v1.8

fbertran · Aug 23, 2019 · df59bb7 · df59bb7
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -16,3 +16,4 @@
 ^fullrespdf*$
 ^inst/animation*$
 ^articles*$
+^review*$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,9 @@
 Package: Cascade
 Type: Package
 Title: Selection, Reverse-Engineering and Prediction in Cascade Networks
-Version: 1.7
-Date: 2019-02-09
-Depends: R (>= 2.10)
+Version: 1.8
+Date: 2019-08-24
+Depends: R (>= 3.5.0)
 biocViews:
 Imports: abind, animation, cluster, grid, igraph, lars, lattice, 
          limma, magic, methods, nnls, splines, stats4, survival, tnet, VGAM

diff --git a/NEWS b/NEWS
@@ -1,3 +1,5 @@
 1.0 - 1.4 Creation and review of the package 
 1.5 Package and especially its code was transformed to cope with CRAN requirements
 1.6 Package had to be splited and data shiped apart to CRAN in the CascadeData package
+1.7 Help pages were completed and examples added for every function. It required new datasets that were added to the package.
+1.8 Fix discrepancy between datalist and datasets as requested by CRAN.
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# Cascade 1.8
+
+* Fix discrepancy between datalist and datasets as requested by CRAN.
+
 # Cascade 1.7
 
 * Help pages were completed and examples added for every function. It required new datasets that were added to the package.

diff --git a/README.Rmd b/README.Rmd
@@ -124,7 +124,7 @@ Net_inf_C <- Cascade::inference(M, cv.subjects=TRUE)
 
 Heatmap of the coefficients of the Omega matrix of the network
 ```{r heatresults}
-stats::heatmap(Net_inf_C@network, Rowv = NA, Colv = NA, scale="none", revC=TRUE)
+stats::heatmap(Net_inf_C@network, Rowv=NA, Colv=NA, scale="none", revC=TRUE)
 ```
 
 ###Post inferrence network analysis

diff --git a/README.md b/README.md
@@ -47,7 +47,6 @@ Import Cascade Data (repeated measurements on several subjects) from the Cascade
 ```r
 library(Cascade)
 if(!require(CascadeData)){install.packages("CascadeData")}
-#> Loading required package: CascadeData
 data(micro_US)
 micro_US<-as.micro_array(micro_US,time=c(60,90,210,390),subject=6)
 ```
@@ -56,7 +55,6 @@ Get a summay and plots of the data:
 
 ```r
 summary(micro_US)
-#> Loading required package: cluster
 #>    N1_US_T60        N1_US_T90        N1_US_T210       N1_US_T390    
 #>  Min.   :   1.0   Min.   :   1.0   Min.   :   1.0   Min.   :   1.0  
 #>  1st Qu.:  19.7   1st Qu.:  18.8   1st Qu.:  15.2   1st Qu.:  20.9  
@@ -149,11 +147,6 @@ M <- Cascade::gene_expr_simulation(
   time_label=rep(1:4,each=25),
   subject=5,
   level_peak=200)
-#> Loading required package: VGAM
-#> Loading required package: stats4
-#> Loading required package: splines
-#> Loading required package: magic
-#> Loading required package: abind
 ```
 
 Get a summay and plots of the simulated data:
@@ -225,7 +218,6 @@ We infer the new network using subjectwise leave one out cross-validation (all m
 
 ```r
 Net_inf_C <- Cascade::inference(M, cv.subjects=TRUE)
-#> Loading required package: nnls
 #> We are at step :  1
 #> The convergence of the network is (L1 norm) : 0.0068
 #> We are at step :  2
@@ -239,7 +231,7 @@ Net_inf_C <- Cascade::inference(M, cv.subjects=TRUE)
 Heatmap of the coefficients of the Omega matrix of the network
 
 ```r
-stats::heatmap(Net_inf_C@network, Rowv = NA, Colv = NA, scale="none", revC=TRUE)
+stats::heatmap(Net_inf_C@network, Rowv=NA, Colv=NA, scale="none", revC=TRUE)
 ```
 
 <img src="man/figures/README-heatresults-1.png" title="plot of chunk heatresults" alt="plot of chunk heatresults" width="100%" />

diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 1.19.2.1
+pandoc: 2.7.2
 pkgdown: 1.3.0
 pkgdown_sha: ~
 articles: {}

diff --git a/docs/reference/M.html b/docs/reference/M.html