good practice

-additional indentation
- build vignette
- change .Rbuildignore

.Rbuildignore

@@ -3,7 +3,7 @@
 ^LICENSE\.md$
 ^doc$
 ^Meta$
-^codemeta.json$
+^codemeta\.json$
 ^\.github$
 ^CONTRIBUTING\.md$
 ^codecov\.yml$

.Rproj.user/F4975BFA/pcs/files-pane.pper

@@ -5,5 +5,5 @@
             "ascending": true
         }
     ],
-    "path": "~/GitHub/QuadratiK-package/vignettes"
+    "path": "~/GitHub/QuadratiK-package"
 }

.Rproj.user/F4975BFA/pcs/source-pane.pper

@@ -1,3 +1,3 @@
 {
-    "activeTab": 23
+    "activeTab": 3
 }

.Rproj.user/F4975BFA/pcs/windowlayoutstate.pper

@@ -6,7 +6,7 @@
         "windowheight": 619
     },
     "right": {
-        "splitterpos": 319,
+        "splitterpos": 358,
         "topwindowstate": "NORMAL",
         "panelheight": 581,
         "windowheight": 619

.Rproj.user/shared/notebooks/paths

@@ -1,10 +1,14 @@
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/.Rbuildignore="C485D008"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/DESCRIPTION="81DC6CFF"
+C:/Users/sarac/Documents/GitHub/QuadratiK-package/R/QuadratiK-package.R="3289712E"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/R/RcppExports.R="1C52515A"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/R/classes.R="577DA69C"
+C:/Users/sarac/Documents/GitHub/QuadratiK-package/R/critical_value.R="A50610C8"
+C:/Users/sarac/Documents/GitHub/QuadratiK-package/R/h_selection.R="CC326A5C"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/R/kb.test.R="0E2DB6A5"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/R/pk.test.R="3CC5D390"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/R/pkbd_functions.R="1BEA4C49"
+C:/Users/sarac/Documents/GitHub/QuadratiK-package/R/wireless.R="5FF8D491"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/codecov.yml="C78935A5"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/codemeta.json="35775251"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/man/QuadratiK-package.Rd="71173F69"
@@ -15,8 +19,11 @@ C:/Users/sarac/Documents/GitHub/QuadratiK-package/tests/testthat/test-pkbc.R="32
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/tests/testthat/test-rpkb.R="251BDAC0"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/tests/testthat/test-sample_hypersphere.R="599F043F"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/tests/testthat/test.dpkb.R="449F69A9"
+C:/Users/sarac/Documents/GitHub/QuadratiK-package/vignettes/TwoSample_test.R="76EE7DD8"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/vignettes/TwoSample_test.Rmd="77787FE7"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/vignettes/kSample_test.R="81A6DE0C"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/vignettes/kSample_test.Rmd="61D887F6"
+C:/Users/sarac/Documents/GitHub/QuadratiK-package/vignettes/uniformity.R="0370929A"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/vignettes/uniformity.Rmd="89CAEE2E"
+C:/Users/sarac/Documents/GitHub/QuadratiK-package/vignettes/wireless_clustering.R="2C6FE7FD"
 C:/Users/sarac/Documents/GitHub/QuadratiK-package/vignettes/wireless_clustering.Rmd="FC40ACF9"

R/clustering_functions.R

@@ -286,7 +286,7 @@ setMethod("pkbc", signature(dat = "ANY"),
                 memb_best <- apply(normprobMat_best, 1, which.max)
 
                 # Calculate the within-cluster sum of squares
-                wcss <- vapply(1:numClust, function(cl) {
+                wcss <- sapply(1:numClust, function(cl) {
                    idx <- which(memb_best==cl)
 
                    if(length(idx)>0){
@@ -306,7 +306,7 @@ setMethod("pkbc", signature(dat = "ANY"),
 
                 # Calculate the within-cluster sum of squares using cosine 
                 # similarity
-                wcss_cos <- vapply(1:numClust, function(cl) {
+                wcss_cos <- sapply(1:numClust, function(cl) {
                    idx <- which(memb_best==cl)
                    if(length(idx)>0){
                       dat_memb <- matrix(t(dat[idx,]),ncol=numVar, byrow=TRUE)

R/pkbd_functions.R

@@ -181,7 +181,7 @@ rpkb <- function(n, mu, rho, method = 'rejvmf') {
 
    } else if (method == 'rejpsaw') {
 
-      retvals <- vapply(1:n, function(x){
+      retvals <- sapply(1:n, function(x){
          lambda <- (2*rho)/(1+rho^2)
          # pSaw: log-density and derivatives
          lpdf <- function(t) {-p*log(1-lambda*t) + (p-3)*(log(1+t) + log(1-t))}

doc/TwoSample_test.R

@@ -10,7 +10,7 @@ x_2 <- rmvnorm(n, mean = rep(0,d))
 y_2 <- rmsn(n=n, xi=0, Omega = diag(d), alpha=rep(skewness_y,d))
 
 ## -----------------------------------------------------------------------------
-h = 2
+h <- 2
 set.seed(2468)
 two_test <- kb.test(x=x_2, y=y_2, h=h)
 

doc/TwoSample_test.Rmd

@@ -25,7 +25,7 @@ y_2 <- rmsn(n=n, xi=0, Omega = diag(d), alpha=rep(skewness_y,d))
 ```
 
 ```{r}
-h = 2
+h <- 2
 set.seed(2468)
 two_test <- kb.test(x=x_2, y=y_2, h=h)
 ```

doc/TwoSample_test.html

@@ -357,7 +357,7 @@ <h3>Non-parametric two-sample test</h3>
 <span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">2468</span>)</span>
 <span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a>x_2 <span class="ot">&lt;-</span> <span class="fu">rmvnorm</span>(n, <span class="at">mean =</span> <span class="fu">rep</span>(<span class="dv">0</span>,d))</span>
 <span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a>y_2 <span class="ot">&lt;-</span> <span class="fu">rmsn</span>(<span class="at">n=</span>n, <span class="at">xi=</span><span class="dv">0</span>, <span class="at">Omega =</span> <span class="fu">diag</span>(d), <span class="at">alpha=</span><span class="fu">rep</span>(skewness_y,d))</span></code></pre></div>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>h <span class="ot">=</span> <span class="dv">2</span></span>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>h <span class="ot">&lt;-</span> <span class="dv">2</span></span>
 <span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">2468</span>)</span>
 <span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a>two_test <span class="ot">&lt;-</span> <span class="fu">kb.test</span>(<span class="at">x=</span>x_2, <span class="at">y=</span>y_2, <span class="at">h=</span>h)</span></code></pre></div>
 <p>For the two-sample case, the <code>summary</code> function provides

doc/kSample_test.R

@@ -2,7 +2,7 @@
 library(mvtnorm)
 library(QuadratiK)
 sizes <- rep(200,3)
-eps = 1
+eps <- 1
 set.seed(2468)
 x1 <- rmvnorm(sizes[1], mean = c(0,sqrt(3)*eps/3))
 x2 <- rmvnorm(sizes[2], mean = c(-eps/2,-sqrt(3)*eps/6))
@@ -11,7 +11,7 @@ x <- rbind(x1, x2, x3)
 y <- as.factor(rep(c(1,2,3), times=sizes))
 
 ## -----------------------------------------------------------------------------
-h=1.5
+h <- 1.5
 set.seed(2468)
 k_test <- kb.test(x=x, y=y, h=h)
 k_test

doc/kSample_test.Rmd

@@ -15,7 +15,7 @@ We generated three samples, with $n=200$ observations each, from a 2-dimensional
 library(mvtnorm)
 library(QuadratiK)
 sizes <- rep(200,3)
-eps = 1
+eps <- 1
 set.seed(2468)
 x1 <- rmvnorm(sizes[1], mean = c(0,sqrt(3)*eps/3))
 x2 <- rmvnorm(sizes[2], mean = c(-eps/2,-sqrt(3)*eps/6))
@@ -25,7 +25,7 @@ y <- as.factor(rep(c(1,2,3), times=sizes))
 ```
 Recall that the computed test statistics correspond to the omnibus tests.
 ```{r}
-h=1.5
+h <- 1.5
 set.seed(2468)
 k_test <- kb.test(x=x, y=y, h=h)
 k_test

doc/kSample_test.html

@@ -354,7 +354,7 @@ <h3><span class="math inline">\(k\)</span>-sample test</h3>
 <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="fu">library</span>(mvtnorm)</span>
 <span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="fu">library</span>(QuadratiK)</span>
 <span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a>sizes <span class="ot">&lt;-</span> <span class="fu">rep</span>(<span class="dv">200</span>,<span class="dv">3</span>)</span>
-<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a>eps <span class="ot">=</span> <span class="dv">1</span></span>
+<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a>eps <span class="ot">&lt;-</span> <span class="dv">1</span></span>
 <span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">2468</span>)</span>
 <span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a>x1 <span class="ot">&lt;-</span> <span class="fu">rmvnorm</span>(sizes[<span class="dv">1</span>], <span class="at">mean =</span> <span class="fu">c</span>(<span class="dv">0</span>,<span class="fu">sqrt</span>(<span class="dv">3</span>)<span class="sc">*</span>eps<span class="sc">/</span><span class="dv">3</span>))</span>
 <span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a>x2 <span class="ot">&lt;-</span> <span class="fu">rmvnorm</span>(sizes[<span class="dv">2</span>], <span class="at">mean =</span> <span class="fu">c</span>(<span class="sc">-</span>eps<span class="sc">/</span><span class="dv">2</span>,<span class="sc">-</span><span class="fu">sqrt</span>(<span class="dv">3</span>)<span class="sc">*</span>eps<span class="sc">/</span><span class="dv">6</span>))</span>
@@ -363,7 +363,7 @@ <h3><span class="math inline">\(k\)</span>-sample test</h3>
 <span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a>y <span class="ot">&lt;-</span> <span class="fu">as.factor</span>(<span class="fu">rep</span>(<span class="fu">c</span>(<span class="dv">1</span>,<span class="dv">2</span>,<span class="dv">3</span>), <span class="at">times=</span>sizes))</span></code></pre></div>
 <p>Recall that the computed test statistics correspond to the omnibus
 tests.</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>h<span class="ot">=</span><span class="fl">1.5</span></span>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>h <span class="ot">&lt;-</span> <span class="fl">1.5</span></span>
 <span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">2468</span>)</span>
 <span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a>k_test <span class="ot">&lt;-</span> <span class="fu">kb.test</span>(<span class="at">x=</span>x, <span class="at">y=</span>y, <span class="at">h=</span>h)</span>
 <span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a>k_test</span></code></pre></div>

doc/uniformity.R

@@ -7,7 +7,7 @@ z <- matrix(rnorm(n * d), n, d)
 dat_sphere <- z/sqrt(rowSums(z^2))
 
 ## -----------------------------------------------------------------------------
-rho = 0.7
+rho <- 0.7
 set.seed(2468)
 res_unif <- pk.test(x=dat_sphere, rho=rho)
 

doc/uniformity.Rmd

@@ -22,7 +22,7 @@ dat_sphere <- z/sqrt(rowSums(z^2))
 
 The ``pk.test`` is used for testing uniformity of the generated sample. 
 ```{r}
-rho = 0.7
+rho <- 0.7
 set.seed(2468)
 res_unif <- pk.test(x=dat_sphere, rho=rho)
 

doc/uniformity.html

@@ -355,13 +355,14 @@ <h3>Uniformity test on the Sphere</h3>
 <span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a>dat_sphere <span class="ot">&lt;-</span> z<span class="sc">/</span><span class="fu">sqrt</span>(<span class="fu">rowSums</span>(z<span class="sc">^</span><span class="dv">2</span>))</span></code></pre></div>
 <p>The <code>pk.test</code> is used for testing uniformity of the
 generated sample.</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>rho <span class="ot">=</span> <span class="fl">0.7</span></span>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a>rho <span class="ot">&lt;-</span> <span class="fl">0.7</span></span>
 <span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">2468</span>)</span>
 <span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a>res_unif <span class="ot">&lt;-</span> <span class="fu">pk.test</span>(<span class="at">x=</span>dat_sphere, <span class="at">rho=</span>rho)</span>
 <span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a></span>
 <span id="cb2-5"><a href="#cb2-5" tabindex="-1"></a>res_unif</span></code></pre></div>
 <pre><code>## 
-##  Poisson Kernel-based quadratic distance test of Uniformity on the Sphere 
+##  Poisson Kernel-based quadratic distance test of 
+##                         Uniformity on the Sphere 
 ## Selected consentration parameter rho:  0.7 
 ## 
 ## U-statistic:
@@ -381,7 +382,8 @@ <h3>Uniformity test on the Sphere</h3>
 variable with a table of standard descriptive statistics.</p>
 <div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a>summary_unif <span class="ot">&lt;-</span> <span class="fu">summary</span>(res_unif)</span></code></pre></div>
 <pre><code>## 
-##  Poisson Kernel-based quadratic distance test of Uniformity on the Sphere 
+##  Poisson Kernel-based quadratic distance test of 
+##                         Uniformity on the Sphere 
 ##   Test_Statistics Critical_Value Reject_H0
 ## 1      -0.9756673     0.02660107     FALSE
 ## 2      14.8959834    23.22948694     FALSE</code></pre>

tests/testthat/test-kb.test.R

@@ -8,14 +8,14 @@ test_that("Error on invalid method input", {
    expect_error(kb.test(x = matrix(rnorm(100), ncol = 2), h=0.5, 
                         method = "invalid_method"), 
                 "method must be one of 'bootstrap', 'permutation' or 
-                'subsampling'", fixed=TRUE)
+                     'subsampling'", fixed=TRUE)
 })
 
 # Test 2: Verify Error on Invalid b Input
 test_that("Error on invalid b input", {
    expect_error(kb.test(x = matrix(rnorm(100), ncol = 2), h=0.5, b = 10), 
                 "b indicates the proportion used for the subsamples in the 
-                subsampling algoritm. It must be in (0,1]", fixed=TRUE)
+                     subsampling algoritm. It must be in (0,1].", fixed=TRUE)
 })
 
 # Test 3: Error on Invalid alternative Input
@@ -24,9 +24,9 @@ test_that("Error on invalid alternative input", {
    expect_error(kb.test(x = matrix(rnorm(100), ncol= 2), 
                         y = matrix(rnorm(100), ncol= 2), h=0.5, 
                         alternative = "invalid"),
-                "The algorithm for selecting the value of h can be performed 
-                with respect to the following families of alternatives: 
-                'location', 'scale' or 'skewness'", fixed=TRUE)
+                "The algorithm for selecting the value of h can be performed
+                    with respect to the following families of alternatives: 
+                    'location', 'scale' or 'skewness'", fixed=TRUE)
 })
 
 # Test 4: Error on Invalid centeringType Input

tests/testthat/test-pkbc.R

@@ -15,7 +15,9 @@ dat<-rbind(data1$x,data2$x, data3$x)
 
 # Test 1: Verify Error on Invalid nClust
 test_that("Error is thrown for invalid nClust", {
-   expect_error(pkbc(dat, nClust = 0), "nClust must be greater than 0")
+   dat <- matrix(rnorm(100),ncol=2)
+   expect_error(pkbc(dat, nClust = 0), "Values in the input parameter nClust must be 
+                        greater than 0")
 })
 
 # Test 2: Test for valid input