Files in gehara/PipeMaster
Building and Simulating Coalescent models.
.Rbuildignore
A_pis_priors.png
Agkistrodon_example.md
DESCRIPTION
Dermatonotus_example.md
NAMESPACE
PCS_contortrix.png
PCS_piscivorus.png
PCs_mig_models.png
PCs_nomig_models.png
PipeMaster.Rproj
PipeMaster.pdf
PipeMaster_tutorial.md
PipeMaster_tutorial.pdf
PipeMaster_tutorial_PT.md
R/.Rhistory
R/.Rproj.user/3C186D39/build_options
R/.Rproj.user/3C186D39/pcs/debug-breakpoints.pper
R/.Rproj.user/3C186D39/pcs/files-pane.pper
R/.Rproj.user/3C186D39/pcs/source-pane.pper
R/.Rproj.user/3C186D39/pcs/windowlayoutstate.pper
R/.Rproj.user/3C186D39/pcs/workbench-pane.pper
R/.Rproj.user/3C186D39/persistent-state
R/.Rproj.user/3C186D39/rmd-outputs
R/.Rproj.user/3C186D39/saved_source_markers
R/.Rproj.user/3C186D39/sdb/prop/12F230F6
R/.Rproj.user/3C186D39/sdb/prop/13434328
R/.Rproj.user/3C186D39/sdb/prop/14ED0F37
R/.Rproj.user/3C186D39/sdb/prop/17CD2FCB
R/.Rproj.user/3C186D39/sdb/prop/1813E84C
R/.Rproj.user/3C186D39/sdb/prop/18152F42
R/.Rproj.user/3C186D39/sdb/prop/1D0D8758
R/.Rproj.user/3C186D39/sdb/prop/1DCDA45
R/.Rproj.user/3C186D39/sdb/prop/1DD6BB15
R/.Rproj.user/3C186D39/sdb/prop/200C2F67
R/.Rproj.user/3C186D39/sdb/prop/2326BAF3
R/.Rproj.user/3C186D39/sdb/prop/25486C3B
R/.Rproj.user/3C186D39/sdb/prop/26FEF083
R/.Rproj.user/3C186D39/sdb/prop/28C7CBBA
R/.Rproj.user/3C186D39/sdb/prop/2BE44881
R/.Rproj.user/3C186D39/sdb/prop/3051B4C4
R/.Rproj.user/3C186D39/sdb/prop/359ACE6
R/.Rproj.user/3C186D39/sdb/prop/39B31D95
R/.Rproj.user/3C186D39/sdb/prop/3A546D00
R/.Rproj.user/3C186D39/sdb/prop/427AA8F1
R/.Rproj.user/3C186D39/sdb/prop/434C5412
R/.Rproj.user/3C186D39/sdb/prop/4799D607
R/.Rproj.user/3C186D39/sdb/prop/48E6F444
R/.Rproj.user/3C186D39/sdb/prop/4A4AF57A
R/.Rproj.user/3C186D39/sdb/prop/4D93CBA8
R/.Rproj.user/3C186D39/sdb/prop/4FF2C451
R/.Rproj.user/3C186D39/sdb/prop/507715C9
R/.Rproj.user/3C186D39/sdb/prop/508973B8
R/.Rproj.user/3C186D39/sdb/prop/50F2A67
R/.Rproj.user/3C186D39/sdb/prop/517BC41A
R/.Rproj.user/3C186D39/sdb/prop/51A33895
R/.Rproj.user/3C186D39/sdb/prop/532CD7D
R/.Rproj.user/3C186D39/sdb/prop/547DFA26
R/.Rproj.user/3C186D39/sdb/prop/56B245FC
R/.Rproj.user/3C186D39/sdb/prop/622CD3D1
R/.Rproj.user/3C186D39/sdb/prop/62A826C9
R/.Rproj.user/3C186D39/sdb/prop/6557C3C2
R/.Rproj.user/3C186D39/sdb/prop/6ADBC499
R/.Rproj.user/3C186D39/sdb/prop/702EB655
R/.Rproj.user/3C186D39/sdb/prop/705B37DA
R/.Rproj.user/3C186D39/sdb/prop/738810B3
R/.Rproj.user/3C186D39/sdb/prop/74056E52
R/.Rproj.user/3C186D39/sdb/prop/7608D7CA
R/.Rproj.user/3C186D39/sdb/prop/770A7CD3
R/.Rproj.user/3C186D39/sdb/prop/7C2DF0D9
R/.Rproj.user/3C186D39/sdb/prop/83C4DF4F
R/.Rproj.user/3C186D39/sdb/prop/86DEB0C0
R/.Rproj.user/3C186D39/sdb/prop/8958F7FD
R/.Rproj.user/3C186D39/sdb/prop/8A8D8125
R/.Rproj.user/3C186D39/sdb/prop/8B06A227
R/.Rproj.user/3C186D39/sdb/prop/8C14858B
R/.Rproj.user/3C186D39/sdb/prop/8C15EBD9
R/.Rproj.user/3C186D39/sdb/prop/8D99CA22
R/.Rproj.user/3C186D39/sdb/prop/8F98F120
R/.Rproj.user/3C186D39/sdb/prop/903ECB75
R/.Rproj.user/3C186D39/sdb/prop/905187F1
R/.Rproj.user/3C186D39/sdb/prop/92CE5241
R/.Rproj.user/3C186D39/sdb/prop/96D9377C
R/.Rproj.user/3C186D39/sdb/prop/985D0699
R/.Rproj.user/3C186D39/sdb/prop/993ED111
R/.Rproj.user/3C186D39/sdb/prop/9BB28B29
R/.Rproj.user/3C186D39/sdb/prop/9C8A5ADE
R/.Rproj.user/3C186D39/sdb/prop/9E69AA44
R/.Rproj.user/3C186D39/sdb/prop/A654139A
R/.Rproj.user/3C186D39/sdb/prop/A723143C
R/.Rproj.user/3C186D39/sdb/prop/A78FAA44
R/.Rproj.user/3C186D39/sdb/prop/AAA500
R/.Rproj.user/3C186D39/sdb/prop/AAF33021
R/.Rproj.user/3C186D39/sdb/prop/ABC35CDD
R/.Rproj.user/3C186D39/sdb/prop/B0367CEE
R/.Rproj.user/3C186D39/sdb/prop/B08BE1CC
R/.Rproj.user/3C186D39/sdb/prop/B0C62F93
R/.Rproj.user/3C186D39/sdb/prop/B1A62759
R/.Rproj.user/3C186D39/sdb/prop/B1B74052
R/.Rproj.user/3C186D39/sdb/prop/B3E0DB31
R/.Rproj.user/3C186D39/sdb/prop/B5F3F57
R/.Rproj.user/3C186D39/sdb/prop/B778D7A1
R/.Rproj.user/3C186D39/sdb/prop/B822DE4B
R/.Rproj.user/3C186D39/sdb/prop/B870924E
R/.Rproj.user/3C186D39/sdb/prop/BA458DC9
R/.Rproj.user/3C186D39/sdb/prop/BC398155
R/.Rproj.user/3C186D39/sdb/prop/BC63E8CE
R/.Rproj.user/3C186D39/sdb/prop/BED1C328
R/.Rproj.user/3C186D39/sdb/prop/BF03D11E
R/.Rproj.user/3C186D39/sdb/prop/C1BEF9F5
R/.Rproj.user/3C186D39/sdb/prop/C37DC869
R/.Rproj.user/3C186D39/sdb/prop/C3BA298A
R/.Rproj.user/3C186D39/sdb/prop/C5961D32
R/.Rproj.user/3C186D39/sdb/prop/C88852C3
R/.Rproj.user/3C186D39/sdb/prop/C89B3DC8
R/.Rproj.user/3C186D39/sdb/prop/C9146A89
R/.Rproj.user/3C186D39/sdb/prop/CD467D4E
R/.Rproj.user/3C186D39/sdb/prop/D0277746
R/.Rproj.user/3C186D39/sdb/prop/D08C2677
R/.Rproj.user/3C186D39/sdb/prop/D5B66ABE
R/.Rproj.user/3C186D39/sdb/prop/D6B050A8
R/.Rproj.user/3C186D39/sdb/prop/DCE59F4
R/.Rproj.user/3C186D39/sdb/prop/DE0335E4
R/.Rproj.user/3C186D39/sdb/prop/DE4D3721
R/.Rproj.user/3C186D39/sdb/prop/DF425736
R/.Rproj.user/3C186D39/sdb/prop/E0D17040
R/.Rproj.user/3C186D39/sdb/prop/E2292FB2
R/.Rproj.user/3C186D39/sdb/prop/E861078D
R/.Rproj.user/3C186D39/sdb/prop/E919676F
R/.Rproj.user/3C186D39/sdb/prop/E992E1AE
R/.Rproj.user/3C186D39/sdb/prop/EE49034C
R/.Rproj.user/3C186D39/sdb/prop/F04E4F3A
R/.Rproj.user/3C186D39/sdb/prop/F1115273
R/.Rproj.user/3C186D39/sdb/prop/F175DC
R/.Rproj.user/3C186D39/sdb/prop/F43F525B
R/.Rproj.user/3C186D39/sdb/prop/F49DC25F
R/.Rproj.user/3C186D39/sdb/prop/F58B9DD8
R/.Rproj.user/3C186D39/sdb/prop/F5BF8DA2
R/.Rproj.user/3C186D39/sdb/prop/F60FE5B6
R/.Rproj.user/3C186D39/sdb/prop/F711F1D6
R/.Rproj.user/3C186D39/sdb/prop/F748261F
R/.Rproj.user/3C186D39/sdb/prop/FA9C9A1E
R/.Rproj.user/3C186D39/sdb/prop/FCE4FA0E
R/.Rproj.user/3C186D39/sdb/prop/FE1BE9B4
R/.Rproj.user/3C186D39/sdb/prop/FEB880DF
R/.Rproj.user/3C186D39/sdb/prop/FF700BDD
R/.Rproj.user/3C186D39/sdb/prop/INDEX
R/.Rproj.user/3C186D39/session-persistent-state
R/MENU_condition.menu.R
R/MENU_demog.menu.R
R/MENU_gene.menu.R
R/MENU_genomic.menu.R
R/MENU_main.menu.R
R/MENU_mig.menu.R
R/MENU_time.menu.R
R/PipeMaster.R
R/codemography.NGS.R
R/coexpansion_CEA_TH_NCT.R
R/coexpansion_PT.R
R/coexpansion_pulses.R
R/fas2ms2.R
R/format_conversion_functions.R
R/get.data.structure.R
R/get.msABC.R
R/get.pops.R
R/get.ss.pop.name.R
R/hap.div.R
R/iPyrad.alleles.loci2fasta.R
R/ms.commander.forplot.R
R/ms.commander.snp.R
R/ms.commander2.R
R/ms.string.generator.R
R/msABC.commander.R
R/network.sim.R
R/observed.coexp.sumstat.R
R/observed.demog.sumstat.R
R/observed.sumstat.R
R/observed.sumstat.ngs.R
R/parallel.sims.R
R/parameter_samplers.R
R/phybase.dependecies.R
R/pop.planner.R
R/popassign-data.R
R/scrm.commander.R
R/seqs-data.R
R/sim.coaltrees.R
R/sim.msABC.R
R/sim.msABC.sumstat.R
R/sim.sumstat.R
R/single_pop_demog_test.R
R/visualization.tools.R
README.md
R_workshop.pdf
The_coalescent.pdf
data/A_contortrix.RData
data/A_piscivorus.RData
data/hABC.priors.RData
data/models.RData
data/observed_Dermatonotus.RData
data/popassign.RData
data/seqs.RData
hABC_manual.md
images/model.png
inst/PopPlanner.jar
inst/msABClinux
inst/msABCmac
inst/run.msABC.R
man/H.div.Rd
man/PipeMaster.Rd
man/PlotModel.Rd
man/PopPlanner.Rd
man/get.data.structure.Rd
man/get.prior.table.Rd
man/get.tree.info.Rd
man/iPyrad.alleles.loci2fasta.Rd
man/main.menu.Rd
man/ms.to.DNAbin.Rd
man/multiplot.Rd
man/obs.sumstat.ngs.Rd
man/observed.coexp.sumstat.Rd
man/observed.pw.distances.Rd
man/observed.singlepop.sumstat.Rd
man/observed.sumstat.Rd
man/plot.priors.Rd
man/plot.sim.obs.Rd
man/plotPCs.Rd
man/popassign.Rd
man/seqs.Rd
man/sim.coaltrees.Rd
man/sim.coexp.Rd
man/sim.coexp.ngs.Rd
man/sim.coexpPT.Rd
man/sim.ms.sumstat.Rd
man/sim.msABC.sanger.Rd
man/sim.msABC.sumstat.Rd
man/sim.sp.tree.Rd
man/single.pop.demog.Rd
man/update.priors.Rd
model.png
model_plot_IM.png
model_plot_Is.png
msABClinux
pca.png
priors.png
sim.obs.png
