HTTP Pipeline Code (http.pl)

System Requirements

This package provides scripts and APIs in R and works on both Windows and Linux systems

R

All code in this package has been tested on R 3.6.0 and R 4.4.1, but any version of R 3.x or 4.x should be compatible. Other package versions may have an impact due to changes in functionality or API.

The following R packages are required to pull existing HTTP data from MongoDB:

• mongolite - Required for DB access in R
• jsonlite - Required for DB access and handling JSON files
• readr - Required to read in tables and delimited files

Additional R packages are required to support pipelining of new HTTP data:

• doParallel - Required for parallelization of certain functions for users on Linux systems
• foreach - Required for parallelization of certain functions for users on Linux systems
• parallel - Required for parallelization of certain functions for users on Linux systems
• tcplfit2 - Required for concentration-response modeling

Additional R packages are also required to support formatting, plotting and timing for output legibility:

• data.table
• dplyr
• ggplot2
• plyr
• rlist
• stringr
• tibble
• tictoc
• tidyr

Installing htpp.pl

The htpp.pl package is an R package and can be installed using the devtools R package. R package dependencies, described above, should be installed prior to installing htpp.pl

This package can be installed from the public EPA Github or installed locally after cloning the code repository:

Install from Github

1. Run devtools function to install directly from Github:

#load devtools library
library(devtools)

#install from Github
devtools::install_github("USEPA/CompTox-htpp.pl")

library(htpp.pl)

Local installation

1. Clone or download the package from github (TBD):

git clone  https://github.com/USEPA/CompTox-htpp.pl.git

2. Move to the htpp.pl installation location and load the package using devtools functions:

#load devtools library
library(devtools)

#use devtools functions to load package and documentation
devtools::install_local(path="path/to/CompTox-htpp.pl/", build_vignettes=TRUE) #installs package and builds vignette

library(htpp.pl)

Version History

v0.4 (4/30/2025)

• Package installation can use devtools::install_github and devtools::install_local
• Added DB-free functionality for full htpp.pl -- see vignette for details
• Updated Vignette
• Various code improvements and bug fixes

v0.3 (3/4/2024)

• Various code improvements
• Improved roxygen2 documentation
• devtools package load functions work as intended
• Added vignette
• Added README

v0.2 (11/2/2023)

• Various code improvements throughout
• Add parallel capabilities to several functions
• Added external data
• Refined documentation

v0.1.1 (11/1/2023)

• roxygenized all functions and formatted for R package
• General code improvements throughout

v0.1 (8/3/2023)

• Initial version of code adapted from J. Nyffeler

Contributors

• Derik E. Haggard
• Joshua Harrill
• Joshua Witten
• Jo Nyffeler