`../Isabelle2016/bin/isabelle build -v -D . -o threads=8  -b -o document=pdf -c`

All is fine:

```
Started at Sa 6. Aug 11:14:51 CEST 2016 (polyml-5.6_x86_64-linux on vm-10-155-208-123)
ISABELLE_BUILD_OPTIONS=""

ISABELLE_BUILD_JAVA_OPTIONS="-Djava.awt.headless=true -Xms512m -Xmx2560m -Xss4m"

ML_PLATFORM="x86_64-linux"
ML_HOME="/root/Isabelle2016/contrib/polyml-5.6-1/x86_64-linux"
ML_SYSTEM="polyml-5.6"
ML_OPTIONS="-H 1000"

Session Pure/Pure
Session HOL/HOL (main)
Session HOL/HOL-Word (main)
Session AFP/Word_Lib (AFP)
Session Iptables_Semantics/IP_Addresses
Session Iptables_Semantics/Bitmagic
Session Simple_Firewall/Simple_Firewall
Session Unsorted/Routing
Session Iptables_Semantics/Iptables_Semantics
Session Iptables_Semantics/Iptables_Semantics_Documentation
Session Iptables_Semantics/Iptables_Semantics_Examples
Session Iptables_Semantics/Iptables_Semantics_Examples_Large1
Session Iptables_Semantics/Iptables_Semantics_Examples_Large2
Session OpenFlow/OpenFlow
Session OpenFlow/OpenFlow_Documentation
Cleaning Word_Lib ...
Cleaning IP_Addresses ...
Cleaning Simple_Firewall ...
Cleaning Routing ...
Cleaning Iptables_Semantics ...
Cleaning Iptables_Semantics_Documentation ...
Cleaning Iptables_Semantics_Examples ...
Cleaning Iptables_Semantics_Examples_Large1 ...
Cleaning Iptables_Semantics_Examples_Large2 ...
Cleaning OpenFlow ...
Cleaning OpenFlow_Documentation ...
Cleaning Bitmagic ...
Building Word_Lib ...
Word_Lib: theory Sublist
Word_Lib: theory WordBitwise
Word_Lib: theory Prefix_Order
Word_Lib: theory Enumeration
Word_Lib: theory HOL_Lemmas
Word_Lib: theory More_Divides
Word_Lib: theory Hex_Words
Word_Lib: theory Signed_Words
Word_Lib: theory Norm_Words
Word_Lib: theory WordBitwise_Signed
Word_Lib: theory Word_Syntax
Word_Lib: theory Word_Lib
Word_Lib: theory Aligned
Word_Lib: theory Word_Enum
Word_Lib: theory Word_Setup_32
Word_Lib: theory Word_Setup_64
Word_Lib: theory Word_Lemmas
Word_Lib: theory Word_Lemmas_32
Word_Lib: theory Word_Lemmas_64
Timing Word_Lib (8 threads, 69.572s elapsed time, 176.444s cpu time, 5.244s GC time, factor 2.54)
Document at /root/.isabelle/Isabelle2016/browser_info/AFP/Word_Lib/document.pdf
Finished Word_Lib (0:01:47 elapsed time, 0:03:28 cpu time, factor 1.94)
Building IP_Addresses ...
IP_Addresses: theory Char_ord
IP_Addresses: theory Code_Abstract_Nat
IP_Addresses: theory Code_Target_Int
IP_Addresses: theory Infinite_Set
IP_Addresses: theory Multiset
IP_Addresses: theory Option_ord
IP_Addresses: theory Product_Lexorder
IP_Addresses: theory NumberWang_IPv4
IP_Addresses: theory NumberWang_IPv6
IP_Addresses: theory Code_Target_Nat
IP_Addresses: theory Word_More
IP_Addresses: theory Code_Char
IP_Addresses: theory List_More
IP_Addresses: theory Quicksort
IP_Addresses: theory Misc
IP_Addresses: theory Hs_Compat
IP_Addresses: theory Lib_Numbers_toString
IP_Addresses: theory Word_Next
IP_Addresses: theory WordInterval
IP_Addresses: theory Lib_List_toString
IP_Addresses: theory Lib_Word_toString
IP_Addresses: theory IP_Address
IP_Addresses: theory WordInterval_Sorted
IP_Addresses: theory IPv4
IP_Addresses: theory IPv6
IP_Addresses: theory Prefix_Match
IP_Addresses: theory CIDR_Split
IP_Addresses: theory IP_Address_Parser
IP_Addresses: theory IP_Address_toString
Timing IP_Addresses (8 threads, 362.597s elapsed time, 930.688s cpu time, 53.452s GC time, factor 2.57)
Document at /root/.isabelle/Isabelle2016/browser_info/Iptables_Semantics/IP_Addresses/document.pdf
Finished IP_Addresses (0:08:06 elapsed time, 0:17:37 cpu time, factor 2.17)
Building Simple_Firewall ...
Simple_Firewall: theory Iface
Simple_Firewall: theory Firewall_Common_Decision_State
Simple_Firewall: theory GroupF
Simple_Firewall: theory IP_Partition_Preliminaries
Simple_Firewall: theory List_Product_More
Simple_Firewall: theory Lib_Enum_toString
Simple_Firewall: theory IP_Addr_WordInterval_toString
Simple_Firewall: theory L4_Protocol
Simple_Firewall: theory Simple_Packet
Simple_Firewall: theory Primitives_toString
Simple_Firewall: theory SimpleFw_Syntax
Simple_Firewall: theory SimpleFw_Semantics
Simple_Firewall: theory Generic_SimpleFw
Simple_Firewall: theory Shadowed
Simple_Firewall: theory Service_Matrices
Timing Simple_Firewall (8 threads, 31.458s elapsed time, 115.716s cpu time, 10.780s GC time, factor 3.68)
Document at /root/.isabelle/Isabelle2016/browser_info/Simple_Firewall/Simple_Firewall/document.pdf
Finished Simple_Firewall (0:01:33 elapsed time, 0:03:00 cpu time, factor 1.93)
Building Routing ...
Routing: theory Adhoc_Overloading
Routing: theory Linorder_Helper
Routing: theory Monad_Syntax
Routing: theory Routing_Table
Routing: theory IpRoute_Parser
Routing: theory Linux_Router
Timing Routing (8 threads, 7.067s elapsed time, 20.276s cpu time, 0.672s GC time, factor 2.87)
Document at /root/.isabelle/Isabelle2016/browser_info/Unsorted/Routing/document.pdf
Finished Routing (0:00:46 elapsed time, 0:01:00 cpu time, factor 1.30)
Building Iptables_Semantics ...
Iptables_Semantics: theory LaTeXsugar
Iptables_Semantics: theory List_Misc
Iptables_Semantics: theory More_Bits_Int
Iptables_Semantics: theory Negation_Type
Iptables_Semantics: theory WordInterval_Lists
Iptables_Semantics: theory Bits_Integer
Iptables_Semantics: theory Code_Target_Bits_Int
Iptables_Semantics: theory Datatype_Selectors
Iptables_Semantics: theory Conntrack_State
Iptables_Semantics: theory Iface_Attic
Iptables_Semantics: theory Remdups_Rev
Iptables_Semantics: theory Negation_Type_DNF
Iptables_Semantics: theory Firewall_Common
Iptables_Semantics: theory RepeatStabilize
Iptables_Semantics: theory Ternary
Iptables_Semantics: theory L4_Protocol_Flags
Iptables_Semantics: theory SimpleFw_toString
Iptables_Semantics: theory IpAddresses
Iptables_Semantics: theory Word_Upto
Iptables_Semantics: theory Ports
Iptables_Semantics: theory Tagged_Packet
Iptables_Semantics: theory Common_Primitive_Syntax
Iptables_Semantics: theory Semantics
Iptables_Semantics: theory Matching_Ternary
Iptables_Semantics: theory Semantics_Goto
Iptables_Semantics: theory Matching
Iptables_Semantics: theory Semantics_Stateful
Iptables_Semantics: theory Ruleset_Update
Iptables_Semantics: theory Call_Return_Unfolding
Iptables_Semantics: theory Semantics_Ternary
Iptables_Semantics: theory Unknown_Match_Tacs
Iptables_Semantics: theory Matching_Embeddings
Iptables_Semantics: theory Fixed_Action
Iptables_Semantics: theory Common_Primitive_Matcher_Generic
Iptables_Semantics: theory Normalized_Matches
Iptables_Semantics: theory Negation_Type_Matching
Iptables_Semantics: theory Primitive_Normalization
Iptables_Semantics: theory Packet_Set_Impl
Iptables_Semantics: theory Common_Primitive_Matcher
Iptables_Semantics: theory Ipassmt
Iptables_Semantics: theory Routing_IpAssmt
Iptables_Semantics: theory Packet_Set
Iptables_Semantics: theory Optimizing
Iptables_Semantics: theory Common_Primitive_Lemmas
Iptables_Semantics: theory Common_Primitive_toString
Iptables_Semantics: theory Conntrack_State_Transform
Iptables_Semantics: theory Example_Semantics
Iptables_Semantics: theory Interfaces_Normalize
Iptables_Semantics: theory IpAddresses_Normalize
Iptables_Semantics: theory No_Spoof
Iptables_Semantics: theory Protocols_Normalize
Iptables_Semantics: theory Ports_Normalize
Iptables_Semantics: theory Interface_Replace
Iptables_Semantics: theory Transform
Iptables_Semantics: theory Primitive_Abstract
Iptables_Semantics: theory SimpleFw_Compliance
Iptables_Semantics: theory Code_Interface
Iptables_Semantics: theory Semantics_Embeddings
Iptables_Semantics: theory Iptables_Semantics
Iptables_Semantics: theory No_Spoof_Embeddings
Iptables_Semantics: theory Parser
Iptables_Semantics: theory Code_haskell
Timing Iptables_Semantics (8 threads, 222.635s elapsed time, 834.308s cpu time, 86.328s GC time, factor 3
.75)
Document at /root/.isabelle/Isabelle2016/browser_info/Iptables_Semantics/Iptables_Semantics/document.pdf
Finished Iptables_Semantics (0:07:09 elapsed time, 0:17:44 cpu time, factor 2.48)
Building Iptables_Semantics_Documentation ...
Iptables_Semantics_Documentation: theory Documentation
Timing Iptables_Semantics_Documentation (8 threads, 5.470s elapsed time, 6.736s cpu time, 0.128s GC time,
 factor 1.23)
Document at /root/.isabelle/Isabelle2016/browser_info/Iptables_Semantics/Iptables_Semantics_Documentation
/document.pdf
Finished Iptables_Semantics_Documentation (0:00:57 elapsed time, 0:00:58 cpu time, factor 1.01)
Building OpenFlow ...
OpenFlow: theory Sort_Descending
OpenFlow: theory CaesarTheories
OpenFlow: theory List_Group
OpenFlow: theory Semantics_OpenFlow
OpenFlow: theory OpenFlowMatches
OpenFlow: theory FeatherweightOpenFlowComparison
OpenFlow: theory OpenFlowAction
OpenFlow: theory OpenFlowSerialize
OpenFlow: theory LinuxRouterOpenFlowTranslation
OpenFlow: theory OF_conv_test
OpenFlow: theory RFC2544
Timing OpenFlow (8 threads, 125.633s elapsed time, 541.436s cpu time, 50.048s GC time, factor 4.31)
Document at /root/Iptables_Semantics/thy/OpenFlow/of_outp/document.pdf
Finished OpenFlow (0:03:49 elapsed time, 0:10:49 cpu time, factor 2.83)
Building Iptables_Semantics_Examples_Large2 ...
Iptables_Semantics_Examples_Large2: theory IP_Address_Space_Examples_All_Small
Iptables_Semantics_Examples_Large2: theory IP_Address_Space_Examples_All_Large
Timing Iptables_Semantics_Examples_Large2 (8 threads, 6559.377s elapsed time, 31659.924s cpu time, 1506.196s GC time, factor 4.83)
Document at /root/.isabelle/Isabelle2016/browser_info/Iptables_Semantics/Iptables_Semantics_Examples_Large2/document.pdf
Finished Iptables_Semantics_Examples_Large2 (1:58:04 elapsed time, 8:56:26 cpu time, factor 4.54)
Building Iptables_Semantics_Examples_Large1 ...
Iptables_Semantics_Examples_Large1: theory Analyze_TUM_Net_Firewall
Iptables_Semantics_Examples_Large1: theory TUM_Spoofing_new3
Iptables_Semantics_Examples_Large1: theory TUM_Simple_FW
Timing Iptables_Semantics_Examples_Large1 (8 threads, 7090.504s elapsed time, 23443.396s cpu time, 2604.568s GC time, factor 3.31)
Document at /root/.isabelle/Isabelle2016/browser_info/Iptables_Semantics/Iptables_Semantics_Examples_Large1/document.pdf
Finished Iptables_Semantics_Examples_Large1 (2:01:09 elapsed time, 6:33:42 cpu time, factor 3.24)
Building Iptables_Semantics_Examples ...
Iptables_Semantics_Examples: theory Analyze_Ringofsaturn_com
Iptables_Semantics_Examples: theory Analyze_SQRL_Shorewall
Iptables_Semantics_Examples: theory Analyze_medium_sized_company
Iptables_Semantics_Examples: theory IP_Address_Space_Examples_All_Small
Iptables_Semantics_Examples: theory Parser_Test
Iptables_Semantics_Examples: theory SNS_IAS_Eduroam_Spoofing
Iptables_Semantics_Examples: theory SQRL_2015_nospoof
Iptables_Semantics_Examples: theory Analyze_topos_generated
Iptables_Semantics_Examples: theory Parser6
Iptables_Semantics_Examples: theory Ports_Fail
Iptables_Semantics_Examples: theory iptables_Ln_tuned_parsed
Iptables_Semantics_Examples: theory Analyze_Synology_Diskstation
Iptables_Semantics_Examples: theory Parser6_Test
Timing Iptables_Semantics_Examples (8 threads, 1471.027s elapsed time, 4079.832s cpu time, 357.740s GC time, factor 2.77)
Document at /root/.isabelle/Isabelle2016/browser_info/Iptables_Semantics/Iptables_Semantics_Examples/document.pdf
Finished Iptables_Semantics_Examples (0:28:16 elapsed time, 1:11:49 cpu time, factor 2.54)
Building Bitmagic ...
Bitmagic: theory More_Bits_Int
Bitmagic: theory Bits_Integer
Bitmagic: theory Code_Target_Bits_Int
Timing Bitmagic (8 threads, 13.346s elapsed time, 16.284s cpu time, 0.488s GC time, factor 1.22)
Document at /root/.isabelle/Isabelle2016/browser_info/Iptables_Semantics/Bitmagic/document.pdf
Finished Bitmagic (0:00:48 elapsed time, 0:01:15 cpu time, factor 1.56)
Building OpenFlow_Documentation ...
OpenFlow_Documentation: theory OpenFlowDoc
Timing OpenFlow_Documentation (8 threads, 2.741s elapsed time, 4.508s cpu time, 0.092s GC time, factor 1.64)
Document at /root/Iptables_Semantics/thy/OpenFlow/of_doc/document.pdf
Finished OpenFlow_Documentation (0:01:10 elapsed time, 0:01:04 cpu time, factor 0.91)
Finished at Sa 6. Aug 16:08:38 CEST 2016
4:53:47 elapsed time, 17:42:54 cpu time, factor 3.61
```


Where should I place the config file?


codestyle


Sure about this? Write APIs are scary, and I'd like to have *some* kind of oversight. How is it more disruptive than people posting normal feedback messages?

cc @ArtOfCode-


README.md
README.md
@@ -0,0 +1,2 @@
+# musical-octo-invention
+duykhanh1982@users.noreply.github.com
1 comment on commit a954086


only 30 cycles to access memory already in L1 cache. 100 cycles to fetch a new one.


[R/newCode.R:6:1:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L6) *style:* **Variable and function names should be all lowercase.**
```r
readInputData <- function(file, sep) {
^~~~~~~~~~~~~
```
[R/newCode.R:7:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L7) *style:* **Variable and function names should be all lowercase.**
```r
  inputData <-
  ^~~~~~~~~
```
[R/newCode.R:12:17:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L12) *style:* **Commas should never have a space before.**
```r
      sep = sep ,
               ~^
```
[R/newCode.R:17:10:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L17) *style:* **Variable and function names should be all lowercase.**
```r
    nrow(inputData),
         ^~~~~~~~~
```
[R/newCode.R:19:10:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L19) *style:* **Variable and function names should be all lowercase.**
```r
    ncol(inputData),
         ^~~~~~~~~
```
[R/newCode.R:22:24:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L22) *style:* **Variable and function names should be all lowercase.**
```r
  return(as.data.frame(inputData))
                       ^~~~~~~~~
```
[R/newCode.R:26:1:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L26) *style:* **Variable and function names should be all lowercase.**
```r
addTimeScaleToData <- function(iT, fT, data) {
^~~~~~~~~~~~~~~~~~
```
[R/newCode.R:26:32:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L26) *style:* **Variable and function names should be all lowercase.**
```r
addTimeScaleToData <- function(iT, fT, data) {
                               ^~
```
[R/newCode.R:26:36:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L26) *style:* **Variable and function names should be all lowercase.**
```r
addTimeScaleToData <- function(iT, fT, data) {
                                   ^~
```
[R/newCode.R:27:16:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L27) *style:* **Variable and function names should be all lowercase.**
```r
  time <-  seq(iT, fT, length.out = nrow(data))
               ^~
```
[R/newCode.R:27:20:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L27) *style:* **Variable and function names should be all lowercase.**
```r
  time <-  seq(iT, fT, length.out = nrow(data))
                   ^~
```
[R/newCode.R:31:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L31) *style:* **Variable and function names should be all lowercase.**
```r
    iT,
    ^~
```
[R/newCode.R:33:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L33) *style:* **Variable and function names should be all lowercase.**
```r
    fT,
    ^~
```
[R/newCode.R:49:16:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L49) *warning:* **Do not use absolute paths.**
```r
  filename <- "~/Desktop/Trinidad/LTT/fractionOfPopsize2.txt"
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/newCode.R:54:12:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L54) *style:* **Variable and function names should be all lowercase.**
```r
  data <-  readInputData(file = filename, sep = separator)
           ^~~~~~~~~~~~~
```
[R/newCode.R:54:12:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L54) *warning:* **no visible global function definition for ‘readInputData’**
```r
  data <-  readInputData(file = filename, sep = separator)
           ^~~~~~~~~~~~~
```
[R/newCode.R:55:11:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L55) *style:* **Variable and function names should be all lowercase.**
```r
  data <- addTimeScaleToData(iT = itime, fT = ftime, data = data)
          ^~~~~~~~~~~~~~~~~~
```
[R/newCode.R:55:11:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L55) *warning:* **no visible global function definition for ‘addTimeScaleToData’**
```r
  data <- addTimeScaleToData(iT = itime, fT = ftime, data = data)
          ^~~~~~~~~~~~~~~~~~
```
[R/newCode.R:56:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L56) *style:* **Variable and function names should be all lowercase.**
```r
  nDataCols <-
  ^~~~~~~~~
```
[R/newCode.R:59:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L59) *style:* **Commented code should be removed.**
```r
  # source("~/Desktop/Trinidad/LTT/plotStackedAreas.R")
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/newCode.R:64:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L64) *style:* **Variable and function names should be all lowercase.**
```r
  plotStackedAreas(data,
  ^~~~~~~~~~~~~~~~
```
[R/newCode.R:70:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L70) *style:* **Variable and function names should be all lowercase.**
```r
  plotStackedAreas(data,
  ^~~~~~~~~~~~~~~~
```
[R/newCode.R:77:11:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L77) *style:* **Commented code should be removed.**
```r
  #       install.packages("RColorBrewer")
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/newCode.R:78:11:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L78) *style:* **Commented code should be removed.**
```r
  #       library(RColorBrewer)
          ^~~~~~~~~~~~~~~~~~~~~
```
[R/newCode.R:82:4:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L82) *style:* **Commented code should be removed.**
```r
  #myColours= brewer.pal(8,"Set1")
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/newCode.R:83:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = (grDevices::rainbow(nDataCols, start = 0.11))
  ^~~~~~~~~
```
[R/newCode.R:83:13:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L83) *style:* **Use <-, not =, for assignment.**
```r
  myColours = (grDevices::rainbow(nDataCols, start = 0.11))
            ^
```
[R/newCode.R:83:35:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L83) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = (grDevices::rainbow(nDataCols, start = 0.11))
                                  ^~~~~~~~~
```
[R/newCode.R:84:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L84) *style:* **Variable and function names should be all lowercase.**
```r
  plotStackedAreas(
  ^~~~~~~~~~~~~~~~
```
[R/newCode.R:89:15:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L89) *style:* **Variable and function names should be all lowercase.**
```r
    colours = myColours,
              ^~~~~~~~~
```
[R/newCode.R:91:21:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L91) *style:* **Variable and function names should be all lowercase.**
```r
    areaBorderCol = myColours #use area colours to hide borders
                    ^~~~~~~~~
```
[R/newCode.R:96:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L96) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  ^~~~~~~~~
```
[R/newCode.R:96:13:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L96) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:96:34:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L96) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
                                 ^~~~~~~~~
```
[R/newCode.R:97:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L97) *style:* **Variable and function names should be all lowercase.**
```r
  plotStackedAreas(
  ^~~~~~~~~~~~~~~~
```
[R/newCode.R:102:15:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L102) *style:* **Variable and function names should be all lowercase.**
```r
    colours = myColours,
              ^~~~~~~~~
```
[R/newCode.R:104:21:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L104) *style:* **Variable and function names should be all lowercase.**
```r
    areaBorderCol = myColours,
                    ^~~~~~~~~
```
[R/newCode.R:112:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L112) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  ^~~~~~~~~
```
[R/newCode.R:112:13:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L112) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:112:34:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L112) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
                                 ^~~~~~~~~
```
[R/newCode.R:113:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L113) *style:* **Variable and function names should be all lowercase.**
```r
  myOrder = sample(1:nDataCols, nDataCols) #random selection of data columns
  ^~~~~~~
```
[R/newCode.R:113:11:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L113) *style:* **Use <-, not =, for assignment.**
```r
  myOrder = sample(1:nDataCols, nDataCols) #random selection of data columns
          ^
```
[R/newCode.R:113:22:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L113) *style:* **Variable and function names should be all lowercase.**
```r
  myOrder = sample(1:nDataCols, nDataCols) #random selection of data columns
                     ^~~~~~~~~
```
[R/newCode.R:113:33:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L113) *style:* **Variable and function names should be all lowercase.**
```r
  myOrder = sample(1:nDataCols, nDataCols) #random selection of data columns
                                ^~~~~~~~~
```
[R/newCode.R:114:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L114) *style:* **Variable and function names should be all lowercase.**
```r
  plotStackedAreas(
  ^~~~~~~~~~~~~~~~
```
[R/newCode.R:119:15:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L119) *style:* **Variable and function names should be all lowercase.**
```r
    colours = myColours,
              ^~~~~~~~~
```
[R/newCode.R:121:21:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L121) *style:* **Variable and function names should be all lowercase.**
```r
    areaBorderCol = myColours,
                    ^~~~~~~~~
```
[R/newCode.R:125:13:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L125) *style:* **Variable and function names should be all lowercase.**
```r
    order = myOrder,
            ^~~~~~~
```
[R/newCode.R:131:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L131) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  ^~~~~~~~~
```
[R/newCode.R:131:13:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L131) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:131:34:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L131) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
                                 ^~~~~~~~~
```
[R/newCode.R:132:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L132) *style:* **Variable and function names should be all lowercase.**
```r
  plotStackedAreas(
  ^~~~~~~~~~~~~~~~
```
[R/newCode.R:137:15:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L137) *style:* **Variable and function names should be all lowercase.**
```r
    colours = myColours,
              ^~~~~~~~~
```
[R/newCode.R:139:21:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L139) *style:* **Variable and function names should be all lowercase.**
```r
    areaBorderCol = myColours,
                    ^~~~~~~~~
```
[R/newCode.R:149:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L149) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  ^~~~~~~~~
```
[R/newCode.R:149:13:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L149) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:149:34:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L149) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
                                 ^~~~~~~~~
```
[R/newCode.R:150:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L150) *style:* **Variable and function names should be all lowercase.**
```r
  plotStackedAreas(
  ^~~~~~~~~~~~~~~~
```
[R/newCode.R:155:15:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L155) *style:* **Variable and function names should be all lowercase.**
```r
    colours = myColours,
              ^~~~~~~~~
```
[R/newCode.R:157:21:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L157) *style:* **Variable and function names should be all lowercase.**
```r
    areaBorderCol = myColours,
                    ^~~~~~~~~
```
[R/newCode.R:169:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L169) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  ^~~~~~~~~
```
[R/newCode.R:169:13:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L169) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:169:34:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L169) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
                                 ^~~~~~~~~
```
[R/newCode.R:170:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L170) *style:* **Variable and function names should be all lowercase.**
```r
  plotStackedAreas(
  ^~~~~~~~~~~~~~~~
```
[R/newCode.R:175:15:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L175) *style:* **Variable and function names should be all lowercase.**
```r
    colours = myColours,
              ^~~~~~~~~
```
[R/newCode.R:177:21:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L177) *style:* **Variable and function names should be all lowercase.**
```r
    areaBorderCol = myColours,
                    ^~~~~~~~~
```
[R/newCode.R:193:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L193) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  ^~~~~~~~~
```
[R/newCode.R:193:13:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L193) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:193:34:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L193) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
                                 ^~~~~~~~~
```
[R/newCode.R:194:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L194) *style:* **Variable and function names should be all lowercase.**
```r
  plotStackedAreas(
  ^~~~~~~~~~~~~~~~
```
[R/newCode.R:199:15:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L199) *style:* **Variable and function names should be all lowercase.**
```r
    colours = myColours,
              ^~~~~~~~~
```
[R/newCode.R:201:21:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L201) *style:* **Variable and function names should be all lowercase.**
```r
    areaBorderCol = myColours,
                    ^~~~~~~~~
```
[R/newCode.R:223:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L223) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  ^~~~~~~~~
```
[R/newCode.R:223:13:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L223) *style:* **Use <-, not =, for assignment.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
            ^
```
[R/newCode.R:223:34:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L223) *style:* **Variable and function names should be all lowercase.**
```r
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
                                 ^~~~~~~~~
```
[R/newCode.R:224:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L224) *style:* **Variable and function names should be all lowercase.**
```r
  myColours[length(myColours)] = "white"
  ^~~~~~~~~
```
[R/newCode.R:224:20:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L224) *style:* **Variable and function names should be all lowercase.**
```r
  myColours[length(myColours)] = "white"
                   ^~~~~~~~~
```
[R/newCode.R:224:32:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L224) *style:* **Use <-, not =, for assignment.**
```r
  myColours[length(myColours)] = "white"
                               ^
```
[R/newCode.R:225:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L225) *style:* **Variable and function names should be all lowercase.**
```r
  plotStackedAreas(
  ^~~~~~~~~~~~~~~~
```
[R/newCode.R:230:15:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L230) *style:* **Variable and function names should be all lowercase.**
```r
    colours = myColours,
              ^~~~~~~~~
```
[R/newCode.R:232:21:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/newCode.R#L232) *style:* **Variable and function names should be all lowercase.**
```r
    areaBorderCol = myColours,
                    ^~~~~~~~~
```
[R/plotStackedAreas.R:23:1:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L23) *style:* **Variable and function names should be all lowercase.**
```r
runBeast <- function(commandLine = "") {
^~~~~~~~
```
[R/plotStackedAreas.R:23:22:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L23) *style:* **Variable and function names should be all lowercase.**
```r
runBeast <- function(commandLine = "") {
                     ^~~~~~~~~~~
```
[R/plotStackedAreas.R:25:31:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L25) *style:* **Variable and function names should be all lowercase.**
```r
    strings <- rJava::.jarray(commandLine)
                              ^~~~~~~~~~~
```
[R/plotStackedAreas.R:30:1:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L30) *style:* **Variable and function names should be all lowercase.**
```r
plotStackedAreas <- function(
^~~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:36:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L36) *style:* **Variable and function names should be all lowercase.**
```r
  areaBorderWidth= NA,
  ^~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:37:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L37) *style:* **Variable and function names should be all lowercase.**
```r
  areaBorderCol="black",
  ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:39:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L39) *style:* **Variable and function names should be all lowercase.**
```r
  addAxisSpace=FALSE,
  ^~~~~~~~~~~~
```
[R/plotStackedAreas.R:40:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L40) *style:* **Variable and function names should be all lowercase.**
```r
  addLegend=NA,
  ^~~~~~~~~
```
[R/plotStackedAreas.R:45:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L45) *style:* **Variable and function names should be all lowercase.**
```r
  pdfW=7,
  ^~~~
```
[R/plotStackedAreas.R:46:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L46) *style:* **Variable and function names should be all lowercase.**
```r
  pdfH=5,
  ^~~~
```
[R/plotStackedAreas.R:47:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L47) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
  legend.pt.cex=1,
  ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:52:4:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L52) *style:* **Use <-, not =, for assignment.**
```r
  X= data$time
   ^
```
[R/plotStackedAreas.R:52:4:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L52) *style:* **Put spaces around all infix operators.**
```r
  X= data$time
  ~^
```
[R/plotStackedAreas.R:54:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L54) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(stacked100){
    ^
```
[R/plotStackedAreas.R:55:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L55) *style:* **Variable and function names should be all lowercase.**
```r
    sumDataCols<- function(X){
    ^~~~~~~~~~~
```
[R/plotStackedAreas.R:55:16:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L55) *style:* **Put spaces around all infix operators.**
```r
    sumDataCols<- function(X){
              ~^
```
[R/plotStackedAreas.R:58:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L58) *style:* **Variable and function names should be all lowercase.**
```r
    dataSums= apply(data, MARGIN=1, FUN=sumDataCols)
    ^~~~~~~~
```
[R/plotStackedAreas.R:58:13:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L58) *style:* **Use <-, not =, for assignment.**
```r
    dataSums= apply(data, MARGIN=1, FUN=sumDataCols)
            ^
```
[R/plotStackedAreas.R:58:13:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L58) *style:* **Put spaces around all infix operators.**
```r
    dataSums= apply(data, MARGIN=1, FUN=sumDataCols)
           ~^
```
[R/plotStackedAreas.R:58:33:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L58) *style:* **Put spaces around all infix operators.**
```r
    dataSums= apply(data, MARGIN=1, FUN=sumDataCols)
                               ~^~
```
[R/plotStackedAreas.R:58:40:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L58) *style:* **Put spaces around all infix operators.**
```r
    dataSums= apply(data, MARGIN=1, FUN=sumDataCols)
                                      ~^~
```
[R/plotStackedAreas.R:58:41:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L58) *style:* **Variable and function names should be all lowercase.**
```r
    dataSums= apply(data, MARGIN=1, FUN=sumDataCols)
                                        ^~~~~~~~~~~
```
[R/plotStackedAreas.R:59:6:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L59) *style:* **Use <-, not =, for assignment.**
```r
    Y= data[,2:ncol(data)]/dataSums
     ^
```
[R/plotStackedAreas.R:59:6:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L59) *style:* **Put spaces around all infix operators.**
```r
    Y= data[,2:ncol(data)]/dataSums
    ~^
```
[R/plotStackedAreas.R:59:14:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L59) *style:* **Commas should always have a space after.**
```r
    Y= data[,2:ncol(data)]/dataSums
             ^
```
[R/plotStackedAreas.R:59:27:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L59) *style:* **Put spaces around all infix operators.**
```r
    Y= data[,2:ncol(data)]/dataSums
                         ~^~
```
[R/plotStackedAreas.R:59:28:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L59) *style:* **Variable and function names should be all lowercase.**
```r
    Y= data[,2:ncol(data)]/dataSums
                           ^~~~~~~~
```
[R/plotStackedAreas.R:61:6:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L61) *style:* **Use <-, not =, for assignment.**
```r
    Y= data[,2:ncol(data)]
     ^
```
[R/plotStackedAreas.R:61:6:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L61) *style:* **Put spaces around all infix operators.**
```r
    Y= data[,2:ncol(data)]
    ~^
```
[R/plotStackedAreas.R:61:14:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L61) *style:* **Commas should always have a space after.**
```r
    Y= data[,2:ncol(data)]
             ^
```
[R/plotStackedAreas.R:63:12:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L63) *style:* **Use <-, not =, for assignment.**
```r
  ndatacols= ncol(Y)
           ^
```
[R/plotStackedAreas.R:63:12:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L63) *style:* **Put spaces around all infix operators.**
```r
  ndatacols= ncol(Y)
          ~^
```
[R/plotStackedAreas.R:66:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L66) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(sum(Y<0)>=1) stop("Data columns can not have negative values.")
    ^
```
[R/plotStackedAreas.R:66:11:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L66) *style:* **Put spaces around all infix operators.**
```r
  if(sum(Y<0)>=1) stop("Data columns can not have negative values.")
         ~^~
```
[R/plotStackedAreas.R:66:14:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L66) *style:* **Put spaces around all infix operators.**
```r
  if(sum(Y<0)>=1) stop("Data columns can not have negative values.")
            ~^~~
```
[R/plotStackedAreas.R:67:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L67) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(sum(X<0)>=1) stop("Time scale can not have negative values.")
    ^
```
[R/plotStackedAreas.R:67:11:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L67) *style:* **Put spaces around all infix operators.**
```r
  if(sum(X<0)>=1) stop("Time scale can not have negative values.")
         ~^~
```
[R/plotStackedAreas.R:67:14:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L67) *style:* **Put spaces around all infix operators.**
```r
  if(sum(X<0)>=1) stop("Time scale can not have negative values.")
            ~^~~
```
[R/plotStackedAreas.R:68:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L68) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(nrow(Y)==0) stop("Data columns appear to be empty.")
    ^
```
[R/plotStackedAreas.R:68:13:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L68) *style:* **Put spaces around all infix operators.**
```r
  if(nrow(Y)==0) stop("Data columns appear to be empty.")
           ~^~~
```
[R/plotStackedAreas.R:69:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L69) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(X)==0) stop("Time scale appears to be empty.")
    ^
```
[R/plotStackedAreas.R:69:15:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L69) *style:* **Put spaces around all infix operators.**
```r
  if(length(X)==0) stop("Time scale appears to be empty.")
             ~^~~
```
[R/plotStackedAreas.R:72:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L72) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(is.na(areaBorderWidth)) areaBorderWidth<- 1
    ^
```
[R/plotStackedAreas.R:72:12:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L72) *style:* **Variable and function names should be all lowercase.**
```r
  if(is.na(areaBorderWidth)) areaBorderWidth<- 1
           ^~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:72:30:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L72) *style:* **Variable and function names should be all lowercase.**
```r
  if(is.na(areaBorderWidth)) areaBorderWidth<- 1
                             ^~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:72:45:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L72) *style:* **Put spaces around all infix operators.**
```r
  if(is.na(areaBorderWidth)) areaBorderWidth<- 1
                                           ~^
```
[R/plotStackedAreas.R:73:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L73) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(colours)==1){
    ^
```
[R/plotStackedAreas.R:73:21:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L73) *style:* **Put spaces around all infix operators.**
```r
  if(length(colours)==1){
                   ~^~~
```
[R/plotStackedAreas.R:74:7:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L74) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(is.na(colours)) colours <- grDevices::rainbow(ndatacols)
      ^
```
[R/plotStackedAreas.R:76:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L76) *style:* **Variable and function names should be all lowercase.**
```r
  areaBorderCol <- as.vector(matrix(areaBorderCol, nrow=ndatacols, ncol=1))
  ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:76:37:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L76) *style:* **Variable and function names should be all lowercase.**
```r
  areaBorderCol <- as.vector(matrix(areaBorderCol, nrow=ndatacols, ncol=1))
                                    ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:76:56:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L76) *style:* **Put spaces around all infix operators.**
```r
  areaBorderCol <- as.vector(matrix(areaBorderCol, nrow=ndatacols, ncol=1))
                                                      ~^~
```
[R/plotStackedAreas.R:76:72:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L76) *style:* **Put spaces around all infix operators.**
```r
  areaBorderCol <- as.vector(matrix(areaBorderCol, nrow=ndatacols, ncol=1))
                                                                      ~^~
```
[R/plotStackedAreas.R:77:44:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L77) *style:* **Put spaces around all infix operators.**
```r
  colours <- as.vector(matrix(colours, nrow=ndatacols, ncol=1))
                                          ~^~
```
[R/plotStackedAreas.R:77:60:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L77) *style:* **Put spaces around all infix operators.**
```r
  colours <- as.vector(matrix(colours, nrow=ndatacols, ncol=1))
                                                          ~^~
```
[R/plotStackedAreas.R:78:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L78) *style:* **Variable and function names should be all lowercase.**
```r
  areaBorderWidth <- as.vector(matrix(areaBorderWidth, nrow=ndatacols, ncol=1))
  ^~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:78:39:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L78) *style:* **Variable and function names should be all lowercase.**
```r
  areaBorderWidth <- as.vector(matrix(areaBorderWidth, nrow=ndatacols, ncol=1))
                                      ^~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:78:60:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L78) *style:* **Put spaces around all infix operators.**
```r
  areaBorderWidth <- as.vector(matrix(areaBorderWidth, nrow=ndatacols, ncol=1))
                                                          ~^~
```
[R/plotStackedAreas.R:78:76:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L78) *style:* **Put spaces around all infix operators.**
```r
  areaBorderWidth <- as.vector(matrix(areaBorderWidth, nrow=ndatacols, ncol=1))
                                                                          ~^~
```
[R/plotStackedAreas.R:80:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L80) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(length(order)>1) {
    ^
```
[R/plotStackedAreas.R:80:19:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L80) *style:* **Put spaces around all infix operators.**
```r
  if(length(order)>1) {
                 ~^~
```
[R/plotStackedAreas.R:81:1:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L81) *style:* **lines should not be more than 80 characters.**
```r
    if(length(order)!=ndatacols) stop("Order array must be the length of data columns.")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:81:7:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L81) *style:* **Place a space before left parenthesis, except in a function call.**
```r
    if(length(order)!=ndatacols) stop("Order array must be the length of data columns.")
      ^
```
[R/plotStackedAreas.R:81:21:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L81) *style:* **Put spaces around all infix operators.**
```r
    if(length(order)!=ndatacols) stop("Order array must be the length of data columns.")
                   ~^~~
```
[R/plotStackedAreas.R:84:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L84) *style:* **Variable and function names should be all lowercase.**
```r
    areaBorderWidth <- areaBorderWidth[order]
    ^~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:84:24:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L84) *style:* **Variable and function names should be all lowercase.**
```r
    areaBorderWidth <- areaBorderWidth[order]
                       ^~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:85:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
    areaBorderCol<- areaBorderCol[order]
    ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:85:18:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L85) *style:* **Put spaces around all infix operators.**
```r
    areaBorderCol<- areaBorderCol[order]
                ~^
```
[R/plotStackedAreas.R:85:21:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L85) *style:* **Variable and function names should be all lowercase.**
```r
    areaBorderCol<- areaBorderCol[order]
                    ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:88:3:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L88) *style:* **Variable and function names should be all lowercase.**
```r
  upperPrevious <- X*0
  ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:88:21:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L88) *style:* **Put spaces around all infix operators.**
```r
  upperPrevious <- X*0
                   ~^~
```
[R/plotStackedAreas.R:89:23:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L89) *style:* **Put spaces around all infix operators.**
```r
  areas <- vector(mode="list", ndatacols)
                     ~^~
```
[R/plotStackedAreas.R:90:6:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L90) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in seq(areas)){
     ^
```
[R/plotStackedAreas.R:91:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L91) *style:* **Variable and function names should be all lowercase.**
```r
    upperThis <- upperPrevious + Y[,i]
    ^~~~~~~~~
```
[R/plotStackedAreas.R:91:18:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L91) *style:* **Variable and function names should be all lowercase.**
```r
    upperThis <- upperPrevious + Y[,i]
                 ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:91:37:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L91) *style:* **Commas should always have a space after.**
```r
    upperThis <- upperPrevious + Y[,i]
                                    ^
```
[R/plotStackedAreas.R:92:25:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L92) *style:* **Put spaces around all infix operators.**
```r
    areas[[i]] <- list(x=c(X, rev(X)), y=c(upperPrevious, rev(upperThis)))
                       ~^~
```
[R/plotStackedAreas.R:92:41:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L92) *style:* **Put spaces around all infix operators.**
```r
    areas[[i]] <- list(x=c(X, rev(X)), y=c(upperPrevious, rev(upperThis)))
                                       ~^~
```
[R/plotStackedAreas.R:92:44:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L92) *style:* **Variable and function names should be all lowercase.**
```r
    areas[[i]] <- list(x=c(X, rev(X)), y=c(upperPrevious, rev(upperThis)))
                                           ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:92:63:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L92) *style:* **Variable and function names should be all lowercase.**
```r
    areas[[i]] <- list(x=c(X, rev(X)), y=c(upperPrevious, rev(upperThis)))
                                                              ^~~~~~~~~
```
[R/plotStackedAreas.R:93:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L93) *style:* **Variable and function names should be all lowercase.**
```r
    upperPrevious <- upperThis
    ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:93:22:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L93) *style:* **Variable and function names should be all lowercase.**
```r
    upperPrevious <- upperThis
                     ^~~~~~~~~
```
[R/plotStackedAreas.R:96:7:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L96) *style:* **Use <-, not =, for assignment.**
```r
  xaxs="r"
      ^
```
[R/plotStackedAreas.R:96:7:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L96) *style:* **Put spaces around all infix operators.**
```r
  xaxs="r"
     ~^~
```
[R/plotStackedAreas.R:97:7:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L97) *style:* **Use <-, not =, for assignment.**
```r
  yaxs="r"
      ^
```
[R/plotStackedAreas.R:97:7:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L97) *style:* **Put spaces around all infix operators.**
```r
  yaxs="r"
     ~^~
```
[R/plotStackedAreas.R:98:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L98) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!addAxisSpace){
    ^
```
[R/plotStackedAreas.R:98:7:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L98) *style:* **Variable and function names should be all lowercase.**
```r
  if(!addAxisSpace){
      ^~~~~~~~~~~~
```
[R/plotStackedAreas.R:99:9:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L99) *style:* **Use <-, not =, for assignment.**
```r
    xaxs="i"
        ^
```
[R/plotStackedAreas.R:99:9:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L99) *style:* **Put spaces around all infix operators.**
```r
    xaxs="i"
       ~^~
```
[R/plotStackedAreas.R:100:9:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L100) *style:* **Use <-, not =, for assignment.**
```r
    yaxs="i"
        ^
```
[R/plotStackedAreas.R:100:9:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L100) *style:* **Put spaces around all infix operators.**
```r
    yaxs="i"
       ~^~
```
[R/plotStackedAreas.R:103:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L103) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.na(file)){
    ^
```
[R/plotStackedAreas.R:104:9:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L104) *style:* **Use <-, not =, for assignment.**
```r
    file=paste(file,".pdf",sep="")
        ^
```
[R/plotStackedAreas.R:104:9:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L104) *style:* **Put spaces around all infix operators.**
```r
    file=paste(file,".pdf",sep="")
       ~^~
```
[R/plotStackedAreas.R:104:21:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L104) *style:* **Commas should always have a space after.**
```r
    file=paste(file,".pdf",sep="")
                    ^
```
[R/plotStackedAreas.R:104:28:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L104) *style:* **Commas should always have a space after.**
```r
    file=paste(file,".pdf",sep="")
                           ^
```
[R/plotStackedAreas.R:104:31:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L104) *style:* **Put spaces around all infix operators.**
```r
    file=paste(file,".pdf",sep="")
                             ~^~
```
[R/plotStackedAreas.R:105:34:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L105) *style:* **Variable and function names should be all lowercase.**
```r
    grDevices::pdf(file, width = pdfW, height = pdfH, bg="white")
                                 ^~~~
```
[R/plotStackedAreas.R:105:49:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L105) *style:* **Variable and function names should be all lowercase.**
```r
    grDevices::pdf(file, width = pdfW, height = pdfH, bg="white")
                                                ^~~~
```
[R/plotStackedAreas.R:105:57:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L105) *style:* **Put spaces around all infix operators.**
```r
    grDevices::pdf(file, width = pdfW, height = pdfH, bg="white")
                                                       ~^~
```
[R/plotStackedAreas.R:108:34:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L108) *style:* **Put spaces around all infix operators.**
```r
  graphics::layout(matrix(1, ncol=1, byrow=TRUE))
                                ~^~
```
[R/plotStackedAreas.R:108:43:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L108) *style:* **Put spaces around all infix operators.**
```r
  graphics::layout(matrix(1, ncol=1, byrow=TRUE))
                                         ~^~
```
[R/plotStackedAreas.R:109:20:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L109) *style:* **Put spaces around all infix operators.**
```r
  graphics::par(mar=c(4, 4, 2, 2), cex=0.9)
                  ~^~
```
[R/plotStackedAreas.R:109:39:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L109) *style:* **Put spaces around all infix operators.**
```r
  graphics::par(mar=c(4, 4, 2, 2), cex=0.9)
                                     ~^~
```
[R/plotStackedAreas.R:111:59:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L111) *style:* **Put spaces around all infix operators.**
```r
  ylim <- range(sapply(areas, function(x) range(x$y, na.rm=TRUE)), na.rm=TRUE)
                                                         ~^~
```
[R/plotStackedAreas.R:111:73:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L111) *style:* **Put spaces around all infix operators.**
```r
  ylim <- range(sapply(areas, function(x) range(x$y, na.rm=TRUE)), na.rm=TRUE)
                                                                       ~^~
```
[R/plotStackedAreas.R:112:1:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L112) *style:* **lines should not be more than 80 characters.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:112:20:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L112) *style:* **Commas should always have a space after.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                   ^
```
[R/plotStackedAreas.R:112:23:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L112) *style:* **Commas should always have a space after.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                      ^
```
[R/plotStackedAreas.R:112:31:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                             ~^~
```
[R/plotStackedAreas.R:112:42:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                                        ~^~
```
[R/plotStackedAreas.R:112:53:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                                                   ~^~
```
[R/plotStackedAreas.R:112:61:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                                                           ~^~
```
[R/plotStackedAreas.R:112:71:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                                                                     ~^~
```
[R/plotStackedAreas.R:112:82:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                                                                                ~^~
```
[R/plotStackedAreas.R:112:93:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L112) *style:* **Put spaces around all infix operators.**
```r
  graphics::plot(X,Y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", xaxs=xaxs, yaxs=yaxs, main=main)
                                                                                ~^~
```
[R/plotStackedAreas.R:113:6:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L113) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  for(i in seq(areas)){
     ^
```
[R/plotStackedAreas.R:114:1:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L114) *style:* **lines should not be more than 80 characters.**
```r
    graphics::polygon(areas[[i]], border=areaBorderCol[i], col=colours[i], lwd=areaBorderWidth[i])
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:114:41:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L114) *style:* **Put spaces around all infix operators.**
```r
    graphics::polygon(areas[[i]], border=areaBorderCol[i], col=colours[i], lwd=areaBorderWidth[i])
                                       ~^~
```
[R/plotStackedAreas.R:114:42:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L114) *style:* **Variable and function names should be all lowercase.**
```r
    graphics::polygon(areas[[i]], border=areaBorderCol[i], col=colours[i], lwd=areaBorderWidth[i])
                                         ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:114:63:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L114) *style:* **Put spaces around all infix operators.**
```r
    graphics::polygon(areas[[i]], border=areaBorderCol[i], col=colours[i], lwd=areaBorderWidth[i])
                                                             ~^~
```
[R/plotStackedAreas.R:114:79:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L114) *style:* **Put spaces around all infix operators.**
```r
    graphics::polygon(areas[[i]], border=areaBorderCol[i], col=colours[i], lwd=areaBorderWidth[i])
                                                                             ~^~
```
[R/plotStackedAreas.R:114:80:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L114) *style:* **Variable and function names should be all lowercase.**
```r
    graphics::polygon(areas[[i]], border=areaBorderCol[i], col=colours[i], lwd=areaBorderWidth[i])
                                                                               ^~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:117:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L117) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.na(addLegend)){
    ^
```
[R/plotStackedAreas.R:117:13:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L117) *style:* **Variable and function names should be all lowercase.**
```r
  if(!is.na(addLegend)){
            ^~~~~~~~~
```
[R/plotStackedAreas.R:118:10:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L118) *style:* **Use <-, not =, for assignment.**
```r
    names= colnames(Y)
         ^
```
[R/plotStackedAreas.R:118:10:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L118) *style:* **Put spaces around all infix operators.**
```r
    names= colnames(Y)
        ~^
```
[R/plotStackedAreas.R:119:1:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **lines should not be more than 80 characters.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
```
[R/plotStackedAreas.R:119:22:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **Variable and function names should be all lowercase.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                     ^~~~~~~~~
```
[R/plotStackedAreas.R:119:39:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                     ~^~
```
[R/plotStackedAreas.R:119:50:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                ~^~
```
[R/plotStackedAreas.R:119:58:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                        ~^~
```
[R/plotStackedAreas.R:119:73:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                       ~^~
```
[R/plotStackedAreas.R:119:89:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:119:90:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **Words within variable and function names should be separated by '_' rather than '.'.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ^~~~~~~~~~~~~
```
[R/plotStackedAreas.R:119:111:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:119:118:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:119:125:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:119:137:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:119:144:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:119:159:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L119) *style:* **Put spaces around all infix operators.**
```r
    graphics::legend(addLegend, legend=names, pch=22, col="black", pt.bg=colours, pt.cex=legend.pt.cex, pt.lwd=1, lwd=0, lty=NA, box.lwd=NA, bg=legend.bg, cex=legend.cex)
                                                                                ~^~
```
[R/plotStackedAreas.R:122:20:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L122) *style:* **Put spaces around all infix operators.**
```r
  graphics::box(lwd=boxlwd)
                  ~^~
```
[R/plotStackedAreas.R:124:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L124) *style:* **Place a space before left parenthesis, except in a function call.**
```r
  if(!is.na(file)){
    ^
```
[R/plotStackedAreas.R:125:5:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/plotStackedAreas.R#L125) *warning:* **local variable ‘a’ assigned but may not be used**
```r
    a <- grDevices::dev.off()
    ^
```
[R/readBeast2Trees.R:6:1:](https://github.com/beast-dev/RBeast/blob/7f8646b44bb1e42d740b05d2aed565202bc7d67b/R/readBeast2Trees.R#L6) *style:* **Use two spaces to indent, never tabs.**
```r
	tmp			<- readLines(file, n=2e3, warn = FALSE)
^
```


should be order of 100x faster (matching relative cache fetch cycles)


`12>CSC : error CS2001: Source file 'WowPacketParser\WowPacketParserModule.V7_0_3_22248\Parsers\CharacterHandler.cs' could not be found.`


lots more useful examples there -hash tables etc


Yay! 🍻


Are you sure it won't skip the next element? Maybe the array should be iterated in reverse?


Cool. I'll do it that way.


test should be tests, as per dir naming policy, IIRC

Looks good otherwise, please push upstream.


ng-click compartilha  a função do controller cadastrarProdutos passando todos os atributos da view de cadastro a cima.


para saan to gema??


@HyGlobalHD Yeah sorry, I wrote hell but corrected it afterwards. :D
When I'm back home I should have some time. What project are we talking about?


Cambios necesarios luego de deprecar @api.one


@SubJunk That's a great idea, i'm shameful to didn't have it myself ;-)
I'm not sure if it can help but i founded that:
https://github.com/yakka34/Unofficial-cpubenchmark.net-API


think you.