Run RiskPaths Model from R - openmpp/openmpp.github.io GitHub Wiki
It is a convenient to use GNU R to prepare model parameters and analyze output values. There are two different R APIs which we can use for openM++ models:
- openMpp package: simple and convenient specially for desktop users, upstream and downstream analysis;
-
omsJSON web-service API: preferable choice to run models on computational clusters and in cloud.
Below is an example how to do advanced parameters analysis and run RiskPaths model on desktop using openMpp R package. There is an identical example to:
OpenM++ provides R package openMpp to simplify access to openM++ database for R developers. To find out more about openMpp R package please check:
There is also an excelent R package created by Matthew T. Warkentin available at: oncology-outcomes/openmpp.
Following R example is running "RiskPaths" model to analyze childlessness by varying two parameters:
- Age baseline for first union formation
- Relative risks of union status on first pregnancy by following scale factor:
scaleValues <- seq(from = 0.44, to = 1.00, by = 0.02)Please keep in mind, scaling above result in 841 runs of RiskPaths model and task may take long time to be completed. If you want to get results faster scale values by 0.08 instead of 0.02.
# use openMpp library for openM++ database access
library(DBI)
library("openMpp")
library("RSQLite")
#
# Using RiskPaths model
# to analyze contribution of delayed union formations
# versus decreased fertility on childlessness
#
# Input parameters:
# AgeBaselineForm1: age baseline for first union formation
# UnionStatusPreg1: relative risks of union status on first pregnancy
# Output value:
# T05_CohortFertility: Cohort fertility, expression 1
#
##################################################################
# To run this example please uncomment and/or change values below
# to match your hardware and file system environment:
#
# model_exe <- path to the model executable, i.e.: "./RiskPaths" or "RiskPaths.exe"
# model_sqlite <- path to the model.sqlite database: "RiskPaths.sqlite"
# model_args <- optional arguments to control model run, for example:
# -OpenM.SubValues 8 <- number of simation members
# -OpenM.Threads 4 <- number of computatinal threads
#
### For running on a local machine using the working directory in R
#
# For the following values to work, you must first set the R Working directory
# to the directory containing the RiskPaths executable and the SQLite database.
# In RStudio Session > Set Working Directory > Choose Directory,
# then navigate to location, e.g.: /OM_ROOT/models/RiskPaths/ompp/bin
# Alternatively, one may use setwd(), e.g.: setwd("/OM_ROOT/models/RiskPaths/ompp/bin")
#
model_exe = "./RiskPaths"
model_sqlite = "RiskPaths.sqlite"
model_args = " " # default: 1 simulation member and 1 thread
# model_args = " -OpenM.SubValues 8 -OpenM.Threads 4"
#
### For running on a local machine using explicit paths
#
# model_exe = "/path/to/executable/model/RiskPaths"
# model_sqlite = "/path/to/SQLite/database/RiskPaths.sqlite"
#
### For running on cluster (change to match your cluster)
#
# model_exe = "mpiexec"
# model_sqlite = "/mirror/RiskPaths.sqlite"
# model_args = "-n 8 /mirror/RiskPaths -OpenM.SubValues 16 -OpenM.Threads 2"
##################################################################
#
# connect to database to model databes
#
theDb <- dbConnect(RSQLite::SQLite(), model_sqlite, synchronous = "full")
invisible(dbGetQuery(theDb, "PRAGMA busy_timeout = 86400")) # recommended
# find RiskPaths model in database and get model dictionaries ("modelDic", "typeDic", etc...)
defRs <- getModel(theDb, "RiskPaths")
#
# create a copy of default model parameters
#
baseRunId <- getFirstRunId(theDb, defRs)
if (baseRunId <= 0)
stop("no run results found for the model ", defRs$modelDic$model_name, " ", defRs$modelDic$model_digest)
#
# get default values for AgeBaselineForm1 and UnionStatusPreg1 parameters
# by reading it from first model run results
# assuming first run of the model done with default set of parameters
#
ageFirstUnionRs <- selectRunParameter(theDb, defRs, baseRunId, "AgeBaselineForm1")
unionStatusPregRs <- selectRunParameter(theDb, defRs, baseRunId, "UnionStatusPreg1")
#
# create modeling task with
# all input parameters same as model default except of
# AgeBaselineForm1, UnionStatusPreg1 and SimulationCases parameters
#
casesParam <- list(name = "SimulationCases", value = 1000L) # number of simulation cases
taskTxt <- data.frame( # name (auto generated), description and notes for the task
name = NA,
lang = "EN",
descr = "Analyzing childlessness",
note = NA,
stringsAsFactors = FALSE
)
taskId <- createTask(theDb, defRs, taskTxt)
if (taskId <= 0L) stop("task creation failed: ", defRs$modelDic$model_name, " ", defRs$modelDic$model_digest)
# parameters scale
#
# scaleValues <- seq(from = 0.50, to = 1.00, by = 0.50) # tiny set of runs for quick test
#
scaleValues <- seq(from = 0.44, to = 1.00, by = 0.02)
UnionStatusMultipler = rep(1, length(unionStatusPregRs$param_value)) # vector of 1's
for (scAgeBy in scaleValues)
{
print(c("Scale age: ", scAgeBy))
for (scUnionBy in scaleValues)
{
ageParam <- list(name = "AgeBaselineForm1", value = ageFirstUnionRs$param_value * scAgeBy)
UnionStatusMultipler[1:2] = scUnionBy # scale first two values of parameter vector
unionParam <- list(name = "UnionStatusPreg1", value = unionStatusPregRs$param_value * UnionStatusMultipler )
# Append new working set of parameters into the task. A corresponding setId is generated.
setId <- createWorksetBasedOnRun(theDb, defRs, baseRunId, NA, ageParam, unionParam, casesParam)
setReadonlyWorkset(theDb, defRs, TRUE, setId)
taskId <- updateTask(theDb, defRs, taskId, setIds = setId)
}
}
#
# run the model on cluster or local desktop
# consult your cluster admin on how to use computational grid
print(paste("Run the model:", model_exe, "...please wait..."))
system2(
model_exe,
paste(
model_args,
" -OpenM.TaskId ", taskId,
" -OpenM.LogToConsole false",
" -OpenM.LogToFile true",
" -OpenM.ProgressPercent 100",
sep = ""
)
)
#
# read results of task run from database
# cohort fertility: T05_CohortFertility.Expr1
#
taskRunId <- getTaskLastRunId(theDb, taskId) # most recent task run id
taskRunRs <- selectTaskRun(theDb, taskRunId) # get result id's
#
# taskRunId
# [1] 111
# taskRunRs$taskRunSet # Content for "tiny set of runs"
# task_run_id run_id set_id task_id
# 1 108 109 104 103
# 2 108 110 105 103
# 3 108 111 106 103
# 4 108 112 107 103
# Main scenario task_id 103 comes with 4 sets of parameters set_id 104, 105, 106, 107 (e.g. PSA)
# The main scenario/task was run (task_run_id 108) which spins out 4 runs run_id 109, 110, 111, 112
scaleLen <- length(scaleValues)
childlessnessMat <- matrix(data = NA, nrow = scaleLen, ncol = scaleLen, byrow = TRUE)
runPos <- 1
for (k in 1:scaleLen)
{
for (j in 1:scaleLen)
{
# cohort fertility: T05_CohortFertility.Expr1
expr1Rs <- selectRunOutputValue(theDb, defRs, taskRunRs$taskRunSet$run_id[runPos], "T05_CohortFertility", "Expr1")
childlessnessMat[k, j] = expr1Rs$expr_value
runPos <- runPos + 1
}
}
dbDisconnect(theDb) # close database connection
#
# display the results
#
persp(
x = scaleValues,
y = scaleValues,
z = childlessnessMat,
xlab = "Decreased union formation",
ylab = "Decreased fertility",
zlab = "Childlessness",
theta = 30, phi = 30, expand = 0.5, ticktype = "detailed",
col = "lightgreen",
cex.axis = 0.7
)