mdes.bird2r1 <- function(score = NULL, dists = "normal", k1 = -6, k2 = 6,
order = 1, interaction = FALSE, treat.lower = TRUE, cutoff = 0, p = NULL,
power = .80, alpha = .05, two.tailed = TRUE, df = n2 - g2 - 1,
rho2, omega2, r21 = 0, r2t2 = 0, g2 = 0,
rate.tp = 1, rate.cc = 0, n1, n2) {
user.parms <- as.list(match.call())
.error.handler(user.parms)
if(df < 1) stop("Insufficient degrees of freedom", call. = FALSE)
if(!is.null(score) & order == 0) warning("Ignoring information from the 'score' object \n", call. = FALSE)
if(order == 0) {
d <- 1
if(is.null(p)) stop("'p' cannot be NULL in random assignment designs", call. = FALSE)
idx.score <- intersect(c("dists", "k1", "k2", "interaction", "treat.lower", "cutoff"), names(user.parms))
if(length(idx.score) > 0) cat("\nCAUTION: Ignoring argument(s):",
sQuote(names(user.parms[idx.score])), "\n")
ifelse(treat.lower, cutoff <- p, cutoff <- 1 - p)
interaction <- FALSE
dists <- "uniform"
k1 <- 0
k2 <- 1
} else if(order %in% 1:8) {
if(is.null(score)) {
score <- inspect.score(order = order, interaction = interaction,
treat.lower = treat.lower, cutoff = cutoff,
p = p, k1 = k1, k2 = k2, dists = dists)
} else {
if("p" %in% names(user.parms)) warning("Using 'p' from the 'score' object, ignoring 'p' in the function call", call. = FALSE)
if(!inherits(score, "score")) {
score <- inspect.score(score = score, order = order, interaction = interaction,
treat.lower = treat.lower, cutoff = cutoff,
p = p, k1 = k1, k2 = k2, dists = dists)
} else {
idx.score <- intersect(c("dists", "k1", "k2", "order", "interaction", "treat.lower", "p", "cutoff"), names(user.parms))
if(length(idx.score) > 0) cat("\nCAUTION: 'score' object overwrites argument(s):",
sQuote(names(user.parms[idx.score])), "\n")
}
}
d <- score$rdde
p <- score$p
cutoff <- score$cutoff
treat.lower <- score$treat.lower
order <- score$order
interaction <- score$interaction
dists <- score$parms$dists
k1 <- score$parms$k1
k2 <- score$parms$k2
} else if(order > 8) {
stop("'order' > 8 is not allowed", call. = FALSE)
}
sse <- (1/(rate.tp - rate.cc)) * sqrt(rho2 * omega2 * (1 - r2t2) / n2 +
d * (1 - rho2) * (1 - r21) / (p * (1 - p) * n2 * n1))
mdes <- .mdes(power, alpha, sse, df, two.tailed)
colnames(mdes) <- c("mdes", paste0(100 * (1 - round(alpha, 2)), "%lcl"),
paste0(100 * (1 - round(alpha, 2)), "%ucl"))
mdes.out <- list(parms = list(dists = dists, k1 = k1, k2 = k2,
order = order, interaction = interaction,
treat.lower = treat.lower, p = p, cutoff = cutoff,
power = power, alpha = alpha, two.tailed = two.tailed,
rho2 = rho2, omega2 = omega2, r21 = r21, r2t2 = r2t2,
g2 = g2, rate.tp = rate.tp, rate.cc = rate.cc, n1 = n1, n2 = n2),
df = df,
sse = sse,
mdes = mdes)
.summary.mdes(mdes.out)
class(mdes.out) <- c("mdes", "bird2r1")
return(invisible(mdes.out))
}
mdes.bird2 <- mdes.bird2r1
power.bird2r1 <- function(score = NULL, dists = "normal", k1 = -6, k2 = 6,
order = 1, interaction = FALSE, treat.lower = TRUE, cutoff = 0, p = NULL,
es = .25, alpha = .05, two.tailed = TRUE, df = n2 - g2 - 1,
rho2, omega2, r21 = 0, r2t2 = 0, g2 = 0,
rate.tp = 1, rate.cc = 0, n1, n2) {
user.parms <- as.list(match.call())
.error.handler(user.parms)
if(df < 1) stop("Insufficient degrees of freedom", call. = FALSE)
if(!is.null(score) & order == 0) warning("Ignoring information from the 'score' object \n", call. = FALSE)
if(order == 0) {
d <- 1
if(is.null(p)) stop("'p' cannot be NULL in random assignment designs", call. = FALSE)
idx.score <- intersect(c("dists", "k1", "k2", "interaction", "treat.lower", "cutoff"), names(user.parms))
if(length(idx.score) > 0) cat("\nCAUTION: Ignoring argument(s):",
sQuote(names(user.parms[idx.score])), "\n")
ifelse(treat.lower, cutoff <- p, cutoff <- 1 - p)
interaction <- FALSE
dists <- "uniform"
k1 <- 0
k2 <- 1
} else if(order %in% 1:8) {
if(is.null(score)) {
score <- inspect.score(order = order, interaction = interaction,
treat.lower = treat.lower, cutoff = cutoff,
p = p, k1 = k1, k2 = k2, dists = dists)
} else {
if("p" %in% names(user.parms)) warning("Using 'p' from the 'score' object, ignoring 'p' in the function call", call. = FALSE)
if(!inherits(score, "score")) {
score <- inspect.score(score = score, order = order, interaction = interaction,
treat.lower = treat.lower, cutoff = cutoff,
p = p, k1 = k1, k2 = k2, dists = dists)
} else {
idx.score <- intersect(c("dists", "k1", "k2", "order", "interaction", "treat.lower", "p", "cutoff"), names(user.parms))
if(length(idx.score) > 0) cat("\nCAUTION: 'score' object overwrites argument(s):",
sQuote(names(user.parms[idx.score])), "\n")
}
}
d <- score$rdde
p <- score$p
cutoff <- score$cutoff
treat.lower <- score$treat.lower
order <- score$order
interaction <- score$interaction
dists <- score$parms$dists
k1 <- score$parms$k1
k2 <- score$parms$k2
} else if(order > 8) {
stop("'order' > 8 is not allowed", call. = FALSE)
}
sse <- (1/(rate.tp - rate.cc)) * sqrt(rho2 * omega2 * (1 - r2t2) / n2 +
d * (1 - rho2) * (1 - r21) / (p * (1 - p) * n2 * n1))
power <- .power(es, alpha, sse, df, two.tailed)
power.out <- list(parms = list(dists = dists, k1 = k1, k2 = k2,
order = order, interaction = interaction,
treat.lower = treat.lower, p = p, cutoff = cutoff,
es = es, alpha = alpha, two.tailed = two.tailed,
rho2 = rho2, omega2 = omega2, r21 = r21, r2t2 = r2t2,
g2 = g2, rate.tp = rate.tp, rate.cc = rate.cc,
n1 = n1, n2 = n2),
df = df,
sse = sse,
power = power)
names(power) <- "power"
.summary.power(power.out)
class(power.out) <- c("power", "bird2r1")
return(invisible(power.out))
}
power.bird2 <- power.bird2r1
cosa.bird2r1 <- function(score = NULL, dists = "normal", k1 = -6, k2 = 6, rhots = NULL,
order = 1, interaction = FALSE,
treat.lower = TRUE, cutoff = 0, p = NULL,
cn1 = 0, cn2 = 0, cost = NULL,
n1 = NULL, n2 = NULL, n0 = c(10, 100), p0 = .499,
constrain = "power", round = TRUE, max.power = FALSE,
local.solver = c("LBFGS", "SLSQP"),
power = .80, es = .25, alpha = .05, two.tailed = TRUE,
rho2, omega2, g2 = 0, r21 = 0, r2t2 = 0) {
user.parms <- as.list(match.call())
.error.handler(user.parms, fun = "cosa")
if(!is.null(rhots)) {
if(rhots == 0) {
if(order != 0) {
order <- 0
warning("'order' argument is ignored, forcing 'order = 0' because 'rhots = 0'", call. = FALSE)
}
} else {
stop("'rhots' argument will be removed in the future, arbitrary correlations are not allowed,
use inspect.score() function instead", call. = FALSE)
}
}
if(!is.null(score) & order == 0) warning("Ignoring information from the 'score' object \n", call. = FALSE)
if(order == 0) {
d <- 1
idx.score <- intersect(c("dists", "k1", "k2", "interaction", "treat.lower", "cutoff"), names(user.parms))
if(length(idx.score) > 0) cat("\nCAUTION: Ignoring argument(s):",
sQuote(names(user.parms[idx.score])), "\n")
cutoff <- NA
interaction <- FALSE
dists <- "uniform"
k1 <- 0
k2 <- 1
} else if(order %in% 1:8) {
if(is.null(score)) {
score <- inspect.score(order = order, interaction = interaction,
treat.lower = treat.lower, cutoff = cutoff,
p = p, k1 = k1, k2 = k2, dists = dists)
} else {
if("p" %in% names(user.parms)) warning("Using 'p' from the 'score' object, ignoring 'p' in the function call", call. = FALSE)
if(!inherits(score, "score")) {
score <- inspect.score(score = score, order = order, interaction = interaction,
treat.lower = treat.lower, cutoff = cutoff,
p = p, k1 = k1, k2 = k2, dists = dists)
} else {
idx.score <- intersect(c("dists", "k1", "k2", "order", "interaction", "treat.lower", "p", "cutoff"), names(user.parms))
if(length(idx.score) > 0) cat("\nCAUTION: 'score' object overwrites argument(s):",
sQuote(names(user.parms[idx.score])), "\n")
}
}
d <- score$rdde
p <- score$p
cutoff <- score$cutoff
treat.lower <- score$treat.lower
order <- score$order
interaction <- score$interaction
dists <- score$parms$dists
k1 <- score$parms$k1
k2 <- score$parms$k2
} else if(order > 8) {
stop("'order' > 8 is not allowed", call. = FALSE)
}
fun <- "cosa.bird2r1"
lb <- c(1, g2 + 2)
if(!is.null(n2)) {
if(n2[1] < lb[2]) stop("Lower bound for 'n2' violate minimum degrees of freedom requirement", call. = FALSE)
}
.df <- quote(n2 - g2 - 1)
.sse <- quote(sqrt(rho2 * omega2 * (1 - r2t2) / n2 +
d * (1 - rho2) * (1 - r21) / (p * (1 - p) * n2 * n1)))
.cost <- quote(n2 * cn2 +
n2 * n1 * (cn1[2] + p * (cn1[1] - cn1[2])))
.var.jacob <- expression(
c(
-d * (1 - rho2) * (1 - r21) / (p * (1 - p) * n2 * n1^2),
-rho2 * omega2 * (1 - r2t2) / n2^2 -
d * (1 - rho2) * (1 - r21) / (p * (1 - p) * n2^2 * n1),
-(1 - 2 * p) * d * (1 - rho2) * (1 - r21) / ((1 - p)^2 * p^2 * n2 * n1)
)
)
.cost.jacob <- expression(
c(
n2 * (p * cn1[1] + (1 - p) * cn1[2]),
cn2 +
n1 * (p * cn1[1] + (1 - p) * cn1[2]),
n2 * n1 * (cn1[1] - cn1[2])
)
)
if(all(cn1 == 0) & is.null(p)) p <- .50
cosa <- .cosa(order = order, interaction = interaction,
cn1 = cn1, cn2 = cn2, cost = cost,
constrain = constrain, round = round,
max.power = max.power, local.solver = local.solver,
power = power, es = es, alpha = alpha, two.tailed = two.tailed,
rho2 = rho2, omega2 = omega2, r21 = r21, r2t2 = r2t2,
g2 = g2, p0 = p0, p = p, n0 = n0, n1 = n1, n2 = n2)
cosa.out <- list(parms = list(dists = dists, k1 = k1, k2 = k2,
order = order, interaction = interaction,
treat.lower = treat.lower, cutoff = cutoff,
cn1 = cn1, cn2 = cn2, cost = cost,
constrain = constrain, round = round,
max.power = max.power, local.solver = local.solver,
power = power, es = es, alpha = alpha, two.tailed = two.tailed,
rho2 = rho2, omega2 = omega2, r21 = r21, r2t2 = r2t2,
g2 = g2, p0 = p0, p = p, n0 = n0, n1 = n1, n2 = n2),
cosa = cosa)
class(cosa.out) <- c("cosa", "bird2r1")
.summary.cosa(cosa.out)
return(invisible(cosa.out))
}
cosa.bird2 <- cosa.bird2r1
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