Coordinated Entry By-Name-List using HMIS CSV 5.1, R, and SQL

This is a build out of TX-601’s Coordinated Entry By-Name List.  The report is written using SQLDF inside of an R environment.

Homebase Function

homebase <- function(
  hmisDataPath,
  vispdatDataPath,
  staffInfoDataPath,
  executionPath,
  hmisFunctionsFilePath,
  viSpdat2DataPath,
  clientContactInfoPath) {

  library("tcltk")
  
  # Load the weights for progress bar
  loadingPackagesIncrement <- 2
  loadingHMISDataIncrement <- 10
  addDisabilitiesIncrement <- 5
  householdIdIncrement <- 4
  calculatingAgeIncrement <- 1
  gettingEnrollmentsIncrement <- 10
  gettingStaffInfoIncrement <- 5
  calculatingCHIncrement <- 10
  addVispdatIncrement <- 5
  getFamilyWithChildIncrement <- 5
  loadServicesIncrement <- 15
  nbnStaysIncrement <- 5
  outreachContactsIncrement <- 5
    outreachAndNbnCountIncrement <- 5
    clientContactinfoIncrement <- 3
  makeHmisCodesReadableIncrement <- 2
  formatHomebaseIncrement <- 1
  
  # Find the progress bar max.
  total <- (loadingPackagesIncrement +
              loadingHMISDataIncrement +
              addDisabilitiesIncrement +
              householdIdIncrement +
              calculatingAgeIncrement +
              gettingEnrollmentsIncrement +
              gettingStaffInfoIncrement +
              calculatingCHIncrement +
              addVispdatIncrement +
              getFamilyWithChildIncrement +
              loadServicesIncrement +
              nbnStaysIncrement +
              outreachAndNbnCountIncrement +
              makeHmisCodesReadableIncrement +
              formatHomebaseIncrement +
              clientContactinfoIncrement
  )
      # Initialize progress bar
  pbCounter = 0
  pb <- tkProgressBar(title = "Homebase Function", min = 0,
                      max = total, width = 300)
  
  ###### START ##########
  setTkProgressBar(pb, pbCounter, label = "Loading Packages")

  # There needs to be a lot of allocated memory for Java for
  # XLConnect to work.
    options(java.parameters = "-Xmx14336m") ## memory set to 14 GB

  library(sqldf)
  library(XLConnect)
  library(xlsx)


  # Load the HMIS functions.
  source(hmisFunctionsFilePath)
  
  # Return to execution path.
  setwd(executionPath)
  
  # Update progress bar
  pbCounter <- pbCounter + loadingPackagesIncrement
  setTkProgressBar(pb, pbCounter, label = "Loading HMIS Data")
  
  # Load HMIS Data
  client <- loadClient(hmisDataPath)
  enrollment <- loadEnrollment(hmisDataPath)
  disabilities <- loadDisabilities(hmisDataPath)
  exit <- loadExit(hmisDataPath)
  project <- loadProject(hmisDataPath)
  enrollmentCoc <- loadEnrollmentCoc(hmisDataPath)

  # Return to execution path.
  setwd(executionPath)
  
  pbCounter <- pbCounter + loadingHMISDataIncrement
  setTkProgressBar(pb, pbCounter, label = "Getting Disabilities")
  
  # Takes the Disabilities.csv and breaks out the disabilities reported
  # for each participants into individual elements with binary resposnes.
  client <- addDisabilityInfoToClient(client, disabilities)
  
  # Update progress bar
  pbCounter <- pbCounter + addDisabilitiesIncrement
  setTkProgressBar(pb, pbCounter, label = "Getting Household IDs")
  
  # Gets the PersonalIDs of participants with a HUD Entry or Update in last 90 days.
  enrollmentCoc <- getMostRecentRecordsPerId(enrollmentCoc, "PersonalID", "DateCreated")
  enrollmentCoc$DateCreated <- as.character(enrollmentCoc$DateCreated)
  
  # Get Household IDs from EnrollmentCoc.csv
  client_HHIDs <- sqldf("SELECT DISTINCT a.PersonalID, b.HouseholdID
                  FROM client a
                  LEFT JOIN enrollmentCoc b
                  ON a.PersonalID=b.PersonalID
                  WHERE HouseholdID != 'NA'
                  ")

  client_HHIDs <- sqldf("SELECT PersonalID, MAX(HouseholdID) As 'HouseholdID' FROM client_HHIDs GROUP BY PersonalID")

  # Update progress bar
  pbCounter <- pbCounter + householdIdIncrement
  setTkProgressBar(pb, pbCounter, label = "Calculating Age")
  
  # Calculate age
  client <- sqldf("SELECT DISTINCT *, (DATE('NOW') - DATE(DOB)) As 'Age' FROM client")
  
  pbCounter <- pbCounter + calculatingAgeIncrement
  setTkProgressBar(pb, pbCounter, label = "Getting Enrollments")

  # Filters to most recent HUD Assessment per participant
  df1 <- getMostRecentRecordsPerId(enrollment, "PersonalID", "EntryDate")

  ## Adds a 'MaxEntryDate' flag to enrollment
  #enrollment <- sqldf("SELECT a.*, b.MaxEntryDate
                      #FROM enrollment a
                      #LEFT JOIN df1 b
                      #ON a.ProjectEntryID=b.ProjectEntryID
                      #")


    # Adds a 'MaxEntryDate' flag to enrollment
    enrollment <- sqldf("SELECT a.*, b.MaxEntryDate
                      FROM enrollment a
                      LEFT JOIN df1 b
                      ON a.ProjectEntryID=b.ProjectEntryID
                      WHERE b.MaxEntryDate = 'Yes'
                      ")
  
  # Get Project Info for Enrollment
  enrollmentCoc <- addProjectInfoToEnrollment(enrollmentCoc, project)
  
  df3 <- sqldf("SELECT PersonalID, DateCreated As 'MostRecentHUDAssess', UserID As 'StaffID', ProjectName, ProjectType
               FROM enrollmentCoc")
  df3 <- makeProjectTypeReadable(df3)
  pbCounter <- pbCounter + gettingStaffInfoIncrement
  setTkProgressBar(pb, pbCounter, label = "Calculating Chronically Homeless")
  
  # Adds a ChronicallyHomeless flag
  df4 <- addChronicallyHomelessFlagToClient(client, df1)
  # Adds a ActiveInPh flag
  df5 <- getClientsInPH(loadEnrollment(hmisDataPath), exit, project)
  
  # Returns flags to clientDf
  targetClient <- sqldf("SELECT DISTINCT a.*, b.'ActiveInPh', c.EntryDate
                        FROM df4 a
                        LEFT JOIN df5 b
                        ON a.PersonalID=b.PersonalID
                        LEFT JOIN enrollment c
                        ON a.PersonalID=c.PersonalID
                        ")

  colnames(targetClient)[which(colnames(targetClient) == "EntryDate")] <- "RecentHUDEntryDate"
  
  # Load staff information
  staffInfo <- readWorksheetFromFile(staffInfoDataPath, sheet = 1, startRow = 1)
  colnames(staffInfo)[1] <- "StaffID"
  staffInfo <- sqldf("SELECT DISTINCT StaffID, Name, Email FROM staffInfo")
  
  # Find the staff information for who completed each HUD Assessment.
  df7 <- sqldf("SELECT a.*, b.Name As 'StaffName', b.Email As 'StaffEmail'
               FROM df3 a
               LEFT JOIN staffInfo b
               ON a.StaffID=b.StaffID
               ")
  remove(list = c("staffInfo"))
  
  # Add the Staff and Project information back to client list.
  targetClient <- sqldf("SELECT a.*, b.MostRecentHUDAssess, b.StaffName, b.StaffEmail, b.ProjectName As 'LastProgramInContact', b.ReadableProjectType As 'LastProjectTypeContacted'
                        FROM targetClient a
                        LEFT JOIN df7 b
                        ON a.PersonalID=b.PersonalID
                        ")
  
  targetClient <- subset(targetClient)
  
  # Cleanup
  remove(list = c("df4", "df3", "df5", "df1", "enrollmentCoc"))
  
  pbCounter <- pbCounter + calculatingCHIncrement
  setTkProgressBar(pb, pbCounter, label = "Adding VI-SPDAT")
  
  # Load VI-SPDAT information
  viSpdat <- readWorksheetFromFile(vispdatDataPath, sheet = 1, startRow = 1)
  viSpdat2 <- readWorksheetFromFile(viSpdat2DataPath, sheet = 1, startRow = 1)

  # Clean up VI-SPDAT1 formatting
  colnames(viSpdat)[6] <- "DateOfVISPDAT"
  viSpdat$DateOfVISPDAT <- as.character(viSpdat$DateOfVISPDAT)
  viSpdat$Participant.Enterprise.Identifier <- gsub("-", "", viSpdat$Participant.Enterprise.Identifier)
  viSpdat$Family.Enterprise.Identifier <- gsub("-", "", viSpdat$Family.Enterprise.Identifier)
  viSpdat$Family.Enterprise.Identifier <- gsub("\\{", "", viSpdat$Family.Enterprise.Identifier)
    viSpdat$Family.Enterprise.Identifier <- gsub("\\}", "", viSpdat$Family.Enterprise.Identifier)
    colnames(viSpdat)[1] <- "PersonalID"

  # Clean up VI-SPDAT2 formatting
  viSpdat2$DateOfVISPDAT <- as.character(viSpdat2$DateOfVISPDAT)
  viSpdat2$PersonalID <- gsub("-", "", viSpdat2$PersonalID)
    
    # Get most recent VI-SPDAT per client.
  viSpdat <- getMostRecentRecordsPerId(viSpdat, "PersonalID", "DateOfVISPDAT")
  viSpdat2 <- getMostRecentRecordsPerId(viSpdat2, "PersonalID", "DateOfVISPDAT")

    # Shape VI-SPDAT to look like VI-SPDAT 2
    viSpdat <- sqldf("SELECT PersonalID, DateOfVISPDAT As 'DateOfVISPDAT', '' As VISPDATTotalFamilyScore, '' As VISPDATTotalYouthScore, ScoreVISPDAT As 'VISPDATTotalIndividualScore', 'Individual' As TypeOfViSpdat FROM viSpdat")
    viSpdat2 <- sqldf("SELECT PersonalID, DateOfVISPDAT, VISPDATTotalFamilyScore, VISPDATTotalYouthScore, VISPDATTotalIndividualScore, TypeOfViSpdat FROM viSpdat2")

    allVispdat <- rbind(viSpdat, viSpdat2)

    # Get max between new and old VI-SPDAT
    allVispdat <- getMostRecentRecordsPerId(allVispdat, "PersonalID", "DateOfVISPDAT")

    allVispdat <- unique(allVispdat)

   
    allVispdat$VISPDATTotalIndividualScore[allVispdat$VISPDATTotalIndividualScore == ''] <- '0'
    allVispdat$VISPDATTotalFamilyScore[allVispdat$VISPDATTotalFamilyScore == ''] <- '0'
    allVispdat$VISPDATTotalYouthScore[allVispdat$VISPDATTotalYouthScore == ''] <- '0'

    allVispdat$VISPDATTotalIndividualScore[is.na(allVispdat$VISPDATTotalIndividualScore)] <- '0'
    allVispdat$VISPDATTotalFamilyScore[is.na(allVispdat$VISPDATTotalFamilyScore)] <- '0'
    allVispdat$VISPDATTotalYouthScore[is.na(allVispdat$VISPDATTotalYouthScore)] <- '0'


    allVispdat$VISPDATTotalIndividualScore <- as.integer(allVispdat$VISPDATTotalIndividualScore)
    allVispdat$VISPDATTotalFamilyScore <- as.integer(allVispdat$VISPDATTotalFamilyScore)
    allVispdat$VISPDATTotalYouthScore <- as.integer(allVispdat$VISPDATTotalYouthScore)
    
    allVispdat <- subset(allVispdat)
    # Make one column for score.
    #allVispdat <- sqldf("SELECT *, CASE 
                                    #WHEN (VISPDATTotalFamilyScore IS '' 
                                          #AND VISPDATTotalYouthScore IS '') 
                                          #THEN VISPDATTotalIndividualScore
                                    #WHEN (VISPDATTotalFamilyScore IS '' 
                                          #AND VISPDATTotalIndividualScore IS '') 
                                          #THEN VISPDATTotalYouthScore
                                          #ELSE VISPDATTotalFamilyScore
                                   #END As 'ScoreVISPDAT'
                        #FROM allVispdat
                        #ORDER BY ScoreVISPDAT DESC
                      #")

    allVispdat <- sqldf("SELECT *, CASE 
                                    WHEN (VISPDATTotalFamilyScore <= VISPDATTotalIndividualScore
                                          AND VISPDATTotalYouthScore <= VISPDATTotalIndividualScore) 
                                          THEN VISPDATTotalIndividualScore
                                    WHEN (VISPDATTotalFamilyScore <= VISPDATTotalYouthScore
                                          AND VISPDATTotalIndividualScore <= VISPDATTotalYouthScore) 
                                          THEN VISPDATTotalYouthScore
                                          ELSE VISPDATTotalFamilyScore
                                   END As 'ScoreVISPDAT'
                        FROM allVispdat
                        ORDER BY ScoreVISPDAT DESC
                      ")

    allVispdat$ScoreVISPDAT <- as.numeric(allVispdat$ScoreVISPDAT)

  targetClient <- subset(targetClient)


  # Add VI-SPDAT scores and dates to the client list.
  targetClient <- sqldf("SELECT a.*, b.ScoreVISPDAT, b.DateOfVISPDAT, b.TypeOfVispdat
                        FROM targetClient a
                        LEFT JOIN allVispdat b
                        ON a.PersonalID=b.PersonalID
                        ")
  
  # Just in case, make date SQLite friendly.
  targetClient$DateOfVISPDAT <- as.character(targetClient$DateOfVISPDAT)
  
  remove(list = c("viSpdat", "viSpdat2", "allVispdat"))
  
  pbCounter <- pbCounter + addVispdatIncrement
  setTkProgressBar(pb, pbCounter, label = "Getting Family with Child")

 client <- sqldf("SELECT a.*, b.HouseholdID 
                  FROM client a
                  LEFT JOIN client_HHIDs b 
                  ON a.PersonalID=b.PersonalID")
 targetClient <- sqldf("SELECT a.*, b.HouseholdID 
                  FROM targetClient a
                  LEFT JOIN client_HHIDs b 
                  ON a.PersonalID=b.PersonalID")

    remove(client)
    remove(enrollment)

    client <- loadClient(hmisDataPath)
    enrollment <- loadEnrollment(hmisDataPath)

    family_flag_builder <- sqldf("SELECT DISTINCT PersonalID, HouseholdID, RelationshipToHoH FROM enrollment")

    family_flag_builder <- family_flag_builder[!is.na(family_flag_builder$HouseholdID),]
    family_flag_builder <- sqldf("SELECT HouseholdID, 
        (CASE WHEN RelationshipToHoH = 1 THEN 'Yes' ELSE 'No' END) As 'Adult', 
        (CASE WHEN RelationshipToHoH = 2 THEN 'Yes' ELSE 'No' END) As 'Child' 
        FROM family_flag_builder")
    hhids_of_adults <- sqldf("SELECT DISTINCT HouseholdID, Adult FROM family_flag_builder WHERE Adult = 'Yes'")
    hhids_of_child <- sqldf("SELECT DISTINCT HouseholdID, Child FROM family_flag_builder WHERE Child = 'Yes'")
    family_flag_builder <- sqldf("SELECT a.HouseholdID, a.Adult, b.Child
                         FROM hhids_of_adults a
                         INNER JOIN hhids_of_child b
                         ON a.HouseholdID=b.HouseholdID  
                         ")

    family_flag_builder <- sqldf("SELECT HouseholdID, 'Yes' As FamilyWithChildren FROM family_flag_builder WHERE Adult = 'Yes' AND Child = 'Yes' GROUP BY HouseholdID")
   
  # Add the family flag back to the client list.
  targetClient <- sqldf("SELECT DISTINCT a.*, b.FamilyWithChildren
                        FROM targetClient a
                        LEFT JOIN family_flag_builder b
                        ON a.HouseholdID=b.HouseholdID
                        ")
  
  remove(list = c("family_flag_builder"))
  
  targetClient <- subset(targetClient)
  pbCounter <- pbCounter + getFamilyWithChildIncrement
  setTkProgressBar(pb, pbCounter, label = "Loading Services")
  
  
  # Free up some memory before attempting Services.csv
  remove(list = c("client", "enrollment", "disabilities", "exit", "project"))
  
  setwd(hmisDataPath)
  
  # Load services -- large files.
  services <- loadServices()
  
  pbCounter <- pbCounter + loadServicesIncrement
  setTkProgressBar(pb, pbCounter, label = "Getting Night-by-Night Stays")
  
  # Get all of te NBN service entries.
  clientNbn <- sqldf("SELECT *
                     FROM services
                     WHERE RecordType = 200
                     ")
  # Count the number of NBN check-ins per client.  Make sure the date as distinct, due to ETO duplicate bed
  # stays when data is pulled using a program-group including two-shelters.
  daysCheckedInNBN <- sqldf("SELECT DISTINCT(PersonalID), COUNT (DISTINCT(DateProvided)) As 'NonProgramShelterNights'
                            FROM clientNbn
                            GROUP BY PersonalID
                            ")
  
  pbCounter <- pbCounter + nbnStaysIncrement
  setTkProgressBar(pb, pbCounter, label = "Getting Outreach Contacts")
  
  # Get all Outreach Contact services.
  clientOutreach <- sqldf("SELECT *
                          FROM services
                          WHERE RecordType = 12
                          ")
  
  # Count all Outreach Contacts per client.  Count distinct is to get around ETO bug when data is
  # pulled using a program group which includes two outreach agencies.
  outreachContacts <- sqldf("SELECT DISTINCT(PersonalID), COUNT (DISTINCT(DateProvided)) As 'NumberOutreachContacts'
                            FROM clientOutreach
                            GROUP BY PersonalID
                            ")
  
  pbCounter <- pbCounter + outreachContactsIncrement
  setTkProgressBar(pb, pbCounter, label = "Adding Outreach and NBN Count")
  
  # Add NBN stays to client list.
  targetClient <- sqldf("SELECT a.*, b.NonProgramShelterNights
                        FROM targetClient a
                        LEFT JOIN daysCheckedInNBN b
                        ON a.PersonalID=b.PersonalID
                        ")
  
  # Add Outreach Contacts to client list.
  targetClient <- sqldf("SELECT a.*, b.NumberOutreachContacts
                        FROM targetClient a
                        LEFT JOIN outreachContacts b
                        ON a.PersonalID=b.PersonalID
                        ")
  
  remove(list = c("services", "clientOutreach", "daysCheckedInNBN", "clientNbn", "outreachContacts"))

    pbCounter <- pbCounter + outreachAndNbnCountIncrement
    setTkProgressBar(pb, pbCounter, label = "Add Client Contact Info")

  # Add client contact information
  clientContactInfo <- readWorksheetFromFile(clientContactInfoPath, sheet = 1, startRow = 1)
  colnames(clientContactInfo)[1] <- "PersonalID"
  colnames(clientContactInfo)[2] <- "ProgramStartDate"
  colnames(clientContactInfo)[3] <- "ClientEmail"
    colnames(clientContactInfo)[4] <- "ClientPhone"
    clientContactInfo$PersonalID <- gsub("-", "", clientContactInfo$PersonalID)

  clientContactInfo <- getMostRecentRecordsPerId(clientContactInfo, "PersonalID", "ProgramStartDate")

  targetClient <- sqldf("SELECT a.*, b.ClientEmail, b.ClientPhone 
                        FROM targetClient a
                        LEFT JOIN clientContactInfo b
                        ON a.PersonalID=b.PersonalID
                        ")

  pbCounter <- pbCounter + clientContactinfoIncrement
  setTkProgressBar(pb, pbCounter, label = "Make HMIS Codes Readable")
  
  setwd(executionPath)
  
  # Make HMIS codes human readable.
  targetClient <- combineRaceColumnsAndMakeReadable(targetClient)
  targetClient <- makeGenderReadable(targetClient)
  targetClient <- makeEthnicityReadable(targetClient)
  targetClient <- makeVeteranStatusReadable(targetClient)
  
  
  pbCounter <- pbCounter + makeHmisCodesReadableIncrement
  setTkProgressBar(pb, pbCounter, label = "Format Homebase Dataframe")
  
  # Pull and format the client list.
  homebase_all <- sqldf("SELECT DISTINCT
                        PersonalID,
                        FirstName,
                        MiddleName,
                        LastName,
                        ClientEmail,
                        ClientPhone,
                        NameSuffix,
                        SSN,
                        DOB,
                        Age,
                        Gender,
                        Race,
                        Ethnicity,
                        VeteranStatus,
                        HouseholdID,
                        ChronicallyHomeless,
                        NumberOutreachContacts,
                        NonProgramShelterNights,
                        RecentHUDEntryDate,
                        MostRecentHUDAssess,
                        FamilyWithChildren,
                        ScoreVISPDAT,
                        TypeOfViSpdat,
                        DateOfVISPDAT,
                        PhysicalDisability,
                        DevelopmentalDisability,
                        ChronicHealthCondition,
                        a.'HIV/AIDS',
                        MentalHealthProblem,
                        SubstanceAbuse,
                        StaffName,
                        StaffEmail,
                        LastProgramInContact,
                        LastProjectTypeContacted,
                        ActiveInPH
                        FROM targetClient a
                        ")

    pbCounter <- pbCounter + formatHomebaseIncrement
    setTkProgressBar(pb, pbCounter, label = "Homebase Complete")

    # Clean up

    close(pb)
    rm(list = setdiff(ls(), "homebase_all"))
    # Retun list.
    homebase_all
}

Homebase Report

options(java.parameters = "-Xmx14336m") ## memory set to 14 GB

developmentLog <- c("REPORT DETAILS -- DO NOT DELETE THIS TAB",
                    "For development information please visit ladvien.com",

                    "5/30/17",
                    "Added order by for PSH and RRH -- should match operations manual.",
                    "Changed 90-day filter for VI-SPDAT to only need at least one VI-SPDAT to keep participant in 'active'",
                    "Added client contact information",


                    "5/10/2017",
                    "Changed EnrollmentCoC max date function to look at DateCreated not InformationDate",
                    "Changed the Enrollment max date function to look at EntryDate and not DateCreated",
                    "",
                                      
                    "05/07/2017",
                    "Automated Formatting",
                    "Added descending on VeteranStatus, FamilyWithChildren, ScoreVISPDAT in respective order.",
                    "Added Graphic Dashboard",
                    "",
                    
                    "05/07/2017",
                    "Switched from using Client.DOB -> Age for establishing family to Enrollment.RelationshipToHoH.  This seems to have addressed the families not flagging.",
                    "",
                    
                    "03/15/2017",
                    "Incorporated VI-SPDAT2",
                    "",
                    
                    "02/01/2017",
                    "Initial Report",
                    ""
                    )
# Argument guide
  # 1 = Name of Report
  # 2 = Folder path for HMIS data
  # 3 = VI-SPDAT File data
  # 4 = Staff Info File data
  # 5 = Executing directory path

# args <- commandArgs(trailingOnly = TRUE)
# nameOfReport <- args[1]
# hmisDataPath <- args[2]
# vispdatDataPath <- args[3]
# staffInfoDataPath <- args[4]
# executionPath <- args[5]
# viSpdat2DataPath <- args[6]
# 
# outputPath <- executionPath
# homebaseFunctionFilePath <- paste(executionPath, "\\Homebase_Function.R", sep ="")
# hmisFunctionsFilePath <- paste(executionPath, "\\HMIS_R_Functions.R", sep = "")

# PC
nameOfReport <- "Homebase_Report.R"
hmisDataPath <- "E:/Dropbox/HMIS/Warehouse/All Program 2016 Program Group  3-1-2017 - 5-30-2017"
vispdatDataPath <- "E:/Dropbox/HMIS/Warehouse/VI-SPDAT and HUD Flat Export for SQL -- 3-6-2017.xlsx"
staffInfoDataPath <- "E:/Dropbox/HMIS/Warehouse/Staff Contact Info for SQL -- 3-6-2017.xlsx"
executionPath <- "E:/Dropbox/HMIS/Coordinated_Entry_Report"
hmisFunctionsFilePath <- "E:/Dropbox/HMIS/HMIS_R_Functions/HMIS_R_Functions.R"
homebaseFunctionFilePath <- "E:/Dropbox/HMIS/Coordinated_Entry_v2_TX-601/Coordinated_Entry_v2_TX-601/Homebase_Function.R"
outputPath <- "E:/Dropbox/HMIS/Warehouse"
viSpdat2DataPath <- "E:/Dropbox/HMIS/Warehouse/VI-SPDAT v2.0 -- 04-05-17 -- TB.xlsx"
clientContactInfoPath <- "E:/Dropbox/HMIS/Warehouse/Client Contact for SQL -- 5-30-17 -- TB.xlsx"
outputPath <- "E:/Dropbox/HMIS/Warehouse"
# Mac PC
 #nameOfReport <- "Homebase_Report.R"
 #hmisDataPath <- "C:/Users/Ladvien/Desktop/Homebase 04-18-2017/data"
 #vispdatDataPath <- "C:/Users/Ladvien/Dropbox/HMIS/Warehouse/VI-SPDAT and HUD Flat Export for SQL -- 3-6-2017.xlsx"
 #staffInfoDataPath <- "C:/Users/Ladvien/Dropbox/HMIS/Warehouse/Staff Contact Info for SQL -- 3-6-2017.xlsx"
 #executionPath <- "C:/Users/Ladvien/Dropbox/HMIS/Coordinated_Entry_Report"
 #hmisFunctionsFilePath <- "C:/Users/Ladvien/Dropbox/HMIS/HMIS_R_Functions/HMIS_R_Functions.R"
 #homebaseFunctionFilePath <- "C:/Users/Ladvien/Dropbox/HMIS/Coordinated_Entry_v2_TX-601/Coordinated_Entry_v2_TX-601/Homebase_Function.R"
 #viSpdat2DataPath <- "C:/Users/Ladvien/Dropbox/HMIS/Warehouse/VI-SPDAT v2.0 -- 04-05-17 -- TB.xlsx"
 #outputPath <- "C:/Users/Ladvien/Desktop"
# Mac
#nameOfReport <- "Homebase_Report.R"
#hmisDataPath <- "/Users/user/Dropbox/HMIS/Coordinated_Entry_Report/All Programs 12-18-2016 to 03-18-2017"
#vispdatDataPath <- "/Users/user/Dropbox/HMIS/Coordinated_Entry_Report/VI-SPDAT and HUD Flat Export for SQL -- 3-6-2017.xlsx"
#staffInfoDataPath <- "/Users/user/Dropbox/HMIS/Coordinated_Entry_Report/Staff Contact Info for SQL -- 3-6-2017.xlsx"
#executionPath <- "/Users/user/Dropbox/HMIS/Coordinated_Entry_Report"
#hmisFunctions <- "/Users/user/Dropbox/HMIS/HMIS_R_Functions/HMIS_R_Functions.R"
cat("arg1: ")
cat(nameOfReport)
cat("\n") 
cat("arg2: ")
cat(hmisDataPath)
cat("\n") 
cat("arg3: ")
cat(vispdatDataPath)
cat("\n")
cat("arg4: ")
cat(staffInfoDataPath)
cat("\n")
cat("arg5: ")
cat(executionPath)
cat("\n")
cat("arg6: ")
cat(viSpdat2DataPath)
cat("\n")


source(homebaseFunctionFilePath)

homebase_all <- homebase(hmisDataPath,
                 vispdatDataPath,
                 staffInfoDataPath,
                 executionPath,
                 hmisFunctionsFilePath,
                 viSpdat2DataPath,
                 clientContactInfoPath)

######## WIP: Aggregates ##########
numberOfHudAssessmentsPerStaff <- sqldf("SELECT StaffName, COUNT(StaffName) FROM homebase_all GROUP BY StaffName")
#countOfChronicallyHomeless <- sqldf("SELECT COUNT(PersonalID) As CountOfChronic FROM homebase_all WHERE ChronicallyHomeless = 'Yes'")
#countOfGender <- sqldf("SELECT DISTINCT(Gender), COUNT(Gender) FROM homebase_all GROUP BY Gender")
#ageCounts <- sqldf("SELECT CASE
                        #WHEN Age < 5 THEN 1
                        #WHEN Age > 4 AND Age < 13 THEN 2
                        #WHEN Age > 13 AND Age < 18 THEN 3
                        #WHEN Age > 17 AND Age < 25 THEN 4
                        #WHEN Age > 24 AND Age < 35 THEN 5
                        #WHEN Age > 34 AND Age < 45 THEN 6
                        #WHEN Age > 44 AND Age < 55 THEN 7
                        #WHEN Age > 54 AND Age < 62 THEN 8
                        #WHEN Age > 61 THEN 9
                        #END As AgeType
                    #FROM homebase_all 
    #")

#aggregates <- cbind(numberOfHudAssessmentsPerStaff, countOfChronicallyHomeless)
homebase_housed <- sqldf("SELECT *
                         FROM homebase_all
                         WHERE ActiveInPH IS 'Yes'
                         ORDER BY VeteranStatus DESC,
                                  FamilyWithChildren DESC,
                                  ScoreVISPDAT DESC
                         ")

# Filter client to PersonalIDs with Entry or Update in last 90 days
homebase_active <- sqldf("SELECT *
                  FROM homebase_all
                  WHERE (
                          RecentHUDEntryDate > DATE('NOW', '-90 DAY')
                          OR (MostRecentHUDAssess > DATE('NOW', '-90 DAY'))
                        ) 
                        AND
                        (
                          (DateOfVISPDAT != '')
                        )
                  AND
                  ActiveInPH IS NOT 'Yes'
                  ORDER BY VeteranStatus DESC,
                           FamilyWithChildren DESC,
                           ScoreVISPDAT DESC
                  ")

tmp_possibly_active <- sqldf("SELECT *
                             FROM homebase_all
                             WHERE (( MostRecentHUDAssess > DATE('NOW', '-90 DAY')) 
                             OR
                             (
                              (DateOfVISPDAT > DATE('NOW', '-90 DAY'))
                             ))
                             AND
                             ActiveInPH IS NOT 'Yes'
                             ORDER BY VeteranStatus DESC,
                                      FamilyWithChildren DESC,
                                      ScoreVISPDAT DESC
                             ")

homebase_possibly_active <- sqldf("SELECT a.*
                                  FROM tmp_possibly_active a
                                  LEFT JOIN homebase_active b
                                  ON a.PersonalID=b.PersonalID
                                  WHERE b.PersonalID IS NULL
                                  ORDER BY VeteranStatus DESC,
                                           FamilyWithChildren DESC,
                                           ScoreVISPDAT DESC
                                  ")

homebase_psh <- sqldf("SELECT *
                      FROM homebase_active
                      WHERE ChronicallyHomeless = 'Yes'
                      ORDER BY MostRecentHUDAssess DESC                    
                      ")


homebase_psh <- sqldf("SELECT * FROM homebase_psh ORDER BY 
                                          ScoreVISPDAT DESC, 
                                          NonProgramShelterNights DESC
                                        ")


homebase_rrh <- sqldf("SELECT *
                      FROM homebase_active
                      WHERE ChronicallyHomeless IS NOT 'Yes'
                      ")

tmp_rrh_vets <- sqldf("SELECT * FROM homebase_rrh WHERE VeteranStatus = 'Yes'")
tmp_rrh_youth <- sqldf("SELECT * FROM homebase_rrh WHERE Age > 17 AND Age < 26")
tmp_rrh_families <- sqldf("SELECT * FROM homebase_rrh WHERE FamilyWithChildren = 'Yes'")
tmp_rrh_singles <- sqldf("SELECT * FROM homebase_rrh WHERE VeteranStatus IS NOT 'Yes' 
                                                           AND FamilyWithChildren IS NOT 'Yes'
                                                           AND Age < 18 OR Age > 25
                                                          ")


tmp_rrh_vets <- sqldf("SELECT * FROM tmp_rrh_vets ORDER BY
                                                ScoreVISPDAT DESC,
                                                NonProgramShelterNights DESC, 
                                                MostRecentHUDAssess DESC
                                                ")

tmp_rrh_youth <- sqldf("SELECT * FROM tmp_rrh_youth ORDER BY
                                                ScoreVISPDAT DESC,
                                                NonProgramShelterNights DESC, 
                                                MostRecentHUDAssess DESC
                                                ")

tmp_rrh_families <- sqldf("SELECT * FROM tmp_rrh_families ORDER BY
                                                ScoreVISPDAT DESC,
                                                NonProgramShelterNights DESC, 
                                                MostRecentHUDAssess DESC
                                                ")

tmp_rrh_singles <- sqldf("SELECT * FROM tmp_rrh_singles ORDER BY
                                                ScoreVISPDAT DESC,
                                                NonProgramShelterNights DESC, 
                                                MostRecentHUDAssess DESC
                                                ")

homebase_rrh <- rbind(tmp_rrh_vets, tmp_rrh_youth, tmp_rrh_families, tmp_rrh_singles)

homebase_assistToList <- sqldf("SELECT DISTINCT StaffName, COUNT(StaffName) As 'AssistToList'
                    FROM homebase_active
                    WHERE ActiveInPH IS NOT 'Yes'
                    GROUP BY StaffName
                    ORDER BY AssistToList DESC
                    ")


#library("ggplot2")

#df1 <- homebase_all$LastProjectTypeContacted

#ggplot(homebase_all, aes(NumberOutreachContacts, LastProgramInContact)) +
  #geom_raster(aes(fill = Age), interpolate = FALSE)


detach("package:XLConnect", unload = TRUE)
detach("package:xlsx", unload = TRUE)
library(openxlsx)

reportDetails <- data.frame(developmentLog)
colnames(reportDetails)[1] <- "Development Log"

ch_count <- sqldf("SELECT 'Chronically\nHomeless' As 'Category', 
    SUM(CASE ChronicallyHomeless WHEN 'Yes' THEN 1 ELSE 0 END) As 'Count'
    FROM homebase_psh")

vet_count <- sqldf("SELECT 'Veteran' As 'Category', 
    SUM(CASE VeteranStatus WHEN 'Yes' THEN 1 ELSE 0 END) As 'Count'
    FROM homebase_psh")

female_count <- sqldf("SELECT 'Female' As 'Category', 
    SUM(CASE Gender WHEN 'Female' THEN 1 ELSE 0 END) As 'Count'
    FROM homebase_psh")

male_count <- sqldf("SELECT 'Male' As 'Category', 
    SUM(CASE Gender WHEN 'Male' THEN 1 ELSE 0 END) As 'Count'
    FROM homebase_psh")

development_count <- sqldf("SELECT 'Developmental\nDisability' As 'Category', 
    SUM(CASE DevelopmentalDisability WHEN 'Yes' THEN 1 ELSE 0 END) As 'Count'
    FROM homebase_psh")
chronic_health_count <- sqldf("SELECT 'Chronic Health\nCondition' As 'Category', 
    SUM(CASE ChronicHealthCondition WHEN 'Yes' THEN 1 ELSE 0 END) As 'Count'
    FROM homebase_psh")
hiv_aids_count <- sqldf("SELECT 'HIV/AIDS' As 'Category', 
    SUM(CASE 'HIV/AIDS' WHEN 'Yes' THEN 1 ELSE 0 END) As 'Count'
    FROM homebase_psh")
mental_health_count <- sqldf("SELECT 'Mental Health\nProblem' As 'Category', 
    SUM(CASE MentalHealthProblem WHEN 'Yes' THEN 1 ELSE 0 END) As 'Count'
    FROM homebase_psh")
substance_abuse_count <- sqldf("SELECT 'Substance\nAbuse' As 'Category', 
    SUM(CASE SubstanceAbuse WHEN 'Yes' THEN 1 ELSE 0 END) As 'Count'
    FROM homebase_psh")

#fleeing_dv_count <-

family_count <- sqldf("SELECT 'Family With Children' As 'Category', 
    SUM(CASE FamilyWithChildren WHEN 'Yes' THEN 1 ELSE 0 END) As 'Count'
    FROM homebase_psh")


counts <- rbind(ch_count,
                vet_count,
                female_count,
                male_count,
                development_count,
                chronic_health_count,
                hiv_aids_count,
                mental_health_count,
                substance_abuse_count,
                family_count)

counts$val <- seq()
counts$Category <- factor(counts$Category, levels = counts$Category[order(counts$val)])

###########################################
# Calculate Housing Vacancy               #
###########################################

project <- loadProject(hmisDataPath)
enrollment <- loadEnrollment(hmisDataPath)
exit <- loadExit(hmisDataPath)
inventory <- loadInventory(hmisDataPath)

enrollmentAndProject <- addProjectInfoToEnrollment(enrollment, project)
activeInHousing <- sqldf("SELECT a.ProjectEntryID, a.PersonalID, a.ProjectType, a.ProjectName, a.ProjectID, b.ExitDate
                          FROM enrollmentAndProject a
                          LEFT JOIN exit b
                          ON a.ProjectEntryID=b.ProjectEntryID
                          WHERE (a.ProjectType = 2 OR a.ProjectType = 3 OR a.ProjectType = 9 OR a.ProjectType = 13)
                          ")

activeInHousing$ExitDate[is.na(activeInHousing$ExitDate)] <- 0
activeInHousing <- sqldf("SELECT DISTINCT * FROM activeInHousing WHERE ExitDate = 0")
aggregatedActiveInHousing <- sqldf("SELECT ProjectName, ProjectID, COUNT(ProjectName) As 'Enrolled' 
                                    FROM activeInHousing 
                                    GROUP BY ProjectName
                                    ORDER BY Enrolled DESC")

tmp <- sqldf("SELECT ProjectID, SUM(HMISParticipatingBeds) As 'Beds' FROM inventory GROUP BY ProjectID")

aggregatedActiveInHousing <- sqldf("SELECT a.*, b.Beds 
                                    FROM aggregatedActiveInHousing a
                                    LEFT JOIN tmp b
                                    ON a.ProjectID=b.ProjectID
                                   ")

projectVacancy <- sqldf("SELECT ProjectName, Enrolled, Beds, (CAST(Enrolled As FLOAT) / CAST(Beds As Float)) As 'OccupancyPercentage' FROM aggregatedActiveInHousing ORDER BY 'Vacancy %' DESC")
projectVacancy <- projectVacancy[order(projectVacancy$OccupancyPercentage),]
projectVacancy <- subset(projectVacancy)
projectWithVacancy <- sqldf("SELECT * FROM projectVacancy WHERE OccupancyPercentage < 1")
projectWithVacancy <- subset(projectWithVacancy)

###########################################
# Create some Awesome Graphs              #
###########################################

library("ggplot2")
library("RColorBrewer")
png("rrhCountsGraph.png", height = 1200, width = 1200, res = 250, pointsize = 8)
rrhCountsGraph <- ggplot(data = counts, aes(x = Category, y = Count, fill = Category)) +
    geom_bar(stat = "identity") +
    labs(title = "Permanent Supportive Housing Eligibe") +
    theme(axis.text.x = element_text(angle = 45, hjust = 1),
        legend.position = "none") +
    scale_fill_brewer(palette = "Spectral")
dev.off()

n <- 60
qual_col_pals = brewer.pal.info[brewer.pal.info$category == 'qual',]
col_vector = unlist(mapply(brewer.pal, qual_col_pals$maxcolors, rownames(qual_col_pals)))
levels <- seq(nrow(projectVacancy))
projectVacancy$Order <- levels
png("projectVacancy.png", height = 1200, width = 1200, res = 250, pointsize = 8)
projectVacancyGraph <- ggplot(data = projectVacancy, aes(x = reorder(ProjectName, -projectVacancy$Order), y = OccupancyPercentage, fill = ProjectName)) +
    geom_bar(stat = "identity") +
    labs(title = "Occupancy by Housing Projects") +
    theme(axis.text.x = element_text(angle = 90, hjust = 1),
        legend.position = "none") +
    coord_flip()
dev.off()
print(projectVacancyGraph)


n <- 60
qual_col_pals = brewer.pal.info[brewer.pal.info$category == 'qual',]
col_vector = unlist(mapply(brewer.pal, qual_col_pals$maxcolors, rownames(qual_col_pals)))
levels <- seq(nrow(projectWithVacancy))
projectWithVacancy$Order <- levels

vacancyPal <- c("#70AD47", "#47A3AD", "#AD5147", "#8447AD")

png("projectWithVacancy.png", height = 1200, width = 1200, res = 250, pointsize = 8)
projectWithVacancyGraph <- ggplot(data = projectWithVacancy,
        aes(x = reorder(ProjectName, Order), y = OccupancyPercentage, fill = OccupancyPercentage)) +
    geom_bar(stat = "identity", width = 1, color = vacancyPal[4]) +
    scale_fill_gradient2(low = "green", mid = vacancyPal[1], high = vacancyPal[2]) +
    labs(title = "Occupancy by Project") +
    xlab("Current Occupancy %") +
    ylab("Occupancy %") +
    theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 16),
          axis.text.y = element_text(hjust = 1),
        legend.position = "none") +
    coord_flip()
dev.off()
ggsave("projectWithVacancy.png")
print(projectWithVacancyGraph)

###########################################
# Format Workbook, Add Graphs, and Write  #`
###########################################
library("openxlsx")
setwd(outputPath)
# Theme
color_column_background <- "#70AD47"
color_header_font_color <- "#FFFFFF"
column_header_font_size <- 18

## Header Styles
headerStyle1 <- createStyle(fgFill = color_column_background,
                            valign = "top",
                            halign = "CENTER",
                            fontColour = color_header_font_color,
                            fontSize = column_header_font_size)

# Create the Workbook
homebaseWorkbook <- createWorkbook()

# Add the needed sheets.
addWorksheet(homebaseWorkbook, sheetName = "Dashboard")
addWorksheet(homebaseWorkbook, sheetName = "EligibleForPSH")
addWorksheet(homebaseWorkbook, sheetName = "EligibleForRRH")
addWorksheet(homebaseWorkbook, sheetName = "Possibly Active")
addWorksheet(homebaseWorkbook, sheetName = "Housed")
addWorksheet(homebaseWorkbook, sheetName = "AssistToList")
addWorksheet(homebaseWorkbook, sheetName = "Report Details")

# Add the data to worksheets.
writeDataTable(homebaseWorkbook, sheet = 2, x = homebase_psh, colNames = TRUE, tableStyle = "TableStyleLight9", headerStyle = headerStyle1)
writeDataTable(homebaseWorkbook, sheet = 3, x = homebase_rrh, colNames = TRUE, tableStyle = "TableStyleLight9", headerStyle = headerStyle1)
writeDataTable(homebaseWorkbook, sheet = 4, x = homebase_possibly_active, colNames = TRUE, tableStyle = "TableStyleLight9", headerStyle = headerStyle1)
writeDataTable(homebaseWorkbook, sheet = 5, x = homebase_housed, colNames = TRUE, tableStyle = "TableStyleLight9", headerStyle = headerStyle1)
writeDataTable(homebaseWorkbook, sheet = 6, x = homebase_assistToList, colNames = TRUE, tableStyle = "TableStyleLight9", headerStyle = headerStyle1)
writeDataTable(homebaseWorkbook, sheet = 7, x = reportDetails, colNames = TRUE, tableStyle = "TableStyleLight9", headerStyle = headerStyle1)

# Format the columns for readability.
setColWidths(homebaseWorkbook, 2, cols = 2:ncol(homebase_psh), widths = "auto")
setColWidths(homebaseWorkbook, 3, cols = 2:ncol(homebase_rrh), widths = "auto")
setColWidths(homebaseWorkbook, 4, cols = 2:ncol(homebase_possibly_active), widths = "auto")
setColWidths(homebaseWorkbook, 5, cols = 2:ncol(homebase_housed), widths = "auto")
setColWidths(homebaseWorkbook, 6, cols = 2:ncol(homebase_assistToList), widths = "auto")
setColWidths(homebaseWorkbook, 7, cols = 2:ncol(reportDetails), widths = "auto")

# Format first column statically.  For some reason, 'auto' clips the PersonalID
setColWidths(homebaseWorkbook, 2, cols = 1:1, widths = 38)
setColWidths(homebaseWorkbook, 3, cols = 1:1, widths = 38)
setColWidths(homebaseWorkbook, 4, cols = 1:1, widths = 38)
setColWidths(homebaseWorkbook, 5, cols = 1:1, widths = 38)
setColWidths(homebaseWorkbook, 6, cols = 1:1, widths = 38)
setColWidths(homebaseWorkbook, 2, cols = 1:1, widths = 38)

# Format rows.
setRowHeights(homebaseWorkbook, 2, rows = 1:1, height = 40)
setRowHeights(homebaseWorkbook, 3, rows = 1:1, height = 40)
setRowHeights(homebaseWorkbook, 4, rows = 1:1, height = 40)
setRowHeights(homebaseWorkbook, 5, rows = 1:1, height = 40)
setRowHeights(homebaseWorkbook, 6, rows = 1:1, height = 40)
setRowHeights(homebaseWorkbook, 7, rows = 1:1, height = 40)

# Freeze the top row
freezePane(homebaseWorkbook, sheet = 2, firstRow = TRUE)
freezePane(homebaseWorkbook, sheet = 3, firstRow = TRUE)
freezePane(homebaseWorkbook, sheet = 4, firstRow = TRUE)
freezePane(homebaseWorkbook, sheet = 5, firstRow = TRUE)
freezePane(homebaseWorkbook, sheet = 6, firstRow = TRUE)

##################################
#### Add Graphs to Workbook ######
##################################  
print(rrhCountsGraph) #plot needs to be showing
insertPlot(homebaseWorkbook, 1, width = 7.87, height = 5.5, fileType = "png", units = "in")

# Openxlsx requires zip.exe to save the workbook.  Weird.
Sys.setenv("R_ZIPCMD" = "C:/Rtools/bin/zip.exe")
today <- Sys.Date()
print(outputPath)
saveWorkbook(homebaseWorkbook, paste(outputPath, "\\", "Homebase_v2_", today, ".xlsx", sep =""), overwrite = TRUE)
cat(getwd())

openXL(paste(outputPath, "\\", "Homebase_v2_", today, ".xlsx", sep = ""))

The whole thing relies on some R functions I’ve written to assist:

HMIS Functions

  # Thanks SO. 
# http://stackoverflow.com/questions/9341635/check-for-installed-packages-before-running-install-packages
pkgTest <- function(x)
{
  if (!require(x,character.only = TRUE))
  {
    install.packages(x,dep=TRUE)
    library(x, character.only =  TRUE)
    if(!require(x,character.only = TRUE)) stop("Package not found")
  } else {
    library(x, character.only =  TRUE)
  }
}

pkgTest("sqldf")
pkgTest("tcltk")
pkgTest("zoo")
pkgTest("XLConnect")

loadAffiliation <- function(path = getwd()){
  affiliation <- read.csv(paste(path, "/Affiliation.csv", sep = ""))
}

loadClient <- function(path = getwd()){
  client <- read.csv(paste(path, "/Client.csv", sep = ""))
}

loadDisabilities <- function(path = getwd()) {
  disabilities <- read.csv(paste(path,  "/Disabilities.csv", sep = ""))
}

loadEmployementEducation <- function(path = getwd()) {
  employementEducation <- read.csv(paste(path, "/EmploymentEducation.csv", sep = ""))
}

loadEnrollment <- function(path = getwd()) {
  enrollment <- read.csv(paste(path, "/Enrollment.csv", sep = ""))
}

loadEnrollmentCoc <- function(path = getwd()) {
  enrollmentCoc <- read.csv(paste(path, "/EnrollmentCoC.csv", sep = ""))
}

loadExit <- function(path = getwd()) {
  exit <- read.csv(paste(path, "/Exit.csv", sep = ""))
}

loadExport <- function(path = getwd()) {
  export <- read.csv(paste(path, "/Export.csv", sep = ""))
}

loadFunder <- function(path = getwd()){
  funder <- read.csv(paste(path, "/Funder.csv", sep = ""))
}

loadHealthAndDv <- function(path = getwd()){
  healthAndDv <- read.csv(paste(path, "/HealthAndDV.csv", sep = ""))
}

loadIncomeBenefits <- function(path = getwd()){
  incomeBenefits <- read.csv(paste(path, "/IncomeBenefits.csv", sep = ""))
}

loadInventory <- function(path = getwd()){
  inventory <- read.csv(paste(path, "/Inventory.csv", sep = ""))
}

loadOrganization <- function(path = getwd()){
  organization <- read.csv(paste(path, "/Organization.csv", sep = "")) 
}

loadProject <- function(path = getwd()){
  project <- read.csv(paste(path, "/Project.csv", sep = ""))
}

loadProjectCoc <- function(path = getwd()){
  projectCoc <- read.csv(paste(path, "/ProjectCoC.csv", sep = ""))
}

loadServices <- function(path = getwd()){
  services <- read.csv(paste(path, "/Services.csv", sep = ""))
}

loadSite <- function(path = getwd()){
  site <- read.csv(paste(path, "/Site.csv", sep = ""))
}

# loadHMISCsvs51 <- function(path) {
#   affiliation <- read.csv(paste(path, "/Affiliation.csv", sep = ""))
#   client <- read.csv(paste(path, "/Client.csv", sep = ""))
#   disabilities <- read.csv(paste(path,  "/Disabilities.csv", sep = ""))
#   employementEducation <- read.csv(paste(path, "/EmploymentEducation.csv", sep = ""))
#   enrollment <- read.csv(paste(path, "/Enrollment.csv", sep = ""))
#   exit <- read.csv(paste(path, "/Exit.csv", sep = ""))
#   export <- read.csv(paste(path, "/Export.csv", sep = ""))
#   funder <- read.csv(paste(path, "/Funder.csv", sep = ""))
#   healthAndDv <- read.csv(paste(path, "/HealthAndDV.csv", sep = ""))
#   incomeBenefits <- read.csv(paste(path, "/IncomeBenefits.csv", sep = ""))
#   inventory <- read.csv(paste(path, "/Inventory.csv", sep = ""))
#   organization <- read.csv(paste(path, "/Organization.csv", sep = ""))
#   project <- read.csv(paste(path, "/Project.csv", sep = ""))
#   projectCoc <- read.csv(paste(path, "/ProjectCoC.csv", sep = ""))
#   services <- read.csv(paste(path, "/Services.csv", sep = ""))
#   site <- read.csv(paste(path, "/Site.csv", sep = ""))
#   return(c(services, site))
# }



makeDestinationReadable <- function (df) {
  df <- exit
  df <- sqldf("SELECT *, Destination as 'ReadableDestination' FROM df")
  df$ReadableDestination[df$ReadableDestination == "1"] <- "Emergency shelter, including hotel or motel paid for with emergency shelter voucher"
  df$ReadableDestination[df$ReadableDestination == "2"] <- "Transitional housing for homeless persons (including homeless youth)"
  df$ReadableDestination[df$ReadableDestination == "3"] <- "Permanent housing for formerly homeless persons (such as: CoC project; or HUD legacy programs; or HOPWA PH)"
  df$ReadableDestination[df$ReadableDestination == "4"] <- "Psychiatric hospital or other psychiatric facility"
  df$ReadableDestination[df$ReadableDestination == "5"] <- "Substance abuse treatment facility or detox center"
  df$ReadableDestination[df$ReadableDestination == "6"] <- "Hospital or other residential non-psychiatric medical facility"
  df$ReadableDestination[df$ReadableDestination == "7"] <- "Jail, prison or juvenile detention facility"
  df$ReadableDestination[df$ReadableDestination == "8"] <- "Client doesn’t know"
  df$ReadableDestination[df$ReadableDestination == "9"] <- "Client refused"
  df$ReadableDestination[df$ReadableDestination == "10"] <- "Rental by client, no ongoing housing subsidy"
  df$ReadableDestination[df$ReadableDestination == "11"] <- "Owned by client, no ongoing housing subsidy"
  df$ReadableDestination[df$ReadableDestination == "12"] <- "Staying or living with family, temporary tenure (e.g., room, apartment or house)"
  df$ReadableDestination[df$ReadableDestination == "13"] <- "Staying or living with friends, temporary tenure (e.g., room apartment or house)"
  df$ReadableDestination[df$ReadableDestination == "14"] <- "Hotel or motel paid for without emergency shelter voucher"
  df$ReadableDestination[df$ReadableDestination == "15"] <- "Foster care home or foster care group home"
  df$ReadableDestination[df$ReadableDestination == "16"] <- "Place not meant for habitation (e.g., a vehicle, an abandoned building, bus/train/subway station/airport or anywhere outside)"
  df$ReadableDestination[df$ReadableDestination == "17"] <- "Other"
  df$ReadableDestination[df$ReadableDestination == "18"] <- "Safe Haven"
  df$ReadableDestination[df$ReadableDestination == "19"] <- "Rental by client, with VASH housing subsidy"
  df$ReadableDestination[df$ReadableDestination == "20"] <- "Rental by client, with other ongoing housing subsidy"
  df$ReadableDestination[df$ReadableDestination == "21"] <- "Owned by client, with ongoing housing subsidy"
  df$ReadableDestination[df$ReadableDestination == "22"] <- "Staying or living with family, permanent tenure"
  df$ReadableDestination[df$ReadableDestination == "23"] <- "Staying or living with friends, permanent tenure"
  df$ReadableDestination[df$ReadableDestination == "24"] <- "Deceased"
  df$ReadableDestination[df$ReadableDestination == "25"] <- "Long-term care facility or nursing home"
  df$ReadableDestination[df$ReadableDestination == "26"] <- "Moved from one HOPWA funded project to HOPWA PH"
  df$ReadableDestination[df$ReadableDestination == "27"] <- "Moved from one HOPWA funded project to HOPWA TH"
  df$ReadableDestination[df$ReadableDestination == "28"] <- "Rental by client, with GPD TIP housing subsidy"
  df$ReadableDestination[df$ReadableDestination == "29"] <- "Residential project or halfway house with no homeless criteria"
  df$ReadableDestination[df$ReadableDestination == "30"] <- "No exit interview completed"
  df$ReadableDestination[df$ReadableDestination == "99"] <- "Data not collected"
  
  df
}


makeProjectTypeReadable <- function (df) {
  df <- sqldf("SELECT *, ProjectType as 'ReadableProjectType' FROM df")
  df$ReadableProjectType[df$ReadableProjectType == "1"] <- "Emergency Shelter"
  df$ReadableProjectType[df$ReadableProjectType == "2"] <- "Transitional Housing"
  df$ReadableProjectType[df$ReadableProjectType == "3"] <- "PH - Permanent Supportive Housing"
  df$ReadableProjectType[df$ReadableProjectType == "4"] <- "Street Outreach"
  df$ReadableProjectType[df$ReadableProjectType == "5"] <- "Services Only"
  df$ReadableProjectType[df$ReadableProjectType == "6"] <- "Other"
  df$ReadableProjectType[df$ReadableProjectType == "7"] <- "Safe Haven"
  df$ReadableProjectType[df$ReadableProjectType == "8"] <- "PH – Housing Only"
  df$ReadableProjectType[df$ReadableProjectType == "10"] <- "PH – Housing with Services (no disability required for entry)"
  df$ReadableProjectType[df$ReadableProjectType == "11"] <- "Day Shelter"
  df$ReadableProjectType[df$ReadableProjectType == "12"] <- "Homelessness Prevention"
  df$ReadableProjectType[df$ReadableProjectType == "13"] <- "PH - Rapid Re-Housing"
  df$ReadableProjectType[df$ReadableProjectType == "14"] <- "Coordinated Assessment"
  
  df
}

makeRaceReadable <- function(client){
  client$AmIndAKNativ[client$AmIndAKNative == "1"] <- "American Indian or Alaska Native"
  client$Asian[client$Asian == "1"] <- "Asian"
  client$BlackAfAmerican[client$BlackAfAmerican == "1"] <- "Black or African American"
  client$NativeHIOtherPacific[client$NativeHIOtherPacific == "1"] <- "Native Hawaiian or Other Pacific Islander"
  client$White[client$White == "1"] <- "White"
  client$RaceNone[client$RaceNone == "8"] <- "Client doesnt know"
  client$RaceNone[client$RaceNone == "9"] <- "Client refused"
  client$RaceNone[client$RaceNone == "99"] <- "Data not collected"
  client
}

makeGenderReadable <- function(client) {
  
  # HMIS CSV 5.1
  # 0 Female
  # 1 Male
  # 2 Transgender male to female
  # 3 Transgender female to male
  # 4 Doesn’t identify as male, female, or transgender
  # 8 Client doesn’t know
  # 9 Client refused
  # 99 Data not collected
  
  client$Gender[client$Gender == "0"] <- "Female"
  client$Gender[client$Gender == "1"] <- "Male"
  client$Gender[client$Gender == "2"] <- "Transgender male to female"
  client$Gender[client$Gender == "3"] <- "Transgender female to male"
  client$Gender[client$Gender == "4"] <- "Doesn’t identify as male, female, or transgender"
  client$Gender[client$Gender == "8"] <- "Client doesn’t know"
  client$Gender[client$Gender == "9"] <- "Client refused"
  client$Gender[client$Gender == "99"] <- "Data not collected"
  
  client
}

makeVeteranStatusReadable <- function(client) {
  
  # HMIS CSV 5.1
  # 0 No
  # 1 Yes
  # 8 Client doesn’t know
  # 9 Client refused
  # 99 Data not collected
  
  client$VeteranStatus[client$VeteranStatus == "0"] <- "No"
  client$VeteranStatus[client$VeteranStatus == "1"] <- "Yes"
  client$VeteranStatus[client$VeteranStatus == "8"] <- "Client doesn’t know"
  client$VeteranStatus[client$VeteranStatus == "9"] <- "Client refused"
  client$VeteranStatus[client$VeteranStatus == "99"] <- "Data not collected"
  
  client
}

makeEthnicityReadable <- function(client) {
  
  # HMIS CSV 5.1
  # 0 Non-Hispanic/Non-Latino
  # 1 Hispanic/Latino
  # 8 Client doesn’t know
  # 9 Client refused
  # 99 Data not collected
  
  client$Ethnicity[client$Ethnicity == "0"] <- "Non-Hispanic/Non-Latino"
  client$Ethnicity[client$Ethnicity == "1"] <- "Hispanic/Latino"
  client$Ethnicity[client$Ethnicity == "8"] <- "Client doesn’t know"
  client$Ethnicity[client$Ethnicity == "9"] <- "Client refused"
  client$Ethnicity[client$Ethnicity == "99"] <- "Data not collected"
  
  client
}

combineRaceColumnsAndMakeReadable <- function(client){
  client$AmIndAKNativ[client$AmIndAKNative == "0"] <- ""
  client$Asian[client$Asian == "0"] <- ""
  client$BlackAfAmerican[client$BlackAfAmerican == "0"] <- ""
  client$NativeHIOtherPacific[client$NativeHIOtherPacific == "0"] <- ""
  client$White[client$White == "0"] <- ""  
  client$RaceNone[client$RaceNone == "0"] <- ""
  
  client <- makeRaceReadable(client)
  client$Race <- paste(client$AmIndAKNativ, client$Asian, client$BlackAfAmerican, client$NativeHIOtherPacific, client$White, client$RaceNone, sep = " ")
  client$Race <- gsub(" NA", "",client$Race)
  client <- client[,-which(names(client) == "AmIndAKNative")]
  client <- client[,-which(names(client) == "Asian")] 
  client <- client[,-which(names(client) == "BlackAfAmerican")]
  client <- client[,-which(names(client) == "NativeHIOtherPacific")]
  client <- client[,-which(names(client) == "White")]
  client <- client[,-which(names(client) == "RaceNone")]
  client
}

addDisabilityInfoToClient <- function(client, disabilities){
  
  # From HMIS CSV Programming Specifications 5.1
  # 5 = Physical disability
  clientsWithPhysicalDisability <- sqldf("SELECT *, 'Yes' As PhysicalDisability 
                                         FROM disabilities
                                         WHERE DisabilityType = 5
                                         AND DisabilityResponse = 1
                                         ")
  
  clientsWithPhysicalDisability <- getMostRecentRecordsPerId(clientsWithPhysicalDisability, "PersonalID", "InformationDate")
  
  client <- sqldf("SELECT a.*, b.PhysicalDisability
                  FROM client a
                  LEFT JOIN clientsWithPhysicalDisability b
                  ON a.PersonalID=b.PersonalID
                  ")
  
  client <- subset(client)
  
  # 6 Developmental disability
  clientDevelopmentalDisability <- sqldf("SELECT *, 'Yes' As DevelopmentalDisability 
                                         FROM disabilities
                                            WHERE DisabilityType = 6
                                            AND DisabilityResponse = 1
                                            ")
  
  clientDevelopmentalDisability <- getMostRecentRecordsPerId(clientDevelopmentalDisability, "PersonalID", "InformationDate")
  
  clientDevelopmentalDisability <- subset(clientDevelopmentalDisability)
  
  client <- sqldf("SELECT a.*, b.DevelopmentalDisability
                  FROM client a
                  LEFT JOIN clientDevelopmentalDisability b
                  ON a.PersonalID=b.PersonalID
                  ")
  
  client <- subset(client)
  
  # 7 Chronic health condition
  clientChronicHealthCondition <- sqldf("SELECT *, 'Yes' As ChronicHealthCondition 
                                         FROM disabilities
                                        WHERE DisabilityType = 7
                                        AND DisabilityResponse = 1
                                        ")
  
  clientChronicHealthCondition <- getMostRecentRecordsPerId(clientChronicHealthCondition, "PersonalID", "InformationDate")
  
  client <- sqldf("SELECT a.*, b.ChronicHealthCondition
                  FROM client a
                  LEFT JOIN clientChronicHealthCondition b
                  ON a.PersonalID=b.PersonalID
                  ")
  
  client <- subset(client)
  
  # 8 HIV/AIDS
  clientHivAids         <- sqldf("SELECT *, 'Yes' As 'HIV/AIDS' 
                                         FROM disabilities
                                        WHERE DisabilityType = 8
                                        AND DisabilityResponse = 1
                                        ")
  
  clientHivAids <- getMostRecentRecordsPerId(clientHivAids, "PersonalID", "InformationDate")
  
  client <- sqldf("SELECT a.*, b.'HIV/AIDS'
                  FROM client a
                  LEFT JOIN clientHivAids b
                  ON a.PersonalID=b.PersonalID
                  ")
  
  client <- subset(client)
  
  # 9 Mental health problem
  clientMentalHealthProblem <- sqldf("SELECT *, 'Yes' As MentalHealthProblem 
                                         FROM disabilities
                                     WHERE DisabilityType = 9
                                     AND DisabilityResponse = 1
                                     ")
  
  clientMentalHealthProblem <- getMostRecentRecordsPerId(clientMentalHealthProblem, "PersonalID", "InformationDate")
  
  client <- sqldf("SELECT a.*, b.MentalHealthProblem
                  FROM client a
                  LEFT JOIN clientMentalHealthProblem b
                  ON a.PersonalID=b.PersonalID
                  ")
  
  client <- subset(client)
  
  # 10 Substance abuse
  clientSubstanceAbuse      <- sqldf("SELECT *, 'Yes' As SubstanceAbuse 
                                         FROM disabilities
                                     WHERE DisabilityType = 10
                                     AND DisabilityResponse = 1
                                     ")
  
  clientSubstanceAbuse <- getMostRecentRecordsPerId(clientSubstanceAbuse, "PersonalID", "InformationDate")
  
  client <- sqldf("SELECT a.*, b.SubstanceAbuse
                  FROM client a
                  LEFT JOIN clientSubstanceAbuse b
                  ON a.PersonalID=b.PersonalID
                  ")
  
  client <- subset(client)
  
  client
}


makeDisabilityTypeReadable <- function(disabilities){
  # From HMIS CSV Programming Specifications 5.1
  # 5 Physical disability
  # 6 Developmental disability
  # 7 Chronic health condition
  # 8 HIV/AIDS
  # 9 Mental health problem
  # 10 Substance abuse
  disabilities$DisabilityType[disabilities$DisabilityType == "5"] <- "Physical disability"
  disabilities$DisabilityType[disabilities$DisabilityType == "6"] <- "Developmental disability"
  disabilities$DisabilityType[disabilities$DisabilityType == "7"] <- "PhysicalChronic health condition"
  disabilities$DisabilityType[disabilities$DisabilityType == "8"] <- "Chronic health condition"
  disabilities$DisabilityType[disabilities$DisabilityType == "9"] <- "HIV/AIDS"
  disabilities$DisabilityType[disabilities$DisabilityType == "10"] <- "Substance abuse"
  disabilities  
}

makeTrackingMethodReadable <- function(df) {
  df <- sqldf("SELECT *, ProjectType as 'ReadableTrackingMethod' FROM df")
  df$ReadableProjectType[df$ReadableProjectType == "0"] <- "Entry/Exit Date"
  df$ReadableProjectType[df$ReadableProjectType == "3"] <- "Night-by-Night"
}

# activeRecords <- activeFilter(df, "occStartDate", "occEndDate", "2017-01-23", '2017-01-26')
activeFilter <- function(df, dateVector1, dateVector2, beginRange, endRange){
  df[is.na(df)] <- ""
  df[dateVector1,] <- as.character(df[dateVector1,])
  df[dateVector2,] <- as.character(df[dateVector2,])
  str <- paste("SELECT * FROM df WHERE (", dateVector1, "< '", endRange, "' AND ", dateVector2, " = '') OR (", dateVector1, "< '", endRange, "' AND ", dateVector2, " > '", beginRange, "')", sep = "")
  sqldf(str)
}

# Get active Enrollments
getActiveHudEnrollments <- function(enrollment, exit, project){
  project <- makeProjectTypeReadable(project)
  
  project <- subset(project)
  
  activeEnrollment <- sqldf("SELECT *
                            FROM enrollment a
                            LEFT JOIN exit b
                            ON a.ProjectEntryID=b.ProjectEntryID
                            WHERE b.ProjectEntryID IS NULL")
  
  
  activeEnrollment <- subset(activeEnrollment)
  
  activeEnrollmentsWithProjectInfo <- sqldf("SELECT b.ProjectType, b.ReadableProjectType, b.ProjectID, b.ProjectName, a.*
                                            FROM activeEnrollment a
                                            INNER JOIN project b
                                            ON a.ProjectID=b.ProjectID
                                            ")
  
  activeEnrollmentsWithProjectInfo <- subset(activeEnrollmentsWithProjectInfo)
  activeEnrollmentsWithProjectInfo
}


addProjectInfoToEnrollment <- function(enrollment, project){
  project <- makeProjectTypeReadable(project)
  enrollmentsWithProjectInfo <- sqldf("SELECT a.*, b.ProjectType, b.ReadableProjectType, b.ProjectName, b.TrackingMethod
                                            FROM enrollment a
                                            INNER JOIN project b
                                            ON a.ProjectID=b.ProjectID
                                            ")
  
  enrollmentsWithProjectInfo <- subset(enrollmentsWithProjectInfo)
  enrollmentsWithProjectInfo
}


getMostRecentRecordsPerId <- function(df, idHeader, dateHeader){
  str <- paste("SELECT *, MAX(", dateHeader, "), 'Yes' As Max", dateHeader, " FROM df GROUP BY ", idHeader, sep = "")
  bfr <- sqldf(str)
  sqldf(str)
}

getClientsInPH <- function(enrollment, exit, project) {
  
  ### START ###
  #############################################
  ##### Active in PH Projects #################
  ############## Incomplete ###################
  #############################################
  
  project <- makeProjectTypeReadable(project)
  
  project <- subset(project)
  
  activeEnrollment <- sqldf("SELECT *
                            FROM enrollment a 
                            LEFT JOIN exit b
                            ON a.ProjectEntryID=b.ProjectEntryID
                            WHERE b.ProjectEntryID IS NULL")
  
  
  activeEnrollment <- subset(activeEnrollment)
  
  activeEnrollmentsWithProjectInfo <- sqldf("SELECT b.ProjectType, b.ReadableProjectType, b.ProjectID, b.ProjectName, a.*
                                            FROM activeEnrollment a
                                            INNER JOIN project b
                                            ON a.ProjectID=b.ProjectID
                                            ")
  
  activeEnrollmentsWithProjectInfo <- subset(activeEnrollmentsWithProjectInfo)
  
  # PSH = 3
  # RRH = 13
  clientsActiveInPh <- sqldf("SELECT PersonalID, 'Yes' As 'ActiveInPH'
                             FROM activeEnrollmentsWithProjectInfo
                             WHERE ProjectType = 3
                             OR ProjectType = 13
                             ")
  
  clientsActiveInPh <- subset(clientsActiveInPh)
  clientsActiveInPh
}

getClientsInPHWithinRange <- function(enrollment, exit, project, beginDate, endDate) {
  
  enrollment$EntryDate <- as.character(enrollment$EntryDate)
  exit$ExitDate <- as.character(exit$ExitDate)
  
  project <- makeProjectTypeReadable(project)
  
  project <- subset(project)
  
  enrollmentWithProjectInfo <- sqldf("SELECT b.ProjectType, b.ReadableProjectType, b.ProjectID, b.ProjectName, a.*
                                     FROM enrollment a
                                     INNER JOIN project b
                                     ON a.ProjectID=b.ProjectID
                                     ")

  enrollmentWithProjectInfo <- subset(enrollmentWithProjectInfo)
  
  str <- paste("SELECT * FROM enrollmentWithProjectInfo WHERE (ProjectType = 3 OR ProjectType = 13) AND EntryDate < '", beginDate, "'", sep = "")
  
  phEnrollment <- sqldf(str)

  str2 <- paste("SELECT * FROM exit WHERE ExitDate < '", endDate, "'", sep = "")
  relevantExit <- sqldf(str2)

  activeEnrollment <- sqldf("SELECT *
                            FROM phEnrollment a
                            LEFT JOIN relevantExit b
                            ON a.ProjectEntryID=b.ProjectEntryID
                            WHERE b.ProjectEntryID IS NULL")

  ######################################################################
  ######################################################################
  ######################################################################
  ###################### Left off Here #################################
  ######################################################################
  ######################################################################
  ######################################################################
}

getWeeksBetween <- function(beginDate, endDate){
  difftime(strptime(endDate, format = "%Y-%m-%d"), strptime(beginDate, format = "%Y-%m-%d"), units="weeks") 
}

getMonthsBetween <- function(beginDate, endDate){
  (as.yearmon(strptime(endDate, format = "%Y-%m-%d"))-
     as.yearmon(strptime(beginDate, format = "%Y-%m-%d")))*12
}

getQuartersBetween <- function(beginDate, endDate){
  (as.yearqtr(strptime(endDate, format = "%Y-%m-%d"))-
     as.yearqtr(strptime(beginDate, format = "%Y-%m-%d")))*4
}

getYearsBetween <- function(beginDate, endDate){
  (as.yearmon(strptime(endDate, format = "%Y-%m-%d"))-
     as.yearmon(strptime(beginDate, format = "%Y-%m-%d")))
}

addChronicallyHomelessFlagToClient <- function(client, enrollment){
  #############################################
  ##### Get those with Disabling Condition ###
  #############################################
  enrolledWithDisability <- sqldf("SELECT *
                              FROM enrollment
                              WHERE DisablingCondition = 1")
  
  #############################################
  ##### Length-of-Stay ########################
  #############################################
  # Participants who meet the length-of-stay in homelessness requirement
  # Either through four or more occurences with cumulative duration exceeding a year
  # Or a consequtive year.
  #                 113 = "12 Months"
  #                 114 = "More than 12 Months"
  chronicityDf <- sqldf("SELECT *
                        FROM enrolledWithDisability
                        WHERE (TimesHomelessPastThreeYears = 4
                          AND (
                            MonthsHomelessPastThreeYears = 113
                            OR MonthsHomelessPastThreeYears = 114)
                          )
                            OR (CAST(JULIANDAY('now') - JULIANDAY(DateToStreetESSH) AS Integer) > 364
                            AND (DateToStreetESSH != '')
                          )
                        ")
  
  #############################################
  ##### Chronically Homeless ##################
  #############################################
  # Take the distinct PersonalIDs of individuals who meet both chronicity
  # and disabling condition.
  
  chClient <- sqldf("SELECT DISTINCT(PersonalID), 'Yes' As 'ChronicallyHomeless'
                        FROM chronicityDf
                        ")
  
  # Get client info for chronically homeless.
  chClient <- sqldf("SELECT a.*, b.'ChronicallyHomeless'
                    FROM client a
                    LEFT JOIN chClient b
                    ON a.PersonalID=b.PersonalID
                    ")
  
  chClient <- subset(chClient)
  
  chClient
}
Lumi4 -- LumiCommunication

Lumi Communication

This namespace contains the serial device handling functions.  The goal is to have two abstract classes which define the interaction between the main device and the peripheral  These two classes will be responsible for searching, connecting, exchanging data, closing connections, and device failure handling.  To get going I’m going to take some advice from Mythical Man Month: “Show me your flowcharts and conceal your tables, and I shall continue to be mystified. Show me your tables, and I won’t usually need your flowcharts; they’ll be obvious.”  Well, I don’t have tables, so I guess my charts will have to do.

lumi_communication_central.pngLumiCommunication is largely modeled after Apple’s CoreBluetooth API.  It has abstractions representing both remote and local devices.  These abstractions are inherited in concrete classes for different device types.  Currently, the API is focusing on two device types, BluetoothLE and WiFi (ESP8266).  Though, if the abstraction is effective, it shouldn’t be difficult to provide support for Bluetooth Classic and Wired Serial connections.

The CentralManager’s main responsibilities are to monitor the PC’s device status, initiate searches, connect to devices.

I’m adding a bit to the CoreBluetooth model; I’m writing this code to be hacker friendly as one of my biggest peeves with frameworks meant for interacting with embedded devices is they often don’t allow for easy modification of the device’s behavior.  For example, most SoC-centered device modules (HM-10, ESP8266, etc.) which control radio hardware have firmware allowing for the modification of the module’s behavior.  Often, these are modified through AT Commands.  It struck me one day, why am I not writing code in such a manner?  For example, instead writing concrete code inside the classes which handle searching for BluetoothLE to to automatically connect to known devices, why not create an static object which defines these behaviors, then, when I want to change the behavior of my hardware, I simply pass in a new behavioral definition object. I’ve outlined this in my BehavioralBluetooth project (abaonded for the time being).

LumiCommunication classes will have an object which defines the behavior of the hardware.

lumi_communication.png  
The PeripheralManager is responsible for representing the states and delivered data of the peripheral devices.  There are events associated with data received from the device, confirmation of sent data, device state changes.  Like the CentralManager the PeripheralManager will have a PeripheralBehavior object which will define its actions.  There are received and sent buffers to monitor succesful flow of data between the local and remote device.

Lumi4 - init()

Lumi4

This is the next iteration in a three year project.  Here are the current iterations:

  1. Vorpal Hoff – an attempt at wireless uploading with a HM-11 and LPC1114 combination.  Written in C / C++ (Initialized May 22nd 2014).
  2. HM-1X Aid – this project was meant to be a GUI on top of the HM-1X modules, allowing “easy” editing of the module’s behavior.  It was my first venture into C#.  (It’s sooo bad;although, the serial communication was asynchronous.) (Initialized Dec. 19th 2015)
  3. Lumi1 – this the first successful TinySafeBoot uploader.  It was written in C# using the .NET WinForms.  Unfortunately, it was synchronous.  And I was finished with the USB-to-UART uploader before I realized there was no easy BLE support in WinForm’s .NET. (Initialized  March 2nd 2016)
  4. Lumi2 –  this is where things start getting better.  It is the current version of the TSB wireless bootloader.  It works, is asynchronous, and has BLE support.  Unfortunately, the code turned into spaghetti.  This is largely due to my poor understanding of object-oriented design.  It has god-modules, a horrifically implemented SerialEvent response protocol, poor encapsulation, no polymorphism.  It’s just a mess. (Initialized March 21st 2016)
  5. Lumi3 – this project was stopped early.  It was an attempt to build a multiplatform uploader using Xamarin Forms.  It would have allowed iOS, Android, and Windows versions of the application. Unfortunately, it is a fairly complex project.  Theoretically, the uploader would work by allowing the user to select a HEX file from Dropbox, handshake with TinySafeBoot using BLE or WifI, then upload the HEX file.  And though this is theoretically possible, it would take learning two new APIs: Xamarin Forms and Dropbox.  And my focus is dilberate practice of language conventiosn and OOP, rather hacking through two new APIs.  Most likely, I’ll come back to this project after Lumi4 (Jan 13th 2017)

Why? Seriously, dude

It is important to state the objective of the this three-year project has not been to produce a product which works, although, that’s a close second.  The purpose of these repeated attempts is to improve as a developer.  

Of course, I don’t believe if I try enough and eat my Wheatie I’ll grow into a great developer.  But with each iteration I’m focusing on developing a handful of new skills.  This learning strategy is from the book Peak by Anders Ericsson.  The continued and intentional practice is labeled by Ericsson as “deliberate practice.”  It’s with this mindset I’ve approached this iterative coding project, hoping with each iteration the code improves, but more importantly, my skill as a developer improves.

Focus

Deliberate practice involves selecting particular deficits to focus on.  This is more effective, as the improvement is in a few intentional areas, rather than trying to practice every important nuance of a skill at once.  This seems easy to get behind; especially, when it comes to developer skills.  There are just too many to try and refine all at once.

Sadly, focused practice isn’t something I was intentional about for the first few code bases in this series.  It wasn’t until Lumi3 and Lumi4 did it bubble up as crucial in the process of developing my skills.

Targeted Areas in Lumi4

The areas I’m looking to practice in Lumi4

  • Project Management
  • Project journaling
  • Abstraction
  • Encapsulation
  • Granulization of objects (avoid God-objects)
  • Meaningful names
  • C# Conventions (naming, formatting, placement, etc.)
  • Factory design pattern
  • Observer design pattern
  • Error handling
  • Unit Testing

Some areas which I may take on if all goes well:

  • Integration testing
  • Documentation API

What’s the Plan for Lumi4?

Lumi4 will have three basic components:

  1. Communication handling for BluetoothLE and WiFi (extendedable to Bluetooth Classic and USB-to-UART)
  2. Smart serial display (e.g., recognizes data outside of ASCII range and prints as a hex string)
  3. TinySafeBoot uploader

Learning Assests

Unit and Integration Testing

Testing fascinates me.  When I studied psychometrics there were a battery of tests as to whether and instrument worked as intended. In the psychology world these were the fundemental building blocks of effective research and practice.  Why did we use CPT? Because it passes a variety of tests to demonstrate efficacy.  In the developer world tests still hold my fascination.  They consistently demonstrate a product is capable of completing the task for which it was designed.

Of course, I’ve struggled with adopting testing in projects.  A lot of this has to do with poor understanding of how to design a test to meet a purpose.  It wasn’t until I was listening to a Coding Blocks (#54 – Writing Amazing Unit Tests) episode on writing unit tests did I get more comfortable with testing.  Specifically, when they discussed the differences between unit and integration testing.

When I first attempted to write tests for a project it was unit tests. Unfortunately, this project was the second iteration of my Lumi uploader and the tests resulted in a hot-mess.  This is because I was trying to test functions which relied on inputs from other systems.  

For example,  

    [TestMethod]
    public async Task<bool> shouldStartBLEWatcher()
    {
        // Arrange
        blueTestObject.init();
        await blueTestObject.startBLEWatcher(8);

        return true;
    }

This is as far as I made it writing a unit test on a method which was meant to test whether the StartBLEWatcher() method was working.  In unit testing there should be an assert on the output of the method, but StartBLEWatcher() returned discovered BLE devices (yes, I realize the method could be re-written better, thus the reason for this article).  This is where I got frustrated.  ”How the hell am I suppossed to write unit tests on code which interacts with other hardware!?” I mean, I get it, unit testing is the bread-and-butter of professional programmers.  It helps building big projects which would otherwise collapse under size.  But how the hell do I write unit tests for code which relies on outside systems!?  Saldy, I found the answer too late: You don’t.

In the Coding Blocks episodes there is a discussion on the difference between unit tests and integration tests.  A unit test is meant to test a small piece of code and it should rely on no other code.  An integration tests checks whether a piece of code works as intended. However, unlike unit tests, integration tests do rely on outside systems by their very definition.

When I heard this discussion I went to the first StackOverflow answer on the subject: 

Question: “What is the difference between integration and unit tests?”

Answer (by Nathan Huges)

A unit test is a test written by the programmer to verify that a relatively small piece of code is doing what it is intended to do. They are narrow in scope, they should be easy to write and execute, and their effectiveness depends on what the programmer considers to be useful. The tests are intended for the use of the programmer, they are not directly useful to anybody else, though, if they do their job, testers and users downstream should benefit from seeing fewer bugs.

Part of being a unit test is the implication that things outside the code under test are mocked or stubbed out. Unit tests shouldn’t have dependencies on outside systems. They test internal consistency as opposed to proving that they play nicely with some outside system.

An integration test is done to demonstrate that different pieces of the system work together. Integration tests cover whole applications, and they require much more effort to put together. They usually require resources like database instances and hardware to be allocated for them. The integration tests do a more convincing job of demonstrating the system works (especially to non-programmers) than a set of unit tests can, at least to the extent the integration test environment resembles production.

Actually “integration test” gets used for a wide variety of things, from full-on system tests against an environment made to resemble production to any test that uses a resource (like a database or queue) that isn’t mocked out.

Well, that’s it for a bit.

Lumi3 Debriefing Notes

C# Learning Journal: Refactoring Lumi

Lumi Uploader

I’ve been working on writing my own flash UART uploader since May 2014. Originally, I was trying to write an uploader in C using the GCC compiler. The idea was to upload a Intel HEX file compiled for the LPC1114 to the uC remotely, using a Bluetooth LE connection. Here’s a description of the custom circuit board designed for the project:

*Valdez Mutant Board

Unfortunately, the project was out of my league. After spending months writing C code there it was not usable. Of course, learned a lot about C in the process.

Well, after a couple of years I started on code to upload compiled Atmel ATMega and ATtiny programs using the same method outlined in the Valdez Mutant article. But this time, the uploader was written in C# on Windows. And it interfaced with the TinySafeBootloader on the Atmel uCs.

Strangely, I actually finished the project. The first code-base was written as a C# Forms application. This worked out great! I was actually able to use the System.Devices.Ports to access a CH340G or FTDI chip. The USB-to-UART then shook hands with the bootloader on either an ATMega328P, ATtiny84, or ATtiny85 (others should be supported, but these were the only tested due to the simplicity of the Arduino HAL).

Here’s the code base:

*Lumi Uploader – Windows Forms Version

Of course, there is are a lot of problems with the code. Most center around inexperience writing object-oriented code.

Here are some of the problems I identified:

Mistakes
1\. [God objects](http://sourcemaking.com/antipatterns/the-blob)
2\. [C# Conventions not followed](https://msdn.microsoft.com/en-us/library/ff926074.aspx)
3\. Deprecation (Forms->Universal)
4\. [Synchronous IO](https://msdn.microsoft.com/en-us/library/windows/desktop/aa365683(v=vs.85).aspx)
5\. Poor support for BLE
6\. Poor naming schemes
7\. Improper use of delegate / events
8\. Poor use of object abstraction
9. 

It was really the lack of BluetoothLE support which forced a change in directions. However, the elusive wireless upload to an AVR was just too close to abandon. Reluctantly, I created yet another code base. This time, it was derived from the Windows Universal App platform.

After a few months I had a working version. It was able to upload to ATtiny chips and ATMega chips over Bluetooth LE.

However, when I started trying to add ESP8266 support–well, things went to the Pooh. It seemed of all the problems listed above the only one resolved was the adding of Bluetooth LE support.  My skill was not increasing.

Also, there were two additional issues which arose:

  1. Handling advertisement and connection for Bluetooth.
  2. There was a rather nasty bug around writing to a connected device.

The first issue was a nightmare. I was able to work around it–but, it was horrifically hackish. In short, there are two namespaces which must be used to achieve in app BluetoothLE search and connection, Windows.Devices.Bluetooth and Windows.Devices.Bluetooth.BluetoothAdvertisement. First, to find the BluetoothLE devices you’d need to instialize BluetoothLEAdvertisementWatcher object:

  // Bluetooth LE Discovery
  BluetoothLEAdvertisementWatcher bleAdvertWatcher = new BluetoothLEAdvertisementWatcher();
  public sealed partial class MainPage : Page
  {
        // Create and initialize a new watcher instance.
        bleAdvertWatcher = new BluetoothLEAdvertisementWatcher();
        bleAdvertWatcher.Received += OnAdvertisementReceived;
        bleAdvertWatcher.Stopped += OnAdvertisementWatcherStopped;
        bleAdvertWatcher.ScanningMode = BluetoothLEScanningMode.Active;
        bleAdvertWatcher.Start();
  }

I’ll not dig into the details, but with this sample in mind here is the outline of how I achieved BluetoothLE in-app scan and connect.

  1. When OnAdvertisementReceived fires you get the discovered devices ID from the EventArgs
  2. After the user discovers the device sought, then a user input would start a the asynchronous creation of a BluetoothLEDevice using the ID found from the AdvertisementWatcher.
  3. Here’s where it gets hackish: If the device is successful in connecting, then there is no event–rather, a callback timer should be started with enough time for the BluetoothLEDevice to connect and enumerate.
  4. When the timer callback fires then, using the new var device = await BluetoothLEDevice.FromBluetoothAddressAsync(ID).
  5. After the wait, the services variable should have all of the services found on the BluetoothLEDevice. At this point, all the services on the remote device should be enumerated–and var services = device.GattServices, which includes enumerating services and characteristics.

What the API actually expects is the user will connect to the device using Windows built-in Bluetooth support. This API seems poorly thought out and unfortunate. Even Apple, with all of their “developer guidance”, doesn’t tie the developers’ hands when searching and connecting to BluetoothLE devices. Of course, CoreBluetooth was developed early in BluetoothLE’s lifecycle, so maybe that’s before API developers knew better than turn too much power over to code-consumers? Who knows! But I’ve strong feelings on the matter, given it took me so much time to figure out Microsoft’s intentions.

And with that–I’m closing down the Lumi3 project and starting on Lumi4.

JPS DSRIP Report V2.0

JPS DSRIP Report V2.0

options(java.parameters = "-Xmx14336m")  ## memory set to 14 GB
library("XLConnect")
library("sqldf")
library("tcltk")

startDate <- "2015-10-01"
endDate <- "2016-09-30"

df <- readWorksheetFromFile("JPS_Raw_Data.xlsx", sheet = 1, startRow = 2)

#sampleVector <- sample(1:nrow(df), 30000)
#df2 <- df[sampleVector,]

#write.csv(df2, file="Sample of JPS_Raw_Data (30000).csv", na="")

#df3 <- read.csv("Sample of JPS_Raw_Data (30000).csv")

### Formatting ###################################
df3[is.na(df3)] <- ""
df3$Participant.Enterprise.Identifier <- gsub("-", "", df3$Participant.Enterprise.Identifier)
colnames(df3)[2] <- "peid"
colnames(df3)[5] <- "CaseNumber"
colnames(df3)[7] <- "Gender"
colnames(df3)[8] <- "Race"
colnames(df3)[9] <- "Ethnicity"
colnames(df3)[10] <- "ProgramName"
colnames(df3)[11] <- "SiteName"
colnames(df3)[12] <- "AgreesToShareOne"
colnames(df3)[13] <- "AgreesToShareTwo"
colnames(df3)[17] <- "ScanCardIssuedDate"
colnames(df3)[21] <- "ProgramStartDate"
df3$ProgramStartDate <- as.character(df3$ProgramStartDate)
colnames(df3)[22] <- "ProgramEndDate"
df3$ProgramEndDate <- as.character(df3$ProgramEndDate)
df3$ScanCardIssuedDate <- as.character(df3$ScanCardIssuedDate)
colnames(df3)[19] <- "OutreachContactDate"
df3$OutreachContactDate <- as.character(df3$OutreachContactDate)

##################################################

# Filter to only participants who agree to share information.
df4 <- sqldf("SELECT * FROM df3 
              WHERE (
                 AgreesToShareOne == 'Yes' 
                OR AgreesToShareTwo == 'Yes')
             ")

##################################################
####### Start ####################################
####### Get Most Recent Scancard PEIDs ###########
##################################################

df5a <- sqldf("SELECT * FROM df4 WHERE ScanCardIssuedDate != ''")

# Filter to Scan Card Creations (First time Homeless) or Return in Six Months
str2 <- paste("SELECT * FROM df5a WHERE ScanCardIssuedDate > '", startDate, "' AND ScanCardIssuedDate < '", endDate, "'", sep="")
df5a <- sqldf(str2)

str <- paste("SELECT peid, MAX(ScanCardIssuedDate) AS 'MostRecentScanCardDate', 'Scan-card' As 'DateType', Value_1712 As 'Issuance Type', 'Scan-card' As 'ContactType' FROM df5a WHERE Value_1712 = 'Scan Card Creation (First time homeless clients)' OR  Value_1712 = 'Scan Card Renewal (clients who return to the shelter after six months of being away)' GROUP BY peid ORDER BY MostRecentScanCardDate DESC", sep = "")

df5a <- sqldf(str)
##################################################
####### End = df5a ###############################
####### Get Most Recent Scancard PEIDs ###########
##################################################

##################################################
####### Start ####################################
####### Get most recent Outreach Contact #########
##################################################

df5b <- sqldf("SELECT *
              FROM df4 
              WHERE Outreach_Contact_2478 != ''
              ")

str <- paste("SELECT peid, MAX(Outreach_Contact_2478) As 'MostRecentOutreachContact', 'OutreachContact' As 'DateType' FROM df5b WHERE Outreach_Contact_2478 > '", startDate, "' AND Outreach_Contact_2478  < '", endDate, "' GROUP BY peid ORDER BY MostRecentOutreachContact DESC", sep = "")

df5b <- sqldf(str)
##################################################
####### End = df5a ###############################
####### Get most recent Outreach Contact #########
##################################################

##################################################
####### Start ####################################
####### Get most recent Program Enrollment #######
##################################################

#### 'CD PIT ES LTB' Program Group #######
  # Emergency Youth Shelter
  # ALS Emergency Shelter
  # Employment Program
  # Emergency Shelter
  # PNS-Lowden Schutts Program for Women and Children
  # PNS-Moving Home
  # Veteran's Voice Shelter Based
  # S.T.A.R.T

#### 'TH JPS Project' Program Group
  # Families Together TH
  # ARL.HA -Transitional Housing
  # YWCA-TBLA 114 RRH
  # CEC TH
  # CEC- TBLA 114 Transitional Housing
  # 3CP
  # GRACE-Transitional Housing - TBLA 114
  # NASH TH
  # Liberty House TH
  # MHMR-HS- TBLA 114 TH
  # PNS-Veteran Transitional Living
  # TC-TBLA 114 Transitional Housing TCCD
  # SIMON
  # The Salvation Army Mabee Center -- TBLA 114

#### Individual Program Groups
  # ALS Emergency Shelter
  # Emergency Shelter

df5c <- sqldf("SELECT * 
              FROM df4
              WHERE ProgramName = 'Emergency Youth Shelter'
                 OR ProgramName = 'ALS Emergency Shelter'
                 OR ProgramName = 'Employment Program'
                 OR ProgramName = 'Emergency Shelter'
                 OR ProgramName = 'PNS-Lowden Schutts Program for Women and Children'
                 OR ProgramName = 'PNS-Moving Home'
                 OR ProgramName = 'Veteran''s Voice Shelter Based'
                 OR ProgramName = 'S.T.A.R.T'

                OR ProgramName = 'YWCA-TBLA 114 RRH'
                OR ProgramName = 'CEC TH'
                OR ProgramName = 'CEC- TBLA 114 Transitional Housing'
                OR ProgramName = '3CP'
                OR ProgramName = 'GRACE-Transitional Housing - TBLA 114'
                OR ProgramName = 'NASH TH'
                OR ProgramName = 'Liberty House TH'
                OR ProgramName = 'MHMR-HS- TBLA 114 TH'
                OR ProgramName = 'PNS-Veteran Transitional Living'
                OR ProgramName = 'TC-TBLA 114 Transitional Housing TCCD'
                OR ProgramName = 'SIMON'
                OR ProgramName = 'The Salvation Army Mabee Center -- TBLA 114'

                OR ProgramName = 'ALS Emergency Shelter'
              ")

# TODO: Fix ProgramEndDate to remove HH:MM:SS instead of hacking it.
df5c <- sqldf("SELECT *, date(ProgramEndDate) As ProgramEndDate2 FROM df5c")

#df5c <- sqldf("SELECT * FROM df5c WHERE ProgramStartDate >= '2015-10-01'
#                                  AND ( ProgramEndDate2 = ''
#                                        OR ProgramEndDate2 >= '2015-01'
#                                      ) 
#              ")

df5c <- activeFilter(df5c, 'ProgramStartDate', 'ProgramEndDate2', startDate, endDate)

df5c <- sqldf("SELECT peid, ProgramName, SiteName, MAX(ProgramStartDate) As 'MostRecentProgramStart', ProgramEndDate As 'MostRecentProgramEnd' 
              FROM df5c
              GROUP BY peid
              ORDER BY MostRecentProgramStart
              ")

##################################################
####### Start ####################################
####### Aggregate Outreach, Scancard, Program ####
##################################################

df6 <- sqldf("SELECT * FROM df5a a LEFT JOIN df5b b ON a.peid=b.peid")
df6 <- subset(df6)
df6 <- sqldf("SELECT * FROM df6 a LEFT JOIN df5c b ON a.peid=b.peid")
df6 <- subset(df6)

df6$MostRecentProgramStart[is.na(df6$MostRecentProgramStart)] <- "1900-01-01"
df6$MostRecentOutreachContact[is.na(df6$MostRecentOutreachContact)] <- "1900-01-01"
df6$MostRecentScanCardDate[is.na(df6$MostRecentScanCardDate)] <- "1900-01-01"

#df6 <- sqldf(c("UPDATE df6 SET MostRecentScanCardDate = replace(MostRecentScanCardDate, '', '1900-01-01')", "SELECT * FROM df6"))
#df6 <- sqldf(c("UPDATE df6 SET MostRecentProgramStart = replace(MostRecentProgramStart, '', '1900-01-01')", "SELECT MostRecentProgramStart FROM df6"))

df6 <- sqldf("SELECT DISTINCT(peid), 
             CASE 
                WHEN MostRecentScanCardDate > MostRecentOutreachContact
                AND MostRecentScanCardDate > MostRecentProgramStart
              THEN MostRecentScanCardDate 
                WHEN MostRecentProgramStart > MostRecentOutreachContact
              THEN MostRecentProgramStart
                WHEN MostRecentOutreachContact = MAX(MostRecentScanCardDate, MostRecentProgramStart, MostRecentOutreachContact)
              THEN MostRecentOutreachContact
              ELSE 'Unknown'
              END AS LastContactDate, 
             CASE 
                WHEN MostRecentScanCardDate > MostRecentOutreachContact
                AND MostRecentScanCardDate > MostRecentProgramStart
             THEN 'Scan Card Issuance' 
                WHEN MostRecentProgramStart > MostRecentOutreachContact
             THEN 'Program Start Date'
                WHEN MostRecentOutreachContact = MAX(MostRecentScanCardDate, MostRecentProgramStart, MostRecentOutreachContact)
             THEN 'Outreach Contact'
             ELSE 'Unknown'
             END AS ContactDateType 
             FROM df6
             ")

##################################################
####### End = df6 ################################
####### Aggregate Outreach, Scancard, Program ####
##################################################

##################################################
####### Start ####################################
####### Add Demographics #########################
##################################################

df7 <- sqldf("SELECT DISTINCT(peid), SSN, Name, CaseNumber, DOB, Gender, Race, Ethnicity
             FROM df3
             ")

df7 <- sqldf("SELECT a.*, b.SSN, b.Name, b.CaseNumber, b.DOB, b.Gender, b.Race, b.Ethnicity
             FROM df6 a
             INNER JOIN df7 b
             ON a.peid=b.peid
             ")

# activeRecords <- activeFilter(df, "occStartDate", "occEndDate", "2017-01-23", '2017-01-26')
activeFilter <- function(df, beginDate, endDate, beginRange, endRange){
  df[is.na(df)] <- ""
  str <- paste("SELECT * FROM df WHERE ", beginDate, " >= '", beginRange, "' AND ( ", endDate, " = '' OR ", endDate, " >= '", beginRange, "')", sep = "")
  #print(str)
  df <- sqldf(str)
  df
}