preparing branch for model science review
This commit is contained in:
famulare
Родитель
28f6e4d8c3
Коммит
6448fd5786
|
|
@ -19,23 +19,18 @@ pip-selfcheck.json
|
|||
Thumbs.db
|
||||
ehthumbs.db
|
||||
ehthumbs_vista.db
|
||||
|
||||
# Dump file
|
||||
*.stackdump
|
||||
|
||||
# Folder config file
|
||||
[Dd]esktop.ini
|
||||
|
||||
# Recycle Bin used on file shares
|
||||
$RECYCLE.BIN/
|
||||
|
||||
# Windows Installer files
|
||||
*.cab
|
||||
*.msi
|
||||
*.msix
|
||||
*.msm
|
||||
*.msp
|
||||
|
||||
# Windows shortcuts
|
||||
*.lnk
|
||||
### Python template
|
||||
|
|
@ -43,10 +38,8 @@ $RECYCLE.BIN/
|
|||
__pycache__/
|
||||
*.py[cod]
|
||||
*$py.class
|
||||
|
||||
# C extensions
|
||||
*.so
|
||||
|
||||
# Distribution / packaging
|
||||
.Python
|
||||
build/
|
||||
|
|
@ -65,17 +58,14 @@ wheels/
|
|||
.installed.cfg
|
||||
*.egg
|
||||
MANIFEST
|
||||
|
||||
# PyInstaller
|
||||
# Usually these files are written by a python script from a template
|
||||
# before PyInstaller builds the exe, so as to inject date/other infos into it.
|
||||
*.manifest
|
||||
*.spec
|
||||
|
||||
# Installer logs
|
||||
pip-log.txt
|
||||
pip-delete-this-directory.txt
|
||||
|
||||
# Unit test / coverage reports
|
||||
htmlcov/
|
||||
.tox/
|
||||
|
|
@ -87,41 +77,30 @@ coverage.xml
|
|||
*.cover
|
||||
.hypothesis/
|
||||
.pytest_cache/
|
||||
|
||||
# Translations
|
||||
*.mo
|
||||
*.pot
|
||||
|
||||
# Django stuff:
|
||||
*.log
|
||||
local_settings.py
|
||||
db.sqlite3
|
||||
|
||||
# Flask stuff:
|
||||
instance/
|
||||
.webassets-cache
|
||||
|
||||
# Scrapy stuff:
|
||||
.scrapy
|
||||
|
||||
# Sphinx documentation
|
||||
docs/_build/
|
||||
|
||||
# PyBuilder
|
||||
target/
|
||||
|
||||
# Jupyter Notebook
|
||||
.ipynb_checkpoints
|
||||
|
||||
# pyenv
|
||||
.python-version
|
||||
|
||||
# celery beat schedule file
|
||||
celerybeat-schedule
|
||||
|
||||
# SageMath parsed files
|
||||
*.sage.py
|
||||
|
||||
# Environments
|
||||
.env
|
||||
.venv
|
||||
|
|
@ -130,17 +109,13 @@ venv/
|
|||
ENV/
|
||||
env.bak/
|
||||
venv.bak/
|
||||
|
||||
# Spyder project settings
|
||||
.spyderproject
|
||||
.spyproject
|
||||
|
||||
# Rope project settings
|
||||
.ropeproject
|
||||
|
||||
# mkdocs documentation
|
||||
/site
|
||||
|
||||
# mypy
|
||||
.mypy_cache/
|
||||
### VisualStudioCode template
|
||||
|
|
@ -152,19 +127,16 @@ venv.bak/
|
|||
### Vagrant template
|
||||
# General
|
||||
.vagrant/
|
||||
|
||||
# Log files (if you are creating logs in debug mode, uncomment this)
|
||||
# *.logs
|
||||
### JetBrains template
|
||||
# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and WebStorm
|
||||
# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
|
||||
|
||||
# User-specific stuff
|
||||
.idea/**/workspace.xml
|
||||
.idea/**/tasks.xml
|
||||
.idea/**/dictionaries
|
||||
.idea/**/shelf
|
||||
|
||||
# Sensitive or high-churn files
|
||||
.idea/**/dataSources/
|
||||
.idea/**/dataSources.ids
|
||||
|
|
@ -177,101 +149,74 @@ venv.bak/
|
|||
.idea/**/misc.xml
|
||||
.idea/**/vcs.xml
|
||||
.idea/*.iml
|
||||
|
||||
# Let's allow shared run configurations
|
||||
!**/.idea/**/runConfigurations/
|
||||
|
||||
# Gradle
|
||||
.idea/**/gradle.xml
|
||||
.idea/**/libraries
|
||||
|
||||
# CMake
|
||||
cmake-build-debug/
|
||||
cmake-build-release/
|
||||
|
||||
# Mongo Explorer plugin
|
||||
.idea/**/mongoSettings.xml
|
||||
|
||||
# File-based project format
|
||||
*.iws
|
||||
|
||||
# IntelliJ
|
||||
out/
|
||||
|
||||
# mpeltonen/sbt-idea plugin
|
||||
.idea_modules/
|
||||
|
||||
# JIRA plugin
|
||||
atlassian-ide-plugin.xml
|
||||
|
||||
# Cursive Clojure plugin
|
||||
.idea/replstate.xml
|
||||
|
||||
# Crashlytics plugin (for Android Studio and IntelliJ)
|
||||
com_crashlytics_export_strings.xml
|
||||
crashlytics.properties
|
||||
crashlytics-build.properties
|
||||
fabric.properties
|
||||
|
||||
# Editor-based Rest Client
|
||||
.idea/httpRequests
|
||||
### R template
|
||||
# History files
|
||||
.Rhistory
|
||||
.Rapp.history
|
||||
|
||||
# Session Data files
|
||||
.RData
|
||||
|
||||
# Example code in package build process
|
||||
*-Ex.R
|
||||
|
||||
# Output files from R CMD build
|
||||
/*.tar.gz
|
||||
|
||||
# Output files from R CMD check
|
||||
/*.Rcheck/
|
||||
|
||||
# RStudio files
|
||||
.Rproj.user/
|
||||
.Ruserdata
|
||||
|
||||
# produced vignettes
|
||||
vignettes/*.html
|
||||
vignettes/*.pdf
|
||||
|
||||
# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
|
||||
.httr-oauth
|
||||
|
||||
# knitr and R markdown default cache directories
|
||||
/*_cache/
|
||||
/cache/
|
||||
|
||||
# Temporary files created by R markdown
|
||||
*.utf8.md
|
||||
*.knit.md
|
||||
|
||||
# Shiny token, see https://shiny.rstudio.com/articles/shinyapps.html
|
||||
rsconnect/
|
||||
|
||||
|
||||
*/.idea/*
|
||||
|
||||
api_service/docs_src/seattle_flu*rst
|
||||
data/*
|
||||
.pg_service.conf
|
||||
.pgpass
|
||||
|
||||
#Models database and local folder
|
||||
model_data/*
|
||||
models.db
|
||||
modelDB.tsv
|
||||
|
||||
# Package archives
|
||||
dbViewR_*.tar.gz
|
||||
modelServR_*.tar.gz
|
||||
incidenceMapR_*.tar.gz
|
||||
|
||||
# Test directories
|
||||
test_model_store/*
|
||||
plots/*
|
||||
|
|
@ -279,3 +224,4 @@ test_jobs/*
|
|||
plots/*
|
||||
july_22_plots/*
|
||||
may_22_plots/*
|
||||
.modelStoreToken
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
|
||||
export(addCensusData)
|
||||
export(expandDB)
|
||||
export(loadBingData)
|
||||
export(masterSpatialDB)
|
||||
export(selectFromDB)
|
||||
import(DBI)
|
||||
|
|
@ -11,7 +12,9 @@ import(geojsonio)
|
|||
import(jsonlite)
|
||||
import(lubridate)
|
||||
import(rgdal)
|
||||
import(rgeos)
|
||||
import(sf)
|
||||
import(sp)
|
||||
import(tidycensus)
|
||||
import(tidyr)
|
||||
importFrom(RCurl,getURL)
|
||||
|
|
|
|||
|
|
@ -1,11 +1,9 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/smoothModel - Copy.R, R/smoothModel.R
|
||||
% Please edit documentation in R/smoothModel.R
|
||||
\name{smoothModel}
|
||||
\alias{smoothModel}
|
||||
\title{smoothModel: function to define variable smoothing models from dbViewR object}
|
||||
\usage{
|
||||
smoothModel(db, shp, family = NULL, neighborGraph = NULL)
|
||||
|
||||
smoothModel(db, shp, family = NULL, neighborGraph = NULL)
|
||||
}
|
||||
\arguments{
|
||||
|
|
@ -16,25 +14,9 @@ Smoothing only makes sense by age, location, and time. Factor variables cannot
|
|||
|
||||
\item{family}{non-standard family override (default = NULL).}
|
||||
|
||||
\item{neighborGraph}{non-standard neighbor graph (default = NULL)}
|
||||
|
||||
\item{db}{dbViewR object with valid column names for INLA model.
|
||||
Smoothing only makes sense by age, location, and time. Factor variables cannot be smoothed!}
|
||||
|
||||
\item{shp}{sf object with residence_census_tract shapes (all higher levels assume iid and not local smoothing)}
|
||||
|
||||
\item{family}{non-standard family override (default = NULL).}
|
||||
|
||||
\item{neighborGraph}{non-standard neighbor graph (default = NULL)}
|
||||
}
|
||||
\value{
|
||||
modelDefinition object for modelTrainR, list with fields
|
||||
type = smooth
|
||||
family : as input
|
||||
formula : model definition for INLA
|
||||
inputData : inla-prepared db$observed data
|
||||
neighborGraph : as input or derived from shp during formula construction
|
||||
|
||||
modelDefinition object for modelTrainR, list with fields
|
||||
type = smooth
|
||||
family : as input
|
||||
|
|
@ -43,15 +25,10 @@ modelDefinition object for modelTrainR, list with fields
|
|||
neighborGraph : as input or derived from shp during formula construction
|
||||
}
|
||||
\description{
|
||||
smoothModel: function to define variable smoothing models from dbViewR object
|
||||
|
||||
smoothModel: function to define variable smoothing models from dbViewR object
|
||||
}
|
||||
\examples{
|
||||
return h1n1pdm incidence model by time and location
|
||||
modelDefinition <- smoothModel(db = dbViewR::selectFromDB(), shp = dbViewR::masterSpatialDB())
|
||||
|
||||
return h1n1pdm incidence model by time and location
|
||||
modelDefinition <- smoothModel(db = dbViewR::selectFromDB(), shp = dbViewR::masterSpatialDB())
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,5 +1,16 @@
|
|||
# Generated by roxygen2: do not edit by hand
|
||||
|
||||
export(getHumanReadableModelIdFromModel)
|
||||
export(getHumanReadableModelIdFromQuery)
|
||||
export(getModelIdFromModel)
|
||||
export(getModelIdFromQuery)
|
||||
export(getModelQueryObjectFromModel)
|
||||
export(getModelQueryObjectFromQuery)
|
||||
export(loadModelFileById)
|
||||
export(queryLoadedModel)
|
||||
export(queryModelById)
|
||||
export(returnModel)
|
||||
export(saveModel)
|
||||
import(digest)
|
||||
import(jsonlite)
|
||||
import(logging)
|
||||
|
|
|
|||
|
|
@ -1,9 +1,12 @@
|
|||
# Generated by roxygen2: do not edit by hand
|
||||
|
||||
export(ggplotSmoothEffects)
|
||||
export(ggplotDiagnosticPlots)
|
||||
export(ggplotFixedEffects)
|
||||
export(ggplotLatentMap)
|
||||
export(ggplotSmoothEffects)
|
||||
export(ggplotSmoothMap)
|
||||
export(ggplotSmoothSequential)
|
||||
import(INLAutils)
|
||||
import(dplyr)
|
||||
import(ggplot2)
|
||||
import(grid)
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
% Please edit documentation in R/ggplotWrappers.R
|
||||
\name{ggplotSmoothEffects}
|
||||
\alias{ggplotSmoothEffects}
|
||||
\title{ggplotSmoothEffects: function for plotting data, smoothed model, and fixed effects model next to each other}
|
||||
\title{ggplotSmoothEffects: function for plotting smoothed model and fixed effects model next to each other}
|
||||
\usage{
|
||||
ggplotSmoothEffects(model_smooth, model_effects, shp, censusdb = NULL,
|
||||
title = "", shape_level = "residence_census_tract")
|
||||
|
|
@ -14,12 +14,9 @@ ggplotSmoothEffects(model_smooth, model_effects, shp, censusdb = NULL,
|
|||
ggplot object
|
||||
}
|
||||
\description{
|
||||
NOT YET IMPLEMENTED!
|
||||
ggplotSmoothEffects: function for plotting smoothed model and fixed effects model next to each other
|
||||
}
|
||||
\examples{
|
||||
plotDat <- right_join(model$modeledData,shp, by=c('residence_census_tract'))
|
||||
plotDat$positive[plotDat$positive==0]<-NaN
|
||||
ggplotSmoothSequential(plotDat)
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
Загрузка…
Ссылка в новой задаче