EASIalt: easiOrigin

# easiOrigin and CALM
## OneWay Vignette with Custom Contrasts

source("http://raw.githubusercontent.com/cwendorf/easiOrigin/main/source-easiOrigin.R")
source("http://raw.githubusercontent.com/cwendorf/CALM/main/source-CALM.R")

### Data Management

Factor <- c(rep(1, 4), rep(2, 4), rep(3, 4))
Outcome <- c(0, 0, 3, 5, 4, 7, 4, 9, 9, 6, 4, 9)
Factor <- factor(Factor, levels = c(1, 2, 3), labels = c("Level1", "Level2", "Level3"))
OneWayData <- data.frame(Factor, Outcome)

### Analyses of the Means

#### Confidence Intervals

ciMeans(Outcome ~ Factor)
graphMeans(Outcome ~ Factor)

### Analyses Using CALM Contrast Codes

#### Treatment (First) Contrasts

contrasts(Factor) <- treatment.first
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = treatment.first)
graphContrasts(Outcome ~ Factor, contrasts = treatment.first)
nhstContrasts(Outcome ~ Factor, contrasts = treatment.first)

#### Treatment (Last) Contrasts

contrasts(Factor) <- treatment.last
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = treatment.last)
graphContrasts(Outcome ~ Factor, contrasts = treatment.last)
nhstContrasts(Outcome ~ Factor, contrasts = treatment.last)

#### Control (First) Contrasts

contrasts(Factor) <- control.first
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = control.first)
graphContrasts(Outcome ~ Factor, contrasts = control.first)
nhstContrasts(Outcome ~ Factor, contrasts = control.first)

#### Control (Last) Contrasts

contrasts(Factor) <- control.last
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = control.last)
graphContrasts(Outcome ~ Factor, contrasts = control.last)
nhstContrasts(Outcome ~ Factor, contrasts = control.last)

#### Deviation (First) Contrasts

contrasts(Factor) <- deviation.first
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = deviation.first)
graphContrasts(Outcome ~ Factor, contrasts = deviation.first)
nhstContrasts(Outcome ~ Factor, contrasts = deviation.first)

#### Deviation (Last) Contrasts

contrasts(Factor) <- deviation.last
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = deviation.last)
graphContrasts(Outcome ~ Factor, contrasts = deviation.last)
nhstContrasts(Outcome ~ Factor, contrasts = deviation.last)

#### Helmert (Forward) Contrasts

contrasts(Factor) <- helmert.forward
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = helmert.forward)
graphContrasts(Outcome ~ Factor, contrasts = helmert.forward)
nhstContrasts(Outcome ~ Factor, contrasts = helmert.forward)

#### Helmert (Reverse) Contrasts

contrasts(Factor) <- helmert.reverse
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = helmert.reverse)
graphContrasts(Outcome ~ Factor, contrasts = helmert.reverse)
nhstContrasts(Outcome ~ Factor, contrasts = helmert.reverse)

#### Repeated (Forward) Contrasts

contrasts(Factor) <- repeated.forward
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = repeated.forward)
graphContrasts(Outcome ~ Factor, contrasts = repeated.forward)
nhstContrasts(Outcome ~ Factor, contrasts = repeated.forward)

#### Repeated (Reverse) Contrasts

contrasts(Factor) <- repeated.reverse
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = repeated.reverse)
graphContrasts(Outcome ~ Factor, contrasts = repeated.reverse)
nhstContrasts(Outcome ~ Factor, contrasts = repeated.reverse)

#### Difference (Forward) Contrasts

contrasts(Factor) <- difference.forward
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = difference.forward)
graphContrasts(Outcome ~ Factor, contrasts = difference.forward)
nhstContrasts(Outcome ~ Factor, contrasts = difference.forward)

#### Difference (Reverse) Contrasts

contrasts(Factor) <- difference.reverse
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = difference.reverse)
graphContrasts(Outcome ~ Factor, contrasts = difference.reverse)
nhstContrasts(Outcome ~ Factor, contrasts = difference.reverse)

### Analyses Using Custom Contrasts

#### Orthogonal Contrasts

GM <- c(1 / 3, 1 / 3, 1 / 3)
H1 <- c(1, -1 / 2, -1 / 2)
H2 <- c(0, 1, -1)
ex_custom.orthogonal <- rbind(GM, H1, H2)
custom.orthogonal <- calm.encode(ex_custom.orthogonal)
custom.orthogonal

contrasts(Factor) <- custom.orthogonal[, -1]
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = custom.orthogonal[, -1])
graphContrasts(Outcome ~ Factor, contrasts = custom.orthogonal[, -1])
nhstContrasts(Outcome ~ Factor, contrasts = custom.orthogonal[, -1])

#### Nonorthogonal Contrasts

GM <- c(1, 0, 0)
H1 <- c(1, -1 / 2, -1 / 2)
H2 <- c(1, -1, 0)
ex_custom.nonorthogonal <- rbind(GM, H1, H2)
custom.nonorthogonal <- calm.encode(ex_custom.nonorthogonal)
custom.nonorthogonal

contrasts(Factor) <- custom.nonorthogonal[, -1]
ciCoefficients(Outcome ~ Factor)
graphCoefficients(Outcome ~ Factor)
nhstCoefficients(Outcome ~ Factor)

ciContrasts(Outcome ~ Factor, contrasts = custom.nonorthogonal[, -1])
graphContrasts(Outcome ~ Factor, contrasts = custom.nonorthogonal[, -1])
nhstContrasts(Outcome ~ Factor, contrasts = custom.nonorthogonal[, -1])