trialist.nof1.dpu

A JAGS based DPU

Use in R

A DPU is simply an R function that is designed to be called either locally or remotely.

#install
library(devtools)
install_github("trialist.nof1.dpu", "openmhealth")

#use
library("trialist.nof1.dpu")
mydata <- data.frame(
  Pain = c(22, 18, 21,16, 22, 15, 23, 14), 
  Fatigue = c(7,4,9,3,7,4,8,3), 
  Drowsy = c(5,5,5,4,5,5,4,5), 
  Sleep = c(4,2,4,1,4,1,4,1), 
  Thinking = c(5,2,6,1,8,4,7,6), 
  Constipation = c(10,7,10,6,9,5,10,3),
  Treat = c(0,1,0,1,0,1,0,1)
)

nof1 <- wrap.norm2(
  observations = mydata,
  alphaprior = list("norm",0,1e-6),
  betaprior = list("norm",0,1e-6),
  varprior = list("sd","unif"),
  varprior.params = c(0,5)
)

Call remotely as DPU through OpenCPU

For the observations argument, we can either pass a set of rows (which is conventional in JSON):

curl https://pilots.ohmage.org/ocpu/github/openmhealth/trialist.nof1.dpu/R/wrap.norm2/json \
-H 'Content-Type: application/json' \
-d '{"observations":[
  {"Pain":22,"Fatigue":7,"Drowsy":5,"Sleep":4,"Thinking":5,"Constipation":10,"Treat":0},
  {"Pain":18,"Fatigue":4,"Drowsy":5,"Sleep":2,"Thinking":2,"Constipation":7,"Treat":1},
  {"Pain":21,"Fatigue":9,"Drowsy":5,"Sleep":4,"Thinking":6,"Constipation":10,"Treat":0},
  {"Pain":16,"Fatigue":3,"Drowsy":4,"Sleep":1,"Thinking":1,"Constipation":6,"Treat":1},
  {"Pain":22,"Fatigue":7,"Drowsy":5,"Sleep":4,"Thinking":8,"Constipation":9,"Treat":0},
  {"Pain":15,"Fatigue":4,"Drowsy":5,"Sleep":1,"Thinking":4,"Constipation":5,"Treat":1},
  {"Pain":23,"Fatigue":8,"Drowsy":4,"Sleep":4,"Thinking":7,"Constipation":10,"Treat":0},
  {"Pain":14,"Fatigue":3,"Drowsy":5,"Sleep":1,"Thinking":6,"Constipation":3,"Treat":1}
], "conv.limit": 1.05, "niters":10000, "setsize":1000, "alphaprior":["norm",0, 1e-6], 
"betaprior": ["norm", 0, 1e-6], "varprior" : ["sd", "unif"], "varprior.params":[0,5]}'

Or we can call the same function can using a list of columns:

curl https://pilots.ohmage.org/ocpu/github/openmhealth/trialist.nof1.dpu/R/wrap.norm2/json \
-H 'Content-Type: application/json' \
-d '{"observations":{
  "Pain":[22,18,21,16,22,15,23,14], 
  "Fatigue":[7,4,9,3,7,4,8,3], 
  "Drowsy":[5,5,5,4,5,5,4,5], 
  "Sleep":[4,2,4,1,4,1,4,1], 
  "Thinking": [5,2,6,1,8,4,7,6], 
  "Constipation":[10,7,10,6,9,5,10,3], 
  "Treat":[0,1,0,1,0,1,0,1] 
}, "conv.limit":1.05, "niters":10000, "setsize":1000, "alphaprior":["norm",0, 1e-6], 
"betaprior": ["norm", 0, 1e-6], "varprior" : ["sd", "unif"], "varprior.params":[0,5]}'

Old DPU wrapper

The old wrapper wrap.norm has been superseded by wrap.norm2 above. This is how the old wrapper is called:

curl https://public.opencpu.org/ocpu/github/openmhealth/trialist.nof1.dpu/R/wrap.norm/json \
-H 'Content-Type: application/json' \
-d '{"Pain":[22, 18, 21,16, 22, 15, 23, 14],"Fatigue":[7,4,9,3,7,4,8,3], "Drowsy":[5,5,5,4,5,5,4,5], "Sleep":[4,2,4,1,4,1,4,1], "Thinking" : [5,2,6,1,8,4,7,6], "Constipation":[10,7,10,6,9,5,10,3], "Treat": [0,1,0,1,0,1,0,1], "conv.limit": 1.05, "niters":10000, "setsize":1000, "alphaprior":["norm",0, 1e-6], "betaprior": ["norm", 0, 1e-6], "varprior" : ["sd", "unif"], "varprior.params":[0,5]}'