Add cran-comments

cran-comments.md

@@ -1,35 +1,26 @@
-## Resubmission
-# plinkQC 0.3.2
-## minor changes
-* Add checks and tests in `evaluate_check_ancestry` for missing non-reference samples
-[5c03971](https://github.com/meyer-lab/plinkQC/commit/5c03971b92341b5a8cb26a1d5f2e37d637f5cbd7)
-* Clarified tutorials:
-  * R internal file.copy instead of systems `cp` command to make run on windows: [6c91ef3](https://github.com/meyer-lab/plinkQC/commit/6c91ef3368f601658967f88bc20db94a28307fce),
-  fixes [#26](https://github.com/meyer-lab/plinkQC/issues/26) 
-  * Add additional filter for A->T, C->G variants as suggested in [#24](https://github.com/meyer-lab/plinkQC/issues/24); [11e0375](https://github.com/meyer-lab/plinkQC/commit/11e03756852215915310a836d2e73dbcedf12bfc)
-* Fixed plotting issues in PCA plot of ancestry check:
-  * allow for supplying names of European reference population [ae09e64](https://github.com/meyer-lab/plinkQC/commit/ae09e64ee2eaeb8337b60b24b126a9c049d6315f)
-  * provide argument to specify number of populations per legend row [c7fe85d](https://github.com/meyer-lab/plinkQC/commit/c7fe85d555c256bf8be3843803ff1cc445f7898f)
-  * Ensure correct ordering of population colors when reference population is not HapMap [86275b7](https://github.com/meyer-lab/plinkQC/commit/86275b7c281835681f38ab16672db61c288cfed9)
-
-# plinkQC 0.3.1
-## minor changes
-
-* Fixed dead links in vignettes (caused by migration of repository): [da987d8](https://github.com/meyer-lab/plinkQC/commit/da987d8f225aa6aca0596b9c4f6a2484b102bdb6)
-* Added note about chrY in Hapmap data (vignette): [e8afbb9](https://github.com/meyer-lab/plinkQC/commit/e8afbb9842ed9421461a8114ac0a00f7955cf0c0)
-* Added note about recommended use of plink1.9 (vs 2.0):
-[b69d3d7](https://github.com/meyer-lab/plinkQC/commit/b69d3d71d23e9b161176a635fcb2b5a2b524591f)
-
 ## Test environments
-* local R installation, R 4.0.0
-* ubuntu 16.04 (on travis-ci), R 4.0.0
+* local R installation, R 4.0.2
+* ubuntu 16.04 (on travis-ci), R 4.0.2
 * win-builder (devel)
 
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note
 
-## Comments
-* This is a minor release
-* Mostly updates to vignettes and documentation
-* Some additional checks and tests on ancestry check
+* This is a new release, addressing some minor bug fixes and adding some more
+functionality.
+
+# plinkQC 0.3.3
+## major changes
+* Output all IBD estimates in `run_check_relatedness` not just fail IBD
+estimates [d009da90](https://github.com/meyer-lab/plinkQC/commit/d009da90434a83cb4867881e3772b518d17dc2dd)
+* Add midp modifier for --hwe and --hardy as recommended on [plink hwe documentation](https://www.cog-genomics.org/plink/1.9/filter#hwe) and discussed in issue [#27](https://github.com/meyer-lab-cshl/plinkQC/issues/27); [43230a6c](https://github.com/meyer-lab/plinkQC/commit/43230a6ce5f079b46c85b1a7a526213177db1f1b)
+
+## minor changes
+* Add checks in `cleanData` that can distinguish between miss-sepcified filters and non-failing samples [7432b1ee](https://github.com/meyer-lab/plinkQC/commit/7432b1ee880ad14c7a078f3a0379f7fdcff1684b); addresses issue [#31](https://github.com/meyer-lab-cshl/plinkQC/issues/31) 
+* Add checks and tests in `check_snp_missingness`, `check_maf` and `check_hwe` 
+in cases where all samples pass `perIndividualQC`.
+[31ed6f65](https://github.com/meyer-lab/plinkQC/commit/31ed6f653902857a0a78ae723e786dd84d240b75); related to issue [#31](https://github.com/meyer-lab-cshl/plinkQC/issues/31) 
+* Add checks and tests in `evaluate_check_sex` and `evaluate_check_het_imiss`
+for all passing samples and accordingly, no fail samples label in plot.
+[d071a43](https://github.com/meyer-lab/plinkQC/commit/d071a4341b0d4c40220b42f81c412da4d320b8ec)