Update to Version 2.0.0

*05/06/2022*

Update the data with the Expert Panel annotations and the
R Markdown for this manuscript:

* Garcia et al. (2022 - Submitted). "Development of Training Materials for Pathologists to Provide Machine Learning Validation Data of Tumor-Infiltrating Lymphocytes in Breast Cancer," *Cancers*.

Changes include:

1. New `modalityID = "camic-expert"` that denotes the annotations from our
Expert Panel.
2. Two new batches, `batch = "FDA-HTT-Train001"` and `"FDA-HTT-Train002"`. These
batches contain the ROIs scored by the Expert Panel.
3. New `readerID` of the experts appear as `“expert****”`
4. The R Markdown used to create the figures in the Cancers paper and a
copy of the PDF output are available in the folder
`inst/extra/20220506-GarciaCancersPaper` to simplify reproducibility of the paper
in case some data formatting changes in the current `pilotHTT` data frame.

README.md

@@ -5,6 +5,8 @@ Truthing project (HTT project). The "inst" directory
 will be used to archive scripts that reproduce the
 analyses done for different presentations and publications.
 
+Project hub space: https://ncihub.org/groups/eedapstudies
+
 To install this package from the R command line: install_github('DIDSR/HTT')
 
 #### Data and Code Repository
@@ -13,16 +15,21 @@ To install this package from the R command line: install_github('DIDSR/HTT')
 #### Manual documenting the data and functions in the R package:
 * [https://github.com/DIDSR/HTT/tree/main/inst/manual](https://github.com/DIDSR/HTT/tree/main/inst/manual)
 
+#### Webinar tour of the data: [Link to video](https://ncihub.org/groups/eedapstudies/wiki/Presentation2021:TourofHTTData)
+
+---
+
 #### Manuscript describing the project:
-* S. N. Dudgeon et al., “A Pathologist-Annotated Dataset for Validating Artificial Intelligence: A Project Description and Pilot Study,” arXiv:2010.06995, 2020. Accepted for publication by the Journal of Pathology Informatics, 2021. [https://arxiv.org/abs/2010.06995](https://arxiv.org/abs/2010.06995)
+* Dudgeon et al. (2020), "A Pathologist-Annotated Dataset for Validating Artificial Intelligence: A Project Description and Pilot Study," *Journal of Pathology Informatics*, **12**, p. 45. https://www.doi.org/10.4103/jpi.jpi_83_20
+
+#### Manuscript describing expert panel:
+
+* Garcia et al. (2022 - Submitted). "Development of Training Materials for Pathologists to Provide Machine Learning Validation Data of Tumor-Infiltrating Lymphocytes in Breast Cancer," *Cancers*.
 
-#### Webinar tour of the data: [Video here](https://ncihub.org/groups/eedapstudies/wiki/Presentation2021:TourofHTTData)
+#### Pathology Informatics Presentation:
 
-#### Version 1.0: Pathology Informatics Presentation:
-Version 1.0 of this repository holds the data, scripts, and functions that were used for the following presentation.
-* B. D. Gallas and et al., “High Throughput Truthing (HTT): pathologist agreement from a pilot study,” presented at the Pathology Informatics Summit, 2021.  [https://ncihub.org/groups/eedapstudies/wiki/Presentation2021:PathologyInformaticsSummitHTTproject](https://ncihub.org/groups/eedapstudies/wiki/Presentation2021:PathologyInformaticsSummitHTTproject)
-* R markdown to create the figures from this presentation
-can be found in this folder: [https://github.com/DIDSR/HTT/tree/main/inst/extra/20210505-PathologyInformatics](https://github.com/DIDSR/HTT/tree/main/inst/extra/20210505-PathologyInformatics)
+* B. D. Gallas and et al., “High Throughput Truthing (HTT): pathologist agreement from a pilot study,” presented at the Pathology Informatics Summit, 2021.  https://ncihub.org/groups/eedapstudies/wiki/Presentation2021:PathologyInformaticsSummitHTTproject
+* R markdown to create the figures from this presentation can be found in this folder: `inst/extra/20210505-PathologyInformatics`
 
 
 [comment]: <> "[![Github All Releases](https://img.shields.io/github/downloads/DIDSR/HTT/total)]()"

UPDATE.md

@@ -0,0 +1,24 @@
+
+## Version 2.0.0
+*05/06/2022*
+
+Update the data with the Expert Panel annotations and the 
+R Markdown for this manuscript:
+
+* Garcia et al. (2022 - Submitted). "Development of Training Materials for Pathologists to Provide Machine Learning Validation Data of Tumor-Infiltrating Lymphocytes in Breast Cancer," *Cancers*.
+
+
+Changes include:
+
+1. New `modalityID = "camic-expert"` that denotes the annotations from our 
+Expert Panel.
+2. Two new batches, `batch = "FDA-HTT-Train001"` and `"FDA-HTT-Train002"`. These
+batches contain the ROIs scored by the Expert Panel.
+3. New `readerID` of the experts appear as `“expert****”`
+4. The R Markdown used to create the figures in the Cancers paper and a
+copy of the PDF output are available in the folder 
+`inst/extra/20220506-GarciaCancersPaper` to simplify reproducibility of the paper
+in case some data formatting changes in the current `pilotHTT` data frame.
+
+## Version 1.0.0
+Creation of the HTT Project's Pilot Study annotation dataset.