From c85e3b49ec32def37898528a217657cdd23b828e Mon Sep 17 00:00:00 2001
From: aduvermy <arnaud.duvermy@ens-lyon.fr>
Date: Thu, 18 Jan 2024 16:39:19 +0100
Subject: [PATCH] improvment page website
---
NEWS.md | 34 +++++++++++++++-------------------
README.md | 4 +++-
inst/pkgdown/_pkgdown.yml | 12 +++++++++---
3 files changed, 27 insertions(+), 23 deletions(-)
diff --git a/NEWS.md b/NEWS.md
index 04fcf38..a33c645 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,34 +1,30 @@
-
# v1.0.0 : End of core development, Ready for beta testing
-The functions, tests, and vignettes are fully functional and operational!
-To do:
- - conducting installation tests
- - seeking out beta testers for further evaluation.
+* The functions, tests, and vignettes are fully functional and operational!
+* To do: 1) conducting installation tests , 2)seeking out beta testers for further evaluation.
# v1.0.1 : few enhancements
- - The metrics_plot function has been updated to display histograms instead of density plots.
- - The identity plot's point shape has been modified, enhancing the visual clarity of comparisons between HTRfit and DESeq2 results.
- - Similar to the identity plot, the dispersion plot also benefits from improved point shape, contributing to a more effective visual analysis.
- - Add xlab/ylab to ROC plot
- - The vignette section now includes a new topic, "About mixed model evaluation".
+* The metrics_plot function has been updated to display histograms instead of density plots.
+* The identity plot's point shape has been modified, enhancing the visual clarity of comparisons between HTRfit and DESeq2 results.
+* Similar to the identity plot, the dispersion plot also benefits from improved point shape, contributing to a more effective visual analysis.
+* Add xlab/ylab to ROC plot
+* The vignette section now includes a new topic, "About mixed model evaluation".
# v1.0.2 : R files reorganization, log file enhancement and versioning
- - R files have been restructured to enhance clarity.
- - The log file location has been relocated to the R temporary directory.
- - A bug that was causing issues with writing the 'group' information in log files during model update has been fixed.
- - Fix NOTE "no visible binding for global variable" linked to ggplot2
- - Fix bug with packageVersion("HTRfit")
+* R files have been restructured to enhance clarity.
+* The log file location has been relocated to the R temporary directory.
+* A bug that was causing issues with writing the 'group' information in log files during model update has been fixed.
+* Fix NOTE "no visible binding for global variable" linked to ggplot2
+* Fix bug with packageVersion("HTRfit")
# v2.0.0 : Enhanced evaluation metrics
- - Improved Documentation: Clearer and more comprehensive information on HTRfit functionalities and usage.
- - Additional Metrics: Added PR curve, precision, recall, accuracy, and R2 for enhanced model evaluation.
- - Reduced Dependencies: Streamlined installation by removing the need for plotROC.
-
+* Improved Documentation: Clearer and more comprehensive information on HTRfit functionalities and usage.
+* Additional Metrics: Added PR curve, precision, recall, accuracy, and R2 for enhanced model evaluation.
+* Reduced Dependencies: Streamlined installation by removing the need for plotROC.
diff --git a/README.md b/README.md
index 051c2be..f7892c2 100644
--- a/README.md
+++ b/README.md
@@ -43,7 +43,9 @@ The following depandencies are required:
```r
## -- required
-install.packages(c('parallel', 'data.table', 'ggplot2', 'gridExtra', 'glmmTMB', 'magrittr', 'MASS', 'reshape2', 'rlang', 'stats', 'utils', 'BiocManager', 'car'))
+install.packages(c('parallel', 'data.table', 'ggplot2', 'gridExtra',
+ 'glmmTMB', 'magrittr', 'MASS', 'reshape2',
+ 'rlang', 'stats', 'utils', 'BiocManager', 'car'))
BiocManager::install('S4Vectors', update = FALSE)
## -- optional
BiocManager::install('DESeq2', update = FALSE)
diff --git a/inst/pkgdown/_pkgdown.yml b/inst/pkgdown/_pkgdown.yml
index c2d3600..f33af03 100644
--- a/inst/pkgdown/_pkgdown.yml
+++ b/inst/pkgdown/_pkgdown.yml
@@ -1,5 +1,11 @@
+repo:
+ url:
+ home: https://gitbio.ens-lyon.fr/LBMC/yvertlab/vortex/plasticity_mutation/HTRfit
navbar:
structure:
- left: [intro, reference, articles , tutorials, news]
- right: [search, github]
-
+ left: [home, intro, reference, articles, tutorials, news]
+ right: [gitlab]
+ components:
+ gitlab:
+ icon: fab fa-gitlab fa-lg
+ href: https://gitbio.ens-lyon.fr/LBMC/yvertlab/vortex/plasticity_mutation/HTRfit
\ No newline at end of file
--
GitLab