From f9295865f4cc8f8f8db5d22d9ba5fe20cc257b17 Mon Sep 17 00:00:00 2001 From: Waldir Leoncio Date: Tue, 24 Mar 2020 15:54:48 +0100 Subject: [PATCH] Updated TODOs --- R/admix1.R | 9 ++++----- TODO.md | 3 ++- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/R/admix1.R b/R/admix1.R index 4ea8146..abc24e5 100644 --- a/R/admix1.R +++ b/R/admix1.R @@ -25,7 +25,7 @@ admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0), cat('---------------------------------------------------\n'); message('Reading mixture result from: ', pathname_filename, '...') } - Sys.sleep(0.0001) #ASK: what for? + Sys.sleep(0.0001) #TODO: remove # ASK: what is this supposed to do? What do graphic obj have to do here? # h0 = findobj('Tag','filename1_text'); @@ -50,7 +50,7 @@ admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0), # Redirect the call to the linkage admixture function. # call function noindex to remove the index column c$data <- noIndex(c$data, c$noalle) - # linkage_admix(c) # ASK: translate this function to R or drop? + # linkage_admix(c) # TODO: obsolete. remove. # return stop("linkage_admix not implemented") } @@ -371,9 +371,8 @@ admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0), } } - # ASK: Remove? are these plotting functions? - tulostaAdmixtureTiedot(proportionsIt, uskottavuus, alaRaja, iterationCount) - viewPartition(proportionsIt, popnames) + tulostaAdmixtureTiedot(proportionsIt, uskottavuus, alaRaja, iterationCount) # TODO: textual outputs. probably not necessary. translate nonetheless + viewPartition(proportionsIt, popnames) # TODO: adapt talle = inputdlg('Do you want to save the admixture results? [Y/n]', 'y') if (talle %in% c('y', 'Y', 'yes', 'Yes')) { diff --git a/TODO.md b/TODO.md index 5b3568c..a70586d 100644 --- a/TODO.md +++ b/TODO.md @@ -16,9 +16,10 @@ Note to contributors: as tasks get finished, please update this file with an `x` The list below contains non-essential but nice-to-have tasks for the next stable release. +- [ ] Implement sparse matrix optimizations from [`fastbaps`](https://github.com/gtonkinhill/fastbaps) +- [ ] Implement plotting functionality from [`starmie`](https://github.com/sa-lee/starmie) - [ ] Standardize capitalization of function names - [ ] Standardize capitalization of function arguments -- [ ] Implement optimizations from `fastbaps` - [ ] Replace redundant functions (ex.: `randga`) # Known pitfalls