library(data.table)
load("example.RData")
col = "ground.temp.min"
filter.zeros.thresh.K = 3
obs[.(check.regions$stn, check.regions$date), by = check.regions$g, (col) :=
     {v = get(col)
      if (!any(!is.na(v) &
              !zero &
              abs(v) <= filter.zeros.thresh.K))
          v[date == median(date)] = NA
      v}]

 *** caught segfault ***
address 0x56386f5fd8dc, cause 'memory not mapped'

Traceback:
 1: `[.data.table`(obs, .(check.regions$stn, check.regions$date),     by = check.regions$g, `:=`((col), {        v = get(col)        if (!any(!is.na(v) & !zero & abs(v) <= filter.zeros.thresh.K))             v[date == median(date)] = NA        v    }))
 2: obs[.(check.regions$stn, check.regions$date), by = check.regions$g,     `:=`((col), {        v = get(col)        if (!any(!is.na(v) & !zero & abs(v) <= filter.zeros.thresh.K))             v[date == median(date)] = NA        v    })]

R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] data.table_1.13.6

loaded via a namespace (and not attached):
[1] compiler_4.0.2