inst/r/finch2018.R

In ICTatRTI/PersonAlyticsPower: Power Analysis and Simulation for PersonAlytics

library(PersonAlyticsPower)

finch2018 <- polyICT$new(
  groups            = c(group1=25, group2=25)      ,
  phases            = makePhase(c(5,4))                ,
  propErrVar        = c(randFx=.5, res=.5, mserr=.0)   ,
  randFxOrder       = 1                                ,
  randFxCor         = 0.1                              ,
  randFxVar         = c(1, 1)                          ,
  error             = armaErr$new()                    ,
  merror            = armaErr$new(list())              ,
  ySD               = NULL                             ,
  yMean             = NULL                             ,
)

finch2018$inputMat[finch2018$inputMat$Phase=='phase1' &
                     finch2018$inputMat$Group=='group1', 'Mean1'] <- .75/5

finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group1', 'Mean0'] <- .75
finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group1', 'Mean1'] <- .375/4

finch2018$inputMat[finch2018$inputMat$Phase=='phase1' &
                     finch2018$inputMat$Group=='group2', 'Mean1'] <- .25/5

finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group2', 'Mean0'] <- .25
finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group2', 'Mean1'] <- .125/4


finch2018$inputMat
finch2018$designCheck()

interactions = list()
ints <- c("group1_phase1_slope",
          "group1_phase2_int"  , "group1_phase2_slope",
          "group2_phase1_slope",
          "group2_phase2_int"  , "group2_phase2_slope")
finch2018formula <- list()
finch2018formula$fixed <- formula(paste("y1 ~ -1 +", paste(ints, collapse = "+")))
finch2018formula$random <- formula(~Time | id)

alignPhase = "none"

ICTpower(outfile = c("Finch_et_al._2018", "csv"),
         design  = finch2018,
         userFormula = finch2018formula,
         interactions = interactions,
         alignPhase = alignPhase,
         B = 1000,
         seed = 6841353)

ICTpower(outfile = c("Finch_et_al._2018", "csv"),
         design  = finch2018,
         userFormula = finch2018formula,
         interactions = interactions,
         alignPhase = alignPhase,
         B = 1000,
         seed = 1)

################################################################################
# Other examples
################################################################################

# raw inputs (not standardized)
finch2018 <- polyICT$new(
  groups            = c(group1=2500, group2=2500)      ,
  phases            = makePhase(c(5,4))                ,
  propErrVar        = c(randFx=.5, res=.5, mserr=.0)   ,
  randFxOrder       = 1                                ,
  randFxCor         = 0.1                              ,
  randFxVar         = c(1, 1)                          ,
  error             = armaErr$new()                    ,
  merror            = armaErr$new(list())              ,
  ySD               = 1                                ,
  yMean             = 0                                ,
)

finch2018$inputMat[finch2018$inputMat$Phase=='phase1' &
                     finch2018$inputMat$Group=='group1', 'Mean1'] <- .75

finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group1', 'Mean0'] <- 3.75
finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group1', 'Mean1'] <- .25

finch2018$inputMat[finch2018$inputMat$Phase=='phase1' &
                     finch2018$inputMat$Group=='group2', 'Mean1'] <- .375

finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group2', 'Mean0'] <- 1.875
finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group2', 'Mean1'] <- .125


finch2018$inputMat
finch2018$designCheck()

interactions = list()
ints <- c("group1_phase1_slope",
          "group1_phase2_int"  , "group1_phase2_slope",
          "group2_phase1_slope",
          "group2_phase2_int"  , "group2_phase2_slope")
finch2018formula <- list()
finch2018formula$fixed <- formula(paste("y1 ~ -1 +", paste(ints, collapse = "+")))
finch2018formula$random <- formula(~Time | id)

alignPhase = "none"

ICTpower(outfile = c("Finch_et_al._2018", "csv"),
         design  = finch2018,
         userFormula = finch2018formula,
         interactions = interactions,
         alignPhase = alignPhase,
         B = 100,
         seed = 90423)

# large sample demonstration
finch2018 <- polyICT$new(
  groups            = c(group1=500, group2=500)      ,
  phases            = makePhase(c(5,4))                ,
  propErrVar        = c(randFx=.5, res=.5, mserr=.0)   ,
  randFxOrder       = 1                                ,
  randFxCor         = 0.1                              ,
  randFxVar         = c(1, 1)                          ,
  error             = armaErr$new()                    ,
  merror            = armaErr$new(list())              ,
  ySD               = NULL                             ,
  yMean             = NULL                             ,
)

finch2018$inputMat[finch2018$inputMat$Phase=='phase1' &
                     finch2018$inputMat$Group=='group1', 'Mean1'] <- .75/5

finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group1', 'Mean0'] <- .75
finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group1', 'Mean1'] <- .375/4

finch2018$inputMat[finch2018$inputMat$Phase=='phase1' &
                     finch2018$inputMat$Group=='group2', 'Mean1'] <- .25/5

finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group2', 'Mean0'] <- .25
finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group2', 'Mean1'] <- .125/4


finch2018$inputMat
finch2018$designCheck()

interactions = list()
ints <- c("group1_phase1_slope",
          "group1_phase2_int"  , "group1_phase2_slope",
          "group2_phase1_slope",
          "group2_phase2_int"  , "group2_phase2_slope")
finch2018formula <- list()
finch2018formula$fixed <- formula(paste("y1 ~ -1 +", paste(ints, collapse = "+")))
finch2018formula$random <- formula(~Time | id)

alignPhase = "none"

ICTpower(outfile = c("Finch_et_al._2018", "csv"),
         design  = finch2018,
         userFormula = finch2018formula,
         interactions = interactions,
         alignPhase = alignPhase,
         B = 100,
         seed = 90423)


# actual power analysis with a different scale
finch2018 <- polyICT$new(
  groups            = c(group1=25, group2=25)      ,
  phases            = makePhase(c(5,4))                ,
  propErrVar        = c(randFx=.5, res=.5, mserr=.0)   ,
  randFxOrder       = 1                                ,
  randFxCor         = 0.1                              ,
  randFxVar         = c(1, 1)                          ,
  error             = armaErr$new()                    ,
  merror            = armaErr$new(list())              ,
  ySD               = 1                             ,
  yMean             = 2                             ,
)

finch2018$inputMat[finch2018$inputMat$Phase=='phase1' &
                     finch2018$inputMat$Group=='group1', 'Mean1'] <- .75/5

finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group1', 'Mean0'] <- .75
finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group1', 'Mean1'] <- .375/4

finch2018$inputMat[finch2018$inputMat$Phase=='phase1' &
                     finch2018$inputMat$Group=='group2', 'Mean1'] <- .25/5

finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group2', 'Mean0'] <- .25
finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group2', 'Mean1'] <- .125/4


finch2018$inputMat
finch2018$designCheck()

interactions = list()
ints <- c("group1_phase1_slope",
          "group1_phase2_int"  , "group1_phase2_slope",
          "group2_phase1_slope",
          "group2_phase2_int"  , "group2_phase2_slope")
finch2018formula <- list()
finch2018formula$fixed <- formula(paste("y1 ~ -1 +", paste(ints, collapse = "+")))
finch2018formula$random <- formula(~Time | id)

alignPhase = "none"

ICTpower(outfile = c("Finch_et_al._2018", "csv"),
         design  = finch2018,
         userFormula = finch2018formula,
         interactions = interactions,
         alignPhase = alignPhase,
         B = 1000,
         seed = 12202236)

# actual power analysis with a min/max scale
finch2018 <- polyICT$new(
  groups            = c(group1=25, group2=25)      ,
  phases            = makePhase(c(5,4))                ,
  propErrVar        = c(randFx=.5, res=.5, mserr=.0)   ,
  randFxOrder       = 1                                ,
  randFxCor         = 0.1                              ,
  randFxVar         = c(1, 1)                          ,
  error             = armaErr$new()                    ,
  merror            = armaErr$new(list())              ,
  yMin              = 0                             ,
  yMax              = 5                             ,
)

finch2018$inputMat[finch2018$inputMat$Phase=='phase1' &
                     finch2018$inputMat$Group=='group1', 'Mean1'] <- .75/5

finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group1', 'Mean0'] <- .75
finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group1', 'Mean1'] <- .375/4

finch2018$inputMat[finch2018$inputMat$Phase=='phase1' &
                     finch2018$inputMat$Group=='group2', 'Mean1'] <- .25/5

finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group2', 'Mean0'] <- .25
finch2018$inputMat[finch2018$inputMat$Phase=='phase2' &
                     finch2018$inputMat$Group=='group2', 'Mean1'] <- .125/4


finch2018$inputMat
finch2018$designCheck() # fails!

interactions = list()
ints <- c("group1_phase1_slope",
          "group1_phase2_int"  , "group1_phase2_slope",
          "group2_phase1_slope",
          "group2_phase2_int"  , "group2_phase2_slope")
finch2018formula <- list()
finch2018formula$fixed <- formula(paste("y1 ~ -1 +", paste(ints, collapse = "+")))
finch2018formula$random <- formula(~Time | id)

alignPhase = "none"

ICTpower(outfile = c("Finch_et_al._2018", "csv"),
         design  = finch2018,
         userFormula = finch2018formula,
         interactions = interactions,
         alignPhase = alignPhase,
         B = 1000,
         seed = 12202236)