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#' Kernel causality summary of evidence for causal paths
#' from three criteria using new exact stochastic dominance.
#'
#'
#'
#' The function develops a unanimity index for deciding which
#' flip (y on xi) or (xi on y) is best. Relevant signs determine the
#' causal direction and unanimity index among three criteria.
#' While allowing the researcher to keep some variables as controls,
#' or outside the scope of causal path determination
#' (e.g., age or latitude) this function produces detailed causal path information
#' in a 5 column matrix identifying the names of variables,
#' causal path directions, path strengths re-scaled to be in the
#' range [--100, 100], (table reports absolute values of the strength)
#' plus Pearson correlation and its p-value.
#' The `2' in the name of the function suggests a second implementation
#' where exact stochastic dominance, decileVote, and momentVote are used
#' and where we avoid Anderson's trapezoidal approximation.
#'
#'
#' The algorithm determines causal path directions
#' from the sign
#' of the strength index and strength index values by comparing
#' three aspects of flipped kernel regressions:
#' [x1 on f(x2, x3, .. xp)] and its flipped version [x2 on f(x1, x3, .. xp)]
#' We compare (i) formal exogeneity test criterion, (ii) absolute residuals, and
#' (iii) R-squares of the flipped regressions implying three criteria Cr1, to Cr3.
#' The criteria are quantified by newer exact methods using four orders
#' of stochastic dominance, SD1 to SD4. See Vinod's (2021) SSRN papers. In portfolio
#' applications of stochastic dominance, one wants higher values. Here, we are
#' comparing two probability distributions of absolute residuals for two
#' flipped models. We choose that flip, which has smaller absolute residuals
#' that will have a better fit.
#'
#' @param mtx {The data matrix with many columns, y the first column
#' is fixed and then
#' paired with all columns, one by one, and still called x for the
#' purpose of flipping.}
#' @param nam {vector of column names for \code{mtx}. Default: colnames(mtx)}
#' @param ctrl {data matrix for designated control variable(s) outside causal paths}
#' @param dig {Number of digits for reporting (default \code{dig}=6).}
#' @return If there are p columns in the input matrix, x1, x2, .., xp, say,
#' and if we keep x1 as a common member of all causal direction pairs
#' (x1, x(1+j)) for (j=1, 2, .., p-1) which can be flipped. That is, either x1 is
#' the cause or x(1+j) is the cause in a chosen pair.
#' The control
#' variables are not flipped. The printed output of this function
#' reports the results for p-1 pairs indicating which variable
#' (by name) causes which other variable (also by name).
#' It also prints a signed summary strength index in the range [-100,100].
#' A positive sign of the strength index means x1 kernel causes x(1+j),
#' whereas a negative strength index means x(1+j) kernel causes x1. The function
#' also prints the Pearson correlation and its p-value. In short, function returns
#' a matrix of p-1 rows and 5 columns entitled:
#' ``cause", ``response", ``strength", ``corr." and ``p-value", respectively
#' with self-explanatory titles. The first two columns have names of variables
#' x1 or x(1+j), depending on which is the cause. The `strength' column
#' reports the absolute value of the summary index, in the range [0,100],
#' providing a summary of causal results
#' based on the preponderance of evidence from Cr1 to Cr3
#' from four orders of stochastic dominance, moments, deciles,
#' etc. The order of input columns in mtx matters.
#' The fourth column, `corr.' of `out', reports the Pearson correlation coefficient.
#' The fifth column has the p-value for testing the null of zero Pearson coeff.
#' This function calls \code{silentPair2}, allowing for control variables.
#' The output of this function can be sent to `xtable' for a nice Latex table.
#' @importFrom stats complete.cases
#' @author Prof. H. D. Vinod, Economics Dept., Fordham University, NY.
#' @seealso See \code{\link{siPair2Blk}} for a block version
#' @seealso See \code{\link{causeSummary}} is subject to trapezoidal approximation.
#' @seealso see \code{\link{silentPair2}} called by this function.
#' @references Vinod, H. D. 'Generalized Correlation and Kernel Causality with
#' Applications in Development Economics' in Communications in
#' Statistics -Simulation and Computation, 2015,
#' \doi{10.1080/03610918.2015.1122048}
#' @references Vinod, H. D. 'New exogeneity tests and causal paths,'
#' Chapter 2 in 'Handbook of Statistics: Conceptual Econometrics
#' Using R', Vol.32, co-editors: H. D. Vinod and C.R. Rao. New York:
#' North Holland, Elsevier Science Publishers, 2019, pp. 33-64.
#'
#' @references Vinod, H. D. Causal Paths and Exogeneity Tests
#' in {Generalcorr} Package for Air Pollution and Monetary Policy
#' (June 6, 2017). Available at SSRN:
#' \url{https://www.ssrn.com/abstract=2982128}
#'
#' @references Vinod, Hrishikesh D., R Package GeneralCorr
#' Functions for Portfolio Choice
#' (November 11, 2021). Available at SSRN:
#' https://ssrn.com/abstract=3961683
#'
#' @references Vinod, Hrishikesh D., Stochastic Dominance
#' Without Tears (January 26, 2021). Available at
#' SSRN: https://ssrn.com/abstract=3773309
#'
#' @concept causal path
#' @concept stochastic dominance orders
#' @concept summary index
#' @note The European Crime data has all three criteria correctly suggesting that a
#' high crime rate kernel causes the deployment of a large number of police officers.
#' Since Cr1 to Cr3 nearly unanimously suggest `crim' as the cause of `off',
#' strength index 100 suggests unanimity among the criteria.
#' \code{attach(EuroCrime); causeSummary(cbind(crim,off))}
#'
#' @examples
#'
#'
#' \dontrun{
#' mtx=as.matrix(mtcars[,1:3])
#' ctrl=as.matrix(mtcars[,4:5])
#' causeSummary2(mtx,ctrl,nam=colnames(mtx))
#' }
#'
### \dontrun{
#'options(np.messages=FALSE)
#'set.seed(234)
#'z=runif(10,2,11)# z is independently created
#'x=sample(1:10)+z/10 #x is somewhat indep and affected by z
#'y=1+2*x+3*z+rnorm(10)
#'w=runif(10)
#'x2=x;x2[4]=NA;y2=y;y2[8]=NA;w2=w;w2[4]=NA
#'causeSummary2(mtx=cbind(x2,y2), ctrl=cbind(z,w2))
### }
#'
#'
#' @export
causeSummary2 = function(mtx, nam = colnames(mtx),
ctrl = 0, dig = 6)
{
# require(generalCorr); require(PerformanceAnalytics); options(np.messages=FALSE)
p = NCOL(mtx)
if (p < 2)
stop("too few columns in input to summaryCause mtx")
#Task 1 compute corr and p-val with pairwise deletion of NAs
pv=rep(NA,p-1)
pearson=rep(NA,p-1)
for ( i in 2:p){
x=mtx[,1]
y=mtx[,i]
ok=complete.cases(x,y) #non-missing data rows pairwise
c1 = cor.test(x[ok], y[ok])
pv[i] = c1$p.value
pearson[i] = c1$estimate
}
si0 = silentPair2(mtx, ctrl = ctrl, dig = dig)
# print(si0)
si = round(100 * as.numeric(si0)/3, 3)
out = matrix(NA, nrow = (p - 1), ncol = 5)
for (i in 2:p) {
if (si[i - 1] < 0) {
print(c(nam[i], "causes", nam[1], "strength=", si[i - 1]), quote = FALSE)
out[i - 1, 1] = nam[i]
out[i - 1, 2] = nam[1]
out[i - 1, 3] = abs(si[i - 1]) #abs strength in out matrix
}
if (si[i - 1] > 0) {
print(c(nam[1], "causes", nam[i], "strength=", si[i - 1]), quote = FALSE)
out[i - 1, 1] = nam[1]
out[i - 1, 2] = nam[i]
out[i - 1, 3] = abs(si[i - 1]) #abs value in the out matrix
}
print(c("corr=", round(pearson[i], 4), "p-val=", round(pv[i], 5)), quote = FALSE)
out[i - 1, 4] = round(pearson[i], 4)
out[i - 1, 5] = round(pv[i], 5)
} #end i loop
colnames(out) = c("cause","response","strength","corr.","p-value")
return(out)
} #end function
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