(Shared by Tom and Hazim, so either can run regardless of which office they are sitting in.)
Create a project in RStudio (easiest to call it global_report) and download these files to the root folder of the project. Make sure you have your version of set_environment.r set up and saved in the project root folder (see notes further below).
To create an .RData file from the database, do in R:
> source("create_rdata_file.r")
To create tables, figures and maps for the global report, do in R:
> source("create_tables_figures.r")
This will create a series of folders (or add to them if they are already created) with the following uses:
- CPFigs These are formatted PDF files for the country profiles for the graphic designer.
- FigData These are CSV files of the data behind each figure in case specific numbers are needed.
- Figs These are dated PDF files for sending to the graphic designer.
- Tables These are dated HTM files for sending to the graphic designer.
Then run the following scripts to create the tables, figures and profile figures respectively:
> source("Tables.r")
> source("Figures.r")
> source("profile_figures.r")
To create CSV files for the web annex tables, do in R:
> source("create_tables_annex_for_web.r")
To re-assemble PDF files for the web annex tables, do in R:
> source("split_rename_PDFs_annex_for_web.r")
You need to create this in your project's root folder to match your local computing environment. It sets up the paths to input and output folders and the connection string to the database (if available).
Here is a template to use:
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Set up the running environment for creating the tables and figures
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
scripts_folder <- getwd() # when running in an RStudio project this will be the root folder of the project.
# Decide whether to take data directly from the database instead of from a .RData file
use_live_db <- FALSE
# Location and name of .RData file (if used)
rdata_folder <- "D:/Example/rdata/"
rdata_name <- "data_2015-07-29.Rdata"
# ODBC connection string for the global TB database (if used), where:
# sssss = SQL-Server name on local network
# ddddd = SQL-Server database name
# uuuuu = SQL-Server username to log into the database
# ppppp = SQL-Server password to log into the database
connection_string <- "driver={SQL Server};server=sssssss;database=ddddddd;uid=uuuuuuu;pwd=pppppppp"
# Folder containing output subfolders for tables,figures and maps:
figures_folder <- "D:/Example/tables_figures/"
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Paths, etc for creating the CSV files for the annex tables to be
# published in the global report and also on the web, and also for splitting/merging PDFs
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Parent folder fo CSV, Excel and PDF files for annex 4 tables in the printed report
annex4_folder <- "D:/Example/Annex_4_data_tables/"
# Folder for CSV files sent to the GHO
gho_folder <- "D:/Example/GHO"
# Parent folder for CSV and PDF files:
annexweb_folder <- "D:/Example/annex_for_web/"
# Define input/output PDF subfolder locations:
pdforigin_folder <- file.path(annexweb_folder, "PDF_by_table")
pdfoutput_folder <- file.path(annexweb_folder, "PDF_by_region")
# PDFsam folder and DOS launch command:
pdfsamfolder <- "C:/Program Files/PDF Split And Merge Basic/bin/"
pdfsamcmd <- 'C:\\Progra~2\\Java\\jre7\\bin\\java.exe -Xmx256m -Dlog4j.configuration=console-log4j.xml -classpath "..\\lib\\pdfsam-console-2.4.3e.jar" org.pdfsam.console.ConsoleClient'