From 8ac39246e8c541c5e9b95df7c0823d5cfb570977 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Tue, 9 Feb 2021 11:58:29 +0000 Subject: [PATCH 1/8] Updated README installation instructions, article link and package info --- README.md | 26 +++++++++++++++++++++----- 1 file changed, 21 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 0290616..5a74bf3 100644 --- a/README.md +++ b/README.md @@ -17,14 +17,30 @@ Two oak decline indexes have been developed to quantitatively describe and diffe This package provides the tools generate these decline indexes using machine learning algorithm random forest. -Install the package from GitHub: +The methodology is outlined in the article: +[Finch, J.P., Brown, N., Beckmann, M., Denman, S. and Draper, J., 2021. Index measures for oak decline severity using phenotypic descriptors. Forest Ecology and Management, 485, p.118948.](https://www.sciencedirect.com/science/article/pii/S0378112721000372) + +### Installation + +The package can be installed from CRAN using: + +``` r +install.packages('pdi') ``` + +Or this development version of the package can be installed from GitHub: + +``` r devtools::install_github('jasenfinch/pdi',build_vignettes = TRUE) ``` -See the vignette for how to generate a phenotypic decline index (PDI) for oak decline severity using example data: +### Learn more -``` -vignette('pdi-example',package = 'pdi') -``` +The package documentation can be browsed online at . + +If this is your first time using `pdi` see the [Generating phenotypic decline indexes using the pdi package](https://jasenfinch.github.io/pdi/articles/pdi-example.html) vignette for information on how to get started. + +If you believe you've found a bug in `pdi`, please file a bug (and, if +possible, a [reproducible example](https://reprex.tidyverse.org)) at +. From e949cd225d8f7c3e72f0720816a7a036d4b1f7c9 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Tue, 9 Feb 2021 12:09:34 +0000 Subject: [PATCH 2/8] Added article DOI to description --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index cadf67c..83767a3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ Type: Package Title: Phenotypic Index Measures for Oak Decline Severity Version: 0.4.1 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6070-7476")) -Description: Oak declines are complex disease syndromes and consist of many visual indicators that include aspects of tree size, crown condition and trunk condition. This can cause difficulty in the manual classification of symptomatic and non-symptomatic trees from what is in reality a broad spectrum of oak tree health condition. Two phenotypic oak decline indexes have been developed to quantitatively describe and differentiate oak decline syndromes in Quercus robur. This package provides a toolkit to generate these decline indexes from phenotypic descriptors using the machine learning algorithm random forest. +Description: Oak declines are complex disease syndromes and consist of many visual indicators that include aspects of tree size, crown condition and trunk condition. This can cause difficulty in the manual classification of symptomatic and non-symptomatic trees from what is in reality a broad spectrum of oak tree health condition. Two phenotypic oak decline indexes have been developed to quantitatively describe and differentiate oak decline syndromes in Quercus robur. This package provides a toolkit to generate these decline indexes from phenotypic descriptors using the machine learning algorithm random forest. The methodology for generating these indexes is outlined in Finch et al. (2121) . URL: https://jasenfinch.github.io/pdi BugReports: https://github.com/jasenfinch/pdi/issues License: GPL-3 From 55a1a8086ccaaeed0586b21486b42370549d2c43 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Tue, 9 Feb 2021 12:10:22 +0000 Subject: [PATCH 3/8] added article link to vignette --- vignettes/pdi-example.Rmd | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/vignettes/pdi-example.Rmd b/vignettes/pdi-example.Rmd index 8295fb0..e2032e3 100644 --- a/vignettes/pdi-example.Rmd +++ b/vignettes/pdi-example.Rmd @@ -30,6 +30,10 @@ These include: * **Decline Acuteness Index (DAI)** - a measure to differentiate between Chronic Oak Decline (COD) and Acute Oak Decline with a score between -1 and 1. Acutely declining trees having a score closer to 1 and chronically declining trees having a score closer to -1. +For more information on the methodology behind generating these decline indexes, see the article: + +[Finch, J.P., Brown, N., Beckmann, M., Denman, S. and Draper, J., 2021. Index measures for oak decline severity using phenotypic descriptors. Forest Ecology and Management, 485, p.118948.](https://www.sciencedirect.com/science/article/pii/S0378112721000372) + This vignette will provide an example framework of how to generate these decline indexes based on the machine learning algorithm random forest, using an example set of phenotypic descriptors. To begin, load the package: From cf0162cdaefb2262c0cd694eb66b68a06ccf3728 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Tue, 9 Feb 2021 12:33:44 +0000 Subject: [PATCH 4/8] updated pkgdown site --- _pkgdown.yml | 2 +- docs/404.html | 16 +- docs/LICENSE-text.html | 6 +- docs/articles/index.html | 6 +- docs/articles/pdi-example.html | 167 ++++++++++-------- .../empty-anchor.js | 15 -- .../figure-html/DBH_site_adjusted_plot-1.png | Bin 15723 -> 27698 bytes .../figure-html/DBH_site_plot-1.png | Bin 16197 -> 28794 bytes .../figure-html/contributions_plot-1.png | Bin 53853 -> 169567 bytes .../figure-html/crown_volume_plot-1.png | Bin 23042 -> 39273 bytes .../figure-html/unnamed-chunk-3-1.png | Bin 17143 -> 26542 bytes .../header-attrs-2.6/header-attrs.js | 12 ++ docs/authors.html | 6 +- docs/index.html | 35 +++- docs/pkgdown.css | 4 +- docs/pkgdown.yml | 9 +- docs/reference/Rplot001.png | Bin 0 -> 1011 bytes docs/reference/agrilusExitHoleDensity.html | 11 +- docs/reference/bleedPrevalence.html | 11 +- docs/reference/calcDIs.html | 68 +++---- docs/reference/crownCondition.html | 11 +- docs/reference/crownProductionEfficiency.html | 11 +- docs/reference/crownSurfaceArea.html | 11 +- docs/reference/crownVolume.html | 11 +- docs/reference/descriptorContributions.html | 65 +++---- docs/reference/index.html | 6 +- docs/reference/liveCrownRatio.html | 11 +- docs/reference/makeAnalysisTable.html | 59 ++++--- docs/reference/mds.html | 63 +++---- docs/reference/minMaxScale.html | 15 +- docs/reference/phenotypingTemplate.html | 15 +- docs/reference/preparePhenotypeData.html | 19 +- docs/reference/readPhenotypeSheet.html | 17 +- docs/reference/reexports.html | 8 +- docs/reference/rf.html | 61 +++---- docs/reference/siteAdjustment.html | 31 ++-- docs/reference/siteAdjustmentFactors.html | 33 ++-- docs/sitemap.xml | 66 +++++++ 38 files changed, 503 insertions(+), 378 deletions(-) delete mode 100644 docs/articles/pdi-example_files/accessible-code-block-0.0.1/empty-anchor.js create mode 100644 docs/articles/pdi-example_files/header-attrs-2.6/header-attrs.js create mode 100644 docs/reference/Rplot001.png create mode 100644 docs/sitemap.xml diff --git a/_pkgdown.yml b/_pkgdown.yml index 6ef5f5a..5baa4a2 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1 +1 @@ -destination: docs +url: https://jasenfinch.github.io/pdi/ diff --git a/docs/404.html b/docs/404.html index 2e0723c..00fe3b8 100644 --- a/docs/404.html +++ b/docs/404.html @@ -18,8 +18,8 @@ - - + + @@ -33,8 +33,8 @@ - - + + @@ -70,7 +70,7 @@ - pdi + pdi 0.4.1 @@ -79,7 +79,7 @@
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