Prepare Release of Version 1.7.2-0 (#28)

* update files generated by Rcpp

* update travis config

* download master branch for updating the source

* remove special character from source

* Update vignette

* update travis config

.travis.yml

@@ -6,13 +6,18 @@ r:
   - release
   - devel
 
-r_github_packages:
-  - jimhester/lintr 
-  - jimhester/covr
+r_packages:
+  - lintr
+  - covr
 
 after_success:
-  - Rscript tools/lint-and-covr.R
+  - Rscript -e "lintr::lint_package()"
+  - Rscript -e "library(covr); coveralls()"
 
 notifications:
   email: false
 
+# Set CXX1X for R-devel, as R-devel does currently not detect CXX1X support for gcc 4.6.3
+# Check if we can remove this at some point in 2017
+before_install:
+- if [[ "$TRAVIS_R_VERSION_STRING" = 'devel' ]]; then mkdir ~/.R && echo 'CXX1X=g++ -std=c++0x -g -O2 -fPIC' > ~/.R/Makevars; fi

R/RcppExports.R

@@ -1,4 +1,4 @@
-# This file was generated by Rcpp::compileAttributes
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 #' Simulate the evolution of biological sequences

scrmr.Rproj → scrm-r.Rproj

@@ -1,8 +1,8 @@
 Version: 1.0
 
-RestoreWorkspace: No
-SaveWorkspace: No
-AlwaysSaveHistory: Yes
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
 UseSpacesForTab: Yes
@@ -12,10 +12,6 @@ Encoding: UTF-8
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
 
-AutoAppendNewline: Yes
-StripTrailingWhitespace: Yes
-
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace

src/RcppExports.cpp

@@ -1,4 +1,4 @@
-// This file was generated by Rcpp::compileAttributes
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
 // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 #include <Rcpp.h>
@@ -9,44 +9,44 @@ using namespace Rcpp;
 List scrm(std::string args, std::string file);
 RcppExport SEXP scrm_scrm(SEXP argsSEXP, SEXP fileSEXP) {
 BEGIN_RCPP
-    Rcpp::RObject __result;
-    Rcpp::RNGScope __rngScope;
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< std::string >::type args(argsSEXP);
     Rcpp::traits::input_parameter< std::string >::type file(fileSEXP);
-    __result = Rcpp::wrap(scrm(args, file));
-    return __result;
+    rcpp_result_gen = Rcpp::wrap(scrm(args, file));
+    return rcpp_result_gen;
 END_RCPP
 }
 // test_RRG_sample
 double test_RRG_sample();
 RcppExport SEXP scrm_test_RRG_sample() {
 BEGIN_RCPP
-    Rcpp::RObject __result;
-    Rcpp::RNGScope __rngScope;
-    __result = Rcpp::wrap(test_RRG_sample());
-    return __result;
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    rcpp_result_gen = Rcpp::wrap(test_RRG_sample());
+    return rcpp_result_gen;
 END_RCPP
 }
 // test_RRG_sampleUnitExpo
 double test_RRG_sampleUnitExpo();
 RcppExport SEXP scrm_test_RRG_sampleUnitExpo() {
 BEGIN_RCPP
-    Rcpp::RObject __result;
-    Rcpp::RNGScope __rngScope;
-    __result = Rcpp::wrap(test_RRG_sampleUnitExpo());
-    return __result;
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    rcpp_result_gen = Rcpp::wrap(test_RRG_sampleUnitExpo());
+    return rcpp_result_gen;
 END_RCPP
 }
 // test_RRG_sampleExpoExpoLimit
 double test_RRG_sampleExpoExpoLimit(double lambda, double b, double limit);
 RcppExport SEXP scrm_test_RRG_sampleExpoExpoLimit(SEXP lambdaSEXP, SEXP bSEXP, SEXP limitSEXP) {
 BEGIN_RCPP
-    Rcpp::RObject __result;
-    Rcpp::RNGScope __rngScope;
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< double >::type lambda(lambdaSEXP);
     Rcpp::traits::input_parameter< double >::type b(bSEXP);
     Rcpp::traits::input_parameter< double >::type limit(limitSEXP);
-    __result = Rcpp::wrap(test_RRG_sampleExpoExpoLimit(lambda, b, limit));
-    return __result;
+    rcpp_result_gen = Rcpp::wrap(test_RRG_sampleExpoExpoLimit(lambda, b, limit));
+    return rcpp_result_gen;
 END_RCPP
 }

src/scrm/model.cc

@@ -489,7 +489,7 @@ std::ostream& operator<<(std::ostream& os, Model& model) {
     for (size_t i = 0; i < n_pops; ++i) {
       for (size_t j = 0; j < n_pops; ++j) {
         if (model.single_mig_pop(i, j) != 0) {
-          os << " " << model.single_mig_pop(i, j) * 100 << "% of pop "
+          os << " " << model.single_mig_pop(i, j) << " of pop "
              << i + 1 << " move to pop " << j + 1 << std::endl;
         }
       }

tools/update-source.sh

@@ -4,8 +4,15 @@
 # with files from scrm's git repo supposed to be at
 # ../scrm
 
+mkdir tmp
+git clone https://github.com/scrm/scrm tmp/
+
+
 rsync -rvcA --exclude '.*'\
             --include '*/'\
             --include '*.cc' --include '*.h'\
             --exclude='*'\
-            ../scrm/src/* src/scrm/
+            tmp/src/* src/scrm/
+
+rm -rf tmp
+

vignettes/scrm-Arguments.Rmd

@@ -59,9 +59,10 @@ decline in population sizes.
 ### Summary Statistics
 
 * `-t < $\theta$ >`: Set the mutation rate to $\theta = 4N_0u$, where _u_ is the neutral mutation rate per locus. If this options is given, scrm generates the segregating sites output.
+* `-transpose-segsites` or `--transpose-segsites`: If given, the segregating sites are printed with each row representing a mutation and each column representing a haplotype, rather than the other way round. Additionally, the time at which a mutation occurred is reported (in units of _4 * N0_ generations) [since v1.7.0].
 * `-T`: Print the local genealogies in newick format.
 * `-O`: Print the local genealogies in the `oriented forest` format as described in [Kelleher _et al._ (2014)](http://dx.doi.org/10.1016/j.tpb.2014.05.001) [since v1.2].
-* `-L`: Print the TMRCA and the local tree length for each segment (behaves different to ms).
+* `-L`: Print the TMRCA and the local tree length for each segment (behaves different to ms). Both values are scaled in coalescent time units, e.g. in _4 * N0_ generations.
 * `-oSFS`: Print the site frequency spectrum. Requires that the mutation rate $\theta$ is given with the '-t' option.
 * `-SC [ms|rel|abs]`: Scaling of sequence positions. Either relative to the locus length between 0 and 1 (`rel`), absolute in base pairs (`abs`) or `ms`'s scaling (default) where the positions in the _segregating sites_ output are relative, and the positions in the trees output are absolute (`ms`) [since v1.3.0].