From c645588961965766acf32a3ff3c30fb01ebb5ee0 Mon Sep 17 00:00:00 2001
From: elizaharris <plasmodialslime@gmail.com>
Date: Wed, 15 Nov 2023 11:00:57 +0100
Subject: [PATCH] docs
---
DESCRIPTION | 7 +++++--
README.md | 11 +++++++++--
boma_application/RunBoma_TimeFRAME.R | 5 +++++
gen-e_example/RunGenE_TimeFRAME.R | 3 +++
...Data_TimeFRAME.R => RunIncubationData_TimeFRAME.R} | 5 +++++
5 files changed, 27 insertions(+), 4 deletions(-)
rename incubation_application/{RunDominikaData_TimeFRAME.R => RunIncubationData_TimeFRAME.R} (97%)
diff --git a/DESCRIPTION b/DESCRIPTION
index f29fce4..e1214de 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,11 @@
Package: TimeFRAME
Title: Bayesian Data Analysis of Isotopic Measurement Time Series
-Version: 0.0.0.9001
+Version: 0.0.0.9002
Authors@R:
- person("Philipp", "Fischer", , "fischphi@student.ethz.ch", role = c("aut", "cre"))
+ c(
+ person("Philipp", "Fischer", , "philipp.fischer@alumni.ethz.ch", role = c("aut", "cre")),
+ person("Eliza", "Harris", , "eliza.harris@sdsc.ethz.ch", role = c("ctb"))
+)
Description: TimeFRAME is a data analysis package that can be used for Bayesian estimation of source contributions and fractionation of isotopic measurement time series. It uses Bayesian parameter estimation with Stan to estimate uncertainty and produce posterior samples. Additionally, the package provides utility functions to simulate measurements and isotopic signature data for the study of nitrous oxide.
License: GPL (>= 3)
Encoding: UTF-8
diff --git a/README.md b/README.md
index cd8c5f7..a82175b 100644
--- a/README.md
+++ b/README.md
@@ -1,18 +1,19 @@
# TimeFRAME
> R package for the analysis of isotopic time series data using Bayesian hierarchical models implemented in Stan.
+> This package was created by Philipp Fischer during his ETHZ MSc thesis. See original package at: https://github.com/PhilFischer/TimeFRAME
## Installation
Make sure R is updated and install TimeFRAME using the R console. On Windows [RTools](https://cran.r-project.org/bin/windows/Rtools/) will additionally be required.
```
if (!require("devtools")) install.packages("devtools")
-devtools::install_github("PhilFischer/TimeFRAME", build_vignettes = TRUE)
+devtools::install_github("elizaharris/TimeFRAME", build_vignettes = TRUE)
```
TimeFRAME uses Stan as sampling library in the background. If there are any issues regarding this, please refer to the [RStan Documentation](https://mc-stan.org/users/interfaces/rstan).
If you do not need additional documentation of the package provided as vignettes you can omit building them for faster installation times.
```
-devtools::install_github("PhilFischer/TimeFRAME", build_vignettes = FALSE)
+devtools::install_github("elizaharris/TimeFRAME", build_vignettes = FALSE)
```
## Usage
@@ -57,6 +58,12 @@ fit.hdgp <- fit_dgp(model, df, t = t, rho = 0.2, rho.r = 0.5, estim.rho = TRUE)
+## Examples
+
+Download the full TimeFRAME repository or just the relevant example folder from https://gitlab.renkulab.io/eliza.harris/timeframe.
+
+You will find three folders containing example datasets and scripts as described in the TimeFRAME manuscript: gen-e_example, boma_application, incubation_application. Working through these examples will help you get started with TimeFRAME.
+
## References
Original FRAME Model
diff --git a/boma_application/RunBoma_TimeFRAME.R b/boma_application/RunBoma_TimeFRAME.R
index 32eb8df..7566bc1 100644
--- a/boma_application/RunBoma_TimeFRAME.R
+++ b/boma_application/RunBoma_TimeFRAME.R
@@ -1,4 +1,9 @@
+# This script illustrates use of the TimeFRAME package to analyse the boma dataset
+
+# If you've not yet installed TimeFRAME, first run:
+# devtools::install_github("elizaharris/TimeFRAME", build_vignettes = TRUE)
+
rm(list = ls())
require(lubridate)
library(TimeFRAME)
diff --git a/gen-e_example/RunGenE_TimeFRAME.R b/gen-e_example/RunGenE_TimeFRAME.R
index bef176d..00bec06 100644
--- a/gen-e_example/RunGenE_TimeFRAME.R
+++ b/gen-e_example/RunGenE_TimeFRAME.R
@@ -4,6 +4,9 @@
# The models are run using default values, the TimeFRAME documentation describes in detail
# the parameters that can be changed and edited.
+# If you've not yet installed TimeFRAME, first run:
+# devtools::install_github("elizaharris/TimeFRAME", build_vignettes = TRUE)
+
rm(list = ls())
require(lubridate)
library(TimeFRAME)
diff --git a/incubation_application/RunDominikaData_TimeFRAME.R b/incubation_application/RunIncubationData_TimeFRAME.R
similarity index 97%
rename from incubation_application/RunDominikaData_TimeFRAME.R
rename to incubation_application/RunIncubationData_TimeFRAME.R
index ca2f5b1..cf6cd8d 100644
--- a/incubation_application/RunDominikaData_TimeFRAME.R
+++ b/incubation_application/RunIncubationData_TimeFRAME.R
@@ -1,4 +1,9 @@
+# This script illustrates use of the TimeFRAME package to analyse the soil incubation dataset
+
+# If you've not yet installed TimeFRAME, first run:
+# devtools::install_github("elizaharris/TimeFRAME", build_vignettes = TRUE)
+
rm(list = ls())
require(lubridate)
library(TimeFRAME)
--
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