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adding badge for r-universe
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hanecakr committed May 3, 2024
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30 changes: 11 additions & 19 deletions README.Rmd
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<!-- badges: start -->

[![R-CMD-check](https://github.com/ropensci/fellingdater/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/fellingdater/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/ropensci/fellingdater/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ropensci/fellingdater?branch=main)
[![pkgcheck](https://github.com/ropensci/fellingdater/workflows/pkgcheck/badge.svg)](https://github.com/ropensci/fellingdater/actions?query=workflow%3Apkgcheck)
[![Status at rOpenSci Software Peer Review](https://badges.ropensci.org/618_status.svg)](https://github.com/ropensci/software-review/issues/618)
[![status](https://joss.theoj.org/papers/3db8c54ec854b575bf5450336ccb000b/status.svg)](https://joss.theoj.org/papers/3db8c54ec854b575bf5450336ccb000b)
[![R-CMD-check](https://github.com/ropensci/fellingdater/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ropensci/fellingdater/actions/workflows/R-CMD-check.yaml) [![Codecov test coverage](https://codecov.io/gh/ropensci/fellingdater/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ropensci/fellingdater?branch=main) [![pkgcheck](https://github.com/ropensci/fellingdater/workflows/pkgcheck/badge.svg)](https://github.com/ropensci/fellingdater/actions?query=workflow%3Apkgcheck) [![rOpenSci](https://badges.ropensci.org/618_status.svg)](https://github.com/ropensci/software-review/issues/618) [![fellingdateer status badge](https://ropensci.r-universe.dev/badges/fellingdater)](https://ropensci.r-universe.dev) [![JOSS](https://joss.theoj.org/papers/3db8c54ec854b575bf5450336ccb000b/status.svg)](https://joss.theoj.org/papers/3db8c54ec854b575bf5450336ccb000b)

<!-- badges: end -->

This R-package offers a suite of functions designed to assist dendrochronologists in inferring estimates for felling dates, derived from dated tree-ring series. The presence of partially preserved sapwood (*sw*) allows to estimate the missing number of sapwood rings, and to report an interval in which the actual felling date (*fd*) likely falls.
This R-package offers a suite of functions designed to assist dendrochronologists in inferring estimates for felling dates, derived from dated tree-ring series. The presence of partially preserved sapwood (*sw*) allows to estimate the missing number of sapwood rings, and to report an interval in which the actual felling date (*fd*) likely falls.

![](man/figures/cross-section.png)

This procedure can be applied to individual series as well as to a collection of timbers.
This procedure can be applied to individual series as well as to a collection of timbers.

In cases where it can be assumed that a group of historical timbers were all felled simultaneously (i.e., in the same year), but due to the absence of the bark/cambial zone (waney edge) and the final formed tree ring, this cannot be determined, the preserved sapwood rings can be used to establish a date range for the felling event.

Taking into account the observed number of sapwood rings across all analysed samples and combining them into a single estimate, a more accurate and precise estimation of the felling date year for the group of timbers under study is likely to be obtained.

An additional function offers a tool for summing sapwood probability distributions, comparable to 'summed probability densities (SPD)' commonly applied to sets of radiocarbon (^14^C) dates.


## Installation

You can install the latest release of `fellingdater` from [GitHub](https://github.com/ropensci/fellingdater/) or [R-universe](https://ropensci.r-universe.dev/fellingdater):

```r
``` r
# install.packages("pak")
pak::pak("ropensci/fellingdater")
```

```r
``` r
install.packages("fellingdater", repos = "https://ropensci.r-universe.dev")
```

Expand All @@ -65,26 +61,23 @@ trs_example1
sw_combine(trs_example1, plot = TRUE)
```

The light grey distributions represent the probability density function of the felling date range for each individual series. The dark grey distribution is the combined estimate for a common felling date.
The light grey distributions represent the probability density function of the felling date range for each individual series. The dark grey distribution is the combined estimate for a common felling date.

The sapwood model used in the example above to estimate the felling date range, was published by [Hollstein (1980)](https://search.worldcat.org/nl/title/6391864):

```{r model_sapwood_counts, dpi=200}
sw_model("Hollstein_1980", plot = TRUE)
```


## Getting started

You can find an overview of the **main functions** and **sapwood datasets** distributed with the package in the [documentation](https://docs.ropensci.org/fellingdater/reference/).

Some practical examples are provided in the [`Get started`](https://docs.ropensci.org/fellingdater/articles/getting_started.html) vignette.


## The workflow

The `fellingdater`-package allows to fully document the methodology to establish a felling date -- for a single
timber or a group of timbers -- making the whole procedure reproducible. It assists in building standardized workflows when applied to large datasets of historical tree-ring series originating from geographically distinct regions. The package is designed to offer several functions related to each step in the (generalized) workflow when working with tree-ring series from (pre-)historical objects or constructions.
The `fellingdater`-package allows to fully document the methodology to establish a felling date -- for a single timber or a group of timbers -- making the whole procedure reproducible. It assists in building standardized workflows when applied to large datasets of historical tree-ring series originating from geographically distinct regions. The package is designed to offer several functions related to each step in the (generalized) workflow when working with tree-ring series from (pre-)historical objects or constructions.

![](man/figures/workflow.png)

Expand All @@ -101,11 +94,10 @@ To refer to the current version of the package:

> Haneca K (2024). fellingdater: an R-package to facilitate the organisation, analysis and interpretation of tree-ring data from wooden heritage objects and structures. R package, version 1.0.0, <https://docs.ropensci.org/fellingdater>.

## Comments and contributions

- Please report any issues or bugs here: <https://github.com/ropensci/fellingdater/issues>.
- Please report any issues or bugs here: <https://github.com/ropensci/fellingdater/issues>.

- Get citation information for `fellingdater` in R typing `citation(package = 'fellingdater')`.
- Get citation information for `fellingdater` in R typing `citation(package = 'fellingdater')`.

- Please note that the `fellingdater` package is released with a [Contributor Code of Conduct](https://github.com/ropensci/fellingdater/blob/main/.github/CONTRIBUTING.md). By contributing to this project, you agree to abide by its terms.
- Please note that the `fellingdater` package is released with a [Contributor Code of Conduct](https://github.com/ropensci/fellingdater/blob/main/.github/CONTRIBUTING.md). By contributing to this project, you agree to abide by its terms.
8 changes: 5 additions & 3 deletions README.md
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[![Codecov test
coverage](https://codecov.io/gh/ropensci/fellingdater/branch/main/graph/badge.svg)](https://app.codecov.io/gh/ropensci/fellingdater?branch=main)
[![pkgcheck](https://github.com/ropensci/fellingdater/workflows/pkgcheck/badge.svg)](https://github.com/ropensci/fellingdater/actions?query=workflow%3Apkgcheck)
[![Status at rOpenSci Software Peer
Review](https://badges.ropensci.org/618_status.svg)](https://github.com/ropensci/software-review/issues/618)
[![status](https://joss.theoj.org/papers/3db8c54ec854b575bf5450336ccb000b/status.svg)](https://joss.theoj.org/papers/3db8c54ec854b575bf5450336ccb000b)
[![rOpenSci](https://badges.ropensci.org/618_status.svg)](https://github.com/ropensci/software-review/issues/618)
[![fellingdateer status
badge](https://ropensci.r-universe.dev/badges/fellingdater)](https://ropensci.r-universe.dev)
[![JOSS](https://joss.theoj.org/papers/3db8c54ec854b575bf5450336ccb000b/status.svg)](https://joss.theoj.org/papers/3db8c54ec854b575bf5450336ccb000b)

<!-- badges: end -->

This R-package offers a suite of functions designed to assist
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