library(matrixTests)

#--- special argument cases ----------------------------------------------------

# x and y can be vectors
x <- rnorm(9)
y <- rnorm(9)
X <- matrix(x, nrow=1)
Y <- matrix(y, nrow=1)
stopifnot(all.equal(row_t_paired(x, y), row_t_paired(X, Y)))

# x and y can be numeric data frames
x <- iris[1:50,1:4]
y <- iris[51:100,1:4]
X <- as.matrix(x)
Y <- as.matrix(y)
stopifnot(all.equal(row_t_paired(x, y), row_t_paired(X, Y)))

# x and y can have 0 rows
x <- matrix(0, nrow=0, ncol=4)
y <- matrix(0, nrow=0, ncol=4)
stopifnot(all.equal(nrow(row_t_paired(x, y)), 0))

# x and y can have 0 rows and 0 columns
x <- matrix(0, nrow=0, ncol=0)
y <- matrix(0, nrow=0, ncol=0)
stopifnot(all.equal(nrow(row_t_paired(x, y)), 0))

# alternative values can be partially completed
x <- rnorm(5)
y <- rnorm(5)
stopifnot(all.equal(row_t_paired(x, y, alternative="greater"), row_t_paired(x, y, alternative="g")))

# null can be +Inf
x <- rnorm(5)
y <- rnorm(5)
res <- row_t_paired(x, y, null=Inf)
stopifnot(all.equal(res$pvalue, 0))
stopifnot(all.equal(res$statistic, -Inf))

# null can be -Inf
x <- rnorm(5)
y <- rnorm(5)
res <- row_t_paired(x, y, null=-Inf)
stopifnot(all.equal(res$pvalue, 0))
stopifnot(all.equal(res$statistic, Inf))

# conf.level can be 0
x <- rnorm(5)
y <- rnorm(5)
res <- row_t_paired(x, y, conf.level=0)
stopifnot(all.equal(res$conf.low, res$conf.high))

# conf.level can be 1
x <- rnorm(5)
y <- rnorm(5)
res <- row_t_paired(x, y, conf.level=1)
stopifnot(all.equal(res$conf.low, -Inf))
stopifnot(all.equal(res$conf.high, Inf))

# conf.level can be NA
x <- rnorm(5)
y <- rnorm(5)
res <- row_t_paired(x, y, conf.level=NA)
stopifnot(all.equal(res$conf.level, NA_real_))
stopifnot(all.equal(res$conf.low, NA_real_))
stopifnot(all.equal(res$conf.high, NA_real_))


#--- recycling -----------------------------------------------------------------

# y can be a vector when x is a matrix
x <- matrix(rnorm(10), nrow=2)
y <- 1:5
res1 <- row_t_paired(x, y)
res2 <- row_t_paired(x, rbind(y,y))
stopifnot(all.equal(res1, res2))

# null can be specified for each row
x <- matrix(rnorm(10), nrow=2)
y <- matrix(rnorm(10), nrow=2)
res1 <- row_t_paired(x, y, null=2)
res2 <- row_t_paired(x, y, null=c(2,2))
stopifnot(all.equal(res1, res2))

# alternative can be specified for each row
x <- matrix(rnorm(10), nrow=2)
y <- matrix(rnorm(10), nrow=2)
res1 <- row_t_paired(x, y, alternative="g")
res2 <- row_t_paired(x, y, alternative=c("g","g"))
stopifnot(all.equal(res1, res2))

# conf.level can be specified for each row
x <- matrix(rnorm(10), nrow=2)
y <- matrix(rnorm(10), nrow=2)
res1 <- row_t_paired(x, y, conf.level=0.98)
res2 <- row_t_paired(x, y, conf.level=c(0.98,0.98))
stopifnot(all.equal(res1, res2))


#--- missing values ------------------------------------------------------------

# missing values in x are removed
x <- c(NA,NA,rnorm(7),NA)
y <- rnorm(10)
res1 <- row_t_paired(x, y)
res2 <- row_t_paired(x[!is.na(x)], y[!is.na(x)])
res2[,c(2,5,8)]  <- res1[,c(2,5,8)]   # NOTE: row_t_paired uses all values to calculate stats (even the ones that do not have a pair)
stopifnot(all.equal(res1, res2))

# missing values in y are removed
x <- rnorm(10)
y <- c(NA,NA,rnorm(7),NA)
res1 <- row_t_paired(x, y)
res2 <- row_t_paired(x[!is.na(y)], y[!is.na(y)])
res2[,c(1,4,7)]  <- res1[,c(1,4,7)]   # NOTE: row_t_paired uses all values to calculate stats (even the ones that do not have a pair)
stopifnot(all.equal(res1, res2))

# missing values from both x and y are removed
x <- c(NA,NA,rnorm(7),NA)
y <- c(NA,rnorm(7),NA,NA)
res1 <- row_t_paired(x, y)
res2 <- row_t_paired(x[!is.na(x) & !is.na(y)], y[!is.na(x) & !is.na(y)])
res2[,c(1,2,4,5,7,8)]  <- res1[,c(1,2,4,5,7,8)]  # NOTE: row_t_paired uses all values to calculate stats (even the ones that do not have a pair)
stopifnot(all.equal(res1, res2))
stopifnot(all.equal(res1$obs.paired, 6))

# no difference between NA and NaN
x1 <- c(NA,NA,1,2,1:5,NA)
x2 <- c(NaN,NaN,1,2,1:5,NaN)
y1 <- c(NA,NA,8:2,NA)
y2 <- c(NaN,NaN,8:2,NaN)
res1 <- row_t_paired(x1, y1)
res2 <- row_t_paired(x2, y2)
stopifnot(all.equal(res1, res2))

# everything can be NA
x <- rep(NA_integer_, 4)
y <- rep(NA_integer_, 4)
res <- suppressWarnings(row_t_paired(x, y))
stopifnot(all.equal(res$obs.paired, 0))


#--- rownames ------------------------------------------------------------------

# when not provided - numbers are used instead.
x <- matrix(rnorm(20), nrow=2)
y <- matrix(rnorm(20), nrow=2)
res <- row_t_paired(x, y)
stopifnot(all.equal(rownames(res), c("1", "2")))

# when not provided - not taken from y
x <- matrix(rnorm(20), nrow=2)
y <- matrix(rnorm(20), nrow=2, dimnames=list(c("A", "B")))
res <- row_t_paired(x, y)
stopifnot(all.equal(rownames(res), c("1","2")))

# when provided - preserved (matrix)
x <- matrix(rnorm(20), nrow=2, dimnames=list(c("A", "B")))
y <- matrix(rnorm(20), nrow=2)
res <- row_t_paired(x, y)
stopifnot(all.equal(rownames(res), rownames(x)))

# when provided - preserved (data.frame)
x <- data.frame(matrix(rnorm(20), nrow=2, dimnames=list(c("A", "B"))))
y <- matrix(rnorm(20), nrow=2)
res <- row_t_paired(x, y)
stopifnot(all.equal(rownames(res), rownames(x)))

# when duplicated - made unique
x <- matrix(rnorm(20), nrow=4, dimnames=list(c("A", "A", "B", "B")))
y <- matrix(rnorm(20), nrow=4)
res <- row_t_paired(x, y)
stopifnot(all.equal(rownames(res), make.unique(rownames(x))))