Fix missing imports

DESCRIPTION

@@ -1,14 +1,25 @@
 Package: SPARK
 Type: Package
 Title: Spatial Pattern Recognition via Kernels
-Version: 1.1.0
-Date: 2020-10-07
+Version: 1.1.1
+Date: 2021-02-02
 Author: Shiquan Sun, Jiaqiang Zhu, and Xiang Zhou
 Maintainer: Jiaqiang Zhu <[email protected]>
 Description: SPARK is an efficient tool for identifying spatial expression patterns. SPARK directly models raw count data generated from various spatial resolved transcriptomic techniques. With a new efficient penalized quasi-likelihood based algorithm, SPARK is scalable to data sets with tens of thousands of genes measured on thousands of samples. Build upon a non-parametric framework, SPARK-X is scalable to large-scale data sets with tens of thousands of genes measured on hundred thousands of samples.
 License: GPL-3
 Depends: R (>= 3.4.0), methods
-Imports: Rcpp (>= 1.0.5),foreach,doParallel,parallel,Matrix,CompQuadForm,matlab,pracma
+Imports: 
+    Rcpp (>= 1.0.5),
+    foreach,
+    doParallel,
+    parallel,
+    Matrix,
+    CompQuadForm,
+    matlab,
+    pracma,
+    doSNOW,
+    pbmcapply,
+    RcppArmadillo
 LinkingTo: Rcpp, RcppArmadillo
 NeedsCompilation: yes
 RoxygenNote: 7.1.1

NAMESPACE

@@ -38,11 +38,11 @@ importFrom(stats,resid)
 importFrom(stats,pcauchy)
 importFrom(stats,model.matrix)
 importFrom(stats,var)
-importFrom(stats,median)
+importFrom(stats,median,quantile)
 importFrom(utils,globalVariables)
 importFrom(utils,installed.packages)
 importFrom(utils,packageVersion)
 importFrom(utils,read.table)
 importFrom(utils,setTxtProgressBar)
 importFrom(utils,txtProgressBar)
-importFrom("methods", "as", "new")
+importFrom("methods", "as", "new", "is")

docs/pages/02_SPARK_Example.md

@@ -6,11 +6,12 @@ permalink: /02_SPARK_Example/
 
 ### Example Analysis with SPARK: Breast Cancer Data
 
-Load the `SPARK` package and Breast cancer data set, which can be downloaded [here](https://github.com/xzhoulab/SPARK/blob/master/data/Layer2_BC_Count.rds).
+Load the `SPARK` package and Breast cancer dataset (included with the package;
+can be also downloaded [here](https://github.com/xzhoulab/SPARK/blob/master/inst/extdata/Layer2_BC_Count.rds)).
+
 ```R
     library('SPARK')
-    load("./Layer2_BC_Count.rds")
-
+    load(system.file("extdata", "Layer2_BC_Count.rds", package = "SPARK"))
 ```
 View the expression count matrix `rawcount`, each row denotes a gene and each column represents a cell/spot.
 ```R