Organize minimal project tree where data is taken from Postgres database via flexdashboard

[vincenzovvv]

Hi all,

I would like to show my current workflow and get some suggestion about how to improve it.
I created a flexdashboard using some data I take from a Postgres database.
I feel it is full of errors and bad practices and I would like to have some suggestions about how to refactor my code.

Here how my project structure looks like:

.
└── my_awesome_report
    ├── set_up.R
    ├── get_data.R
    ├── data
    │     └── my_data.RData
    ├── my_awesome_report.Rmd
    └── .gitignore

• set_up.R contains libraries & database connection via RPostgres.
  This file starts with rm(list=ls()); I know, but where to find some resources on how to correct this error?
• get_data.R gets data via dbGetQuery(db, query), closes the connections via dbDisconnect(db), applies transformations via dplyr then saves the final dataframe in the /data folder as my_data.RData.
• I show my data in a flexdashboard template, hosted on shinyapp.io.
  In r setup, I load my libraries (again!) and data, run and show some tables via kable and some other nice things, and then publish it.

{r setup, include=FALSE}
# load libraries 
library(plotly)
library(knitr)
library(kable)

# load data 
load('data/my_data.RData')

I want my dashboard to be updated on a daily basis; or add a button that the user can press like "Update dashboard" and refreshes the whole dashboard data.
And here is where my process gets very cumbersome.

I run manually:

1. set_up.R
2. get_data.R
3. render my flexdashbaord
4. publish it on the shinyapp.io

How can I make this process automatic, with a chronjob?
The main structure is there but I feel that the whole process is approached in the wrong way.

please let me know your opinion.

Vincenzo