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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -3,5 +3,6 @@ | |
| *.Rproj | ||
| *.so | ||
| *.Rprofile | ||
| devel/* | ||
| Pedixplorer.Rcheck | ||
| *.lintr | ||
| Pedixplorer* | ||
| devel | ||
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| @@ -0,0 +1,50 @@ | ||
| { | ||
| // Use IntelliSense to learn about possible attributes. | ||
| // Hover to view descriptions of existing attributes. | ||
| // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 | ||
| "version": "0.2.0", | ||
| "configurations": [ | ||
| { | ||
| "type": "R-Debugger", | ||
| "name": "Launch R-Workspace", | ||
| "request": "launch", | ||
| "debugMode": "workspace", | ||
| "workingDirectory": "${workspaceFolder}" | ||
| }, | ||
| { | ||
| "type": "R-Debugger", | ||
| "name": "Debug R-File", | ||
| "request": "launch", | ||
| "debugMode": "file", | ||
| "workingDirectory": "${workspaceFolder}", | ||
| "file": "${file}" | ||
| }, | ||
| { | ||
| "type": "R-Debugger", | ||
| "name": "Debug R-Function", | ||
| "request": "launch", | ||
| "debugMode": "function", | ||
| "workingDirectory": "${workspaceFolder}", | ||
| "file": "${file}", | ||
| "mainFunction": "main", | ||
| "allowGlobalDebugging": false | ||
| }, | ||
| { | ||
| "type": "R-Debugger", | ||
| "name": "Debug R-Package", | ||
| "request": "launch", | ||
| "debugMode": "workspace", | ||
| "workingDirectory": "${workspaceFolder}", | ||
| "includePackageScopes": true, | ||
| "loadPackages": [ | ||
| "." | ||
| ] | ||
| }, | ||
| { | ||
| "type": "R-Debugger", | ||
| "request": "attach", | ||
| "name": "Attach to R process", | ||
| "splitOverwrittenOutput": true | ||
| } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| Package: Pedixplorer | ||
| Version: 0.99.2 | ||
| Date: 2023-09-19 | ||
| Version: 1.1.0 | ||
| Date: 2023-11-15 | ||
| Title: Pedigree Functions | ||
| Authors@R: c( | ||
| person("Louis", "Le Nézet", email="[email protected]", | ||
|
|
@@ -24,7 +24,9 @@ Imports: | |
| dplyr, | ||
| tidyr, | ||
| quadprog, | ||
| Matrix | ||
| Matrix, | ||
| S4Vectors, | ||
| testthat | ||
| Description: Routines to handle family data with a Pedigree object. The initial purpose | ||
| was to create correlation structures that describe family relationships such | ||
| as kinship and identity-by-descent, which can be used to model family data | ||
|
|
@@ -38,39 +40,39 @@ RoxygenNote: 7.2.3 | |
| Roxygen: list(markdown = TRUE) | ||
| VignetteBuilder: knitr | ||
| Suggests: | ||
| testthat (>= 3.0.0), | ||
| diffviewer, | ||
| vdiffr, | ||
| rmarkdown, | ||
| vdiffr, | ||
| rmarkdown, | ||
| BiocStyle, | ||
| knitr, | ||
| withr | ||
| withr, | ||
| magick | ||
| Config/testthat/edition: 3 | ||
| biocViews: Software, DataRepresentation, Genetics, Alignment | ||
| BugReports: https://github.com/LouisLeLezet/Pedixplorer/issues | ||
| url: https://github.com/LouisLeNezet/Pedixplorer | ||
| URL: https://github.com/LouisLeNezet/Pedixplorer | ||
| BiocType: Software | ||
| Collate: | ||
| 'Pedigree.R' | ||
| 'AllValidity.R' | ||
| 'AllClass.R' | ||
| 'kindepth.R' | ||
| 'kinship.R' | ||
| 'utils.R' | ||
| 'AllConstructor.R' | ||
| 'AllAccessors.R' | ||
| 'AllGeneric.R' | ||
| 'Pedixplorer-package.R' | ||
| 'alignped4.R' | ||
| 'alignped3.R' | ||
| 'alignped2.R' | ||
| 'alignped1.R' | ||
| 'validity.R' | ||
| 'pedigreeClass.R' | ||
| 'check_hints.R' | ||
| 'kindepth.R' | ||
| 'auto_hint.R' | ||
| 'align.R' | ||
| 'best_hint.R' | ||
| 'bit_size.R' | ||
| 'data.R' | ||
| 'descendants.R' | ||
| 'make_famid.R' | ||
| 'family_check.R' | ||
| 'kinship.R' | ||
| 'utils.R' | ||
| 'find_unavailable.R' | ||
| 'find_avail_affected.R' | ||
| 'find_avail_noninform.R' | ||
|
|
@@ -79,6 +81,7 @@ Collate: | |
| 'generate_colors.R' | ||
| 'ibd_matrix.R' | ||
| 'is_informative.R' | ||
| 'make_famid.R' | ||
| 'min_dist_inf.R' | ||
| 'norm_data.R' | ||
| 'num_child.R' | ||
|
|
@@ -88,6 +91,6 @@ Collate: | |
| 'plot_fromdf.R' | ||
| 'plot.R' | ||
| 'shrink.R' | ||
| 'trim.R' | ||
| 'unrelated.R' | ||
| 'useful_inds.R' | ||
| LazyData: false | ||
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