In skgallagher/InfectionTrees: Sample, Analyze, and Plot Infection Trees

knitr::opts_chunk$set(echo = TRUE,
                      cache = TRUE,
                      warning = FALSE,
                      message = FALSE)
knitr::opts_knit$set(root.dir = "~/InfectionTrees")
devtools::load_all()
library(InfectionTrees)
library(tidyr)
library(dplyr)
library(kableExtra)
library(ggplot2)
theme_set(theme_bw() + theme(axis.title = element_text()))

Preliminaries

1. Make sure InfectionTrees is installed (devtools::install_github("skgallagher/InfectionTrees")) and loaded along with the following libraries

library(InfectionTrees)
library(ggplot2)
library(knitr)
library(kableExtra)
library(tidyr)
library(dplyr)

1. If there are any occurrences of devtools::load_all(), remove them and replace with library(InfectionTrees).

2. Expected run time is an approximation for of estimated time to run the script. They were originally run on a laptop with the following specs unless otherwise specified.

Distributor ID: Ubuntu
Description:    Ubuntu 20.04.2 LTS
Release:    20.04
Codename:   focal

Architecture:                    x86_64
CPU op-mode(s):                  32-bit, 64-bit
Byte Order:                      Little Endian
Address sizes:                   39 bits physical, 48 bits virtual
CPU(s):                          8
On-line CPU(s) list:             0-7
Thread(s) per core:              2
Core(s) per socket:              4
Socket(s):                       1
NUMA node(s):                    1
Vendor ID:                       GenuineIntel
CPU family:                      6
Model:                           142
Model name:                      Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz
Stepping:                        12
CPU MHz:                         1281.004
CPU max MHz:                     4900.0000
CPU min MHz:                     400.0000
BogoMIPS:                        4599.93
Virtualization:                  VT-x
L1d cache:                       128 KiB
L1i cache:                       128 KiB
L2 cache:                        1 MiB
L3 cache:                        8 MiB
NUMA node0 CPU(s):               0-7
Vulnerability Itlb multihit:     KVM: Mitigation: VMX disabled
Vulnerability L1tf:              Not affected
Vulnerability Mds:               Not affected
Vulnerability Meltdown:          Not affected
Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled v
                                 ia prctl and seccomp
Vulnerability Spectre v1:        Mitigation; usercopy/swapgs barriers and __user
                                  pointer sanitization
Vulnerability Spectre v2:        Mitigation; Enhanced IBRS, IBPB conditional, RS
                                 B filling
Vulnerability Srbds:             Mitigation; TSX disabled
Vulnerability Tsx async abort:   Not affected
Flags:                           fpu vme de pse tsc msr pae mce cx8 apic sep mtr
                                 r pge mca cmov pat pse36 clflush dts acpi mmx f
                                 xsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rd
                                 tscp lm constant_tsc art arch_perfmon pebs bts 
                                 rep_good nopl xtopology nonstop_tsc cpuid aperf
                                 mperf pni pclmulqdq dtes64 monitor ds_cpl vmx e
                                 st tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid sse4_
                                 1 sse4_2 x2apic movbe popcnt tsc_deadline_timer
                                  aes xsave avx f16c rdrand lahf_lm abm 3dnowpre
                                 fetch cpuid_fault epb invpcid_single ssbd ibrs 
                                 ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpr
                                 iority ept vpid ept_ad fsgsbase tsc_adjust bmi1
                                  avx2 smep bmi2 erms invpcid mpx rdseed adx sma
                                 p clflushopt intel_pt xsaveopt xsavec xgetbv1 x
                                 saves dtherm ida arat pln pts hwp hwp_notify hw
                                 p_act_window hwp_epp md_clear flush_l1d arch_ca
                                 pabilities

File Structure

All code for reproducing our revised paper results may be found here.

Please clone the entire repository into your local directory and set your working directory to revised_paper_results/

The results include the following:

1. Table 1 results. table1-binary-cov-base-model-sims/ a. Base model simulation results. run-base-sims.R b. Base model simulation bootstrap results. run-base-sims-boot.R c. Table output for base model simulation. analyze-base-sims.R
2. Table 2 results. table2-binary-cov-mot-model-sims/ a. Multiple outside transmissions model simulation results. outsider-sims.R c. Table output for base model simulation. analyze-mot-sims.R
3. The TB data results. md-tb/ a. Tables 3 and 4. tab3-4-data-eda.R b. Tables 5 and 6. i. Results from base and multiple outside transmissions model. tb-data-base-and-mot.R ii. Bootstrap standard error for base and multiple outside transmissions model. bootstrap-sims.R iii. Naive model results. data-naive-model.R iv. Naive model bootstrap error. data-naive-boot.R v. Table outputs for the three models combined. analyze-data-big-table.R c. Figure 4, most likely trees for the base model. fig4-most-likely-trees.R
4. Algorithm to compute whether we have enough samples enough-MC-trees/sampling-enough-mc-trees.R

Code for results and expected run time

Table 1 results. table1-binary-cov-base-model-sims/

This table was produced by running the following three files in order.

Base model simulation results. run-base-sims.R

tb1_fn <- "~/InfectionTrees/revised_paper_results/table1-binary-cov-base-model-sims/run-base-sims.R"

Expected run-time: ~3-5 hours

Base model bootstrap simulation results. run-base-sims-boot.R

tb1_fn <- "~/InfectionTrees/revised_paper_results/table1-binary-cov-base-model-sims/run-base-sims-boot.R"

Expected run-time: ~12-18 hours

Table output for base model simulation. analyze-base-sims.R

tb1_fn <- "~/InfectionTrees/revised_paper_results/table1-binary-cov-base-model-sims/analyze-base-sims.R"

Expected run-time: ~seconds, given the above completed results.

Table 2 results. table2-binary-cov-mot-model-sims/

This table was produced by running the following two files in order.

Multiple outside transmissions model simulation results. outsider-sims.R

tb1_fn <- "~/InfectionTrees/revised_paper_results/table1-binary-cov-base-model-sims/run-base-sims.R"

Expected run-time: ~30 hours

Table output for multiple outside transmissions model simulation. analyze-mot-sims.R

tb1_fn <- "~/InfectionTrees/revised_paper_results/table2-binary-cov-mot-model-sims/analyze-mot-sims.R"

Expected run-time: ~seconds, given the above completed results.

The TB data results. md-tb/

Tables 3 and 4. tab3-4-data-eda.R

tb1_fn <- "~/InfectionTrees/revised_paper_results/md-tb/tab3-4-data-eda.R"

Expected run-time: ~seconds

Tables 5 and 6.

To get these results, we need to run the three models (base, multiple outside transmissions, and naive) and then combine them together.

Results from base and multiple outside transmissions model. tb-data-base-and-mot.R

tb1_fn <- "~/InfectionTrees/revised_paper_results/md-tb/tb-data-base-and-mot.R"

Expected run-time: ~30 hours

Bootstrap standard error for base and multiple outside transmissions model. bootstrap-sims.R

tb1_fn <- "~/InfectionTrees/revised_paper_results/md-tb/bootstrap-sims.R"

Expected run-time: 5 days for the longest loop. Each loop was run in parallel on the NIAID supercomputer, Biowulf.

Naive model results. data-naive-model.R

tb1_fn <- "~/InfectionTrees/revised_paper_results/md-tb/data-naive-model.R"

Expected run-time: ~seconds

Naive model bootstrap error. data-naive-boot.R

tb1_fn <- "~/InfectionTrees/revised_paper_results/md-tb/data-naive-boot.R"

Expected run-time: ~15 minutes

Table outputs for the three models combined. analyze-data-big-table.R

tb1_fn <- "~/InfectionTrees/revised_paper_results/md-tb/analyze-data-big-table.R"

Expected run-time: ~seconds, given outputs from above

Figure 4, most likely trees for the base model. fig4-most-likely-trees.R

tb1_fn <- "~/InfectionTrees/revised_paper_results/md-tb/fig4-most-likely-trees.R"

Expected run-time: ~seconds, given outputs from above

Algorithm to compute whether we have enough samples enough-MC-trees/sampling-enough-mc-trees.R

tb1_fn <- "~/InfectionTrees/revised_paper_results/enough-MC-trees/simulations-enough-mc-trees.R"

Expected run-time: ~2 days

skgallagher/InfectionTrees documentation built on July 28, 2021, 2:14 p.m.