Prepare for release

[shntnu]

New functions

#103
#107
#114
#117
#123

[shntnu]

Error on winbuild
Probably similar to this https://www.r-project.org/nosvn/R.check/r-devel-windows-ix86+x86_64/DiffNet-00check.html
Related discussion
https://stat.ethz.ch/pipermail/r-package-devel/2018q3/003037.html

** running examples for arch 'i386' ... ERROR
Running examples in 'cytominer-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: replicate_correlation
> ### Title: Measure replicate correlation of variables.
> ### Aliases: replicate_correlation
> 
> ### ** Examples
> 
> set.seed(123)
> x1 <- rnorm(10)
> x2 <- x1 + rnorm(10) / 100
> y1 <- rnorm(10)
> y2 <- y1 + rnorm(10) / 10
> z1 <- rnorm(10)
> z2 <- z1 + rnorm(10) / 1
> 
> batch <- rep(rep(1:2, each = 5), 2)
> 
> treatment <- rep(1:10, 2)
> 
> replicate_id <- rep(1:2, each = 10)
> 
> sample <-
+   tibble::tibble(
+     x = c(x1, x2), y = c(y1, y2), z = c(z1, z2),
+     Metadata_treatment = treatment,
+     Metadata_replicate_id = replicate_id,
+     Metadata_batch = batch
+   )
> 
> head(sample)
# A tibble: 6 x 6
        x      y      z Metadata_treatment Metadata_replicate_id Metadata_batch
    <dbl>  <dbl>  <dbl>              <int>                 <int>          <int>
1 -0.560  -1.07  -0.695                  1                     1              1
2 -0.230  -0.218 -0.208                  2                     1              1
3  1.56   -1.03  -1.27                   3                     1              1
4  0.0705 -0.729  2.17                   4                     1              1
5  0.129  -0.625  1.21                   5                     1              1
6  1.72   -1.69  -1.12                   6                     1              2
> 
> # `replicate_correlation`` returns the median, min, and max
> # replicate correlation (across batches) per variable
> replicate_correlation(
+   sample = sample,
+   variables = c("x", "y", "z"),
+   strata = c("Metadata_treatment"),
+   replicates = 2,
+   split_by = "Metadata_batch",
+   replicate_by = "Metadata_replicate_id",
+   cores = 1
+ )
# A tibble: 3 x 4
  variable median   min   max
  <chr>     <dbl> <dbl> <dbl>
1 x         1.00  1.00  1.00 
2 y         0.996 0.993 0.999
3 z         0.627 0.290 0.964
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("replicate_correlation", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11186 (sockconn)
Execution halted

[shntnu]

#138