change name

LICENSE.txt

@@ -1,2 +1,2 @@
-YEAR: 2020
+YEAR: 2022
 COPYRIGHT HOLDER: Kelsey E Johnson

R/sampler.R

@@ -27,7 +27,7 @@ sampler = function(dists,ac,alphaRec,betaRec,alphaIBD,alpha0,beta0,piPriors,nite
 	piPriors = piPriors/sum(piPriors)
 
 	#partitions from getPartitions
-	part = ibdibsR::getPartitions(ac)
+	part = EVICORD::getPartitions(ac)
 	nrec_k = part$nrec_k
 	nibd1_k = part$nibd1_k
 	nibd2_k = part$nibd2_k
@@ -59,19 +59,19 @@ sampler = function(dists,ac,alphaRec,betaRec,alphaIBD,alpha0,beta0,piPriors,nite
 
 	for (i in 1:niter){
 		#sample beta for ibd
-		beta_i[i+1,1] = ibdibsR::sample_beta(c(t1_i[i,],t2_i[i,]) %>% na.omit(), alphas[1],alpha0,beta0)
+		beta_i[i+1,1] = EVICORD::sample_beta(c(t1_i[i,],t2_i[i,]) %>% na.omit(), alphas[1],alpha0,beta0)
 		beta_i[i+1,2] = betaRec
 
 		#update z,v,t
-		zvt = ibdibsR::sample_t_z_v(alphas,beta_i[i+1,],pi_chain[i,],dists$distL_cM,dists$distR_cM,ac,nibd1_k,nibd2_k,nrec_k,n,nk)
+		zvt = EVICORD::sample_t_z_v(alphas,beta_i[i+1,],pi_chain[i,],dists$distL_cM,dists$distR_cM,ac,nibd1_k,nibd2_k,nrec_k,n,nk)
 		z_chain[i+1,] = zvt$z
 		v_chain[i+1,] = zvt$v
 		t1_i[i+1,] = zvt$t[,1]
 		t2_i[i+1,] = zvt$t[,2]
 		t3_i[i+1,] = zvt$t[,3]
 
 		#update pi
-		pi_chain[i+1,] = sort(ibdibsR::sample_pi(z_chain[i+1,],piPriors,nk),decreasing=T)
+		pi_chain[i+1,] = sort(EVICORD::sample_pi(z_chain[i+1,],piPriors,nk),decreasing=T)
 	}
 
 	outlist = list("nVars"=n,"beta"=beta_i,"pi"=pi_chain,"t1"=t1_i,"t2"=t2_i,"t3"=t3_i,"z"=z_chain,"v"=v_chain)

README.md

@@ -12,9 +12,9 @@ The purpose of this method is to classify variants as likely IBD or non-IBD usin
 ```R
 #install from github
 library(devtools)
-github_install("kelsj/ibdibsR")
+github_install("kelsj/EVICORD")
 #load package
-library(ibdibsR)
+library(EVICORD)
 ```
 
 
@@ -24,13 +24,13 @@ library(ibdibsR)
 1. Load pairwise recombination distances in centimorgans (file format should have 3 columns: varID, distL, distR). The distances should be ordered by variant and by allele pairs. Within each variant, the order fo allele pair recombination distances matters; e.g. for allele count 3, the pairwise distances should be in the order 1-2,1-3,2-3; for allele count 4, the order should be 1-2,1-3,1-4,2-3,2-4,3-4; etc.
 
 ```R
-dists = ibdibsR::load_dists("sim_dists_ex.txt",header=T,ac=4)
+dists = EVICORD::load_dists("sim_dists_ex.txt",header=T,ac=4)
 ```
 
 2. Run the Gibbs sampler on the pairwise recombination distances. Several parameter values must be provided at this step: the allele count (**ac**), values for alpha and beta for recurrent/non-IBD variants (**alphaRec**, **betaRec**; can be calculated with nonIBD\_param\_values.R, see below), alpha for IBD variants (**alphaIBD**; recommended to try multiple values and see how this affects your results), priors for beta for IBD variants (**alpha0**, **beta0**), vector of priors for pi (**piPriors**, should have as many values as there are categories of k; i.e. 1+number of non-IBD partitions), and the number of iterations to run (**niter**).
 
 ```R
-ibdibsR::sampler(dists,ac=4,alphaRec=40,betaRec=0.1,alphaIBD=10,alpha0=1,beta0=10,piPriors=c(0.4,0.4,0.2),niter=100,outfile="gibbs_sampler_out.rds") #returns RDS object of output: gibbs_sampler_out.rds
+EVICORD::sampler(dists,ac=4,alphaRec=40,betaRec=0.1,alphaIBD=10,alpha0=1,beta0=10,piPriors=c(0.4,0.4,0.2),niter=100,outfile="gibbs_sampler_out.rds") #returns RDS object of output: gibbs_sampler_out.rds
 ```
 
 3. Visualize results from gibbs_sampler_out.rds. Required parameters: **filename**, e.g. gibbs\_sampler\_out.rds; **ac**, allele count; **tf** integer to thin chains by for visualization. Output plot panels:
@@ -41,15 +41,15 @@ ibdibsR::sampler(dists,ac=4,alphaRec=40,betaRec=0.1,alphaIBD=10,alpha0=1,beta0=1
     4. empirical cumulative density of the fraction of z samples for each variant greater than x (with x=1,2,3,...); i.e., zGT1 = the fraction of posterior samples that the variant is assigned to be non-IBD.
 
 ```R
-ibdibsR::viz_res(filename="gibbs_sampler_out.rds",ac=4,tf=5,outfile="gibbs_sampler_out_viz.pdf") #saves visualizations in pdf gibbs_sampler_out_viz.pdf
+EVICORD::viz_res(filename="gibbs_sampler_out.rds",ac=4,tf=5,outfile="gibbs_sampler_out_viz.pdf") #saves visualizations in pdf gibbs_sampler_out_viz.pdf
 ```
 
 ## Estimating beta for non-IBD variants from data
 
 Posterior values of alpha and beta for the distribution of TMRCAs for non-IBD variants need to be supplied to run the sampler function above. These can be estimated from the pairwise recombination distances of non-IBD allele pairs from multiallelic or known non-IBD variants using the function nonIBD\_param\_values. Requires input of non-IBD variants' pairwise recombination distance (columns: varID, distL, distR). Several parameter values must be provided: the number of non-IBD allele pair distances provided for each variant (**n_nonIBDpairs**), the value of alpha for non-IBD allele pairs (**alpha**); priors for beta (**alpha0**, **beta0**), the number of iterations to run (**niter**), and the output file name (**outfile**).
 
 ```R
-ibdibsR::nonIBD_param_values(dists,n_nonIBDpairs=3,alpha=40,alpha0=1,beta0=10,niter=500,outfile="sampled_nonIBD_param_values_alpha40") #saves sampled values to RDS file sampled_nonIBD_param_values.rds
+EVICORD::nonIBD_param_values(dists,n_nonIBDpairs=3,alpha=40,alpha0=1,beta0=10,niter=500,outfile="sampled_nonIBD_param_values_alpha40") #saves sampled values to RDS file sampled_nonIBD_param_values.rds
 ```
 
 

example/sample_nonIBD_params_example.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Example for ibdibsR function nonIBD_param_values\n",
+    "# Example for EVICORD function nonIBD_param_values\n",
     "\n",
     "## Set up"
    ]
@@ -17,10 +17,10 @@
    },
    "outputs": [],
    "source": [
-    "library(ibdibsR)\n",
+    "library(EVICORD)\n",
     "library(ggplot2)\n",
     "library(dplyr)\n",
-    "setwd(\"./ibdibsR/example\")"
+    "setwd(\"./EVICORD/example\")"
    ]
   },
   {

example/sampler_example.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Example for ibdibsR sampler"
+    "# Example for EVICORD sampler"
    ]
   },
   {
@@ -15,10 +15,10 @@
    },
    "outputs": [],
    "source": [
-    "library(ibdibsR)\n",
+    "library(EVICORD)\n",
     "library(ggplot2)\n",
     "library(dplyr)\n",
-    "setwd(\"./ibdibsR/example\")"
+    "setwd(\"./EVICORD/example\")"
    ]
   },
   {