[med-svn] [mapdamage] 01/01: add patch to fix quantile call to remove NA and NaNs

[Nadiya Sitdykova]

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rovenskasa-guest pushed a commit to branch master
in repository mapdamage.

commit f96109a086832f1a960d3522b9ddb7ae6e5c77bb
Author: nadiya <nadiya at debian>
Date:   Wed Mar 29 00:23:51 2017 -0400

    add patch to fix quantile call to remove NA and NaNs
---
 debian/patches/01_fix_quantile_na_rm.patch | 20 ++++++++++++++++++++
 debian/patches/series                      |  1 +
 2 files changed, 21 insertions(+)

diff --git a/debian/patches/01_fix_quantile_na_rm.patch b/debian/patches/01_fix_quantile_na_rm.patch
new file mode 100644
index 0000000..30d2ba6
--- /dev/null
+++ b/debian/patches/01_fix_quantile_na_rm.patch
@@ -0,0 +1,20 @@
+Author: Nadiya Sitdykova
+Description: change calcSampleStats such as any NA and Nan's are 
+ removed before quantiles are computed
+Last-Update: 2017-03-28
+
+Index: mapdamage/mapdamage/Rscripts/stats/function.R
+===================================================================
+--- mapdamage.orig/mapdamage/Rscripts/stats/function.R	2017-03-29 00:02:46.538470957 -0400
++++ mapdamage/mapdamage/Rscripts/stats/function.R	2017-03-29 00:11:09.141025051 -0400
+@@ -595,8 +595,8 @@
+                       pos=da[,"Pos"],
+                       mea=apply(X,1,mean),
+                       med=apply(X,1,median),
+-                      loCI=apply(X,1,quantile,c(0.025)),
+-                      hiCI=apply(X,1,quantile,c(0.975))
++                      loCI=apply(X,1,quantile,c(0.025),na.rm=TRUE),
++                      hiCI=apply(X,1,quantile,c(0.975),na.rm=TRUE)
+                       ))
+ }
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 8ac87a5..f14293f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 use_debian_packaged_seqtk.patch
+01_fix_quantile_na_rm.patch

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