Create metaData/EML file

[RFlazcano]

I am working on trying to create an EML file using the EML package but I am receiving an error when I run the example code: Has anyone found a way around this issue?

library(EML) library(markdown) title <- "Sparkling Lake, Wisconsin, daily metabolism calculations 2014" pubDate <- "2016" abstract <- as(set_TextType("SparklingAbstract_NEP.docx"), "abstract")

error: pandoc.exe: SparklingAbstract_NEP.docx: openBinaryFile: does not exist (No such file or directory)

Error: pandoc document conversion failed with error 1

[clnsmth]

@RFlazcano what is your sessionInfo()?

[RFlazcano]

This is my sessionInfo():

sessionInfo(package = NULL) R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages: [1] rmarkdown_2.7 EML_2.0.5 LakeMetabolizer_1.5.0 [4] lubridate_1.7.10 rLakeAnalyzer_1.11.4.1 tidyr_1.1.2
[7] dplyr_1.0.0 readr_1.4.0

loaded via a namespace (and not attached): [1] jsonld_2.2 Rcpp_1.0.5 emld_0.5.1 prettyunits_1.1.1 [5] ps_1.3.3 assertthat_0.2.1 rprojroot_1.3-2 digest_0.6.25
[9] utf8_1.1.4 V8_3.4.0 R6_2.4.1 plyr_1.8.6
[13] backports_1.1.7 evaluate_0.14 ggplot2_3.3.2 pillar_1.4.4
[17] rlang_0.4.6 lazyeval_0.2.2 curl_4.3 uuid_0.1-4
[21] rstudioapi_0.11 callr_3.5.1 desc_1.2.0 jqr_1.2.0
[25] munsell_0.5.0 tinytex_0.29 compiler_4.0.2 xfun_0.21
[29] pkgconfig_2.0.3 pkgbuild_1.2.0 htmltools_0.5.1.1 tidyselect_1.1.0 [33] tibble_3.0.1 fansi_0.4.1 crayon_1.3.4 withr_2.4.1
[37] grid_4.0.2 jsonlite_1.7.1 gtable_0.3.0 lifecycle_0.2.0
[41] magrittr_1.5 scales_1.1.1 cli_2.0.2 fs_1.5.0
[45] remotes_2.2.0 testthat_2.3.2 xml2_1.3.2 ellipsis_0.3.1
[49] generics_0.0.2 vctrs_0.3.1 tools_4.0.2 glue_1.4.1
[53] purrr_0.3.4 hms_0.5.3 processx_3.4.5 pkgload_1.1.0
[57] yaml_2.2.1 colorspace_1.4-1 sessioninfo_1.1.1 memoise_1.1.0
[61] knitr_1.30

[clnsmth]

Thanks @RFlazcano. Looks like there are two issues here:

1. set_TextType() can't find "SparklingAbstract_NEP.docx". Try running the function with a full path to the file.
2. The as() constructor doesn't work with EML versions > 2.0.0. Try abstract <- set_TextType(file). See the "Creating EML" vignette for a crash course in the new methods.

Where is this "example" you are working from? Sounds like it needs an update.

[RFlazcano]

Thank you! yes, it's from 2016, my PI got it from a colleague that went to a GLEON workshop.
createMetadata.pdf

[clnsmth]

@RFlazcano Ah yes ... that's the same document my supervisor (cgries) shared with me as an introduction to creating EML with R. If this document is publicly posted somewhere I recommend sending a request to deprecate it since the methods no longer work. It could be updated, but the vignette I posted above is probably enough.

For what purposes are you creating EML via R? If it's a time series dataset to be published at regular intervals, then you're on the right path. A programmatic approach like this simplifies EML versioning and supports automation. If you're new to EML, you might check out the EMLassemblyline R package, which is a rapper around EML R, abstracts away complexity of the schema, and inherits best practices from the US LTER information management community. On the other hand, if this is just a one-off data publication, EDI has a simple web-based editor (ezEML) you may want to consider. Under a user account, you can create and manage multiple EML documents, and publish these along with your data to a repository other than EDI if you wish.

[RFlazcano]

I have just been going through those tutorials to later apply the methods to data we will be collecting later on this year. It will be time-series data for gas flux in a lake.

Thank you, this is really helpful as I learn my way around the package.