updates for CRAN submission

rikardn · Dec 29, 2015 · 797c678 · 797c678
1 parent f8c3cc0
commit 797c678
Show file tree

Hide file tree

Showing 16 changed files with 69 additions and 42 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -5,5 +5,5 @@
 ^.*\.o$
 ^tools$
 ^shinyapp$
-
+^cran-comments.md$
 ^\.travis\.yml$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PopED
 Type: Package
 Title: Population (and Individual) Optimal Experimental Design
-Version: 0.2.0.9003
+Version: 0.3.0
 Depends:
     ggplot2
 Imports:

diff --git a/NEWS b/NEWS
@@ -1,5 +1,15 @@
 PopED News/Changelog
 
+PopED 0.3.0
+===========
+
+* Added new optimization methods and tools, see `?poped_optim()`. This function incorporates the new optimization routines `optim_ARS()` and `optim_LS` which are optimized versions of previous optimization algorithms used in PopED. Both can be run with parallelization. `poped_optim()` also incorporates the genetic algorithm from `GA::ga()`, which can also be run with parallelization, and the "L-BFGS-B" method from `stats::optim()`. `poped_optim()` should be more efficient and faster than `poped_optimize()`.
+
+* Changed the default objective function to be the log of the determinant of the FIM.  `create.poped.database(ofv_calc_type=4)`
+
+* Various small changes and bug fixes.
+
+
 PopED 0.2.0
 ===========
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -0,0 +1,17 @@
+## Test environments
+* local OS X (10.11.2) install, R 3.2.3
+* ubuntu 12.04 (on travis-ci), R 3.2.3
+* win-builder (devel and release)
+
+## R CMD check results
+There were no ERRORs, WARNINGs or NOTEs. 
+
+## Downstream dependencies
+I have also run R CMD check on downstream dependencies of PopED 
+(https://github.com/wch/checkresults/blob/master/httr/r-release). 
+All packages that I could install passed except:
+
+  * Ecoengine: this appears to be a failure related to config on 
+that machine. I couldn't reproduce it locally, and it doesn't 
+seem to be related to changes in httr (the same problem exists 
+                                       with httr 0.4).
diff --git a/man/calc_ofv_and_fim.Rd b/man/calc_ofv_and_fim.Rd
diff --git a/man/evaluate.e.ofv.fim.Rd b/man/evaluate.e.ofv.fim.Rd
diff --git a/man/evaluate.fim.Rd b/man/evaluate.fim.Rd
diff --git a/man/feps.add.Rd b/man/feps.add.Rd
diff --git a/man/feps.add.prop.Rd b/man/feps.add.prop.Rd
diff --git a/man/feps.prop.Rd b/man/feps.prop.Rd
diff --git a/man/model_prediction.Rd b/man/model_prediction.Rd
diff --git a/man/ofv_fim.Rd b/man/ofv_fim.Rd
diff --git a/man/plot_efficiency_of_windows.Rd b/man/plot_efficiency_of_windows.Rd
diff --git a/man/plot_model_prediction.Rd b/man/plot_model_prediction.Rd
diff --git a/tests/testthat/test_distributions.R b/tests/testthat/test_distributions.R
@@ -35,7 +35,7 @@ test_that("pargen works", {
   expect_true(all(pars.ln.1==pars.ln.2))
 
   p.vals <- apply(pars.ln[,1:3],2,function(x) shapiro.test(log(x))[["p.value"]])
-  expect_that(all(p.vals > 0.8), is_true())
+  expect_that(all(p.vals > 0.05), is_true())
 
   # Adding 10% Uncertainty to fixed effects normal-distribution (not Favail)
   # with normal distributions
@@ -50,7 +50,7 @@ test_that("pargen works", {
   expect_that(all(var.diff.n[1:3]<50),is_true())
 
   p.vals <- apply(pars.n[,1:3],2,function(x) shapiro.test(x)[["p.value"]])
-  expect_that(all(p.vals > 0.8), is_true())
+  expect_that(all(p.vals > 0.05), is_true())
 
   # Adding 10% Uncertainty to fixed effects uniform-distribution (not Favail)
   mean.diff.u <- (colMeans(pars.u) - bpop_vals_ed_u[,2])/bpop_vals_ed_u[,2]*100

diff --git a/tools/build_poped/To build PopED in R.docx b/tools/build_poped/To build PopED in R.docx