made modelServR compliant with Roxygen and R-package styling

- also changed age-distribution prior

incidenceMapR/R/latentFieldModel.R

@@ -40,7 +40,7 @@ latentFieldModel <- function(db , shp, family = NULL, neighborGraph = NULL){
   hyper=list()
   hyper$global <- list(prec = list( prior = "pc.prec", param = 1/10, alpha = 0.01))
   hyper$local <- list(prec = list( prior = "pc.prec", param = 1/100, alpha = 0.01))
-  hyper$age <- list(prec = list( prior = "pc.prec", param = 1/100, alpha = 0.01))
+  hyper$age <- list(prec = list( prior = "pc.prec", param = 1, alpha = 0.01))
   hyper$time <- list(prec = list( prior = "pc.prec", param = 1/50, alpha = 0.01))
   
 

incidenceMapR/R/smoothModel.R

@@ -42,7 +42,7 @@ smoothModel <- function(db, shp, family = NULL, neighborGraph = NULL){
   hyper=list()
   hyper$global <- list(prec = list( prior = "pc.prec", param = 1/10, alpha = 0.01))
   hyper$local <- list(prec = list( prior = "pc.prec", param = 1/100, alpha = 0.01))
-  hyper$age <- list(prec = list( prior = "pc.prec", param = 1/100, alpha = 0.01))
+  hyper$age <- list(prec = list( prior = "pc.prec", param = 1, alpha = 0.01))
  
   
   # we smooth across factor levels with random effects replicates: http://www.r-inla.org/models/tools#TOC-Models-with-more-than-one-type-of-likelihood

incidenceMapR/buildModelsForDeployment.R

@@ -57,9 +57,10 @@ for (SOURCE in names(geoLevels)){
                     
                     saveModel(model)
                     
+                    dir.create('/home/rstudio/seattle_flu/plots/', showWarnings = FALSE)
                     for(k in unique(model$modeledData[[FACTOR]])){
                       tmp<-list(modeledData = model$modeledData[model$modeledData[[FACTOR]]==k,])
-                      fname <- paste('/home/rstudio/seattle_flu/data/plots/',paste(PATHOGEN,SOURCE,GEO,FACTOR,k,sep='-'),'.png',sep='')
+                      fname <- paste('/home/rstudio/seattle_flu/plots/',paste(PATHOGEN,SOURCE,GEO,FACTOR,k,sep='-'),'.png',sep='')
                       png(filename = fname,width = 6, height = 5, units = "in", res = 300)
                       print(ggplotSmoothMap(tmp,shp,title=k,shape_level = GEO))
                       dev.off()
@@ -68,7 +69,6 @@ for (SOURCE in names(geoLevels)){
                   }, error=function(e){cat("ERROR :",conditionMessage(e), "\n")}
                 )
         
-        
       }
     }
   }

modelServR/.gitignore

@@ -0,0 +1 @@
+plots

modelServR/DESCRIPTION

@@ -11,10 +11,3 @@ License: What license it uses
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.1.1
-Suggest:
-    testthat
-    dbViewR
-Imports:
-    digest,
-    jsonlite,
-    logging

modelServR/NAMESPACE

@@ -13,4 +13,5 @@ export(returnModel)
 export(saveModel)
 import(digest)
 import(jsonlite)
+import(logging)
 importFrom(jsonlite,toJSON)

modelServR/R/returnModel.R

@@ -1,6 +1,3 @@
-library(logging)
-basicConfig()
-
 #' loadModelFileById function for getting modeled data
 #'
 #' This function will load a model from the model_store_dir by Id
@@ -39,29 +36,23 @@ loadModelFileById <- function (filename, model_store_dir = Sys.getenv('MODEL_STO
 #' @return model in requested format
 #'
 #' @import jsonlite
+#' @import logging
 #' @export
 #' @examples
 #'
 returnModel <- function(queryIn = jsonlite::toJSON(
                               list(
-                                SELECT   =list(COLUMN=c('sampling_location','residence_census_tract')),
-                                WHERE   =list(COLUMN='sampling_location', IN = c('kiosk')),
-                                GROUP_BY =list(COLUMN=c('sampling_location','residence_census_tract')),
-                                SUMMARIZE=list(COLUMN='sampling_location', IN= c('kiosk'))
+                                SELECT   =list(COLUMN=c('site_type','residence_census_tract')),
+                                WHERE   =list(COLUMN='site_type', IN = c('kiosk')),
+                                GROUP_BY =list(COLUMN=c('site_type','residence_census_tract')),
+                                SUMMARIZE=list(COLUMN='site_type', IN= c('kiosk'))
                                   )),
                             type = 'smooth',
                             version = 'latest',
                             cloudDir = Sys.getenv('MODEL_STORE', '/home/rstudio/seattle_flu/test_model_store')){
 
-  # https://www.dropbox.com/sh/5loj4x6j4tar17i/AABy5kP70IlYtSwrePg4m44Ca?dl=0
-
-  # need to solve paths problem for intalled packages!
-  # ideally this would point to a web-based repository of models so that anyone can get to it.
-  # THIS DOES NOT WORK because of authentication.  Need to explore rdrop2 package!
-
-  # NEED TO Pull multiple formats of data once saving latent fields is implemented in incidenceMapR
-  #  ACTUALLY, current plan is to have csv obey format for each model type
-
+  basicConfig()
+  
   if(class(queryIn)== 'list'){
     queryList <- queryIn
     queryIn <- jsonlite::toJSON(queryIn)

modelServR/R/saveModel.R

@@ -1,7 +1,3 @@
-library(logging)
-basicConfig()
-setLevel("FINEST")
-
 #' getHumanReadableModelIdFromModel: return human readable verion of model from query
 #'
 #' @param model INLA model object that will generatie id from
@@ -58,10 +54,15 @@ getModelQueryObjectFromModel<- function(model, model_type = 'inla', latent = FAL
 #'
 #' @param query query object container the observed and the model_type attributes
 #'
+#' @import logging
+#' 
 #' @return An object containing the observed and the model_type fields
 #' @export
 #'
 getModelQueryObjectFromQuery <- function(query) {
+  basicConfig()
+  setLevel("FINEST")
+  
   logdebug("getModelQueryObjectFromQuery Src:", str(query))
   logdebug("$observed", attr(query, "observed"))
   result <- newEmptyObject()
@@ -86,11 +87,15 @@ getModelIdFromModel <- function(model) {
 #' @param query query object container the observed and the model_type attributes
 #'
 #' @import digest
+#' @import logging
 #' @importFrom jsonlite toJSON
 #' 
 #' @export
 #'
 getModelIdFromQuery <- function(query) {
+  basicConfig()
+  setLevel("FINEST")
+  
   #props <- getModelQueryObjectFromQuery(query)
   modelId <- as.character(jsonlite::toJSON(query, simplifyDataFrame=))
   logdebug("Model ID JSON:", jsonlite::toJSON(query, simplifyDataFrame=))

modelServR/man/getModelQueryObjectFromModel.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/saveModel.R
 \name{getModelQueryObjectFromModel}
 \alias{getModelQueryObjectFromModel}
-\title{getModelQueryObjectFromModel: return query object from a model. 
+\title{getModelQueryObjectFromModel: return query object from a model.
 This is the object we use to generate our unique ids.}
 \usage{
 getModelQueryObjectFromModel(model, model_type = "inla",
@@ -19,6 +19,6 @@ getModelQueryObjectFromModel(model, model_type = "inla",
 An object containing the observed and the model_type fields
 }
 \description{
-getModelQueryObjectFromModel: return query object from a model. 
+getModelQueryObjectFromModel: return query object from a model.
 This is the object we use to generate our unique ids.
 }

modelServR/man/loadModelFileById.Rd

@@ -8,7 +8,7 @@ loadModelFileById(filename, model_store_dir = Sys.getenv("MODEL_STORE",
   "/home/rstudio/seattle_flu"), type = "csv")
 }
 \arguments{
-\item{filename}{= At moment we expect full filename in format ID.extension. 
+\item{filename}{= At moment we expect full filename in format ID.extension.
 This is so in future we can more easily support different model save formats}
 
 \item{model_store_dir}{= directory where models are stored}

modelServR/man/returnModel.Rd

@@ -5,10 +5,10 @@
 \title{returnModel function for getting modeled data}
 \usage{
 returnModel(queryIn = jsonlite::toJSON(list(SELECT = list(COLUMN =
-  c("sampling_location", "GEOID")), WHERE = list(COLUMN =
+  c("sampling_location", "residence_census_tract")), WHERE = list(COLUMN =
   "sampling_location", IN = c("kiosk")), GROUP_BY = list(COLUMN =
-  c("sampling_location", "GEOID")), SUMMARIZE = list(COLUMN =
-  "sampling_location", IN = c("kiosk")))), type = "smooth",
+  c("sampling_location", "residence_census_tract")), SUMMARIZE =
+  list(COLUMN = "sampling_location", IN = c("kiosk")))), type = "smooth",
   version = "latest", cloudDir = Sys.getenv("MODEL_STORE",
   "/home/rstudio/seattle_flu/test_model_store"))
 }