esmprep: esmprep: A package for preparing raw data in research that...

In mmiche/esmprep: Data Preparation During and After the Use of the Experience Sampling Methodology (ESM)

Description

The 'esmprep' package helps to prepare a raw ESM dataset for statistical analysis. Preparation includes the handling of errors (mostly due to technological reasons) and the generating of new variables that are necessary and/or helpful in meeting the conditions when statistically analyzing ESM data. The functions in 'esmprep' are meant to hierarchically lead from bottom, i.e. the raw (separated) ESM dataset(s), to top, i.e. a single ESM dataset ready for statistical analysis.

'esmprep' functions

The 'esmprep' functions have an hierarchical order, in which they should be run. See Examples for the function's hiararchy.

Examples

## Not run: 
# -o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-
# N O T E.
# DEAR USER OF THE 'esmprep' PACKAGE,
# THE FOLLOWING CODE IS AN EXAMPLE OF ALL THE PACKAGE'S FUNCTIONS, WHICH ARE
# LARGELY INTERDEPENDENT AND WHICH ARE SUPPOSED TO RUN IN AN HIERARCHICAL ORDER.
# AFTER HAVING LOADED THE PACKAGE YOU CAN COPY PASTE THE ENTIRE CODE INTO YOUR
# CONSOLE OR INTO A SCRIPT AND THEN RUN IT.
# -o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-
# ---------------------------------------------------------------------------------
# Load the 'esmprep' package => library(esmprep)
# ---------------------------------------------------------------------------------
# FUNCTION NAME: relevantREFVN
# --------------
# This is function 1 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# ------------------------------------------------------
# Run function 1 of 29; see esmprep functions' hierarchy.
# ------------------------------------------------------
# With date and time as separate arguments
relRef <- relevantREFVN(ID="id", IMEI="imei", ST="st",
STARTDATE="start_date", STARTTIME="start_time",
ENDDATE="end_date", ENDTIME="end_time")
# With date-time objects instead of separate date and time
relRef <- relevantREFVN(ID="id", IMEI="imei", ST="st",
START_DATETIME="start_dateTime", END_DATETIME="end_dateTime")
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: setREF
# --------------
# This is function 2 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute setREF. Start  ------------------
relRef <- relevantREFVN(ID="id", IMEI="imei", ST="st",
STARTDATE="start_date", STARTTIME="start_time",
ENDDATE="end_date", ENDTIME="end_time")
# Prerequisites in order to execute setREF. End ---------------------
# ------------------------------------------------------
# Run function 2 of 29; see esmprep functions' hierarchy.
# ------------------------------------------------------
# 4 is the number of daily prompts.
# relRef is the result of function 'relevantREFVN'
# Relevant variables names of reference dataset.
(RELEVANTVN_REF <- setREF(4, relRef))
# With date-time objects instead of separate date and time
relRef <- relevantREFVN(ID="id", IMEI="imei", ST="st",
START_DATETIME="start_dateTime", END_DATETIME="end_dateTime")
(RELEVANTVN_REF <- setREF(4, relRef))
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: relevantESVN
# --------------
# This is function 3 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# ------------------------------------------------------
# Run function 3 of 29; see esmprep functions' hierarchy.
# ------------------------------------------------------
# With date and time as separate arguments
relEs <- relevantESVN(svyName="survey_name", IMEI="IMEI",
STARTDATE="start_date", STARTTIME="start_time",
ENDDATE="end_date", ENDTIME="end_time")
# With date-time objects instead of separate date and time
relEs <- relevantESVN(svyName="survey_name", IMEI="IMEI",
START_DATETIME="start_dateTime", END_DATETIME="end_dateTime")
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: setES
# --------------
# This is function 4 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute setES. Start --------------------
relEs <- relevantESVN(svyName="survey_name", IMEI="IMEI",
STARTDATE="start_date", STARTTIME="start_time",
ENDDATE="end_date", ENDTIME="end_time")
# Prerequisites in order to execute setES. End ----------------------
# ------------------------------------------------------
# Run function 4 of 29; see esmprep functions' hierarchy.
# ------------------------------------------------------
# imeiNumbers is the vector containing all IMEI numbers used in
# the ESM study; use the respective entries in the referenceDf.
imeiNumbers <- as.character(referenceDf$imei)
# surveyNames is the vector containing all ESM version names.
surveyNames <- c(
# Test group
   "morningTestGroup", "dayTestGroup", "eveningTestGroup",
# Control group
   "morningControlGroup", "dayControlGroup", "eveningControlGroup")
# 4 is the number of daily prompts
# relEs is the result of function 'relevantESVN'
RELEVANT_ES <- setES(4, imeiNumbers, surveyNames, relEs)
# Extract relevant ESM general information
RELEVANTINFO_ES <- RELEVANT_ES[["RELEVANTINFO_ES"]]
# Extract list of relevant variables names of raw ESM datasets.
RELEVANTVN_ES <- RELEVANT_ES[["RELEVANTVN_ES"]]

# With date-time objects instead of separate date and time
relEs <- relevantESVN(svyName="survey_name", IMEI="IMEI",
START_DATETIME="start_dateTime", END_DATETIME="end_dateTime")
RELEVANT_ES <- setES(4, imeiNumbers, surveyNames, relEs)
# Extract relevant ESM general information
RELEVANTINFO_ES <- RELEVANT_ES[["RELEVANTINFO_ES"]]
# Extract list of relevant variables names of raw ESM datasets.
RELEVANTVN_ES <- RELEVANT_ES[["RELEVANTVN_ES"]]
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: esList
# --------------
# This is function 5 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute esList. Start --------------------
# Generate argument RELEVANTVN_ES
relEs <- relevantESVN(svyName="survey_name", IMEI="IMEI",
STARTDATE="start_date", STARTTIME="start_time",
ENDDATE="end_date", ENDTIME="end_time")
imeiNumbers <- as.character(referenceDf$imei)
surveyNames <- c("morningTestGroup", "dayTestGroup", "eveningTestGroup",
"morningControlGroup", "dayControlGroup", "eveningControlGroup")
RELEVANT_ES <- setES(4, imeiNumbers, surveyNames, relEs)
RELEVANTVN_ES <- RELEVANT_ES[["RELEVANTVN_ES"]]
# Prerequisites in order to execute esList. End ----------------------
# ------------------------------------------------------
# Run function 6 of 29; see esmprep functions' hierarchy.
# ------------------------------------------------------
# 6 exemplary raw ESM (sub-)datasets.
esLs <- esList(list(morningControl, dayControl, eveningControl,
morningTest, dayTest, eveningTest), RELEVANTVN_ES)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: genKey
# --------------
# This is function 6 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute genKey. Start -------------------
relEs <- relevantESVN(svyName="survey_name", IMEI="IMEI",
STARTDATE="start_date", STARTTIME="start_time",
ENDDATE="end_date", ENDTIME="end_time")
imeiNumbers <- as.character(referenceDf$imei)
surveyNames <- c("morningTestGroup", "dayTestGroup", "eveningTestGroup",
"morningControlGroup", "dayControlGroup", "eveningControlGroup")
RELEVANT_ES <- setES(4, imeiNumbers, surveyNames, relEs)
RELEVANTVN_ES <- RELEVANT_ES[["RELEVANTVN_ES"]]
esLs <- esList(list(morningControl, dayControl, eveningControl,
morningTest, dayTest, eveningTest), RELEVANTVN_ES)
# Prerequisites in order to execute genKey. End ---------------------
# ------------------------------------------------------
# Run function 6 of 29; see esmprep functions' hierarchy.
# ------------------------------------------------------
# esLs is the result of function 'esList'.
keyLs <- genKey(esLs)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: genDateTime
# --------------
# This is function 7 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute genDateTime. Start --------------
relEs <- relevantESVN(svyName="survey_name", IMEI="IMEI",
STARTDATE="start_date", STARTTIME="start_time",
ENDDATE="end_date", ENDTIME="end_time")
imeiNumbers <- as.character(referenceDf$imei)
surveyNames <- c("morningTestGroup", "dayTestGroup", "eveningTestGroup",
"morningControlGroup", "dayControlGroup", "eveningControlGroup")
RELEVANT_ES <- setES(4, imeiNumbers, surveyNames, relEs)
RELEVANTINFO_ES <- RELEVANT_ES[["RELEVANTINFO_ES"]]
RELEVANTVN_ES <- RELEVANT_ES[["RELEVANTVN_ES"]]
esLs <- esList(list(morningControl, dayControl, eveningControl,
morningTest, dayTest, eveningTest), RELEVANTVN_ES)
keyLs <- genKey(esLs)
relRef <- relevantREFVN(ID="id", IMEI="imei", ST="st",
STARTDATE="start_date", STARTTIME="start_time",
ENDDATE="end_date", ENDTIME="end_time")
RELEVANTVN_REF <- setREF(4, relRef)
# Prerequisites in order to execute genDateTime. End ----------------
# ------------------------------------------------------
# Run function 7 of 29; see esmprep functions' hierarchy.
# ------------------------------------------------------
# Applying function to reference dataset (7a of 29)
referenceDfList <- genDateTime(referenceDf, "REF", RELEVANTINFO_ES, RELEVANTVN_ES,
RELEVANTVN_REF)

# Extract reference dataset from output
referenceDfNew <- referenceDfList[["refOrEsDf"]]

# Extract extended list of relevant variables names of reference dataset
RELEVANTVN_REF <- referenceDfList[["extendedVNList"]]

# Applying function to raw ESM dataset(s) (7b of 29)
# keyLs is the result of function 'genKey'.
keyList <- genDateTime(keyLs, "ES", RELEVANTINFO_ES, RELEVANTVN_ES,
RELEVANTVN_REF)

# Extract list of raw ESM datasets from output
keyLsNew <- keyList[["refOrEsDf"]]

# Extract extended list of relevant variables names of raw ESM datasets
RELEVANTVN_ES <- keyList[["extendedVNList"]]
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: refPlausible
# --------------
# This is function 8 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute refPlausible. Start ------
# Use example list delivered with the package
RELEVANTVN_REF <- RELEVANTVN_REFext
# Prerequisites in order to execute refPlausible. End --------
# ------------------------------------------------------
# Run function 8 of 29; see esmprep functions' hierarchy.
# ------------------------------------------------------
# In an ESM study all participants answer questionnaires during a time period which
# usually is equal across all participants (e.g. seven days). This function enables the
# user to check whether in the reference dataset the ESM period is plausible. For
# instance, a negative ESM time period would clearly be implausible, e.g. the user
# setting the beginning of the ESM time period after the end of it (which is
# impossible unless a functioning time machine is involved :-) ).
referenceDfNew1 <- refPlausible(refDf=referenceDfNew, units="days", RELEVANTVN_REF)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: rmInvalid
# --------------
# This is function 9 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute rmInvalid. Start ----------------
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# keyLsNew is a list of datasets, also delivered with the package
# Prerequisites in order to execute rmInvalid. End ------------------
# ------------------------------------------------------
# Run function 9 of 29; see esmprep functions' hierarchy.
# ------------------------------------------------------
# keyLsNew is the result of function 'genDateTime' (or of function 'splitDateTime').
rmInvLs <- rmInvalid(keyLsNew, RELEVANTVN_ES)
# Result of function 'rmInvalid' is a list with 4 elements:
names(rmInvLs)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: printRmInvalid
# --------------
# This is function 10 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute printRmInvalid. Start -----------
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# keyLsNew is a list of datasets, also delivered with the package
rmInvLs <- rmInvalid(keyLsNew, RELEVANTVN_ES)
# Prerequisites in order to execute printRmInvalid. End -------------
# ------------------------------------------------------
# Run function 10 of 29; see esmprep functions' hierarchy.
# ------------------------------------------------------
# rmInvLs is the result of function 'rmInvalid'. Display its result
# in the console both tablulated and in detail.
key_rmLs <- printRmInvalid(rmInvLs, smr="both", RELEVANTVN_ES)
# Display the list containing the KEY values of all questionnaires
# that have been removed.
key_rmLs
# Since there have been warning messages in 4 of the 6 datasets,
# the first ESM item (name: V1) was automatically converted to class
# character, although it is numeric. So we'll re-convert V1's class.
# Check V1 prior to conversion
str(rmInvLs[["dfValid"]][[2]][1:2])
rmInvLs[["dfValid"]] <- sapply(rmInvLs[["dfValid"]], function(x) {
     x[,"V1"] <- as.numeric(x[,"V1"])
     return(x) } )
# Check V1 after conversion
str(rmInvLs[["dfValid"]][[2]][1:2])
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: esItems
# --------------
# This is function 11 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute esItems. Start ------------------
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# keyLsNew is a list of datasets, also delivered with the package
rmInvLs <- rmInvalid(keyLsNew, RELEVANTVN_ES)
# Prerequisites in order to execute esItems. End --------------------
# -------------------------------------------------------
# Run function 11 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# Extract the item names of the raw ESM datasets. rmInvLs[["dfValid"]]
# is one of the results from function 'rmInvalid'
plausibItems <- esItems(dfList=rmInvLs[["dfValid"]], RELEVANTVN_ES)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: esPlausible
# --------------
# This is function 12 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute esPlausible. Start --------------
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# keyLsNew is a list of datasets, also delivered with the package
rmInvLs <- rmInvalid(keyLsNew, RELEVANTVN_ES)
plausibItems <- esItems(dfList=rmInvLs[["dfValid"]], RELEVANTVN_ES)
# Prerequisites in order to execute esPlausible. End ----------------
# -------------------------------------------------------
# Run function 12 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# Help checking the plausibility of items in the raw ESM datasets. rmInvLs[["dfValid"]]
# is one of the results from function 'rmInvalid'.
# plausibItems is the result of function 'esItems'.
plausibLs <- esPlausible(dfList=rmInvLs[["dfValid"]], itemVecList=plausibItems)
# Display the results (4 data frames) to the console
# plausibNames gives an overview of the item names across all ESM versions
plausibLs[["plausibNames"]]
# plausibClass gives an overview of the variable types of all items
plausibLs[["plausibClass"]]
# plausibRowNa shows for each ESM version the number of lines in the raw
# ESM datasets and how much percent of the data is missing (NAs).
plausibLs[["plausibRowNa"]]
# plausibMinMax shows for each numeric variable the minimum and maximum.
plausibLs[["plausibMinMax"]]
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: esComplete
# --------------
# This is function 13 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute esComplete. Start ---------------
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# keyLsNew is a list of datasets, also delivered with the package
rmInvLs <- rmInvalid(keyLsNew, RELEVANTVN_ES)
plausibItems <- esItems(dfList=rmInvLs[["dfValid"]], RELEVANTVN_ES)
# Prerequisites in order to execute esComplete. End -----------------
# -------------------------------------------------------
# Run function 13 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# Generate second argument of function 'esComplete'. It's strongly recommended
# to read the explantion of this 2nd argument in the esmprep vignette, function
# 'esComplete'.
lastItemList <- list(
# If in survey version "morningTestGroup" variable "V6" contains the value 0,
# then variable "V6_1" is the last item expected to contain data, else "V6" is the last item
# expected to contain data.
list("morningTestGroup", "V6", 0, "V6_1"),
# In survey version "dayTestGroup" variable "V7" is the last item expected to contain data;
# unlike above, no conditions; NA as 2nd and 3rd element of the inner list are mandatory.
list("dayTestGroup", NA, NA, "V7"),
# Information of all further ESM versions are passed accordingly:
list("eveningTestGroup", "V9", 1, "V9_1"),
list("morningControlGroup", "V6", 0, "V6_1"),
list("dayControlGroup", NA, NA, "V7"),
# The last ESM version has 2 conditions, therefore it is passed 2 times:
# If V8_1 contains a value between 1 and 5, then V8_3 is the last item expected to
# contain data.
list("eveningControlGroup", "V8_1", 1:5, "V8_3"),
# If V8_1 contains the value 0, then V8_2 is the last item expected to contain data.
list("eveningControlGroup", "V8_1", 0, "V8_2"))
# Apply function 'esComplete'. rmInvLs[["dfValid"]] is one of the results of function
# rmInvalid.
isCompleteLs <- esComplete(rmInvLs[["dfValid"]], lastItemList)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: esMerge
# --------------
# This is function 14 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute esMerge. Start ------------------
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# isCompleteLs is a list of datasets, also delivered with the package
# Prerequisites in order to execute esMerge. End --------------------
# -------------------------------------------------------
# Run function 14 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# Merge all raw ESM datasets. isCompleteLs is the result
# of function 'esComplete'.
esMerged <- esMerge(isCompleteLs, RELEVANTVN_ES)
# If preferred convert the 15 digit IMEI number from scientfic notation to text.
esMerged[,RELEVANTVN_ES[["ES_IMEI"]]] <- as.character(esMerged[,RELEVANTVN_ES[["ES_IMEI"]]])
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: findChars
# --------------
# This is function 15 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute findChars. Start ----------------
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# isCompleteLs is a list of datasets, also delivered with the package
esMerged <- esMerge(isCompleteLs, RELEVANTVN_ES)
esMerged[,RELEVANTVN_ES[["ES_IMEI"]]] <- as.character(esMerged[,RELEVANTVN_ES[["ES_IMEI"]]])
# Prerequisites in order to execute findChars. End ------------------
# -------------------------------------------------------
# Run function 15 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# esMerged is the result of function 'esMerge'
findTextIdx <- findChars(esMerged)
# Display structure of function output
str(findTextIdx)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: convertChars
# --------------
# This is function 16 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute convertChars. Start -------------
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# isCompleteLs is a list of datasets, also delivered with the package
esMerged <- esMerge(isCompleteLs, RELEVANTVN_ES)
esMerged[,RELEVANTVN_ES[["ES_IMEI"]]] <- as.character(esMerged[,RELEVANTVN_ES[["ES_IMEI"]]])
findTextIdx <- findChars(esMerged)
# Prerequisites in order to execute convertChars. End ---------------
# -------------------------------------------------------
# Run function 16 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# From result of function 'findChars' select the indices of the items
# in the ESM dataset that contain text answers of the participants.
findTextIdx1 <- findTextIdx[c(1,2,9,10)]
# Use findTextIdx1 to generate the 3rd argument of function 'convertChars'.
textColumns <- names(findTextIdx1)
# Generate data.frame specifying the conversion of single characters.
convertCharsDf <- data.frame(c("ä", "ü"), c("ae", "ue"))
# Apply function. esMerged is the result of function 'esMerge'.
esMerged1 <- convertChars(esMerged, textColumns, convertCharsDf)
# # As default upper and lower case are NOT ignored! If you want them
# # ignored, additionally pass TRUE to the argument ignoreCase, like this:
# convertChars(esMerged, textColumns, convertCharsDf, ignoreCase=TRUE)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: esAssign
# --------------
# This is function 17 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute esAssign. Start -----------------
# esMerged1 is the raw ESM dataset, also delivered with the package
# referenceDfNew is the modified reference dataset, delivered with
# the package.
# RELEVANTINFO_ES is delivered with the package
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# Use example list delivered with the package
RELEVANTVN_REF <- RELEVANTVN_REFext
# Prerequisites in order to execute esAssign. End -------------------
# -------------------------------------------------------
# Run function 17 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# Assign questionnaires contained in the raw ESM dataset to all participants listed
# in the reference dataset. esMerged1 is the result of function 'convertChars',
# referenceDfNew is the result of function 'genDateTime' or of function
# 'splitDateTime'.
# Run only the first 2 out of 8 participants (saves time). The warning message the
# user receives in this case (2 out of 8 participants) is correct.
esAssigned <- esAssign(esDf = esMerged1, refDf = referenceDfNew[1:2,], RELEVANTINFO_ES,
RELEVANTVN_ES, RELEVANTVN_REF)
# # Assign questionnaires contained in the raw ESM dataset to participant P001 listed
# # in the reference dataset.
# esAssigned <- esAssign(esDf = esMerged1, refDf = referenceDfNew, RELEVANTINFO_ES,
# RELEVANTVN_ES, RELEVANTVN_REF, singlePerson="P001")
# More options can be passed to 'esAssign', see parameter description. Note that when
# setting the argument midnightPrompt to TRUE, esAssign takes a bit longer to do its job.
# Output: List with 4 data.frames.
names(esAssigned)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: missingEndDateTime
# --------------
# This is function 18 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute missingEndDateTime. Start -------
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# esAssigned is a list of datasets, delivered with the package. It is
# the result of the assignment of the ESM questionnaires to ALL 8
# participants in the reference dataset.
# Prerequisites in order to execute missingEndDateTime. End ---------
# -------------------------------------------------------
# Run function 18 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# esAssigned[["ES"]] is one of the results of function 'esAssign'.
noEndDf <- missingEndDateTime(esAssigned[["ES"]], RELEVANTVN_ES)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: esIdentical
# --------------
# This is function 19 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute esIdentical. Start --------------
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# esAssigned is a list of datasets, delivered with the package. It is
# the result of the assignment of the ESM questionnaires to ALL 8
# participants in the reference dataset.
noEndDf <- missingEndDateTime(esAssigned[["ES"]], RELEVANTVN_ES)
# Prerequisites in order to execute esIdentical. End ----------------
# -------------------------------------------------------
# Run function 19 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# noEndDf is the result of function 'noEndDateTime'.
identDf <- esIdentical(noEndDf, RELEVANTVN_ES)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: suggestShift
# --------------
# This is function 20 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute suggestShift. Start -------------
# Use example list delivered with the package
RELEVANTINFO_ES <- RELEVANTINFO_ES
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# esAssigned is a list of datasets, delivered with the package. It is
# the result of the assignment of the ESM questionnaires to ALL 8
# participants in the reference dataset.
noEndDf <- missingEndDateTime(esAssigned[["ES"]], RELEVANTVN_ES)
identDf <- esIdentical(noEndDf, RELEVANTVN_ES)
# Prerequisites in order to execute suggestShift. End ---------------
# -------------------------------------------------------
# Run function 20 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# identDf is the result of function 'esIdentical'.
# 100 represents the number of minutes that at least must have passed
# between the scheduled start of an ESM questionnaire at its actual start
# in order for the questionnaire to be eligible for shifting (see function
# makeShift).
sugShift <- suggestShift(identDf, 100, RELEVANTINFO_ES, RELEVANTVN_ES)
# Display output element 'suggestShiftDf':
sugShift$suggestShiftDf
# Display output element 'printShiftDf':
sugShift$printShiftDf
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: printSuggestedShift
# --------------
# This is function 21 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute printSuggestedShift. Start ------
# Use example list delivered with the package
RELEVANTINFO_ES <- RELEVANTINFO_ES
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# esAssigned is a list of datasets, delivered with the package. It is
# the result of the assignment of the ESM questionnaires to ALL 8
# participants in the reference dataset.
noEndDf <- missingEndDateTime(esAssigned[["ES"]], RELEVANTVN_ES)
identDf <- esIdentical(noEndDf, RELEVANTVN_ES)
sugShift <- suggestShift(identDf, 100, RELEVANTINFO_ES, RELEVANTVN_ES)
# Prerequisites in order to execute printSuggestedShift. End --------
# -------------------------------------------------------
# Run function 21 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# Display the result of function 'suggestShift' in the console.
printSuggestedShift(sugShift, RELEVANTVN_ES)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: makeShift
# --------------
# This is function 22 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute makeShift. Start ----------------
# RELEVANTINFO_ES is delivered with the package
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# Use example list delivered with the package
RELEVANTVN_REF <- RELEVANTVN_REFext
# esAssigned is a list of datasets, delivered with the package. It is
# the result of the assignment of the ESM questionnaires to ALL 8
# participants in the reference dataset.
noEndDf <- missingEndDateTime(esAssigned[["ES"]], RELEVANTVN_ES)
identDf <- esIdentical(noEndDf, RELEVANTVN_ES)
sugShift <- suggestShift(identDf, 100, RELEVANTINFO_ES, RELEVANTVN_ES)
# Prerequisites in order to execute makeShift. End -------------------
# -------------------------------------------------------
# Run function 22 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# sugShift is the result of function 'suggestShift'. referenceDfNew is the result
# of function 'genDateTime' or of function 'splitDateTime'.
# keyPromptDf is generated by using part of the output of function suggestShift,
# i.e. by selecting the columns NEW_PROMPT and SHIFTKEY from suggestShiftDf.
keyPromptDf <- sugShift$suggestShiftDf[,c("NEW_PROMPT", "SHIFTKEY")]
madeShift <- makeShift(sugShift, referenceDfNew, keyPromptDf, RELEVANTINFO_ES, RELEVANTVN_REF)
# Tip! Display the result of function 'makeShift' in the console
# in order to check whether the shifting was successful.
printSuggestedShift(madeShift, RELEVANTVN_ES)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: expectedPromptIndex
# --------------
# This is function 23 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute makeShift. Start ----------------
# Use example list delivered with the package
RELEVANTINFO_ES <- RELEVANTINFO_ES
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# Use example list delivered with the package
RELEVANTVN_REF <- RELEVANTVN_REFext
# esAssigned is a list of datasets, delivered with the package. It is
# the result of the assignment of the ESM questionnaires to ALL 8
# participants in the reference dataset.
noEndDf <- missingEndDateTime(esAssigned[["ES"]], RELEVANTVN_ES)
identDf <- esIdentical(noEndDf, RELEVANTVN_ES)
sugShift <- suggestShift(identDf, 100, RELEVANTINFO_ES, RELEVANTVN_ES)
keyPromptDf <- sugShift$suggestShiftDf[,c("NEW_PROMPT", "SHIFTKEY")]
madeShift <- makeShift(sugShift, referenceDfNew, keyPromptDf, RELEVANTINFO_ES, RELEVANTVN_REF)
# Prerequisites in order to execute makeShift. End -------------------
# -------------------------------------------------------
# Run function 23 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# Generate second argument of function 'expectedPromptIndex'. It's strongly
# recommended to read the explanation of this 2nd argument in the esmprep
# vignette, function 'expectedPromptIndex'.
expIdxList <- list(
# I - the user - expect in the ESM version morningTestGroup that
# prompt no.1 is always linked to the value 1.
list("morningTestGroup", 1, 1),
# I - the user - expect in the ESM version dayTestGroup that
# prompt no. 2 and no.3 are always linked to the value 2.
list("dayTestGroup", c(2, 3), 2),
# Information of all further ESM versions are passed accordingly:
list("eveningTestGroup", 4, 3),
list("morningControlGroup", 1, 1),
list("dayControlGroup", c(2,3), 2),
list("eveningControlGroup", 4, 3))
# madeShiftDf$esDf is part of the output of function 'makeShift', if at
# least one questionnaire was shifted to a neighboring prompt index.
expectedDf <- expectedPromptIndex(madeShift$esDf, expIdxList, RELEVANTINFO_ES,
RELEVANTVN_ES)
# If no questionnaire is suggested for shifting (see function suggestShift)
# use the result of function suggestShift as 1st argument, like this:
# expectedDf <- expectedPromptIndex(sugShift$esDf, expIdxList, RELEVANTINFO_ES,
RELEVANTVN_ES)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: intolerable
# --------------
# This is function 24 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute intolerable. Start --------------
# RELEVANTINFO_ES is delivered with the package
# expectedDf is a raw ESM dataset, delivered with the package.
# Prerequisites in order to execute intolerable. End ----------------
# -------------------------------------------------------
# Run function 24 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# Generate second argument of function 'intolerable'
(intoleranceDf <- data.frame(
# Column 'prompt': Prompts that must NEVER be comined with expected categories.
prompt = c(2, 3, 4, 1, 1),
# Column 'expect': Expected categories that must NEVER be combined with the prompts.
expect = c(1, 1, 1, 2, 3)))
# Read: Prompts 2, 3, and 4 must never be combined with expected category 1.
# Read: Prompt 1 must never be combined with expected category 2.
# Read: Prompt 1 must never be combined with expected category 3.
# expectedDf is the result of function 'expectedPromptIndex'.
intolLs <- intolerable(expectedDf, intoleranceDf, RELEVANTINFO_ES)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: randomMultSelection
# --------------
# This is function 25 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute randomMultSelection. Start ------
# RELEVANTINFO_ES is delivered with the package
intoleranceDf <- data.frame(prompt = c(2, 3, 4, 1, 1),
expect = c(1, 1, 1, 2, 3))
# expectedDf is a raw ESM dataset, delivered with the package.
intolLs <- intolerable(expectedDf, intoleranceDf, RELEVANTINFO_ES)
# Prerequisites in order to execute randomMultSelection. End --------
# -------------------------------------------------------
# Run function 25 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# intolLs[["cleanedDf"]] is the result of function 'intolerable'.
randSelLs <- randomMultSelection(intolLs[["cleanedDf"]])
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: computeTimeLag
# --------------
# This is function 26 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute computeTimeLag. Start -----------
# RELEVANTINFO_ES is delivered with the package
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
intoleranceDf <- data.frame(prompt = c(2, 3, 4, 1, 1),
expect = c(1, 1, 1, 2, 3))
# expectedDf is a raw ESM dataset, delivered with the package.
intolLs <- intolerable(expectedDf, intoleranceDf, RELEVANTINFO_ES)
randSelLs <- randomMultSelection(intolLs[["cleanedDf"]])
# Prerequisites in order to execute computeTimeLag. End -------------
# -------------------------------------------------------
# Run function 26 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# randSelLs[["esRandSelIn"]] is the result of function 'randomMultSelection'.
lagDf <- computeTimeLag(randSelLs[["esRandSelIn"]], RELEVANTVN_ES)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: computeDuration
# --------------
# This is function 27 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute computeDuration. Start ----------
# RELEVANTINFO_ES is delivered with the package
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
intoleranceDf <- data.frame(prompt = c(2, 3, 4, 1, 1),
expect = c(1, 1, 1, 2, 3))
# expectedDf is a raw ESM dataset, delivered with the package.
intolLs <- intolerable(expectedDf, intoleranceDf, RELEVANTINFO_ES)
randSelLs <- randomMultSelection(intolLs[["cleanedDf"]])
# Prerequisites in order to execute computeDuration. End ------------
# -------------------------------------------------------
# Run function 27 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# randSelLs[["esRandSelIn"]] is the result of function 'randomMultSelection'.
durDf <- computeDuration(randSelLs[["esRandSelIn"]], RELEVANTVN_ES)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: computeTimeBetween
# --------------
# This is function 28 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute computeTimeBetween. Start -------
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# Use example list delivered with the package
RELEVANTVN_REF <- RELEVANTVN_REFext
intoleranceDf <- data.frame(prompt = c(2, 3, 4, 1, 1),
expect = c(1, 1, 1, 2, 3))
# expectedDf is a raw ESM dataset, delivered with the package.
intolLs <- intolerable(expectedDf, intoleranceDf, RELEVANTINFO_ES)
randSelLs <- randomMultSelection(intolLs[["cleanedDf"]])
# Prerequisites in order to execute computeTimeBetween. End ---------
# -------------------------------------------------------
# Run function 28 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# randSelLs[["esRandSelIn"]] is the result of function 'randomMultSelection'.
tbsqDf <- computeTimeBetween(randSelLs[["esRandSelIn"]], referenceDfNew, RELEVANTVN_ES,
RELEVANTVN_REF)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# FUNCTION NAME: esFinal
# --------------
# This is function 29 of 29 in the hierarchy of 'esmprep' functions.
# ------------------------
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
# Prerequisites in order to execute esFinal. Start ------------------
# RELEVANTINFO_ES is delivered with the package
# Use example list delivered with the package
RELEVANTVN_ES <- RELEVANTVN_ESext
# tbsqDf is a raw ESM dataset, delivered with the package.
# Prerequisites in order to execute esFinal. End --------------------
# -------------------------------------------------------
# Run function 29 of 29; see esmprep functions' hierarchy.
# -------------------------------------------------------
# tbsqDf is the result of function 'computeTimeBetween'.
esDfFin <- esFinal(tbsqDf, esOpt=esAssigned[["ESopt"]], complianceRate=50,
RELEVANTINFO_ES, RELEVANTVN_ES)
# o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o=o
## End(Not run)

mmiche/esmprep documentation built on July 7, 2019, 8:23 p.m.