demonstration/demonstration.md

In NikKrieger/projects: A Project Infrastructure for Researchers

‘projects’ R package demonstration

The user can install the projects package from the Comprehensive R Archive Network (CRAN):

install.packages("projects")

The user then loads the package:

library(projects)

## projects_folder() location:
## projects folder not found. Please run setup_projects()

As the startup message indicates, the user must run setup_projects() in order to initialize the /projects/ folder. The function accepts the path of the directory wherein the user would like for the /projects/ folder to dwell. Here, the user establishes the /projects/ folder in the home directory, whose name is “demonstration”:

setup_projects("~")

## projects folder created at
## /tmp/RtmpS3eJpa/demonstration/projects
## 
## Add affiliations with new_affiliation(),
## then add authors with new_author(),
## then create projects with new_project()

This mock /projects folder has now been created in the user’s home directory, and it is also available for viewing in the demonstration folder on the projects GitHub.

The message suggests adding affiliations and authors before creating projects because it takes marginally more user effort to change an existing project’s authorship than to specify authorship upon a project’s creation.

new_affiliation(
  department_name  = "Department of Physics",
  institution_name = "University of North Science",
  address = "314 Newton Blvd, Springfield CT 06003"
)
new_affiliation(
  department_name  = "Impossibles Investigation Team",
  institution_name = "Creekshirebrook Academy of Thinks",
  address = "Let Gade 27182, 1566 Copenhagen, Denmark"
)
new_affiliation(
  department_name  = "Statistical Consulting Unit",
  institution_name = "Creekshirebrook Academy of Thinks",
  address = "196 Normal Ave, Columbus, OH ",
  id = 50
)
new_author(
  given_names = "Scott",
  last_name = "Bug",
  title = "Professor",
  affiliations = c(2, "Physics"),
  degree = "PhD",
  email = "[e-mail]",
  phone = "965-555-5556"
)
new_author(
  given_names = "Marie",
  last_name = "Curie",
  title = "Chemist",
  affiliations = "Unit",
  phone = "553-867-5309",
  id = 86
)
new_author(
  given_names = "George Washington",
  last_name = "Carver",
  title = "Botanist",
  degree = "MS",
  affiliations = c(1, 2, 50),
  id = 1337
)
new_author(
  given_names = "Leonardo",
  last_name = "da Vinci",
  title = "Mathematician"
)
new_author(
  last_name = "Wu",
  given_names = "Chien-Shiung",
  title = "Physicist",
  affiliations = c("of North", "Statistical Consulting"),
  degree = "PhD",
  email = "[e-mail]"
)
## Output suppressed in knitted file for brevity

affiliations()

# A tibble: 3 x 4
     id department_name        institution_name        address             
  <int> <chr>                  <chr>                   <chr>               
1     1 Department of Physics  University of North Sc… 314 Newton Blvd, Sp…
2     2 Impossibles Investiga… Creekshirebrook Academ… Let Gade 27182, 156…
3    50 Statistical Consultin… Creekshirebrook Academ… "196 Normal Ave, Co…

authors()

# A tibble: 5 x 7
     id given_names     last_name title      degree email          phone   
  <int> <chr>           <chr>     <chr>      <chr>  <chr>          <chr>   
1     1 Scott           Bug       Professor  PhD    scottbug@impo… 965-555…
2     2 Leonardo        da Vinci  Mathemati… <NA>   <NA>           <NA>    
3     3 Chien-Shiung    Wu        Physicist  PhD    [e-mail]       <NA>    
4    86 Marie           Curie     Chemist    <NA>   <NA>           553-867…
5  1337 George Washing… Carver    Botanist   MS     <NA>           <NA>    

We will now create a project called “Creating Cold Fusion”:

new_project(
  title = "Achieving Cold Fusion",
  short_title = "ACF",
  authors = list("Bug", "Chien-Shiung", "Leonardo", 1337, 86),
  current_owner = "Carver",
  corresp_auth = "Bug",
  creator = "Curie",
  stage = "1: design",
  deadline_type = "Pilot study",
  deadline = "2020-12-31",
  id = 12
)

Project 12 has been created at
/tmp/RtmpS3eJpa/demonstration/projects/p0012

# A tibble: 1 x 6
     id title          stage    status    deadline_type deadline           
  <int> <chr>          <prjcts> <chr>     <chr>         <dttm>             
1    12 Achieving Col… 1: desi… just cre… Pilot study   2020-12-31 00:00:00

New project's authors:

# A tibble: 5 x 7
  author_id given_names    last_name title     degree email        phone   
      <int> <chr>          <chr>     <chr>     <chr>  <chr>        <chr>   
1         1 Scott          Bug       Professor PhD    scottbug@im… 965-555…
2         3 Chien-Shiung   Wu        Physicist PhD    [e-mail]     <NA>    
3         2 Leonardo       da Vinci  Mathemat… <NA>   <NA>         <NA>    
4      1337 George Washin… Carver    Botanist  MS     <NA>         <NA>    
5        86 Marie          Curie     Chemist   <NA>   <NA>         553-867…
# A tibble: 1 x 3
  current_owner corresp_auth creator   
  <prjcts_t>    <prjcts_t>   <prjcts_t>
1 1337: Carver  1: Bug       86: Curie

This creates the project folder at /demonstration/projects/p0012/. Provided that the default project folder template was not altered, the /projects folder should be structured as follows:

/tmp/RtmpS3eJpa/demonstration
└── projects
    └── p0012
        ├── data
        ├── data_raw
        ├── figures
        ├── manuscript
        ├── p0012.Rproj
        └── progs
            ├── 01_protocol.Rmd
            ├── 02_datawork.Rmd
            ├── 03_analysis.Rmd
            ├── 04_report.Rmd
            ├── citations.bib
            ├── style.css
            └── styles.docx

The user may now begin work on this project. The demonstration folder on the projects GitHub contains this project folder, with a mock project completed in order to demonstrate workflow from 01_protocol.Rmd to 04_report.Rmd.

NikKrieger/projects documentation built on Aug. 11, 2021, 6:33 p.m.