how to interpolate data within groups in R using seqtime? - r

Question

I am trying to use seqtime (https://github.com/hallucigenia-sparsa/seqtime) to analyze time-serie microbiome data, as follow:
meta = data.table::data.table(day=rep(c(15:27),each=3), condition =c("a","b","c"))
meta<- meta[order(meta$day, meta$condition),]
meta.ts<-as.data.frame(t(meta))
otu=matrix(1:390, ncol = 39)
oturar<-rarefyFilter(otu, min=0)
rarotu<-oturar$rar
time<-meta.ts[1,]
interp.otu<-interpolate(rarotu, time.vector = time,
method = "stineman", groups = meta$condition)
the interpolation returns the following error:
[1] "Processing group a"
[1] "Number of members 13"
intervals
0
12
[1] "Selected interval: 1"
[1] "Length of time series: 13"
[1] "Length of time series after interpolation: 1"
Error in stinepack::stinterp(time.vector, as.numeric(x[i, ]), xout = xout, :
The values of x must strictly increasing
I tried to change method to "hyman", but it returns the error below:
Error in interpolateSub(x = x, time.vector = time.vector, method = method) :
Time points must be provided in chronological order.
I am using R version 3.6.1 and I am a bit new to R.
Please can anyone tell me what I am doing wrong/ how to go around these errors?
Many thanks!

Answer 1

I used quite some time stumbling around trying to figure this out. It all comes down to the data structure of meta and the resulting time variable used as input for the time.vector parameter.
When meta.ts is being converted to a data frame, all strings are automatically converted to factors - this includes day.
To adjust, you can edit your code to the following:
library(seqtime)
meta <- data.table::data.table(day=rep(c(15:27),each=3), condition =c("a","b","c"))
meta <- meta[order(meta$day, meta$condition),]
meta.ts <- as.data.frame(t(meta), stringsAsFactors = FALSE) # Set stringsAsFactors = FALSE
otu <- matrix(1:390, ncol = 39)
oturar <- rarefyFilter(otu, min=0)
rarotu <- oturar$rar
time <- as.integer(meta.ts[1,]) # Now 'day' is character, so convert to integer
interp.otu <- interpolate(rarotu, time.vector = time,
method = "stineman", groups = meta$condition)
As a bonus, read this blogpost for information on the stringsAsFactors parameter. Strings automatically being converted to Factors is a common bewilderment.