Rendering a shipping manifest

I find it to be good practice to include both a shipping manifest and short note to the curators who are receiving material when I ship out my collections. The ‘short notes’ I generally send are slightly post-card-esque, unless working on some big government type project - which the note in the example will be. In general I just like these as a nice little way of adding a bit of personal touch or warmth to the interaction.

The shipping manifests are very important for practical reasons. They allow me to check off material and make sure it is packed. They also seem like a cool old school way of helping people figure what is meant to be where. More feel than another email.

BL has a default template for this process, which automatically combines the transmittal notice with the shipping manifest.
As with the other templates from BL, this one is easily modifiable, and make these changes to a local copy which you have copied out of the packages contents. Unlike the herbarium labels, you will need to manually update some values, and the file itself will be rendered to pdf in whichever location it is found. Theoretically you can probably pass in a few of these args from a user profile or your global settings.

Here we copy the file over to a more ‘natural’ part of the computers file system just like we did with the label templates.

p2libs <- system.file(package = 'BarnebyLives')

folds <- file.path(
  'BarnebyLives', 'rmarkdown', 'templates', 'SoS_transmittal', 'skeleton', 'skeleton.Rmd')

file.copy(from = file.path(p2libs, folds), to =  '.')

Remember, changing the ‘to’ parameter in file.copy will allow it go wherever you want it to. In this example we copy the file into our working directory (‘.’).

Now you have the skeleton for the transmittal notice in your desired directory. Open the skeleton up in a R tab, and fill out the User defined settings. An example is below (do this in the template! not here).

herbarium_code <- 'F' # index herbariorum code
project <- data.frame(
  Name = 'Seeds of Success', # the project name. 
  Project_description = 'native seed conservation and development project',
  # short description
  Organization = 'Chicago Botanic Garden',
  Phone = '312-XXX-0257',
  Person = 'Reed Benkendorf',
  Email = 'rxxkendork@chicagotbotanicxx.org',
  PersonTitle = 'Lead Botanist',
  Sets = 'quadruplicate',
  Permits = 'These materials were collected under the auspices of the US Department of Interiors Bureau of Land Management, unless noted otherwise.'
)

These are your contact details which will go onto the letter head, and provide some context about the collections.

Next you will need to point towards the specimens you want to send. In this case I use a relative path to point towards the output from the BL cleaning pipeline. I select the few fields which matter, and create some empty ones for me to manually check off with a pen as I am packing material.

In the example below I include a little stringr::str_replace call to strip away all but my first initial from my first name. It’s not super safe, For example a first name like ‘McKenna’ would results in ‘MK’ being left behind - modify, or remove it, as desired.

herbarium <- herbaria_info |> 
  dplyr::filter(Abbreviation == herbarium_code)
specimens <- read.csv('../../results/collections-YOUR_NAME.csv') |>
  dplyr::select(Primary_Collector, Collection_number, Full_name) |> 
  dplyr::mutate(
    Packed = "", 
    Received = "", 
    Primary_Collector = stringr::str_replace(Primary_Collector, "[a-z]+", ".")) 

Once you have made all of your changes simply run the job. And once you’ve done that you can ‘knit’ the document using the ‘knit’ button in Rmarkdown’s graphic user interface or Ctrl + Shift + k.