library("matrixStats")

rowCounts_R <- function(x, value = TRUE, na.rm = FALSE, ...) {
  if (is.na(value)) {
    counts <- apply(x, MARGIN = 1L, FUN = function(x)
      sum(is.na(x))
    )
  } else {
    counts <- apply(x, MARGIN = 1L, FUN = function(x)
      sum(x == value, na.rm = na.rm)
    )
  }
  # Preserve names attribute
  names <- names(counts)  
  counts <- as.integer(counts)
  if (useNames && !is.null(names)) names(counts) <- names
  counts
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Data type: integer and numeric
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
for (mode in c("integer", "double")) {
  x <- matrix(runif(10 * 5, min = -3, max = 3), nrow = 10L, ncol = 5L)
  x[sample.int(length(x), size = 7L)] <- 0
  storage.mode(x) <- mode
  
  dimnames = list(letters[1:10], LETTERS[1:5])
  
  # Test with and without dimnames on x
  for (setDimnames in c(TRUE, FALSE)) {
    if (setDimnames) dimnames(x) <- dimnames
    else dimnames(x) <- NULL    
    for (na.rm in c(FALSE, TRUE)) {
      # Check names attribute
      for (useNames in c(TRUE, FALSE)) {
        # Count zeros
        r0 <- rowCounts_R(x, value = 0, na.rm = na.rm, useNames = useNames)
        r1 <- rowCounts(x, value = 0, na.rm = na.rm, useNames = useNames)
        r2 <- colCounts(t(x), value = 0, na.rm = na.rm, useNames = useNames)
        stopifnot(identical(r1, r0))
        stopifnot(identical(r2, r0))
        
        # Count NAs
        r0 <- rowCounts_R(x, value = NA, na.rm = na.rm, useNames = useNames)
        r1 <- rowCounts(x, value = NA, na.rm = na.rm, useNames = useNames)
        r2 <- colCounts(t(x), value = NA, na.rm = na.rm, useNames = useNames)
        stopifnot(identical(r1, r0))
        stopifnot(identical(r2, r0))
        
        if (mode == "integer") {
          ux <- unique(as.vector(x))
          r0 <- r1 <- r2 <- integer(nrow(x))
          for (value in ux) {
            r0 <- r0 + rowCounts_R(x, value = value, na.rm = na.rm, useNames = useNames)
            r1 <- r1 + rowCounts(x, value = value, na.rm = na.rm, useNames = useNames)
            r2 <- r2 + colCounts(t(x), value = value, na.rm = na.rm, useNames = useNames)
            stopifnot(identical(r1, r0))
            stopifnot(identical(r2, r0))
          }
          stopifnot(all(r0 == ncol(x)))
        } # if (mode == "integer")
      } # for (useNames ...)
    } # for (na.rm ...)
  } # for (setDimnames ...)
} # for (mode ...)


# All NAs
na_list <- list(NA_integer_, NA_real_, NaN)
for (na_value in na_list) {
  x <- matrix(na_value, nrow = 10L, ncol = 5L)
  # Test with and without dimnames on x
  for (setDimnames in c(TRUE, FALSE)) {
    if (setDimnames) dimnames(x) <- dimnames
    else dimnames(x) <- NULL    
    for (na.rm in c(FALSE, TRUE)) {
      # Check names attribute
      for (useNames in c(TRUE, FALSE)) {
        r0 <- rowCounts_R(x, na.rm = na.rm, useNames = useNames)
        r1 <- rowCounts(x, na.rm = na.rm, useNames = useNames)
        r2 <- colCounts(t(x), na.rm = na.rm, useNames = useNames)
        stopifnot(identical(r1, r0))
        stopifnot(identical(r2, r0))
        
        # Count NAs
        r0 <- rowCounts_R(x, value = NA, na.rm = na.rm, useNames = useNames)
        r1 <- rowCounts(x, value = NA, na.rm = na.rm, useNames = useNames)
        r2 <- colCounts(t(x), value = NA, na.rm = na.rm, useNames = useNames)
        stopifnot(all(r0 == ncol(x)))
        stopifnot(identical(r1, r0))
        stopifnot(identical(r2, r0))
      }
    }
  }
} # for (na_value ...)


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Data type: logical
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
x <- matrix(FALSE, nrow = 10L, ncol = 4L)
x[7:8, 2:3] <- TRUE
x[1:3, ] <- TRUE
x[, 1] <- TRUE
x[4, ] <- FALSE
x[, 4] <- FALSE
x[2, ] <- FALSE
x[3, ] <- TRUE

# To check names attribute
dimnames <- list(letters[1:10], LETTERS[1:4])

# Test with and without dimnames on x
for (setDimnames in c(TRUE, FALSE)) {
  if (setDimnames) dimnames(x) <- dimnames
  else dimnames(x) <- NULL
  # Row/column counts
  for (na.rm in c(FALSE, TRUE)) {
    # Check names attribute
    for (useNames in c(TRUE, FALSE)) {
      r0 <- rowCounts_R(x, na.rm = na.rm, useNames = useNames)
      r1 <- rowCounts(x, na.rm = na.rm, useNames = useNames)
      r2 <- colCounts(t(x), na.rm = na.rm, useNames = useNames)
      stopifnot(identical(r1, r0))
      stopifnot(identical(r2, r0))
      
      r_true <- rowCounts(x, value = TRUE, na.rm = na.rm, useNames = useNames)
      r_false <- rowCounts(x, value = FALSE, na.rm = na.rm, useNames = useNames)
      stopifnot(r_true + r_false == ncol(x))
      
      c_true <- colCounts(x, value = TRUE, na.rm = na.rm, useNames = useNames)
      c_false <- colCounts(x, value = FALSE, na.rm = na.rm, useNames = useNames)
      stopifnot(c_true + c_false == nrow(x))
      
      # Count NAs
      r0 <- rowCounts_R(x, value = NA, na.rm = na.rm, useNames = useNames)
      r1 <- rowCounts(x, value = NA, na.rm = na.rm, useNames = useNames)
      r2 <- colCounts(t(x), value = NA, na.rm = na.rm, useNames = useNames)
      stopifnot(identical(r1, r0))
      stopifnot(identical(r2, r0))
    }
  }
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Data type: character (not sure if this should be supported)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
x <- matrix(rep(letters, length.out = 10 * 5), nrow = 10L, ncol = 5L)
x[2:3, 3:4] <- NA_character_

# Row/column counts
for (na.rm in c(FALSE, TRUE)) {
  for (value in c("g", NA_character_)) {
    r0 <- rowCounts_R(x, value = value, na.rm = na.rm)
    r1 <- rowCounts(x, value = value, na.rm = na.rm)
    r2 <- colCounts(t(x), value = value, na.rm = na.rm)
    stopifnot(identical(r1, r0))
    stopifnot(identical(r2, r0))

    c <- count(x[1, ], value = value, na.rm = na.rm)
    stopifnot(identical(c, r1[1]))

    c <- count(x[2, ], value = value, na.rm = na.rm)
    stopifnot(identical(c, r1[2]))
  }
}

# NA row
x <- matrix(0, nrow = 2L, ncol = 2L)
x[1, ] <- NA_integer_

dimnames <- list(letters[1:2], LETTERS[1:2])

# Test with and without dimnames on x
for (setDimnames in c(TRUE, FALSE)) {
  if (setDimnames) dimnames(x) <- dimnames
  else dimnames(x) <- NULL    
  # Check names attribute
  for (useNames in c(TRUE, FALSE)) {
    r0 <- rowCounts(x, value = 0, useNames = useNames)
    r1 <- rowCounts_R(x, value = 0, useNames = useNames)
    stopifnot(identical(r0, r1))
  }
}
