NOTE: Only show five estimates, call iNEXT.object$iNextEst. to show complete output.