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def hierarchy_inf(data,par,iter=250000,burn=1000,thin=100): | |
priors={} | |
x0=mc.Uniform('x0',par.x0_min,par.x0_max) | |
tau=mc.Uniform('tau',par.tau_min,par.tau_max) | |
priors["x0"]=x0 | |
priors["tau"]=tau | |
r=mc.Uniform('r',par.r_min,par.r_max) | |
r_delta=mc.Uniform('r_delta',0,(par.r_max-par.r_min)/2) |
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double MCMC_base_truncate_low(double truncate, struct_data *D,struct_para *D_para,struct_priors *D_priors,double *accept,double *h,double para,double (*foo)(struct struct_data *D,struct struct_para *D_para,struct struct_priors *D_priors,double,int,int),int l, int m){ | |
double logu,logaprob,can; | |
//can=rnorm(para,*h); /*can=para+gsl_ran_gaussian(RNG,*h);*/ | |
// if(can<=(truncate)){ | |
// can=para; | |
// } | |
can=truncate-1.0; | |
while(can<=truncate){ | |
can=rnorm(para,*h); |
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# Problem with bedpe file format as generated by bedtools | |
# https://code.google.com/p/bedtools/issues/detail?id=152 | |
#SRR364781 -> wt_sample | |
#SRR364782 -> wt_replicate | |
#SRR364783 -> pol32_sample | |
#SRR364784 -> pol32_replicate | |
#source("https://bioconductor.org/biocLite.R") | |
#biocLite("ShortRead") | |
#biocLite("org.Sc.sgd.db") |
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# Data from Smith & Whitehouse (2012) http://dx.doi.org/10.1038/nature10895 | |
#SRR364781 -> wt_sample | |
#SRR364782 -> wt_replicate | |
#SRR364783 -> pol32_sample | |
#SRR364784 -> pol32_replicate | |
roots=( | |
SRR364781 | |
SRR364782 | |
SRR364783 |
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count_DDY835=c(10,13,9,7,0,15,7,0,7,0,0,10,9,5,0,10,12,6,9,8,0,10,10,0,11,0,0,9,0,0,0,0) | |
count_DDY836=c(15,11,8,17,0,10,7,0,7,0,0,12,8,8,0,9,12,13,10,12,0,13,10,0,8,0,0,10,0,0,0,0) | |
gtype=c("wt","nmd2D","exo1D","rad24D","cdc13D","nmd2_exo1D","nmd2D_rad24D","nmd2D_cdc13D", | |
"exo1D_rad24D","exo1D_cdc13D","rad24D_cdc13D","nmd2D_exo1D_rad24D","nmd2D_exo1D_cdc13D","nmd2D_rad24D_cdc13D", | |
"exo1D_rad24D_cdc13D","nmd2D_exo1D_rad24D_cdc13D","rif1_wt","rif1_nmd2D","rif1_exo1D","rif1_rad24D","rif1_cdc13D", | |
"rif1_nmd2_exo1D","rif1_nmd2D_rad24D","rif1_nmd2D_cdc13D","rif1_exo1D_rad24D","rif1_exo1D_cdc13D","rif1_rad24D_cdc13D","rif1_nmd2D_exo1D_rad24D", | |
"rif1_nmd2D_exo1D_cdc13D","rif1_nmd2D_rad24D_cdc13D","rif1_exo1D_rad24D_cdc13D","rif1_nmd2D_exo1D_rad24D_cdc13D") | |
df=data.frame(gene=gtype,count_DDY835=count_DDY835,count_DDY836=count_DDY836,stringsAsFactors=FALSE) |
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#install.packages(c("mvtnorm","fields")) | |
library(fields) | |
library(mvtnorm) | |
grmf=function(nrow,ncol,sigsq=1,V=1){ | |
pos=expand.grid(row=1:nrow,col=1:ncol) | |
mat=matrix(nrow=nrow,ncol=ncol,0) | |
dists=rdist(pos) | |
#dists[row(dists)==col(dists)]=1 |
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import numpy as np | |
import math | |
import matplotlib.pyplot as plt | |
import webbrowser | |
def makePlot(xvals,yvals,fname="harmonograph.png",fopen=False,w=50,h=50,width=0.1): | |
maxs=[np.max(np.abs(xvals)),np.max(np.abs(yvals))] | |
farthest=max(maxs) | |
drw=plt.figure(1) |
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# Demonstrating significant differences between a | |
# vector of measurements and a single value | |
# Using the statsmodels package for doing test | |
# Using numpy to generate some fake data | |
from statsmodels.stats import weightstats as stests | |
import numpy as np | |
data=np.random.normal(loc=3.4,scale=0.1,size=100) | |
singleValue=3.3 |
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data Cell = Cell {teloLength :: Double, birthDate :: Double, lifeSpan :: Double, seedCell :: Integer} | |
instance Eq Cell where (Cell t1 _ _ _) == (Cell t2 _ _ _) = t1 == t2 | |
instance Ord Cell where (Cell t1 _ _ _) `compare` (Cell t2 _ _ _) = t1 `compare` t2 | |
instance Show Cell where show (Cell t b _ _) = show t ++ " " ++ show b | |
data CellLine x = Senescent | Mother x (CellLine x) (CellLine x) deriving (Show, Read, Eq) | |
-- Functions modelling cell biology | |
shortenTelo :: Cell -> Cell | |
shortenTelo (Cell telo x y oldseed) = Cell (telo - delta) x y newseed |
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import Control.Parallel (par, pseq) | |
import Control.DeepSeq | |
import System.Environment (getArgs) | |
import Data.Time.Clock (diffUTCTime, getCurrentTime) | |
data Tree x = Empty | Node x (Tree x) (Tree x) deriving (Show, Read, Eq) | |
-- Create instance of NFData for Tree data type (defining "normal form") | |
instance NFData a => NFData (Tree a) where | |
rnf Empty = () |