From 08aa084b9c2d32d3517514e6d03a482b024e2607 Mon Sep 17 00:00:00 2001
From: JacobNeumann88 <jn227@nau.edu>
Date: Mon, 20 Sep 2021 05:44:59 -0700
Subject: [PATCH 1/4] Rename examples/HIVdynamics_aMCMC/pt303.bngl to
 examples/HIVdynamics_aMCMC/pt303/pt303.bngl

---
 examples/HIVdynamics_aMCMC/{ => pt303}/pt303.bngl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename examples/HIVdynamics_aMCMC/{ => pt303}/pt303.bngl (99%)

diff --git a/examples/HIVdynamics_aMCMC/pt303.bngl b/examples/HIVdynamics_aMCMC/pt303/pt303.bngl
similarity index 99%
rename from examples/HIVdynamics_aMCMC/pt303.bngl
rename to examples/HIVdynamics_aMCMC/pt303/pt303.bngl
index ca5e25d5..df321487 100644
--- a/examples/HIVdynamics_aMCMC/pt303.bngl
+++ b/examples/HIVdynamics_aMCMC/pt303/pt303.bngl
@@ -55,4 +55,4 @@ end model
 begin actions
 generate_network({overwrite=>1})
 simulate({suffix=>"pt303",method=>"ode",t_end=>36,n_steps=>36,print_functions=>1})
-end actions
\ No newline at end of file
+end actions

From 5de3f2fc3f8d39dc5241577c11652ba412611b12 Mon Sep 17 00:00:00 2001
From: JacobNeumann88 <jn227@nau.edu>
Date: Mon, 20 Sep 2021 05:46:16 -0700
Subject: [PATCH 2/4] Delete examples/HIVdynamics_aMCMC directory

---
 examples/HIVdynamics_aMCMC/README.txt         | 11 ----
 examples/HIVdynamics_aMCMC/pt303.conf         | 38 ------------
 examples/HIVdynamics_aMCMC/pt303.exp          | 10 ----
 examples/HIVdynamics_aMCMC/pt303.sh           | 25 --------
 examples/HIVdynamics_aMCMC/pt303/pt303.bngl   | 58 -------------------
 .../adaptive_files/MLE_params.txt             |  5 --
 .../pt303_output/adaptive_files/diff.txt      |  1 -
 .../adaptive_files/diffMatrix.txt             |  5 --
 examples/HIVdynamics_aMCMC/pt403.bngl         | 58 -------------------
 examples/HIVdynamics_aMCMC/pt403.conf         | 32 ----------
 examples/HIVdynamics_aMCMC/pt403.exp          | 11 ----
 examples/HIVdynamics_aMCMC/pt403.sh           | 24 --------
 .../adaptive_files/MLE_params.txt             |  5 --
 .../pt403_output/adaptive_files/diff.txt      |  1 -
 .../adaptive_files/diffMatrix.txt             |  5 --
 examples/HIVdynamics_aMCMC/pt409.bngl         | 58 -------------------
 examples/HIVdynamics_aMCMC/pt409.conf         | 32 ----------
 examples/HIVdynamics_aMCMC/pt409.exp          | 11 ----
 examples/HIVdynamics_aMCMC/pt409.sh           | 24 --------
 .../adaptive_files/MLE_params.txt             |  5 --
 .../pt409_output/adaptive_files/diff.txt      |  1 -
 .../adaptive_files/diffMatrix.txt             |  5 --
 22 files changed, 425 deletions(-)
 delete mode 100644 examples/HIVdynamics_aMCMC/README.txt
 delete mode 100644 examples/HIVdynamics_aMCMC/pt303.conf
 delete mode 100644 examples/HIVdynamics_aMCMC/pt303.exp
 delete mode 100644 examples/HIVdynamics_aMCMC/pt303.sh
 delete mode 100644 examples/HIVdynamics_aMCMC/pt303/pt303.bngl
 delete mode 100644 examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/MLE_params.txt
 delete mode 100644 examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/diff.txt
 delete mode 100644 examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/diffMatrix.txt
 delete mode 100644 examples/HIVdynamics_aMCMC/pt403.bngl
 delete mode 100644 examples/HIVdynamics_aMCMC/pt403.conf
 delete mode 100644 examples/HIVdynamics_aMCMC/pt403.exp
 delete mode 100644 examples/HIVdynamics_aMCMC/pt403.sh
 delete mode 100644 examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/MLE_params.txt
 delete mode 100644 examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/diff.txt
 delete mode 100644 examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/diffMatrix.txt
 delete mode 100644 examples/HIVdynamics_aMCMC/pt409.bngl
 delete mode 100644 examples/HIVdynamics_aMCMC/pt409.conf
 delete mode 100644 examples/HIVdynamics_aMCMC/pt409.exp
 delete mode 100644 examples/HIVdynamics_aMCMC/pt409.sh
 delete mode 100644 examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/MLE_params.txt
 delete mode 100644 examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/diff.txt
 delete mode 100644 examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/diffMatrix.txt

diff --git a/examples/HIVdynamics_aMCMC/README.txt b/examples/HIVdynamics_aMCMC/README.txt
deleted file mode 100644
index daddd6ff..00000000
--- a/examples/HIVdynamics_aMCMC/README.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-A model parameterization of the two-phase exponential decay model for viral dynamics under therapy 
-generated from published models (1,2).
-
-The first run was done for 100000 iterations to find a suitable covariance matrix and to find convergence. 
-The Warm start following was ran for 200000 total iterations and was able to properly sample the posterior distribution. 
-The configuration of the warm start was preserved and can be found in the configuration file in this folder. 
-The calculated covariance matrix and diffusivity was also saved and can be found in the associated output folder under the adaptive_files
-subdirectory.
-
-1. Perelson,A.S. et al. (1996) HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science, 271, 1582–1586.
-2. Ho,D.D. et al. (1995) Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature, 373, 123–126.
diff --git a/examples/HIVdynamics_aMCMC/pt303.conf b/examples/HIVdynamics_aMCMC/pt303.conf
deleted file mode 100644
index 8fdfb58c..00000000
--- a/examples/HIVdynamics_aMCMC/pt303.conf
+++ /dev/null
@@ -1,38 +0,0 @@
-# A fitting job 
-
-# The directory to which job output will be written
-output_dir=pt303_output
-
-# Model specification
-model = pt303.bngl : pt303.exp
-
-# BNG command - Uncomment and edit this line if you have not set the BNGPATH environment variable
-# bng_command = /path/to/bng2/BNG2.pl
-bng_command = /projects/posner_lab/BioNetGen-2.3.1/BNG2.pl
-
-# Algorithm and objective function choice
-fit_type = am
-objfunc = chi_sq_dynamic # log-normally distributed measurement errors
-
-# Parameters
-uniform_var = A__FREE 0 1
-uniform_var = d1__FREE 0 1
-uniform_var = d2__FREE 0 1
-uniform_var = V0__FREE 0 2000
-uniform_var = sigma__FREE 0 10
-
-# Differential Evolution Parameters
-population_size = 1
-max_iterations = 200000
-adaptive = 50000
-burn_in = 50000
-sample_every = 1
-continue_run = 1
-# Print output to command line
-verbosity = 2
-output_trajectory = lnV
-#starting_params = 0.03826989611517974  0.011463396349503325 0.2337208278613696 88.3204517124641 0.4997243627804076
-
-
-
-
diff --git a/examples/HIVdynamics_aMCMC/pt303.exp b/examples/HIVdynamics_aMCMC/pt303.exp
deleted file mode 100644
index 2c305e56..00000000
--- a/examples/HIVdynamics_aMCMC/pt303.exp
+++ /dev/null
@@ -1,10 +0,0 @@
-# time	lnV
-  0	4.364645373
-  3	4.419146669
-  8	4.323485541
-  11	3.96468535
-  15	2.807668275
-  18	2.183458132
-  22	1.55726096
-  29	1.222021223
-  36	0.916870744
diff --git a/examples/HIVdynamics_aMCMC/pt303.sh b/examples/HIVdynamics_aMCMC/pt303.sh
deleted file mode 100644
index 2c4ee1a2..00000000
--- a/examples/HIVdynamics_aMCMC/pt303.sh
+++ /dev/null
@@ -1,25 +0,0 @@
-#!/bin/bash
-# Example batch script for running MCMC for the degranulation model on a SLURM cluster
-
-# set the number of nodesT
-#SBATCH --nodes=1
-
-# set the number of cpus per node.
-#SBATCH --mincpus=24
-
-#SBATCH --mem=100G
-
-# set max wallclock time for the entire fitting job (3 days)
-#SBATCH --time=2-00:00:00
-
-# set name of job
-#SBATCH --job-name=pybnf
-
-# Enable Anaconda Python 3.5
-# Your cluster might require something different here, or might not require anything. 
-module purge
-module load anaconda3/2020.02
-
-# Run PyBNF
-pybnf -c pt303.conf -t SLURM -o
-
diff --git a/examples/HIVdynamics_aMCMC/pt303/pt303.bngl b/examples/HIVdynamics_aMCMC/pt303/pt303.bngl
deleted file mode 100644
index df321487..00000000
--- a/examples/HIVdynamics_aMCMC/pt303/pt303.bngl
+++ /dev/null
@@ -1,58 +0,0 @@
-begin model
-# pt303
-# c = 0.20 /d t_1/2 = 3.5 d (inferred)
-# c = 0.21 /d t_1/2 = 3.3 d (published estimates)
-begin parameters
-
-##########################################
-A A__FREE # dimensionless
-d1 d1__FREE # /d
-d2 d2__FREE # /d
-V0 V0__FREE # copies per mL 
-sigma sigma__FREE
-end parameters
-begin molecule types
-counter()
-end molecule types
-begin seed species
-counter() 0
-end seed species
-begin observables
-Molecules t counter()
-end observables
-begin functions
-V()=if(t>=7,if(d2<d1,V0*(A*exp(-d1*(t-7))+(1-A)*exp(-d2*(t-7))),V0*(A*exp(-d2*(t-7))+(1-A)*exp(-d1*(t-7)))),V0)
-lnV()=if(t>=7,if(d2<d1,ln(V0*(A*exp(-d1*(t-7))+(1-A)*exp(-d2*(t-7)))),ln(V0*(A*exp(-d2*(t-7))+(1-A)*exp(-d1*(t-7))))),ln(V0))
-S()=if(d2<d1,-d1*A-d2*(1-A),-d2*A-d1*(1-A))
-c()=if(d2<d1,d1*A+d2*(1-A),d2*A+d1*(1-A))
-half_life()=if(d2<d1,ln(2)/(d1*A+d2*(1-A)),ln(2)/(d2*A+d1*(1-A)))
-lnV_tangent()=if(t>=7,if(d2<d1,ln(V0)+(-d1*A-d2*(1-A))*(t-7),ln(V0)+(-d2*A-d1*(1-A))*(t-7)),ln(V0))
-Vdat()=if(t<=0,78.6,\
-       if(t<=3,83.0,\
-       if(t<=8,75.4,\
-       if(t<=11,52.7,\
-       if(t<=15,16.6,\
-       if(t<=18,8.88,\
-       if(t<=22,4.75,\
-       if(t<=29,3.39,\
-       if(t<=36,2.50,\
-       0)))))))))
-lnVdat()=if(t<=0,ln(78.6),\
-         if(t<=3,ln(83.0),\
-         if(t<=8,ln(75.4),\
-         if(t<=11,ln(52.7),\
-         if(t<=15,ln(16.6),\
-         if(t<=18,ln(8.88),\
-         if(t<=22,ln(4.75),\
-         if(t<=29,ln(3.39),\
-         if(t<=36,ln(2.50),\
-         0)))))))))
-end functions
-begin reaction rules
-0->counter() 1
-end reaction rules
-end model
-begin actions
-generate_network({overwrite=>1})
-simulate({suffix=>"pt303",method=>"ode",t_end=>36,n_steps=>36,print_functions=>1})
-end actions
diff --git a/examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/MLE_params.txt b/examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/MLE_params.txt
deleted file mode 100644
index 6f7d83bc..00000000
--- a/examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/MLE_params.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-3.167303185075419636e-01
-8.077267141191819544e-01
-1.174061781468430654e-01
-6.416328782235272854e+01
-8.718178876116529086e-01
diff --git a/examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/diff.txt b/examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/diff.txt
deleted file mode 100644
index 1e29c46c..00000000
--- a/examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/diff.txt
+++ /dev/null
@@ -1 +0,0 @@
-3.687101702274714898e-01
diff --git a/examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/diffMatrix.txt b/examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/diffMatrix.txt
deleted file mode 100644
index 11b9f598..00000000
--- a/examples/HIVdynamics_aMCMC/pt303_output/adaptive_files/diffMatrix.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-4.534231603608707140e-02 -1.477701190727046497e-02 -1.374703071185744488e-02 6.337147325554831623e-01 -1.857957734368396313e-02
--1.477701190727046497e-02 3.743919143614957840e-02 -1.807089247950567634e-02 1.041877657604289853e+00 8.633001504422676761e-03
--1.374703071185744488e-02 -1.807089247950567634e-02 3.975366791195810573e-02 1.399825245102605253e-02 8.232311272357385745e-03
-6.337147325554831623e-01 1.041877657604289853e+00 1.399825245102605253e-02 6.938050124818187214e+02 1.693955950679945532e+00
--1.857957734368396313e-02 8.633001504422676761e-03 8.232311272357385745e-03 1.693955950679945532e+00 3.131008961883107594e-02
diff --git a/examples/HIVdynamics_aMCMC/pt403.bngl b/examples/HIVdynamics_aMCMC/pt403.bngl
deleted file mode 100644
index 048facc9..00000000
--- a/examples/HIVdynamics_aMCMC/pt403.bngl
+++ /dev/null
@@ -1,58 +0,0 @@
-begin model
-# pt403
-# c = 0.23 /d t_1/2 = 3.0 d (inferred)
-# c = 0.32 /d t_1/2 = 2.2 d (published estimates)
-begin parameters
-
-##########################################
-A A__FREE # dimensionless
-d1 d1__FREE # /d
-d2 d2__FREE # /d
-V0 V0__FREE # copies per mL 
-sigma sigma__FREE
-end parameters
-begin molecule types
-counter()
-end molecule types
-begin seed species
-counter() 0
-end seed species
-begin observables
-Molecules t counter()
-end observables
-begin functions
-V()=if(t>=7,if(d2<d1,V0*(A*exp(-d1*(t-7))+(1-A)*exp(-d2*(t-7))),V0*(A*exp(-d2*(t-7))+(1-A)*exp(-d1*(t-7)))),V0)
-lnV()=if(t>=7,if(d2<d1,ln(V0*(A*exp(-d1*(t-7))+(1-A)*exp(-d2*(t-7)))),ln(V0*(A*exp(-d2*(t-7))+(1-A)*exp(-d1*(t-7))))),ln(V0))
-S()=if(d2<d1,-d1*A-d2*(1-A),-d2*A-d1*(1-A))
-c()=if(d2<d1,d1*A+d2*(1-A),d2*A+d1*(1-A))
-half_life()=if(d2<d1,ln(2)/(d1*A+d2*(1-A)),ln(2)/(d2*A+d1*(1-A)))
-lnV_tangent()=if(t>=7,if(d2<d1,ln(V0)+(-d1*A-d2*(1-A))*(t-7),ln(V0)+(-d2*A-d1*(1-A))*(t-7)),ln(V0))
-Vdat()=if(t<=0,145,\
-       if(t<=3,381,\
-       if(t<=8,245,\
-       if(t<=11,158,\
-       if(t<=15,21.0,\
-       if(t<=18,12.0,\
-       if(t<=22,8.98,\
-       if(t<=29,4.58,\
-       if(t<=36,3.42,\
-       0)))))))))
-lnVdat()=if(t<=0,ln(145),\
-         if(t<=3,ln(381),\
-         if(t<=8,ln(245),\
-         if(t<=11,ln(158),\
-         if(t<=15,ln(21.0),\
-         if(t<=18,ln(12.0),\
-         if(t<=22,ln(8.98),\
-         if(t<=29,ln(4.58),\
-         if(t<=36,ln(3.42),\
-         0)))))))))
-end functions
-begin reaction rules
-0->counter() 1
-end reaction rules
-end model
-begin actions
-generate_network({overwrite=>1})
-simulate({suffix=>"pt403",method=>"ode",t_end=>36,n_steps=>36,print_functions=>1})
-end actions
\ No newline at end of file
diff --git a/examples/HIVdynamics_aMCMC/pt403.conf b/examples/HIVdynamics_aMCMC/pt403.conf
deleted file mode 100644
index 9c67f9fe..00000000
--- a/examples/HIVdynamics_aMCMC/pt403.conf
+++ /dev/null
@@ -1,32 +0,0 @@
-# A fitting job 
-
-# The directory to which job output will be written
-output_dir=pt403_output
-
-# Model specification
-model = pt403.bngl : pt403.exp
-
-# BNG command - Uncomment and edit this line if you have not set the BNGPATH environment variable
-# bng_command = /path/to/bng2/BNG2.pl
-bng_command = /projects/posner_lab/BioNetGen-2.3.1/BNG2.pl
-# Algorithm and objective function choice
-fit_type = am
-objfunc = chi_sq_dynamic # log-normally distributed measurement errors
-
-# Parameters
-uniform_var = A__FREE 0 1
-uniform_var = d1__FREE 0 1
-uniform_var = d2__FREE 0 1
-uniform_var = V0__FREE 0 2000
-uniform_var = sigma__FREE 0 10
-# Differential Evolution Parameters
-population_size = 1
-adaptive = 50000
-burn_in = 50000
-sample_every = 1
-max_iterations = 200000
-step_size = 0.01
-continue_run = 1
-# Print output to command line
-verbosity = 2
-output_trajectory = lnV
\ No newline at end of file
diff --git a/examples/HIVdynamics_aMCMC/pt403.exp b/examples/HIVdynamics_aMCMC/pt403.exp
deleted file mode 100644
index b418356c..00000000
--- a/examples/HIVdynamics_aMCMC/pt403.exp
+++ /dev/null
@@ -1,11 +0,0 @@
-# time	lnV
-  0	4.975925412
-  3	5.941840347
-  8	5.502788103
-  11	5.06373586
-  15	3.044095546
-  18	2.487962707
-  22	2.195261213
-  29	1.522047773
-  36	1.229346278
-
diff --git a/examples/HIVdynamics_aMCMC/pt403.sh b/examples/HIVdynamics_aMCMC/pt403.sh
deleted file mode 100644
index d634609b..00000000
--- a/examples/HIVdynamics_aMCMC/pt403.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/bin/bash
-# Example batch script for running MCMC for the degranulation model on a SLURM cluster
-
-# set the number of nodesT
-#SBATCH --nodes=1
-
-# set the number of cpus per node.
-#SBATCH --mincpus=24
-
-#SBATCH --mem=100G
-
-# set max wallclock time for the entire fitting job (3 days)
-#SBATCH --time=01-00:00:00
-
-# set name of job
-#SBATCH --job-name=pybnf
-
-# Enable Anaconda Python 3.5
-# Your cluster might require something different here, or might not require anything. 
-module purge
-module load anaconda3/2020.02
-
-# Run PyBNF
-pybnf -c pt403.conf -t SLURM -o
\ No newline at end of file
diff --git a/examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/MLE_params.txt b/examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/MLE_params.txt
deleted file mode 100644
index 169d36e8..00000000
--- a/examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/MLE_params.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-7.696715061334600261e-01
-7.547077514911814111e-01
-1.126676003661507136e-01
-3.069470715622069292e+02
-4.789248532738739073e-01
diff --git a/examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/diff.txt b/examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/diff.txt
deleted file mode 100644
index e49da49d..00000000
--- a/examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/diff.txt
+++ /dev/null
@@ -1 +0,0 @@
-3.281168740816535201e-01
diff --git a/examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/diffMatrix.txt b/examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/diffMatrix.txt
deleted file mode 100644
index 8a6674a3..00000000
--- a/examples/HIVdynamics_aMCMC/pt403_output/adaptive_files/diffMatrix.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-5.667071652461928150e-02 -7.476167659567871382e-03 -9.691003516377902360e-03 8.539085617392863981e+00 -1.995888550110734572e-02
--7.476167659567871382e-03 6.187943061366321662e-02 -3.992057253876794831e-02 5.511823653704621684e+00 4.216652555757505541e-03
--9.691003516377902360e-03 -3.992057253876794831e-02 6.963562104187673296e-02 3.833024003057170059e+00 1.102011090945406377e-02
-8.539085617392863981e+00 5.511823653704621684e+00 3.833024003057170059e+00 2.895074534531007157e+04 1.599958105614667758e+01
--1.995888550110734572e-02 4.216652555757505541e-03 1.102011090945406377e-02 1.599958105614667758e+01 8.526939850195920656e-02
diff --git a/examples/HIVdynamics_aMCMC/pt409.bngl b/examples/HIVdynamics_aMCMC/pt409.bngl
deleted file mode 100644
index cc5ebaf9..00000000
--- a/examples/HIVdynamics_aMCMC/pt409.bngl
+++ /dev/null
@@ -1,58 +0,0 @@
-begin model
-# pt409
-# c = 0.39 /d t_1/2 = 1.8 d (inferred)
-# c = 0.47 /d t_1/2 = 1.5 d (published estimates)
-begin parameters
-
-##########################################
-A A__FREE # dimensionless
-d1 d1__FREE # /d
-d2 d2__FREE # /d
-V0 V0__FREE # copies per mL
-sigma sigma__FREE
-end parameters
-begin molecule types
-counter()
-end molecule types
-begin seed species
-counter() 0
-end seed species
-begin observables
-Molecules t counter()
-end observables
-begin functions
-V()=if(t>=7,if(d2<d1,V0*(A*exp(-d1*(t-7))+(1-A)*exp(-d2*(t-7))),V0*(A*exp(-d2*(t-7))+(1-A)*exp(-d1*(t-7)))),V0)
-lnV()=if(t>=7,if(d2<d1,ln(V0*(A*exp(-d1*(t-7))+(1-A)*exp(-d2*(t-7)))),ln(V0*(A*exp(-d2*(t-7))+(1-A)*exp(-d1*(t-7))))),ln(V0))
-S()=if(d2<d1,-d1*A-d2*(1-A),-d2*A-d1*(1-A))
-c()=if(d2<d1,d1*A+d2*(1-A),d2*A+d1*(1-A))
-half_life()=if(d2<d1,ln(2)/(d1*A+d2*(1-A)),ln(2)/(d2*A+d1*(1-A)))
-lnV_tangent()=if(t>=7,if(d2<d1,ln(V0)+(-d1*A-d2*(1-A))*(t-7),ln(V0)+(-d2*A-d1*(1-A))*(t-7)),ln(V0))
-Vdat()=if(t<=0,406,\
-       if(t<=3,541,\
-       if(t<=8,555,\
-       if(t<=12,109,\
-       if(t<=15,12.7,\
-       if(t<=19,5.45,\
-       if(t<=22,8.17,\
-       if(t<=29,2.20,\
-       if(t<=36,1.89,\
-       0)))))))))
-lnVdat()=if(t<=0,ln(406),\
-         if(t<=3,ln(541),\
-         if(t<=8,ln(555),\
-         if(t<=12,ln(109),\
-         if(t<=15,ln(12.7),\
-         if(t<=19,ln(5.45),\
-         if(t<=22,ln(8.17),\
-         if(t<=29,ln(2.20),\
-         if(t<=36,ln(1.89),\
-         0)))))))))
-end functions
-begin reaction rules
-0->counter() 1
-end reaction rules
-end model
-begin actions
-generate_network({overwrite=>1})
-simulate({suffix=>"pt409",method=>"ode",t_end=>36,n_steps=>36,print_functions=>1})
-end actions
\ No newline at end of file
diff --git a/examples/HIVdynamics_aMCMC/pt409.conf b/examples/HIVdynamics_aMCMC/pt409.conf
deleted file mode 100644
index c62ed8eb..00000000
--- a/examples/HIVdynamics_aMCMC/pt409.conf
+++ /dev/null
@@ -1,32 +0,0 @@
-# A fitting job 
-
-# The directory to which job output will be writte
-output_dir=pt409_output
-
-# Model specification
-model = pt409.bngl : pt409.exp
-
-# BNG command - Uncomment and edit this line if you have not set the BNGPATH environment variable
-# bng_command = /path/to/bng2/BNG2.pl
-bng_command = /projects/posner_lab/BioNetGen-2.3.1/BNG2.pl
-
-# Algorithm and objective function choice
-fit_type = am
-objfunc = chi_sq_dynamic # log-normally distributed measurement errors
-
-# Parameters
-uniform_var = A__FREE 0 1
-uniform_var = d1__FREE 0 1
-uniform_var = d2__FREE 0 1
-uniform_var = V0__FREE 0 2000
-uniform_var = sigma__FREE 0 10
-# Differential Evolution Parameters
-population_size = 1
-max_iterations = 200000
-adaptive = 50000
-burn_in = 50000
-sample_every = 1
-continue_run = 1
-# Print output to command line
-verbosity = 2
-output_trajectory = lnVV
\ No newline at end of file
diff --git a/examples/HIVdynamics_aMCMC/pt409.exp b/examples/HIVdynamics_aMCMC/pt409.exp
deleted file mode 100644
index 5741499e..00000000
--- a/examples/HIVdynamics_aMCMC/pt409.exp
+++ /dev/null
@@ -1,11 +0,0 @@
-# time	lnV
-  0	6.005743917
-  3	6.293888384
-  8	6.319127314
-  12	4.690795598
-  15	2.540999515
-  19	1.696336617
-  22	2.100580166
-  29	0.789417684
-  36	0.639105827
-
diff --git a/examples/HIVdynamics_aMCMC/pt409.sh b/examples/HIVdynamics_aMCMC/pt409.sh
deleted file mode 100644
index 3170b02f..00000000
--- a/examples/HIVdynamics_aMCMC/pt409.sh
+++ /dev/null
@@ -1,24 +0,0 @@
-#!/bin/bash
-# Example batch script for running MCMC for the degranulation model on a SLURM cluster
-
-# set the number of nodesT
-#SBATCH --nodes=1
-
-# set the number of cpus per node.
-#SBATCH --mincpus=24
-
-#SBATCH --mem=100G
-
-# set max wallclock time for the entire fitting job (3 days)
-#SBATCH --time=01-00:00:00
-
-# set name of job
-#SBATCH --job-name=pybnf
-
-# Enable Anaconda Python 3.5
-# Your cluster might require something different here, or might not require anything. 
-module purge
-module load anaconda3/2020.02
-
-# Run PyBNF
-pybnf -c pt409.conf -t SLURM -r
\ No newline at end of file
diff --git a/examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/MLE_params.txt b/examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/MLE_params.txt
deleted file mode 100644
index aacf4ca5..00000000
--- a/examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/MLE_params.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-5.815154742159475143e-01
-2.077101485011013104e-01
-7.531376976448787008e-01
-4.146112609127258111e+02
-1.163680133793883575e+00
diff --git a/examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/diff.txt b/examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/diff.txt
deleted file mode 100644
index d09c5615..00000000
--- a/examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/diff.txt
+++ /dev/null
@@ -1 +0,0 @@
-3.024784199024603271e-01
diff --git a/examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/diffMatrix.txt b/examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/diffMatrix.txt
deleted file mode 100644
index aefcb2c6..00000000
--- a/examples/HIVdynamics_aMCMC/pt409_output/adaptive_files/diffMatrix.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-4.534840873640461761e-02 -4.299119108419427633e-03 -5.507425699247604084e-03 1.407422925385709256e+01 -3.623749922985950583e-02
--4.299119108419427633e-03 7.120008709763162025e-02 -5.280387730304320765e-02 1.101711924308618684e+01 5.788169077317549191e-03
--5.507425699247604084e-03 -5.280387730304320765e-02 7.330555144133350798e-02 4.480470417752079548e+00 7.506833995255870855e-03
-1.407422925385709256e+01 1.101711924308618684e+01 4.480470417752079548e+00 9.106859090005641337e+04 1.650499769303362285e+01
--3.623749922985950583e-02 5.788169077317549191e-03 7.506833995255870855e-03 1.650499769303362285e+01 1.349485952045679782e-01

From 1b91a2936be4683ea5675fd18fac5175888d93f5 Mon Sep 17 00:00:00 2001
From: JacobNeumann88 <jn227@nau.edu>
Date: Mon, 20 Sep 2021 05:48:32 -0700
Subject: [PATCH 3/4] Add files via upload

---
 examples/HIVdynamics_aMCMC/README.txt         | 13 +++++
 examples/HIVdynamics_aMCMC/pt303/pt303.bngl   | 58 +++++++++++++++++++
 examples/HIVdynamics_aMCMC/pt303/pt303.conf   | 38 ++++++++++++
 examples/HIVdynamics_aMCMC/pt303/pt303.exp    | 10 ++++
 examples/HIVdynamics_aMCMC/pt303/pt303.sh     | 25 ++++++++
 .../adaptive_files/MLE_params.txt             |  5 ++
 .../pt303_output/adaptive_files/diff.txt      |  1 +
 .../adaptive_files/diffMatrix.txt             |  5 ++
 examples/HIVdynamics_aMCMC/pt403/pt403.bngl   | 58 +++++++++++++++++++
 examples/HIVdynamics_aMCMC/pt403/pt403.conf   | 32 ++++++++++
 examples/HIVdynamics_aMCMC/pt403/pt403.exp    | 11 ++++
 examples/HIVdynamics_aMCMC/pt403/pt403.sh     | 24 ++++++++
 .../adaptive_files/MLE_params.txt             |  5 ++
 .../pt403_output/adaptive_files/diff.txt      |  1 +
 .../adaptive_files/diffMatrix.txt             |  5 ++
 examples/HIVdynamics_aMCMC/pt409/pt409.bngl   | 58 +++++++++++++++++++
 examples/HIVdynamics_aMCMC/pt409/pt409.conf   | 32 ++++++++++
 examples/HIVdynamics_aMCMC/pt409/pt409.exp    | 11 ++++
 examples/HIVdynamics_aMCMC/pt409/pt409.sh     | 24 ++++++++
 .../adaptive_files/MLE_params.txt             |  5 ++
 .../pt409_output/adaptive_files/diff.txt      |  1 +
 .../adaptive_files/diffMatrix.txt             |  5 ++
 22 files changed, 427 insertions(+)
 create mode 100644 examples/HIVdynamics_aMCMC/README.txt
 create mode 100644 examples/HIVdynamics_aMCMC/pt303/pt303.bngl
 create mode 100644 examples/HIVdynamics_aMCMC/pt303/pt303.conf
 create mode 100644 examples/HIVdynamics_aMCMC/pt303/pt303.exp
 create mode 100644 examples/HIVdynamics_aMCMC/pt303/pt303.sh
 create mode 100644 examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/MLE_params.txt
 create mode 100644 examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/diff.txt
 create mode 100644 examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/diffMatrix.txt
 create mode 100644 examples/HIVdynamics_aMCMC/pt403/pt403.bngl
 create mode 100644 examples/HIVdynamics_aMCMC/pt403/pt403.conf
 create mode 100644 examples/HIVdynamics_aMCMC/pt403/pt403.exp
 create mode 100644 examples/HIVdynamics_aMCMC/pt403/pt403.sh
 create mode 100644 examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/MLE_params.txt
 create mode 100644 examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/diff.txt
 create mode 100644 examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/diffMatrix.txt
 create mode 100644 examples/HIVdynamics_aMCMC/pt409/pt409.bngl
 create mode 100644 examples/HIVdynamics_aMCMC/pt409/pt409.conf
 create mode 100644 examples/HIVdynamics_aMCMC/pt409/pt409.exp
 create mode 100644 examples/HIVdynamics_aMCMC/pt409/pt409.sh
 create mode 100644 examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/MLE_params.txt
 create mode 100644 examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/diff.txt
 create mode 100644 examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/diffMatrix.txt

diff --git a/examples/HIVdynamics_aMCMC/README.txt b/examples/HIVdynamics_aMCMC/README.txt
new file mode 100644
index 00000000..d1794f85
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/README.txt
@@ -0,0 +1,13 @@
+A model parameterization of the two-phase exponential decay model for viral dynamics under therapy 
+generated from the following publications (1,2).
+
+The first run was done for 100000 iterations to find a suitable covariance matrix and to find convergence. 
+The Warm start following was ran for 200000 total iterations and was able to properly sample the posterior distribution. 
+The configuration of the warm start was preserved and can be found in the configuration file in this folder. 
+The calculated covariance matrix and diffusivity was also saved and can be found in the associated output folder under the adaptive_files
+subdirectory.
+
+A full description of the model can be found in the supplementary methods.
+
+1. Perelson,A.S. et al. (1996) HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science, 271, 1582–1586.
+2. Ho,D.D. et al. (1995) Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature, 373, 123–126.
diff --git a/examples/HIVdynamics_aMCMC/pt303/pt303.bngl b/examples/HIVdynamics_aMCMC/pt303/pt303.bngl
new file mode 100644
index 00000000..ca5e25d5
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt303/pt303.bngl
@@ -0,0 +1,58 @@
+begin model
+# pt303
+# c = 0.20 /d t_1/2 = 3.5 d (inferred)
+# c = 0.21 /d t_1/2 = 3.3 d (published estimates)
+begin parameters
+
+##########################################
+A A__FREE # dimensionless
+d1 d1__FREE # /d
+d2 d2__FREE # /d
+V0 V0__FREE # copies per mL 
+sigma sigma__FREE
+end parameters
+begin molecule types
+counter()
+end molecule types
+begin seed species
+counter() 0
+end seed species
+begin observables
+Molecules t counter()
+end observables
+begin functions
+V()=if(t>=7,if(d2<d1,V0*(A*exp(-d1*(t-7))+(1-A)*exp(-d2*(t-7))),V0*(A*exp(-d2*(t-7))+(1-A)*exp(-d1*(t-7)))),V0)
+lnV()=if(t>=7,if(d2<d1,ln(V0*(A*exp(-d1*(t-7))+(1-A)*exp(-d2*(t-7)))),ln(V0*(A*exp(-d2*(t-7))+(1-A)*exp(-d1*(t-7))))),ln(V0))
+S()=if(d2<d1,-d1*A-d2*(1-A),-d2*A-d1*(1-A))
+c()=if(d2<d1,d1*A+d2*(1-A),d2*A+d1*(1-A))
+half_life()=if(d2<d1,ln(2)/(d1*A+d2*(1-A)),ln(2)/(d2*A+d1*(1-A)))
+lnV_tangent()=if(t>=7,if(d2<d1,ln(V0)+(-d1*A-d2*(1-A))*(t-7),ln(V0)+(-d2*A-d1*(1-A))*(t-7)),ln(V0))
+Vdat()=if(t<=0,78.6,\
+       if(t<=3,83.0,\
+       if(t<=8,75.4,\
+       if(t<=11,52.7,\
+       if(t<=15,16.6,\
+       if(t<=18,8.88,\
+       if(t<=22,4.75,\
+       if(t<=29,3.39,\
+       if(t<=36,2.50,\
+       0)))))))))
+lnVdat()=if(t<=0,ln(78.6),\
+         if(t<=3,ln(83.0),\
+         if(t<=8,ln(75.4),\
+         if(t<=11,ln(52.7),\
+         if(t<=15,ln(16.6),\
+         if(t<=18,ln(8.88),\
+         if(t<=22,ln(4.75),\
+         if(t<=29,ln(3.39),\
+         if(t<=36,ln(2.50),\
+         0)))))))))
+end functions
+begin reaction rules
+0->counter() 1
+end reaction rules
+end model
+begin actions
+generate_network({overwrite=>1})
+simulate({suffix=>"pt303",method=>"ode",t_end=>36,n_steps=>36,print_functions=>1})
+end actions
\ No newline at end of file
diff --git a/examples/HIVdynamics_aMCMC/pt303/pt303.conf b/examples/HIVdynamics_aMCMC/pt303/pt303.conf
new file mode 100644
index 00000000..8fdfb58c
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt303/pt303.conf
@@ -0,0 +1,38 @@
+# A fitting job 
+
+# The directory to which job output will be written
+output_dir=pt303_output
+
+# Model specification
+model = pt303.bngl : pt303.exp
+
+# BNG command - Uncomment and edit this line if you have not set the BNGPATH environment variable
+# bng_command = /path/to/bng2/BNG2.pl
+bng_command = /projects/posner_lab/BioNetGen-2.3.1/BNG2.pl
+
+# Algorithm and objective function choice
+fit_type = am
+objfunc = chi_sq_dynamic # log-normally distributed measurement errors
+
+# Parameters
+uniform_var = A__FREE 0 1
+uniform_var = d1__FREE 0 1
+uniform_var = d2__FREE 0 1
+uniform_var = V0__FREE 0 2000
+uniform_var = sigma__FREE 0 10
+
+# Differential Evolution Parameters
+population_size = 1
+max_iterations = 200000
+adaptive = 50000
+burn_in = 50000
+sample_every = 1
+continue_run = 1
+# Print output to command line
+verbosity = 2
+output_trajectory = lnV
+#starting_params = 0.03826989611517974  0.011463396349503325 0.2337208278613696 88.3204517124641 0.4997243627804076
+
+
+
+
diff --git a/examples/HIVdynamics_aMCMC/pt303/pt303.exp b/examples/HIVdynamics_aMCMC/pt303/pt303.exp
new file mode 100644
index 00000000..2c305e56
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt303/pt303.exp
@@ -0,0 +1,10 @@
+# time	lnV
+  0	4.364645373
+  3	4.419146669
+  8	4.323485541
+  11	3.96468535
+  15	2.807668275
+  18	2.183458132
+  22	1.55726096
+  29	1.222021223
+  36	0.916870744
diff --git a/examples/HIVdynamics_aMCMC/pt303/pt303.sh b/examples/HIVdynamics_aMCMC/pt303/pt303.sh
new file mode 100644
index 00000000..2c4ee1a2
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt303/pt303.sh
@@ -0,0 +1,25 @@
+#!/bin/bash
+# Example batch script for running MCMC for the degranulation model on a SLURM cluster
+
+# set the number of nodesT
+#SBATCH --nodes=1
+
+# set the number of cpus per node.
+#SBATCH --mincpus=24
+
+#SBATCH --mem=100G
+
+# set max wallclock time for the entire fitting job (3 days)
+#SBATCH --time=2-00:00:00
+
+# set name of job
+#SBATCH --job-name=pybnf
+
+# Enable Anaconda Python 3.5
+# Your cluster might require something different here, or might not require anything. 
+module purge
+module load anaconda3/2020.02
+
+# Run PyBNF
+pybnf -c pt303.conf -t SLURM -o
+
diff --git a/examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/MLE_params.txt b/examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/MLE_params.txt
new file mode 100644
index 00000000..6f7d83bc
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/MLE_params.txt
@@ -0,0 +1,5 @@
+3.167303185075419636e-01
+8.077267141191819544e-01
+1.174061781468430654e-01
+6.416328782235272854e+01
+8.718178876116529086e-01
diff --git a/examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/diff.txt b/examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/diff.txt
new file mode 100644
index 00000000..1e29c46c
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/diff.txt
@@ -0,0 +1 @@
+3.687101702274714898e-01
diff --git a/examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/diffMatrix.txt b/examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/diffMatrix.txt
new file mode 100644
index 00000000..11b9f598
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt303/pt303_output/adaptive_files/diffMatrix.txt
@@ -0,0 +1,5 @@
+4.534231603608707140e-02 -1.477701190727046497e-02 -1.374703071185744488e-02 6.337147325554831623e-01 -1.857957734368396313e-02
+-1.477701190727046497e-02 3.743919143614957840e-02 -1.807089247950567634e-02 1.041877657604289853e+00 8.633001504422676761e-03
+-1.374703071185744488e-02 -1.807089247950567634e-02 3.975366791195810573e-02 1.399825245102605253e-02 8.232311272357385745e-03
+6.337147325554831623e-01 1.041877657604289853e+00 1.399825245102605253e-02 6.938050124818187214e+02 1.693955950679945532e+00
+-1.857957734368396313e-02 8.633001504422676761e-03 8.232311272357385745e-03 1.693955950679945532e+00 3.131008961883107594e-02
diff --git a/examples/HIVdynamics_aMCMC/pt403/pt403.bngl b/examples/HIVdynamics_aMCMC/pt403/pt403.bngl
new file mode 100644
index 00000000..048facc9
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt403/pt403.bngl
@@ -0,0 +1,58 @@
+begin model
+# pt403
+# c = 0.23 /d t_1/2 = 3.0 d (inferred)
+# c = 0.32 /d t_1/2 = 2.2 d (published estimates)
+begin parameters
+
+##########################################
+A A__FREE # dimensionless
+d1 d1__FREE # /d
+d2 d2__FREE # /d
+V0 V0__FREE # copies per mL 
+sigma sigma__FREE
+end parameters
+begin molecule types
+counter()
+end molecule types
+begin seed species
+counter() 0
+end seed species
+begin observables
+Molecules t counter()
+end observables
+begin functions
+V()=if(t>=7,if(d2<d1,V0*(A*exp(-d1*(t-7))+(1-A)*exp(-d2*(t-7))),V0*(A*exp(-d2*(t-7))+(1-A)*exp(-d1*(t-7)))),V0)
+lnV()=if(t>=7,if(d2<d1,ln(V0*(A*exp(-d1*(t-7))+(1-A)*exp(-d2*(t-7)))),ln(V0*(A*exp(-d2*(t-7))+(1-A)*exp(-d1*(t-7))))),ln(V0))
+S()=if(d2<d1,-d1*A-d2*(1-A),-d2*A-d1*(1-A))
+c()=if(d2<d1,d1*A+d2*(1-A),d2*A+d1*(1-A))
+half_life()=if(d2<d1,ln(2)/(d1*A+d2*(1-A)),ln(2)/(d2*A+d1*(1-A)))
+lnV_tangent()=if(t>=7,if(d2<d1,ln(V0)+(-d1*A-d2*(1-A))*(t-7),ln(V0)+(-d2*A-d1*(1-A))*(t-7)),ln(V0))
+Vdat()=if(t<=0,145,\
+       if(t<=3,381,\
+       if(t<=8,245,\
+       if(t<=11,158,\
+       if(t<=15,21.0,\
+       if(t<=18,12.0,\
+       if(t<=22,8.98,\
+       if(t<=29,4.58,\
+       if(t<=36,3.42,\
+       0)))))))))
+lnVdat()=if(t<=0,ln(145),\
+         if(t<=3,ln(381),\
+         if(t<=8,ln(245),\
+         if(t<=11,ln(158),\
+         if(t<=15,ln(21.0),\
+         if(t<=18,ln(12.0),\
+         if(t<=22,ln(8.98),\
+         if(t<=29,ln(4.58),\
+         if(t<=36,ln(3.42),\
+         0)))))))))
+end functions
+begin reaction rules
+0->counter() 1
+end reaction rules
+end model
+begin actions
+generate_network({overwrite=>1})
+simulate({suffix=>"pt403",method=>"ode",t_end=>36,n_steps=>36,print_functions=>1})
+end actions
\ No newline at end of file
diff --git a/examples/HIVdynamics_aMCMC/pt403/pt403.conf b/examples/HIVdynamics_aMCMC/pt403/pt403.conf
new file mode 100644
index 00000000..9c67f9fe
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt403/pt403.conf
@@ -0,0 +1,32 @@
+# A fitting job 
+
+# The directory to which job output will be written
+output_dir=pt403_output
+
+# Model specification
+model = pt403.bngl : pt403.exp
+
+# BNG command - Uncomment and edit this line if you have not set the BNGPATH environment variable
+# bng_command = /path/to/bng2/BNG2.pl
+bng_command = /projects/posner_lab/BioNetGen-2.3.1/BNG2.pl
+# Algorithm and objective function choice
+fit_type = am
+objfunc = chi_sq_dynamic # log-normally distributed measurement errors
+
+# Parameters
+uniform_var = A__FREE 0 1
+uniform_var = d1__FREE 0 1
+uniform_var = d2__FREE 0 1
+uniform_var = V0__FREE 0 2000
+uniform_var = sigma__FREE 0 10
+# Differential Evolution Parameters
+population_size = 1
+adaptive = 50000
+burn_in = 50000
+sample_every = 1
+max_iterations = 200000
+step_size = 0.01
+continue_run = 1
+# Print output to command line
+verbosity = 2
+output_trajectory = lnV
\ No newline at end of file
diff --git a/examples/HIVdynamics_aMCMC/pt403/pt403.exp b/examples/HIVdynamics_aMCMC/pt403/pt403.exp
new file mode 100644
index 00000000..b418356c
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt403/pt403.exp
@@ -0,0 +1,11 @@
+# time	lnV
+  0	4.975925412
+  3	5.941840347
+  8	5.502788103
+  11	5.06373586
+  15	3.044095546
+  18	2.487962707
+  22	2.195261213
+  29	1.522047773
+  36	1.229346278
+
diff --git a/examples/HIVdynamics_aMCMC/pt403/pt403.sh b/examples/HIVdynamics_aMCMC/pt403/pt403.sh
new file mode 100644
index 00000000..d634609b
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt403/pt403.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+# Example batch script for running MCMC for the degranulation model on a SLURM cluster
+
+# set the number of nodesT
+#SBATCH --nodes=1
+
+# set the number of cpus per node.
+#SBATCH --mincpus=24
+
+#SBATCH --mem=100G
+
+# set max wallclock time for the entire fitting job (3 days)
+#SBATCH --time=01-00:00:00
+
+# set name of job
+#SBATCH --job-name=pybnf
+
+# Enable Anaconda Python 3.5
+# Your cluster might require something different here, or might not require anything. 
+module purge
+module load anaconda3/2020.02
+
+# Run PyBNF
+pybnf -c pt403.conf -t SLURM -o
\ No newline at end of file
diff --git a/examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/MLE_params.txt b/examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/MLE_params.txt
new file mode 100644
index 00000000..169d36e8
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/MLE_params.txt
@@ -0,0 +1,5 @@
+7.696715061334600261e-01
+7.547077514911814111e-01
+1.126676003661507136e-01
+3.069470715622069292e+02
+4.789248532738739073e-01
diff --git a/examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/diff.txt b/examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/diff.txt
new file mode 100644
index 00000000..e49da49d
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/diff.txt
@@ -0,0 +1 @@
+3.281168740816535201e-01
diff --git a/examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/diffMatrix.txt b/examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/diffMatrix.txt
new file mode 100644
index 00000000..8a6674a3
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt403/pt403_output/adaptive_files/diffMatrix.txt
@@ -0,0 +1,5 @@
+5.667071652461928150e-02 -7.476167659567871382e-03 -9.691003516377902360e-03 8.539085617392863981e+00 -1.995888550110734572e-02
+-7.476167659567871382e-03 6.187943061366321662e-02 -3.992057253876794831e-02 5.511823653704621684e+00 4.216652555757505541e-03
+-9.691003516377902360e-03 -3.992057253876794831e-02 6.963562104187673296e-02 3.833024003057170059e+00 1.102011090945406377e-02
+8.539085617392863981e+00 5.511823653704621684e+00 3.833024003057170059e+00 2.895074534531007157e+04 1.599958105614667758e+01
+-1.995888550110734572e-02 4.216652555757505541e-03 1.102011090945406377e-02 1.599958105614667758e+01 8.526939850195920656e-02
diff --git a/examples/HIVdynamics_aMCMC/pt409/pt409.bngl b/examples/HIVdynamics_aMCMC/pt409/pt409.bngl
new file mode 100644
index 00000000..cc5ebaf9
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt409/pt409.bngl
@@ -0,0 +1,58 @@
+begin model
+# pt409
+# c = 0.39 /d t_1/2 = 1.8 d (inferred)
+# c = 0.47 /d t_1/2 = 1.5 d (published estimates)
+begin parameters
+
+##########################################
+A A__FREE # dimensionless
+d1 d1__FREE # /d
+d2 d2__FREE # /d
+V0 V0__FREE # copies per mL
+sigma sigma__FREE
+end parameters
+begin molecule types
+counter()
+end molecule types
+begin seed species
+counter() 0
+end seed species
+begin observables
+Molecules t counter()
+end observables
+begin functions
+V()=if(t>=7,if(d2<d1,V0*(A*exp(-d1*(t-7))+(1-A)*exp(-d2*(t-7))),V0*(A*exp(-d2*(t-7))+(1-A)*exp(-d1*(t-7)))),V0)
+lnV()=if(t>=7,if(d2<d1,ln(V0*(A*exp(-d1*(t-7))+(1-A)*exp(-d2*(t-7)))),ln(V0*(A*exp(-d2*(t-7))+(1-A)*exp(-d1*(t-7))))),ln(V0))
+S()=if(d2<d1,-d1*A-d2*(1-A),-d2*A-d1*(1-A))
+c()=if(d2<d1,d1*A+d2*(1-A),d2*A+d1*(1-A))
+half_life()=if(d2<d1,ln(2)/(d1*A+d2*(1-A)),ln(2)/(d2*A+d1*(1-A)))
+lnV_tangent()=if(t>=7,if(d2<d1,ln(V0)+(-d1*A-d2*(1-A))*(t-7),ln(V0)+(-d2*A-d1*(1-A))*(t-7)),ln(V0))
+Vdat()=if(t<=0,406,\
+       if(t<=3,541,\
+       if(t<=8,555,\
+       if(t<=12,109,\
+       if(t<=15,12.7,\
+       if(t<=19,5.45,\
+       if(t<=22,8.17,\
+       if(t<=29,2.20,\
+       if(t<=36,1.89,\
+       0)))))))))
+lnVdat()=if(t<=0,ln(406),\
+         if(t<=3,ln(541),\
+         if(t<=8,ln(555),\
+         if(t<=12,ln(109),\
+         if(t<=15,ln(12.7),\
+         if(t<=19,ln(5.45),\
+         if(t<=22,ln(8.17),\
+         if(t<=29,ln(2.20),\
+         if(t<=36,ln(1.89),\
+         0)))))))))
+end functions
+begin reaction rules
+0->counter() 1
+end reaction rules
+end model
+begin actions
+generate_network({overwrite=>1})
+simulate({suffix=>"pt409",method=>"ode",t_end=>36,n_steps=>36,print_functions=>1})
+end actions
\ No newline at end of file
diff --git a/examples/HIVdynamics_aMCMC/pt409/pt409.conf b/examples/HIVdynamics_aMCMC/pt409/pt409.conf
new file mode 100644
index 00000000..c62ed8eb
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt409/pt409.conf
@@ -0,0 +1,32 @@
+# A fitting job 
+
+# The directory to which job output will be writte
+output_dir=pt409_output
+
+# Model specification
+model = pt409.bngl : pt409.exp
+
+# BNG command - Uncomment and edit this line if you have not set the BNGPATH environment variable
+# bng_command = /path/to/bng2/BNG2.pl
+bng_command = /projects/posner_lab/BioNetGen-2.3.1/BNG2.pl
+
+# Algorithm and objective function choice
+fit_type = am
+objfunc = chi_sq_dynamic # log-normally distributed measurement errors
+
+# Parameters
+uniform_var = A__FREE 0 1
+uniform_var = d1__FREE 0 1
+uniform_var = d2__FREE 0 1
+uniform_var = V0__FREE 0 2000
+uniform_var = sigma__FREE 0 10
+# Differential Evolution Parameters
+population_size = 1
+max_iterations = 200000
+adaptive = 50000
+burn_in = 50000
+sample_every = 1
+continue_run = 1
+# Print output to command line
+verbosity = 2
+output_trajectory = lnVV
\ No newline at end of file
diff --git a/examples/HIVdynamics_aMCMC/pt409/pt409.exp b/examples/HIVdynamics_aMCMC/pt409/pt409.exp
new file mode 100644
index 00000000..5741499e
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt409/pt409.exp
@@ -0,0 +1,11 @@
+# time	lnV
+  0	6.005743917
+  3	6.293888384
+  8	6.319127314
+  12	4.690795598
+  15	2.540999515
+  19	1.696336617
+  22	2.100580166
+  29	0.789417684
+  36	0.639105827
+
diff --git a/examples/HIVdynamics_aMCMC/pt409/pt409.sh b/examples/HIVdynamics_aMCMC/pt409/pt409.sh
new file mode 100644
index 00000000..3170b02f
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt409/pt409.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+# Example batch script for running MCMC for the degranulation model on a SLURM cluster
+
+# set the number of nodesT
+#SBATCH --nodes=1
+
+# set the number of cpus per node.
+#SBATCH --mincpus=24
+
+#SBATCH --mem=100G
+
+# set max wallclock time for the entire fitting job (3 days)
+#SBATCH --time=01-00:00:00
+
+# set name of job
+#SBATCH --job-name=pybnf
+
+# Enable Anaconda Python 3.5
+# Your cluster might require something different here, or might not require anything. 
+module purge
+module load anaconda3/2020.02
+
+# Run PyBNF
+pybnf -c pt409.conf -t SLURM -r
\ No newline at end of file
diff --git a/examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/MLE_params.txt b/examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/MLE_params.txt
new file mode 100644
index 00000000..aacf4ca5
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/MLE_params.txt
@@ -0,0 +1,5 @@
+5.815154742159475143e-01
+2.077101485011013104e-01
+7.531376976448787008e-01
+4.146112609127258111e+02
+1.163680133793883575e+00
diff --git a/examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/diff.txt b/examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/diff.txt
new file mode 100644
index 00000000..d09c5615
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/diff.txt
@@ -0,0 +1 @@
+3.024784199024603271e-01
diff --git a/examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/diffMatrix.txt b/examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/diffMatrix.txt
new file mode 100644
index 00000000..aefcb2c6
--- /dev/null
+++ b/examples/HIVdynamics_aMCMC/pt409/pt409_output/adaptive_files/diffMatrix.txt
@@ -0,0 +1,5 @@
+4.534840873640461761e-02 -4.299119108419427633e-03 -5.507425699247604084e-03 1.407422925385709256e+01 -3.623749922985950583e-02
+-4.299119108419427633e-03 7.120008709763162025e-02 -5.280387730304320765e-02 1.101711924308618684e+01 5.788169077317549191e-03
+-5.507425699247604084e-03 -5.280387730304320765e-02 7.330555144133350798e-02 4.480470417752079548e+00 7.506833995255870855e-03
+1.407422925385709256e+01 1.101711924308618684e+01 4.480470417752079548e+00 9.106859090005641337e+04 1.650499769303362285e+01
+-3.623749922985950583e-02 5.788169077317549191e-03 7.506833995255870855e-03 1.650499769303362285e+01 1.349485952045679782e-01

From 07452721040de27881caa35ca461445143157dcf Mon Sep 17 00:00:00 2001
From: JacobNeumann88 <jn227@nau.edu>
Date: Mon, 20 Sep 2021 05:49:06 -0700
Subject: [PATCH 4/4] Update README.txt

---
 examples/HIVdynamics_aMCMC/README.txt | 2 --
 1 file changed, 2 deletions(-)

diff --git a/examples/HIVdynamics_aMCMC/README.txt b/examples/HIVdynamics_aMCMC/README.txt
index d1794f85..6b5e2f67 100644
--- a/examples/HIVdynamics_aMCMC/README.txt
+++ b/examples/HIVdynamics_aMCMC/README.txt
@@ -7,7 +7,5 @@ The configuration of the warm start was preserved and can be found in the config
 The calculated covariance matrix and diffusivity was also saved and can be found in the associated output folder under the adaptive_files
 subdirectory.
 
-A full description of the model can be found in the supplementary methods.
-
 1. Perelson,A.S. et al. (1996) HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science, 271, 1582–1586.
 2. Ho,D.D. et al. (1995) Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature, 373, 123–126.