Merge pull request #21 from lukesonnet/lukesonnet/refactor

Restructure CPP files; rewrite inference

.Rbuildignore

@@ -5,3 +5,4 @@ src/deprecated
 ^\.travis\.yml$
 ^appveyor\.yml$
 ^tests/testthat/test_krlogit_fns\.R$
+^tests/testthat/test_old_krls\.R$

.travis.yml

@@ -29,6 +29,7 @@ matrix:
 
 r_packages:
 - numDeriv
+- KRLS
 
 r_github_packages:
 - r-lib/covr

NAMESPACE

@@ -1,40 +1,23 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(plot,krls2)
+S3method(predict,krls2)
 export(Ktrunc)
 export(bsearch)
 export(chunk)
-export(euc_dist)
-export(fdskrls)
 export(generateK)
 export(getDhat)
 export(inference.krls2)
-export(kern_gauss)
-export(kern_gauss_1d)
-export(krlogit_fn_trunc)
-export(krlogit_gr_trunc)
-export(krlogit_hess_trunc_inv)
 export(krls)
-export(krls_gr_trunc)
-export(krls_hess_trunc_inv)
 export(lambdab.fn)
 export(lambdabsearch)
 export(lambdaline)
 export(lambdasearch)
 export(logistic)
 export(looloss)
-export(mult_diag)
 export(newKernel)
-export(new_gauss_kern)
-export(partial_logit)
-export(predict.krls2)
-export(pwmfx)
-export(pwmfx_novar)
 export(solveForDOptim)
-export(solve_for_d_ls)
-export(solve_for_d_ls_w)
 export(summary.krls2)
-export(trace_mat)
 import(RSpectra)
 importFrom(Rcpp,sourceCpp)
 importFrom(grDevices,devAskNewPage)
@@ -44,6 +27,7 @@ importFrom(graphics,plot)
 importFrom(stats,as.formula)
 importFrom(stats,optim)
 importFrom(stats,optimize)
+importFrom(stats,plogis)
 importFrom(stats,predict)
 importFrom(stats,pt)
 importFrom(stats,quantile)

R/RcppExports.R

@@ -1,83 +1,63 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-#' @export
-mult_diag <- function(x, d) {
-    .Call(`_KRLS2_mult_diag`, x, d)
-}
-
-#' @export
-trace_mat <- function(x) {
-    .Call(`_KRLS2_trace_mat`, x)
-}
-
-#' @export
 krls_gr_trunc <- function(U, D, y, w, fitted, dhat, lambda) {
     .Call(`_KRLS2_krls_gr_trunc`, U, D, y, w, fitted, dhat, lambda)
 }
 
-#' @export
 krls_hess_trunc_inv <- function(U, D, w, lambda) {
     .Call(`_KRLS2_krls_hess_trunc_inv`, U, D, w, lambda)
 }
 
-#' @export
 krlogit_fn_trunc <- function(par, U, D, y, w, lambda) {
     .Call(`_KRLS2_krlogit_fn_trunc`, par, U, D, y, w, lambda)
 }
 
-#' @export
 krlogit_gr_trunc <- function(par, U, D, y, w, lambda) {
     .Call(`_KRLS2_krlogit_gr_trunc`, par, U, D, y, w, lambda)
 }
 
-#' @export
 partial_logit <- function(K, coef, beta0) {
     .Call(`_KRLS2_partial_logit`, K, coef, beta0)
 }
 
-#' @export
 krlogit_hess_trunc_inv <- function(par, U, D, y, w, lambda) {
     .Call(`_KRLS2_krlogit_hess_trunc_inv`, par, U, D, y, w, lambda)
 }
 
-#' @export
+mult_diag <- function(x, d) {
+    .Call(`_KRLS2_mult_diag`, x, d)
+}
+
+trace_mat <- function(x) {
+    .Call(`_KRLS2_trace_mat`, x)
+}
+
 euc_dist <- function(x1, x2) {
     .Call(`_KRLS2_euc_dist`, x1, x2)
 }
 
-#' @export
 kern_gauss_1d <- function(x1, x2, b) {
     .Call(`_KRLS2_kern_gauss_1d`, x1, x2, b)
 }
 
-#' @export
 kern_gauss <- function(x, b) {
     .Call(`_KRLS2_kern_gauss`, x, b)
 }
 
-#' @export
 new_gauss_kern <- function(newx, oldx, b) {
     .Call(`_KRLS2_new_gauss_kern`, newx, oldx, b)
 }
 
-#' @export
+pwmfx <- function(k, x, coefhat, vcovc_mat, p, p2, b) {
+    .Call(`_KRLS2_pwmfx`, k, x, coefhat, vcovc_mat, p, p2, b)
+}
+
 solve_for_d_ls <- function(y, U, D, lambda) {
     .Call(`_KRLS2_solve_for_d_ls`, y, U, D, lambda)
 }
 
-#' @export
 solve_for_d_ls_w <- function(y, U, D, w, lambda) {
     .Call(`_KRLS2_solve_for_d_ls_w`, y, U, D, w, lambda)
 }
 
-#' @export
-pwmfx <- function(k, x, coefhat, vcovc, p, b) {
-    .Call(`_KRLS2_pwmfx`, k, x, coefhat, vcovc, p, b)
-}
-
-#' @export
-pwmfx_novar <- function(k, x, coefhat, p, b) {
-    .Call(`_KRLS2_pwmfx_novar`, k, x, coefhat, p, b)
-}
-