adds metadata, updates supp statement

* by adding zenodo metadata, hopefully we get automatic links to other related repositories
* add an explicit statement to the repository
* updates references to the zenodo software and manuscript repos
* with instructions for installing the zenodo software one in the readme

.Rbuildignore

@@ -0,0 +1,3 @@
+^renv$
+^renv\.lock$
+^LICENSE\.md$

.zenodo.json

@@ -0,0 +1,45 @@
+{
+    "creators": [
+        {
+            "orcid": "0000-0001-8141-7788",
+            "affiliation": "University of Kentucky",
+            "name": "Flight, Robert"
+        },
+        {
+            "orcid": "0000-0003-3995-5368",
+            "affiliation": "University of Kentucky",
+            "name": "Moseley, Hunter"
+        },
+        {
+            "affiliation": "University of Kentucky",
+            "name": "Bhatt, Praneeth"
+        }
+    ],
+
+    "license": "CC-BY 4.0",
+
+    "title": "Information-Content-Informed Kendall-tau Correlation: Utilizing Missing Values",
+
+    "related_identifiers": [
+        {
+            "scheme": "doi",
+            "identifier": "10.5281/zenodo.6311002",
+            "relation": "isSupplementedBy",
+            "resource_type": "software"
+        },
+        {
+            "scheme": "doi",
+            "identifier": "10.5281/zenodo.10570255",
+            "relation": "isSupplementedBy",
+            "resource_type": "software"
+        },
+        {
+            "scheme": "doi",
+            "identifier": "10.5281/zenodo.10570285",
+            "relation": "isSupplementedBy",
+            "resource_type": "software"
+        }
+    ]
+
+
+}

README.md

@@ -5,11 +5,12 @@
 
 All the code for generating the manuscript:
 
-Information-Content-Informed Kendall-tau Correlation: Utilizing Missing Values
-Robert M Flight, Praneeth S Bhatt, Hunter NB Moseley
-[biorxiv](https://doi.org/10.1101/2022.02.24.481854)
+Information-Content-Informed Kendall-tau Correlation: Utilizing Missing Values, Robert M Flight, Praneeth S Bhatt, Hunter NB Moseley [biorxiv](https://doi.org/10.1101/2022.02.24.481854) is contained within this repository.
 
-is contained within this repository.
+## License
+
+The contents of this work are licensed under a CC-BY license.
+If you use any content, you must give attribution to this original work.
 
 ## R Packages Needed
 
@@ -36,6 +37,20 @@ install.packages("renv")
 renv::restore()
 ```
 
+The {ICIKendallTau} package on GitHub is now different than the one used for this manuscript, you should install the one archived on Zenodo (v 0.3.20).
+
+```
+wget https://zenodo.org/records/10580528/files/ICIKendallTau_0.3.20.tar.gz?download=1 --output-document=ICIKendallTau_0.3.20.tar.gz
+tar -xzvf ICIKendallTau_0.3.20.tar.gz
+cd ICIKendallTau
+```
+
+Then start an R session from within the directory, and install it.
+
+```r
+remotes::install_local()
+```
+
 ## Rerun All Underlying Analyses
 
 If you want to rerun everything from the beginning, you can do `tar_make()` on the project, and it should just run it.

doc/ici_kt_manuscript.Rmd

@@ -157,7 +157,7 @@ We examine the effect of missing values on various simulated and real data-sets,
 Given the detrimental effects of including outlier samples in differential analyses, we also evaluate the ability of ICI-Kt to capture sample-sample pairwise similarities and the determination of outlier samples prior to differential analyses.
 Finally, we examine how feature-feature networks derived from various feature-feature correlations change within annotations depending on the correlation method used.
 
-All of the code used for this manuscript is available on zenodo [@flightManuscriptICIKendallTau2022].
+All of the code used for this manuscript is available on zenodo [@flightManuscriptICIKendallTau2024].
 
 ## Methods
 
@@ -257,7 +257,7 @@ In comparison to directly counting the concordant and discordant pairs, some of
 Therefore, we used 64-bit integers and floats where necessary in the *Rcpp* code.
 
 C++ (via *Rcpp* [@eddelbuettel_rcppseamless_2011; @eddelbuettel_seamlessbook_2013; @eddelbuettel_extendingrcpp_2018]) and R code implementations are in the src/kendallc.cpp and R/kendalltau.R files of the ICIKendallTau R package, hosted at https://github.com/MoseleyBioinformaticsLab/ICIKendallTau.
-The version of the package used in this manuscript is available on zenodo [@flightICIKendallTau2022].
+The version of the package used in this manuscript is available on zenodo [@flightICIKendallTau2023].
 
 When a large number of samples need to be compared, it may be useful to split the comparisons across compute instances (across hyperthreaded cores, physical cores, or physical compute nodes).
 The *furrr* R package makes the definition of compute clusters trivial [@vaughanFurrrApplyMapping2021].
@@ -696,4 +696,8 @@ The results shown here are in whole or part based upon data generated by the TCG
 This work was supported in part by grants NSF 2020026 (PI Moseley), NSF ACI1626364 (Griffioen, Moseley), P30 CA177558 (PI Evers) via the Markey Cancer Center Biostatistics and Bioinformatics Shared Resource Facility (MCC BB-SRF), P20 GM121327 (PD St. Clair), and P42 ES007380 (PI Pennell) via the Data Management and Analysis Core (DMAC).
 We are heavily indebted to the University of Kentucky Center for Computational Sciences (CCS) provided Kentucky Research Informatics Cloud (KyRIC), an NSF supported computational resource (NSF ACI1626364) for access to large virtual machines that allowed for methods development and the running of many of the larger datasets in this manuscript.
 
+## Supplemental materials
+
+In addition to the over 30 supplemental figures and tables, the following Zenodo item includes all of the data and code used to generate results: https://zenodo.org/doi/10.5281/zenodo.6309187
+
 ## References

doc/icikt_references.json

@@ -2044,7 +2044,7 @@
 		}
 	},
 	{
-		"id": "flightICIKendallTau2022",
+		"id": "flightICIKendallTau2023",
 		"type": "document",
 		"abstract": "ICIKendallTau version used in the manuscript Information-Content-Informed Kendall-tau Correlation: Utilizing Missing Values Robert M Flight, Praneeth S Bhatt, Hunter NB Moseley",
 		"title": "ICIKendallTau",
@@ -2062,14 +2062,14 @@
 		"issued": {
 			"date-parts": [
 				[
-					"2022",
-					2
+					"2023",
+					12
 				]
 			]
 		}
 	},
 	{
-		"id": "flightManuscriptICIKendallTau2022",
+		"id": "flightManuscriptICIKendallTau2024",
 		"type": "document",
 		"title": "manuscript.ICIKendallTau",
 		"URL": "https://dx.doi.org/10.5281/zenodo.6309187",
@@ -2081,13 +2081,17 @@
 			{
 				"family": "Moseley",
 				"given": "Hunter N. B."
+			},
+			{
+				"family": "Bhatt",
+				"given": "Praneeth S."
 			}
 		],
 		"issued": {
 			"date-parts": [
 				[
-					"2022",
-					2
+					"2024",
+					1
 				]
 			]
 		}