bobmuscarella / EcoInf_Pubs_R_package

An R package to keep track of publications from the Section for Ecoinformatics and Biodiversity at Aarhus University

EcoInf_Pubs_R_package

An R package to keep track of publications from the Section for Ecoinformatics and Biodiversity at Aarhus University

Step-by-step instructions

1. Enter all pending items (papers still with "Submitted" status at end of 2017) to the Google Form here: https://goo.gl/forms/HMlSDEYZ5SEj2XQA3

2. Download the zip file, "EcoInf_publications_archive.zip" from the "Downloads" folder of this repository. (This should eventually be replaced by installation of package directly from GitHub)

3. Unzip that file on your own computer and place the main folder wherever on your computer you'd like this stuff to live.

4. The unzipped folder should hold an R script ("Run_EcoInf_Pubs.R") and three subfolders (archive, package, reports).
   The R script ("Run_EcoInf_Pubs.R") simply includes the code also shown below.

5. In R, set the working directory as the main folder named "EcoInf_publications_archive".
   (You need to edit the "..." below and make sure the working directly ends with '/').

setwd(".../EcoInf_publications_archive/")

6. Run the following code to generate an initial archive of pending papers (i.e., those entered in step 1):

install.packages("googlesheets4")
library(googlesheets4)
url <- "https://docs.google.com/spreadsheets/d/1k_Jyejd4f7E7PWbK9OHI5gkmSOymlfyA54hIfOpIm6g/edit?usp=sharing"
pubs <- as.data.frame(read_sheet(url))
filename <- paste0("archive/EcoInf_publications_", Sys.Date(), ".csv")
write.csv(pubs, file=filename, row.names=F)

7. Install and load the EcoInf Pubs R package:

install.packages("package/EcoinfPubsRpackage_2.1.tar.gz", repos=NULL, type="source")
library(EcoinfPubsRpackage)

8. Set the email options. Here are some examples, you can change as necessary. (Note that the argument "MyEmail" should be replaced with a text string of the Gmail address you plan to use for this.)

MyEmail <- "[e-mail]"
ReportFile <- "EcoInf_publications_2017-11-27.csv"
Deadline <- "Friday Aug 28"
Salutation <- "Kind regards,\nAnne"

9. Send emails to get people to add DOIs to their accepted papers. (Probably no need to do this for the first time since only "submitted" papers are being carried over?).

send.doi.email(ReportFile, 
               SendersEmail = MyEmail,
               Deadline = Deadline,
               Salutation = Salutation,
               DraftOnly = T)

10. Send out emails to get people to update status of their papers.

send.submitted.email(ReportFile, 
                     SendersEmail = MyEmail,
                     Deadline = Deadline,
                     Salutation = Salutation,
                     DraftOnly = T)

You will of course also want to send a general email to everyone providing them with the link to the Google Form: https://goo.gl/forms/HMlSDEYZ5SEj2XQA3

11. Once people have had a chance to reply (i.e., just before making the newsletter), generate the report as a word document.

get.pubslist()

Running this function should create two things:

1. a new .csv file the 'archive' folder
2. a new .docx file to the 'report' folder with the publications for the newsletter

The naming will be based on the date it is generated.