nationalparkservice / drr_template Goto Github PK

We would like to have a look at this template, but the error below appears upon opening.

Clicking yes to recover generates another error.

We tried some additional recovery options but nothing worked.

This helps since folks don't have consistent R configurations. See DRR_Template.Rmd for a location where this should be used.

if (length(pkgList[!inst]) > 0) { install.packages(pkgList[!inst], dep = TRUE, quiet = TRUE, repos = "https://cloud.r-project.org") }

There are *.RData files sprinkled through different subfolders. One is located at: IMD_DRR_Template-master\data\final

I don't think you meant to include. add "*.RData" to the ignore.

The EML Package (also on GitHub) is more flexible and has more robust attribute population capability.

Most folks don't know from where a function comes package-wise and this is handy when debugging. For example:

dplyr::bind_cols()

Update any references to EDI.org to the correct URL of EnvironmentalDataInitiative.org.

remotes::install_github("nationalparkservice/IMD_DRR_Tempate")
give me an 'l'
remotes::install_github("nationalparkservice/IMD_DRR_Template")

PurposeAndScope:

• Spell out 'DOI'.
• Replace 'journals' with 'data journals in 'external peer-reviewed scientific journals' phrase (P2, Background)
• Change 'required' to 'mandated' in 'Note that publication in a data release report series (not required)...' (P3, Background)
• Under 2 Definitions: are there citations for any of these?
• Add definitions for Quality Assurance and Quality Control
• In section 3.1, add links to documents if available
• Ditto for section 3.2 and 3.3
• In section 3.3, is a word missing before or after 'data'? (1st sentence under IMD Reporting and Analysis Guidance)
• In section 4, add a link to the FAIR website

Line 101 (install.packages(RRpackages[!inst], dep = TRUE)) causes an error when knitting. Adding a repos argument should fix the problem: install.packages(RRpackages[!inst], dep = TRUE, repos = "https://cloud.r-project.org")

• I like the idea of splitting the DRR out from QC and metadata generation
  • I know that some people like using the DRR as a place for QC, EDA, etc. so I think it's worth considering how we can support this outside of the DRR
• Ideally we should be able to harvest most of this info from the data package/metadata
• Maybe include this as an Rmd template in NPSdataverse?

Line 146

This is an example of the standard approach we use in standalone scripts and notebooks. I'm not asking for these specific packages, just the fleshing out of their details in this way when they are loaded.

"markdown", # version: 1.1 # links to Sundown rendering library "rmarkdown", # version: 2.7 # newer rendering via pandoc "pander", # version: 0.6.3 # alternative renderer for markdown "knitr", # version: 1.31 # output to HTML, PDF "kableExtra", # version: 1.3.4 # for tables with grouped rows "RODBC", # version: 1.3-17 # connect to ODBC data sources "readxl", # reading xlsx files # version: '1.3.1' "reshape2", # version: '1.4.4' # data re-configuration "maptools", # version 1.1-1 # spatial data handling "httr", # version: 1.4.2 # dealing with HTTP/S connections "vcdExtra", # version 0.7-5 # categorical data viz "gdata", # version: 2.18.0 # data viz "lubridate", # version: '1.7.10' # date handling "plyr", # version: 1.8.6 # split, apply, combine data "dplyr", # data manipulation # version: '1.4.4' "tidyverse", # version: 1.3.0 #data manipulation "ggplot2", # version: '3.2.0' "ggspatial", # version 1.1.5 # spatial awareness for ggplot "RColorBrewer", # version: 1.1-2 # palettes "colorRamps", # version: 2.3 # color ramp tables "htmlwidgets", # version: 1.5.3 # HTML widgets "htmltools", # version: 0.5.1.1 # # HTML utilities "jsonlite", # handling JSON content # version: '1.7.0' "sf", #spatial functions # version: '0.9-5' "sp", #spatial item details# version: '1.4-2' "rgdal", # spatial conversions and interrogation # version: '1.5-16' "raster", # raster handling # version: '3.3-13' "spatialEco", # point in polygon operations # version: '1.2.0' "leaflet", # spatial rendering # version: '2.0.3' "rgbif" # Get gBIF data # version: 3.5.2

after line 112, add:
"remotes", # for install_github()

remove line 110 "EMLassemblyline"...

after line 120 lapply(), insert:

if (! "EMLassemblyline" %in% installed.packages()) remotes::install_github("EDIorg/EMLassemblyline")
require("EMLassemblyline")