diff --git a/DESCRIPTION b/DESCRIPTION index f29fce4b475d4adf8ac7220fe07806519c677312..e1214decf2294a9ada2c22a4203f55ce1a232671 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 cd8c5f79e17c75ca94a3ea164eb742da1d3f021b..a82175b59f5ee88f9a341087772632c51c74f429 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 32eb8df50c589ae12aaf57cb2fb1becb1ef623ad..7566bc112b19a2789706748a95e60f2e70d9e557 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 bef176d46c1b42bfd1a238f9be07ede7117f2851..00bec0612bcf2be0023f5cb7ddc48a7be85ef9b0 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 ca2f5b1c5e8d4cab033877472893b2250ab81d34..cf6cd8d6a71184ea076a5472231f5ad1d2376a0e 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)