paleolimbot / mudata2

Interchange Tools for Multi-Parameter Spatiotemporal Data
https://paleolimbot.github.io/mudata2
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write_mudata_zip() doesn't work inside rmarkdown #28

Closed paleolimbot closed 5 years ago

paleolimbot commented 6 years ago

tdir <- tempfile()
dir.create(tdir)
tf <- file.path(tdir, "temp.Rmd")

writeLines(
  c(
    "---",
    "output: md_document",
    "---",
    "",
    "```{r}",
    "library(mudata2)",
    "getwd()",
    "write_mudata_zip(kentvillegreenwood, 'kg.zip')",
    "write_mudata_json(kentvillegreenwood, 'kg.json')",
    "```",
    ""
  ),
  tf
)

rmarkdown::render(tf)
#> processing file: temp.Rmd
#> output file: temp.knit.md
#> /Applications/RStudio.app/Contents/MacOS/pandoc/pandoc +RTS -K512m -RTS temp.utf8.md --to markdown_strict --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output temp.md --standalone
#> 
#> Output created: temp.md
cat(paste(readLines(file.path(tdir, "temp.md")), collapse = "\n"))
#>     library(mudata2)
#>     getwd()
#>     #> [1] "/private/var/folders/bq/2rcjstv90nx1_wrt8d3gqw6m0000gn/T/Rtmp8WLzt6/filecdbd4b8c12f7"
#>     write_mudata_zip(kentvillegreenwood, 'kg.zip')
#>     write_mudata_json(kentvillegreenwood, 'kg.json')
mudata2::read_mudata_zip(file.path(tdir, "kg.zip"))
#> Error in mudata2::read_mudata_zip(file.path(tdir, "kg.zip")): File /var/folders/bq/2rcjstv90nx1_wrt8d3gqw6m0000gn/T//Rtmp8WLzt6/filecdbd4b8c12f7/kg.zip does not exist
mudata2::read_mudata_json(file.path(tdir, "kg.json"))
#> A mudata object aligned along "date"
#>   distinct_datasets():  "ecclimate"
#>   distinct_locations(): "GREENWOOD A", "KENTVILLE CDA CS"
#>   distinct_params():    "cooldegdays", "dirofmaxgust" ... and 9 more
#>   src_tbls():           "data", "locations" ... and 3 more
#> 
#> tbl_data() %>% head():
#> # A tibble: 6 x 6
#>   dataset   location         param   date       value flags
#>   <chr>     <chr>            <chr>   <date>     <dbl> <chr>
#> 1 ecclimate KENTVILLE CDA CS maxtemp 1999-07-01  28.5 <NA> 
#> 2 ecclimate KENTVILLE CDA CS maxtemp 1999-07-02  30.7 <NA> 
#> 3 ecclimate KENTVILLE CDA CS maxtemp 1999-07-03  26.4 <NA> 
#> 4 ecclimate KENTVILLE CDA CS maxtemp 1999-07-04  28.6 <NA> 
#> 5 ecclimate KENTVILLE CDA CS maxtemp 1999-07-05  26.0 <NA> 
#> 6 ecclimate KENTVILLE CDA CS maxtemp 1999-07-06  25.3 <NA>