[BUGFIX] Refine the package based on the CRAN's feedback (#30)

* CHG: correct the lines based on the CRAN's feedback * CHG: increment the version number * CHG: add cran info; reformat code
egpivo · Nov 13, 2023 · 987a596 · 987a596
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: SpatPCA
 Title: Regularized Principal Component Analysis for Spatial Data
-Version: 1.3.4
+Version: 1.3.5
 Authors@R: c(person(
                 given = "Wen-Ting",
                 family = "Wang",

diff --git a/R/SpatPCA.R b/R/SpatPCA.R
@@ -324,6 +324,7 @@ predict <-
 #'
 #' @param x An spatpca class object for `plot` method
 #' @param ... Not used directly
+#' @return `NULL`.
 #' @seealso \link{spatpca}
 #'
 #' @export

diff --git a/R/helper.R b/R/helper.R
@@ -53,7 +53,7 @@ scaleLocation <- function(location) {
 #' @keywords internal
 #' @param spatpca_object An `spatpca` class object
 #' @param x_new New location matrix.
-#' @return NULL
+#' @return `NULL`.
 #'
 checkNewLocationsForSpatpcaObject <-
   function(spatpca_object, x_new) {
@@ -79,7 +79,7 @@ checkNewLocationsForSpatpcaObject <-
 #' @param Y Data matrix
 #' @param x Location matrix.
 #' @param M Number of folds for cross-validation
-#' @return NULL
+#' @return `NULL`.
 #'
 checkInputData <- function(Y, x, M) {
   x <- as.matrix(x)

diff --git a/R/zzz.R b/R/zzz.R
@@ -2,6 +2,5 @@
   if (!identical(Sys.getenv("NOT_CRAN"), "true")) {
     Sys.setenv(RCPP_PARALLEL_BACKEND = "tinythread")
   }
-
   packageStartupMessage("Welcome to SpatPCA")
 }
diff --git a/README.md b/README.md
@@ -1,5 +1,6 @@
 # SpatPCA Package
-
+[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/SpatPCA)](https://CRAN.R-project.org/package=SpatPCA)
+[![Downloads](http://cranlogs.r-pkg.org/badges/grand-total/SpatPCA)](https://CRAN.R-project.org/package=SpatPCA)
 [![R build status](https://github.com/egpivo/SpatPCA/workflows/R-CMD-check/badge.svg)](https://github.com/egpivo/SpatPCA/actions)
 [![Coverage Status](https://img.shields.io/codecov/c/github/egpivo/SpatPCA/master.svg)](https://app.codecov.io/github/egpivo/SpatpCA?branch=master)
 

diff --git a/man/checkInputData.Rd b/man/checkInputData.Rd
diff --git a/man/checkNewLocationsForSpatpcaObject.Rd b/man/checkNewLocationsForSpatpcaObject.Rd
diff --git a/man/plot.spatpca.Rd b/man/plot.spatpca.Rd
diff --git a/vignettes/demo-two-dim-location.Rmd b/vignettes/demo-two-dim-location.Rmd
@@ -43,14 +43,14 @@ fill_bar <- guides(fill = guide_colourbar(
     label.position = "bottom")
   )
 coltab <- scico(128, palette = 'vik')
-color_scale_limit <- c(-.28, .28)
+color_scale_limit <- c(-.8, .8)
 ```
 #### True spatial pattern (eigenfunction)
 - The underlying spatial pattern below indicates realizations will vary dramatically at the center and be almost unchanged at the both ends of the curve.
 ```{r, out.width = '100%'}
 set.seed(1024)
-p <- 30
-n <- 50
+p <- 25
+n <- 8
 location <-
   matrix(rep(seq(-5, 5, length = p), 2), nrow = p, ncol = 2)
 expanded_location <- expand.grid(location[, 1], location[, 2])
@@ -80,12 +80,13 @@ data.frame(
   - The noise follows the standard normal distribution.
 
 ```{r}
-realizations <- rnorm(n = n, sd = 10) %*% t(true_eigen_fn) + matrix(rnorm(n = n * p^2), n, p^2)
+realizations <- rnorm(n = n, sd = 3) %*% t(true_eigen_fn) + matrix(rnorm(n = n * p^2), n, p^2)
 ```
 
 #### Animate realizations
 - We can see simulated central realizations change in a wide range more frequently than the others.
 ```{r, animation.hook="gifski", out.width = '100%'}
+original_par <- par()
 for (i in 1:n) {
   par(mar = c(3, 3, 1, 1), family = "Times")
   image.plot(
@@ -100,6 +101,7 @@ for (i in 1:n) {
     legend.width=0.5
   )
 }
+par(original_par)
 ```
 
 #### Apply `SpatPCA::spatpca`