John Muschelli muschellij2
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| #!/bin/bash | |
| # https://gist.github.com/muschellij2/64f9104ccec09deb85d4928071b3c9e8 | |
| # set -e | |
| # Comment out this line for quieter output: | |
| # set -x | |
| export cran_set='options(repos = "http://cran.rstudio.com"); ' | |
| # we may be able to change to remotes | |
| export ig_package=devtools |
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| export LD_LIBRARY_PATH=/usr/local/clang/lib:${LD_LIBRARY_PATH} | |
| wget -O travis_helpers.sh http://bit.ly/travis_helpers | |
| source travis_helpers.sh | |
| cat travis_helpers.sh | |
| rm travis_helpers.sh | |
| echo "ANTSR_TRAVIS VERSION 0.6" | |
| # getting original path | |
| export ORIG_PATH=${PATH} | |
| # cmake may not be needed |
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| library(neurobase) | |
| library(papayar) | |
| library(papayaWidget) # from muschellij2/papayaWidget | |
| fname = "training01_01_mprage.nii.gz" | |
| img = readnii(fname) | |
| ortho2(img) | |
| papaya(img) | |
| papayaWidget(img) |
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| rm(list=ls()) | |
| library(ggplot2) | |
| library(ggneuro) | |
| library(RNifti) | |
| library(kirby21.t1) | |
| library(kirby21.fmri) | |
| library(matrixStats) | |
| library(shiny) | |
| library(neurobase) |
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| have_package = function(x) { | |
| x %in% installed.packages() | |
| } | |
| if (!have_package("neurobase")) { | |
| install.packages("neurobase") | |
| } | |
| library(neurobase) | |
| fname = "training01_01_mprage.nii.gz" |
muschellij2
/ fast_fdr.R
Last active
December 15, 2016 20:50
Fast FDR for BHoc (see https://en.wikipedia.org/wiki/False_discovery_rate)
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| library(data.table) | |
| n = 2 * 10^9 | |
| p = runif(n) | |
| big_bh_adjust = function(p) { | |
| n_over_k = NULL | |
| if (any(is.na(p))) { | |
| stop("p-values can't have NA in them for this function") | |
| } | |
| # Get the number of p-values (m) | |
| m = length(p) |
muschellij2
/ dramms_no_affine.R
Created
November 17, 2016 20:09
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| library(extrantsr) | |
| library(neurobase) | |
| library(drammsr) | |
| library(lungct) | |
| base = "19786L_phase1/insp_CT.nii.gz" | |
| base_mask="19786L_phase1/insp_lung_mask.nii.gz" | |
| follow = '19786L_phase2/insp_CT.nii.gz' | |
| follow_mask="19786L_phase2/insp_lung_mask.nii.gz" |
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| ^\..* |
muschellij2
/ Bug_in_read_dcf.R
Last active
November 2, 2016 17:24
Bug for read.dcf - which is a problem with readLines(con = gzfile()) with no newline
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| x = "Package: test | |
| Type: Package | |
| Title: What the Package Does (Title Case)" | |
| ###################################### | |
| # No Newline | |
| ###################################### | |
| file = tempfile() | |
| writeLines(x, file, sep = "") | |
| readLines(file) |
muschellij2
/ sweeney_test.R
Created
October 27, 2016 20:00
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| library(cluster) | |
| m <- 4 #total number of outcomes | |
| n <- 100 #total number of subjects | |
| p <- 10 #total number of covariates | |
| groups.m <- 2 ##number of groups for the columns of B | |
| m.ind <- rep(1:groups.m, each = m/groups.m) | |
| B <- matrix(0, p, m) |