0.9.0: reformatted NEWS.md

Author: slamballais

NEWS.md

@@ -3,82 +3,82 @@
 Version 0.9.0 is the first update after publication of the QDECR manuscript in Frontiers in Neuroinformatics. The latter is based in Lausanne, Switzerland. This version introduces weighted regression and a number of minor tweaks. 
 
 ## New features
-* `qdecr_fastlm` can now take weights via the `weights` argument, which act as observation weights in the linear regression. This argument works similar to `lm`.
+* [#47](https://github.com/slamballais/QDECR/pull/47): `qdecr_fastlm` can now take weights via the `weights` argument, which act as observation weights in the linear regression. This argument works similar to `lm` (addresses [#36](https://github.com/slamballais/QDECR/issues/36)).
 
 ## Bug fixes
-* The specified number of cores is checked against `bigstatsr::nb_cores` (inside `QDECR:::check_cores`). However, it seems that it returns 0 cores when only 1 core is found (given that it always omits 1 core). We thus rewrote `check_cores` to use `parallel::detectCores`, and to make sure that it cannot return 0 cores.
-* Fixed the text in the error message of `QDECR:::check_cores`.
-* Unsmoothed q-cached surface files can now be analyzed. Normally, QDECR would look for files containing `fwhmX`, where X is the FWHM in mm. However, unsmoothed files do not contain this part. The code was rewritten to check if fwhm == 0, and in those cases it will not insert that into the file names. This was fixed by setting `fwhmc` to "" in `QDECR:::qdecr_check`, and by tweaking `QDECR:::qdecr_prep_mgh`.
+* [#43](https://github.com/slamballais/QDECR/pull/43): The specified number of cores is checked against `bigstatsr::nb_cores` (inside `QDECR:::check_cores`). However, it seems that it returns 0 cores when only 1 core is found (given that it always omits 1 core). We thus rewrote `check_cores` to use `parallel::detectCores`, and to make sure that it cannot return 0 cores (fixes [#42](https://github.com/slamballais/QDECR/issues/42)).
+* [#43](https://github.com/slamballais/QDECR/pull/43): Fixed the text in the error message of `QDECR:::check_cores`.
+* [#45](https://github.com/slamballais/QDECR/pull/45): Unsmoothed q-cached surface files can now be analyzed. Normally, QDECR would look for files containing `fwhmX`, where X is the FWHM in mm. However, unsmoothed files do not contain this part. The code was rewritten to check if fwhm == 0, and in those cases it will not insert that into the file names. This was fixed by setting `fwhmc` to "" in `QDECR:::qdecr_check`, and by tweaking `QDECR:::qdecr_prep_mgh` (fixes [#41](https://github.com/slamballais/QDECR/issues/41)).
 
 ## Minor tweaks
-* Tweaked the vertex-wise analysis code (`QDECR:::analysis_chunkedlm`) to be faster and be more memory efficient (`se` is now calculated without the intermediate storage of `s2`).
-* Added an extra check in `QDECR:::qdecr_prep_mgh` so that it also checks whether the .mgh files actually exist. It will output which subjects are missing the surface files (if N < 20) or just say that people are missing surface files (if N >= 20). This adds a little bit of runtime, but it pays off.
-* When there is missing data in the design matrix, `QDECR:::qdecr_fastlm` will throw an error (i.e., `na.action = na.fail`). This is to avoid problems downstream. We opted for `na.fail` and not `na.omit`-like behavior, because users who are unaware of missingness would then only find out after running QDECR that they had missingness.
+* [#46](https://github.com/slamballais/QDECR/pull/46): Tweaked the vertex-wise analysis code (`QDECR:::analysis_chunkedlm`) to be faster and be more memory efficient (`se` is now calculated without the intermediate storage of `s2`) (addresses [#38](https://github.com/slamballais/QDECR/issues/38)).
+* [306826c](https://github.com/slamballais/QDECR/commit/306826c0691fe6d94dd22b1ed6dfa0af96cc9aa0): Added an extra check in `QDECR:::qdecr_prep_mgh` so that it also checks whether the .mgh files actually exist. It will output which subjects are missing the surface files (if N < 20) or just say that people are missing surface files (if N >= 20). This adds a little bit of runtime, but it pays off (fixes [#34](https://github.com/slamballais/QDECR/issues/34)).
+* [26ac549](https://github.com/slamballais/QDECR/commit/26ac549bf05fef9302f20cfb1d177fdfff277954): When there is missing data in the design matrix, `QDECR:::qdecr_fastlm` will throw an error (i.e., `na.action = na.fail`). This is to avoid problems downstream. We opted for `na.fail` and not `na.omit`-like behavior, because users who are unaware of missingness would then only find out after running QDECR that they had missingness.
 
 # QDECR 0.8.5
 
 ## Bug fixes 
-* Fixed a line in `check_id` to explicitly state `drop = TRUE` in `md[, id, drop = TRUE]`. 
-* Fixed that a call to `model.matrix` would supply `stats::contrasts` in `prep_fastlm`; this led to harmless warnings.
+* [cfc9a35](https://github.com/slamballais/QDECR/commit/cfc9a35edbb52586bbd7777865577d49b73368fb): Fixed a line in `check_id` to explicitly state `drop = TRUE` in `md[, id, drop = TRUE]`. 
+* [39b6173](https://github.com/slamballais/QDECR/commit/39b617309913595dc8883bf849085db27fb29912): Fixed that a call to `model.matrix` would supply `stats::contrasts` in `prep_fastlm`; this led to harmless warnings.
 
 ## Minor tweaks
-* To let users analyze custom surface maps, we added the `custom_measure` argument to `qdecr_fastlm`. This argument lets users specify any name for a surface map that they want, provided that [1] it starts with "qdecr_" (e.g. "qdecr_test"), [2] such a file is located in the subj subdirectory of the FreeSurfer output directories, [3] the surface files follow the same naming convention as the other surface maps that FreeSurfer outputs (e.g. "lh.test.fwhm10.fsaverage.mgh").
+* [5043753](https://github.com/slamballais/QDECR/commit/504375366a795926521f6ca640ee6cabc931b757): To let users analyze custom surface maps, we added the `custom_measure` argument to `qdecr_fastlm`. This argument lets users specify any name for a surface map that they want, provided that [1] it starts with "qdecr_" (e.g. "qdecr_test"), [2] such a file is located in the subj subdirectory of the FreeSurfer output directories, [3] the surface files follow the same naming convention as the other surface maps that FreeSurfer outputs (e.g. "lh.test.fwhm10.fsaverage.mgh").
 
 # QDECR 0.8.4
 
 ## Bug fixes
-* Fixed that the model output files (p.mgh, t.mgh, etc) also contained the mcz threshold (e.g. cache.th30).
-* Lots of comments removed/modified, and code was cleaned up a bit.
-* Wrote in a preventative stop for when `dir_out_tree = FALSE` and `clobber = TRUE` are combined. This can easily delete important directories unintentionally, as has happened to the authors.
+* [20d3be2](https://github.com/slamballais/QDECR/commit/20d3be24f92121bfee8f1c114f86494dea51ae65): Fixed that the model output files (p.mgh, t.mgh, etc) also contained the mcz threshold (e.g. cache.th30).
+* [18c9de8](https://github.com/slamballais/QDECR/commit/18c9de8e47bc9af151a5fc3db9ab2fa384358d63): Lots of comments removed/modified, and code was cleaned up a bit.
+* [015d8a1](https://github.com/slamballais/QDECR/commit/015d8a19520aa00a996732b8027d01221f6dc076)/[e0aa3fe](https://github.com/slamballais/QDECR/commit/e0aa3fe9cf5c7ccb7945ff615d5891e77e74b58a): Wrote in a preventative stop for when `dir_out_tree = FALSE` and `clobber = TRUE` are combined. This can easily delete important directories unintentionally, as has happened to the authors.
 
 ## Minor Tweaks
-* Added the `file_out_tree` argument, which controls whether output files also contain the full project name. By default, it is the inverse of `dir_out_tree`.
-* Fixed a lot of the documentation.
+* [e7adb17](https://github.com/slamballais/QDECR/commit/e7adb175575877e573723493d3e78e6aecfc8ea2): Added the `file_out_tree` argument, which controls whether output files also contain the full project name. By default, it is the inverse of `dir_out_tree`.
+* [077e4fd](https://github.com/slamballais/QDECR/commit/077e4fd92bd120bad14c9a75c00f0e8a6f55d63f): Fixed a lot of the documentation.
 
 # QDECR 0.8.3
 
 ## Minor tweaks
-* The `mcz_thr` argument (for `qdecr` and `qdecr_fastlm`) now accepts: 13/1.3/0.05, 20/2.0/0.01, 23/2.3/0.005, 30/3.0/0.001, 33/3.3/0.0005, 40/4.0/0.0001.
-* A new function `qdecr_mcz_thr` makes sure that the value is converted to 13/20/23/30/33/40. 
+* [f019f81](https://github.com/slamballais/QDECR/commit/f019f819c01405bfef0f377ec50fcab03ade3718): The `mcz_thr` argument (for `qdecr` and `qdecr_fastlm`) now accepts: 13/1.3/0.05, 20/2.0/0.01, 23/2.3/0.005, 30/3.0/0.001, 33/3.3/0.0005, 40/4.0/0.0001.
+* [f019f81](https://github.com/slamballais/QDECR/commit/f019f819c01405bfef0f377ec50fcab03ade3718): A new function `qdecr_mcz_thr` makes sure that the value is converted to 13/20/23/30/33/40. 
 
 # QDECR 0.8.2
 
 ## Bug fixes
-* The `fst` package was noted as imported package, but we never implemented functionality from it. Thus, all reference to it was removed.
+* [6638efb](https://github.com/slamballais/QDECR/commit/6638efb2a45492c13e284644b847591b3c9727be): The `fst` package was noted as imported package, but we never implemented functionality from it. Thus, all reference to it was removed.
 
 ## New (minor) tweaks
-* The version is now properly displayed when running `qdecr`. This version is updated dynamically using `packageVersion("QDECR")`. The website (www.qdecr.com) was also added.
-* Exported `load.annot` and the `qdecr_read` functions.
-* Renamed the internal `runMriSurfCluster` function to `run_mri_surf_cluster`.
+* [3d479f4](https://github.com/slamballais/QDECR/commit/3d479f4f47d5ad851ec2de3b8909bd3cd8faa603): The version is now properly displayed when running `qdecr`. This version is updated dynamically using `packageVersion("QDECR")`. The website (www.qdecr.com) was also added.
+* [95a4d90](https://github.com/slamballais/QDECR/commit/95a4d90c6be352be8b7daf734aee126c966b971b): Exported `load.annot` and the `qdecr_read` functions.
+* [fa3de94](https://github.com/slamballais/QDECR/commit/fa3de94b850c3e95f4ca6374f4f9ec3b3486788d): Renamed the internal `runMriSurfCluster` function to `run_mri_surf_cluster`.
 
 # QDECR 0.8.1
 
 ## Bug fixes
-* If the estimated smoothness is below 1, we now increase it to 1 to avoid problems down the line.
-* Fixed a bug in qdecr_clusters where it assumes that there is always at least 1 cluster significant.
-* "w-g.pct" files can now be used as a measure by specifying "qdecr_w_g.pct" (underscore instead of hyphen).
-* Added `fwhm` argument to `qdecr_fastlm`, which was missing before.
+* [e86d2e1](https://github.com/slamballais/QDECR/commit/e86d2e116f9b8976f7004044ed1b3dae7a0df629): If the estimated smoothness is below 1, we now increase it to 1 to avoid problems down the line.
+* [04fcd1b](https://github.com/slamballais/QDECR/commit/04fcd1ba97a770e087c20ff902485122fb292683): Fixed a bug in `qdecr_clusters` where it assumes that there is always at least 1 cluster significant.
+* [251e668](https://github.com/slamballais/QDECR/commit/251e668278fa945e9662675c279dc2d07877ac25): "w-g.pct" files can now be used as a measure by specifying "qdecr_w_g.pct" (underscore instead of hyphen) (fixes [#19](https://github.com/slamballais/QDECR/issues/19)).
+* [dc81b89](https://github.com/slamballais/QDECR/commit/dc81b89ea6bece71831f6abc0e4eebcebc26f51e): Added `fwhm` argument to `qdecr_fastlm`, which was missing before (fixes [#18](https://github.com/slamballais/QDECR/issues/18)).
 
 ## New (minor) features
-* Added `cwp_thr` argument to `qdecr_fastlm` and `qdecr` to set the further cluster-wise p-value adjustment (default is 0.025 due to having 2 hemispheres, thus 0.05 / 2).
-* Automatically output two extra files: "significant_clusters.txt" (the output of `summary(vw, annot = TRUE)`) and "stack_names.txt" (the output of `stacks(vw)` and the corresponding stack numbers).
-* Modified `freeview` and `qdecr_snap`. The `mask` argument is now called `sig`. Furthermore, the ranges for the overlay colors are determined dynamically. Finally, users can now set any arguments to Freeview for manipulating surface files (see `freeview --help` on the command line).
+* [4f024f3](https://github.com/slamballais/QDECR/commit/4f024f38e5bf5a6277c847b9bf2371ffa58521b1): Added `cwp_thr` argument to `qdecr_fastlm` and `qdecr` to set the further cluster-wise p-value adjustment (default is 0.025 due to having 2 hemispheres, thus 0.05 / 2) (fixes [#23](https://github.com/slamballais/QDECR/issues/23)).
+* [08ae63b](https://github.com/slamballais/QDECR/commit/08ae63b23033d0571dfe6509206d95e09863316c): Automatically output two extra files: "significant_clusters.txt" (the output of `summary(vw, annot = TRUE)`) and "stack_names.txt" (the output of `stacks(vw)` and the corresponding stack numbers) (fixes [#17](https://github.com/slamballais/QDECR/issues/17)).
+* [11e2f55](https://github.com/slamballais/QDECR/commit/11e2f55e29a1e0aac0eb39ff5ac3fb92dbbe7f95): Modified `freeview` and `qdecr_snap`. The `mask` argument is now called `sig`. Furthermore, the ranges for the overlay colors are determined dynamically. Finally, users can now set any arguments to Freeview for manipulating surface files (see `freeview --help` on the command line) (fixes [#20](https://github.com/slamballais/QDECR/issues/20)).
 
 # QDECR 0.8.0: Momo
 
 Version 0.8.0 is the first update after public release. It fixes a bunch of mistakes, introduces further modularization, improves the speed and also reduces the RAM load.
 
 ## New functions and features
 
-* Added the input argument `dir_target`, so that the target can be specified flexibly. 
-* Modularized `qdecr_model` and added the input argument `prep_fun`, so that users can choose and create their own prep functions.
-* Modularized `qdecr_analysis` and added the input argument `analysis_fun`, so that users can choose and create their own analysis functions.
-* The internal function to run vertex-wise analyses, called `vertexwise`, now processes regressions in chunks, i.e. more than 1 vertex at a time. This has led to a considerable upgrade in speed, especially for smaller datasets. Chunk size can be controlled with `chunk_size`
+* [#2](https://github.com/slamballais/QDECR/pull/2): Added the input argument `dir_target`, so that the target can be specified flexibly (fixes [#1](https://github.com/slamballais/QDECR/issues/1)). 
+* [#4](https://github.com/slamballais/QDECR/pull/4)/[#6](https://github.com/slamballais/QDECR/pull/6): Modularized `qdecr_model` and added the input argument `prep_fun`, so that users can choose and create their own prep functions (fixes [#3](https://github.com/slamballais/QDECR/issues/3)).
+* [#10](https://github.com/slamballais/QDECR/pull/10): Modularized `qdecr_analysis` and added the input argument `analysis_fun`, so that users can choose and create their own analysis functions.
+* [#10](https://github.com/slamballais/QDECR/pull/10): The internal function to run vertex-wise analyses, called `vertexwise`, now processes regressions in chunks, i.e. more than 1 vertex at a time. This has led to a considerable upgrade in speed, especially for smaller datasets. Chunk size can be controlled with `chunk_size` (fixes [#7](https://github.com/slamballais/QDECR/issues/7)).
 
 ## Bug fixes
 
-* We removed lots of unnecessary dependencies.
-* We fixed the referencing to the default mask.
+* [#10](https://github.com/slamballais/QDECR/pull/10): We removed lots of unnecessary dependencies.
+* [#10](https://github.com/slamballais/QDECR/pull/10): We fixed the referencing to the default mask.
 
 # QDECR 0.7.0: OHBM
 
@@ -87,7 +87,7 @@ Version 0.7.0 is the first version that is publically released. It is also the v
 ## New functions and features
 
 * Creation of the QDECR package (before 0.7.0 it was a series of associated scripts)
-* Creation of the vw object and associated functions
-* Handling of imputed datasets (via imp2list)
+* Creation of the `vw` object and associated functions
+* Handling of imputed datasets (via `imp2list`)
 * Creation of all summary and plot functions
 * Creation of the `stack` concept