mobiodiv/mobsim

Spatial analysis and simulation of ecological communities

Overview

The goal of the package mobsim is to facilitate understanding of scale-dependent biodiversity changes.

The package includes functions to simulate species distributions in space with controlled abundance distributions as well as controlled intraspecific aggregation. For analysis there are functions for species rarefaction and accumulation curves, species-area relationships, endemics-area relationships and the distance-decay of community similarity.

A detailed introduction of the package is available at bioRxiv.

Installation

# The easiest way to get mobsim is to install from CRAN:
install.packages("mobsim")

# Or the development version from GitHub:
# install.packages("devtools")
devtools::install_github("MoBiodiv/mobsim", build_vignettes = TRUE)

Please enter bug reports on github.

Getting help

You can get an overview of the available functions in mobsim:

?mobsim

Or have a look at tutorials in the vignette:

browseVignettes("mobsim")

Examples

Here is an example of how to simulate two communities, which just differ in their spatial aggregation of species, but have the same species abundance distribution and the same total number of individuals.

Simulation of communities

library(mobsim)
comm_rand <- sim_poisson_community(s_pool = 30, n_sim = 300)
comm_agg <- sim_thomas_community(s_pool = 30, n_sim = 300, sigma = 0.05, mother_points = 1)

par(mfrow = c(1,2))
plot(comm_rand)
plot(comm_agg)

Analysis of spatially-explicit community data

mobsim mobsim offer functions to analyse spatially-explicit community data. For example the species-area relationship of a community can be easily evaluated.

sar_rand <- divar(comm_rand)
sar_agg <- divar(comm_agg)

plot(m_species ~ prop_area, data = sar_rand, type = "b", log = "xy",
     xlab = "Proportion of area sampled",ylab = "No. of species",
     ylim = c(3,30))
lines(m_species ~ prop_area, data = sar_agg, type = "b", col = 2)
legend("bottomright", c("Random","Aggregated"), col = 1:2, lwd = 2)

Sampling of communities

Simulated or observed communities can be also sampled inorder to test whether biodiversity changes are correctly detected and revealed by any sampling design.

par(mfrow = c(1,2))
samples_rand <- sample_quadrats(comm_rand, avoid_overlap = TRUE)
samples_agg <- sample_quadrats(comm_agg, avoid_overlap = TRUE)

mobsim's Issues

ToDo minor package maintenance

• Function links in sad_sim() should be consistent
• Maybe sort sim_sad() output by decreasing abundance?

Compiler warning in rThomas_rcpp

@AlbanSagouis I tried to fix the compiler warning problem. In my understanding, it is related to type conversion from Rcpp sugar to C++ data types.
I also simplified by removing one check of n_mother_points.
When it still does not work, we might talk about the logic of the tests before, I try again.

Allow observed SAD as input

A cool feature to possibly add down the line may be the ability for users to specify a full SAD (i.e., a vector of abundances) rather than simply the family S and N.

support functions for handling results of sample_quadrats

In the future it would be cool to add a few support functions for handling the output from the function sample_quadrats. A plot function for the output class could allow a user to examine scale dependence in SADs for example.

Package has been removed from CRAN

Bugs in `Sim.Thomas.Coords`

Hi Felix - I'm using your Sim.Thomas.Coords function in our sensitivity test for mobr, but there seems to be two bugs under the scenario when sigma is large (ie. the Poisson case):

1. xmax and ymax are undefined, and
2. species names are defined differently. Here they are defined as numbers (e.g., from 1 to 100), while in the other scenario they are defined as "species" + numbers (e.g., species1, species2, etc.)

Thanks!

warnings on install

I received the following warnings on install:

Warning: /home/mcglinnd/MoBspatial/man/sample_quadrats.Rd:41: unexpected '}', expecting '{'
Warning: /home/mcglinnd/MoBspatial/man/theme_biodiviz.Rd:20: unknown macro '\item'
Warning: /home/mcglinnd/MoBspatial/man/theme_biodiviz.Rd:22: unknown macro '\item'
Warning: /home/mcglinnd/MoBspatial/man/theme_biodiviz.Rd:24: unexpected section header '\description'
Warning: /home/mcglinnd/MoBspatial/man/theme_biodiviz.Rd:27: unexpected section header '\examples'
Warning: /home/mcglinnd/MoBspatial/man/theme_biodiviz.Rd:39: unexpected END_OF_INPUT '

It looks like some of the man files are a little funky

Trouble with install on ubuntu

Here are the system details

R.version
               _                           
platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          2.3                         
year           2015                        
month          12                          
day            10                          
svn rev        69752                       
language       R                           
version.string R version 3.2.3 (2015-12-10)
nickname       Wooden Christmas-Tree       

I have successfully installed Rcpp. Here is the R install code and resulting error. @rueuntal I think I remember you having some trouble on install as well. Was it something similar?

library(devtools)
install_github('MoBiodiv/MoBspatial')
Downloading GitHub repo MoBiodiv/MoBspatial@master
Installing MoBspatial
'/usr/lib/R/bin/R' --no-site-file --no-environ --no-save --no-restore CMD  \
  INSTALL '/tmp/Rtmp1pDqNX/devtoolse4e454eda54c/MoBiodiv-MoBspatial-4bd41e1'  \
  --library='/home/mcglinnd/R/x86_64-pc-linux-gnu-library/3.2' --install-tests 

* installing *source* package ‘MoBspatial’ ...
** libs
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o MoBspatial.so RcppExports.o SAC_spatial.o rThomas_rcpp.o -L/usr/lib/R/lib -lR
collect2: error: ld terminated with signal 11 [Segmentation fault], core dumped
RcppExports.o:RcppExports.cpp:(.text.startup+0xf): undefined reference to `std::ios_base::Init::Init()'
RcppExports.o:RcppExports.cpp:(.text.startup+0x33): undefined reference to `std::ios_base::ios_base()'
RcppExports.o:RcppExports.cpp:(.text.startup+0x94): undefined reference to `operator new(unsigned long long)'
RcppExports.o:RcppExports.cpp:(.text.startup+0xde): undefined reference to `std::locale::locale()'
RcppExports.o:RcppExports.cpp:(.text.startup+0x113): undefined reference to `std::basic_ios<char, std::char_traits<char> >::init(std::basic_streambuf<char, std::char_traits<char> >*)'
RcppExports.o:RcppExports.cpp:(.text.startup+0x155): undefined reference to `std::ios_base::ios_base()'
RcppExports.o:RcppExports.cpp:(.text.startup+0x1af): undefined reference to `operator new(unsigned long long)'
RcppExports.o:RcppExports.cpp:(.text.startup+0x1f2): undefined reference to `std::locale::locale()'
RcppExports.o:RcppExports.cpp:(.text.startup+0x227): undefined reference to `std::basic_ios<char, std::char_traits<char> >::init(std::basic_streambuf<char, std::char_traits<char> >*)'
RcppExports.o:RcppExports.cpp:(.text.startup+0x27e): undefined reference to `std::ios_base::~ios_base()'
RcppExports.o:RcppExports.cpp:(.text.startup+0x286): undefined reference to `_Unwind_Resume'
RcppExports.o:RcppExports.cpp:(.text.startup+0x2a0): undefined reference to `std::ios_base::~ios_base()'
RcppExports.o:RcppExports.cpp:(.text.startup+0x2a8): undefined reference to `_Unwind_Resume'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0xf): undefined reference to `std::ios_base::Init::Init()'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x33): undefined reference to `std::ios_base::ios_base()'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x3a): relocation truncated to fit: R_X86_64_PC32 against `.refptr._ZTVSt9basic_iosIcSt11char_traitsIcEE'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x94): undefined reference to `operator new(unsigned long long)'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x9b): relocation truncated to fit: R_X86_64_PC32 against `.refptr._ZTVSt15basic_streambufIcSt11char_traitsIcEE'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0xde): undefined reference to `std::locale::locale()'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0xe5): relocation truncated to fit: R_X86_64_PC32 against `vtable for Rcpp::Rstreambuf<true>'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0xf2): relocation truncated to fit: R_X86_64_PC32 against `construction vtable for std::ostream-in-Rcpp::Rostream<true>'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x107): relocation truncated to fit: R_X86_64_PC32 against `construction vtable for std::ostream-in-Rcpp::Rostream<true>'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x113): undefined reference to `std::basic_ios<char, std::char_traits<char> >::init(std::basic_streambuf<char, std::char_traits<char> >*)'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x11a): relocation truncated to fit: R_X86_64_PC32 against `vtable for Rcpp::Rostream<true>'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x128): relocation truncated to fit: R_X86_64_PC32 against `vtable for Rcpp::Rostream<true>'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x155): undefined reference to `std::ios_base::ios_base()'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x1af): undefined reference to `operator new(unsigned long long)'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x1f2): undefined reference to `std::locale::locale()'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x1f9): relocation truncated to fit: R_X86_64_PC32 against `vtable for Rcpp::Rstreambuf<false>'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x206): relocation truncated to fit: R_X86_64_PC32 against `construction vtable for std::ostream-in-Rcpp::Rostream<false>'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x21b): relocation truncated to fit: R_X86_64_PC32 against `construction vtable for std::ostream-in-Rcpp::Rostream<false>'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x227): undefined reference to `std::basic_ios<char, std::char_traits<char> >::init(std::basic_streambuf<char, std::char_traits<char> >*)'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x22e): additional relocation overflows omitted from the output
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x27e): undefined reference to `std::ios_base::~ios_base()'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x286): undefined reference to `_Unwind_Resume'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x2a0): undefined reference to `std::ios_base::~ios_base()'
SAC_spatial.o:SAC_spatial.cpp:(.text.startup+0x2a8): undefined reference to `_Unwind_Resume'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text.startup+0xf): undefined reference to `std::ios_base::Init::Init()'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text.startup+0x33): undefined reference to `std::ios_base::ios_base()'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text.startup+0x94): undefined reference to `operator new(unsigned long long)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text.startup+0xde): undefined reference to `std::locale::locale()'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text.startup+0x113): undefined reference to `std::basic_ios<char, std::char_traits<char> >::init(std::basic_streambuf<char, std::char_traits<char> >*)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text.startup+0x155): undefined reference to `std::ios_base::ios_base()'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text.startup+0x1af): undefined reference to `operator new(unsigned long long)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text.startup+0x1f2): undefined reference to `std::locale::locale()'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text.startup+0x227): undefined reference to `std::basic_ios<char, std::char_traits<char> >::init(std::basic_streambuf<char, std::char_traits<char> >*)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text.startup+0x27e): undefined reference to `std::ios_base::~ios_base()'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text.startup+0x286): undefined reference to `_Unwind_Resume'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text.startup+0x2a0): undefined reference to `std::ios_base::~ios_base()'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text.startup+0x2a8): undefined reference to `_Unwind_Resume'
RcppExports.o:RcppExports.cpp:(.text+0x9e): undefined reference to `std::ios_base::~ios_base()'
RcppExports.o:RcppExports.cpp:(.text+0xa6): undefined reference to `_Unwind_Resume'
RcppExports.o:RcppExports.cpp:(.text+0x12e): undefined reference to `std::ios_base::~ios_base()'
RcppExports.o:RcppExports.cpp:(.text+0x136): undefined reference to `_Unwind_Resume'
RcppExports.o:RcppExports.cpp:(.text+0x14b): undefined reference to `__imp_R_NilValue'
RcppExports.o:RcppExports.cpp:(.text+0x172): undefined reference to `Rf_isNull'
RcppExports.o:RcppExports.cpp:(.text+0x187): undefined reference to `R_PreserveObject'
RcppExports.o:RcppExports.cpp:(.text+0x1a1): undefined reference to `__cxa_guard_acquire'
RcppExports.o:RcppExports.cpp:(.text+0x1d7): undefined reference to `Rf_isNull'
RcppExports.o:RcppExports.cpp:(.text+0x1ec): undefined reference to `R_PreserveObject'
RcppExports.o:RcppExports.cpp:(.text+0x204): undefined reference to `__cxa_guard_acquire'
RcppExports.o:RcppExports.cpp:(.text+0x226): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x24f): undefined reference to `R_GetCCallable'
RcppExports.o:RcppExports.cpp:(.text+0x262): undefined reference to `__cxa_guard_release'
RcppExports.o:RcppExports.cpp:(.text+0x274): undefined reference to `Rf_isNull'
RcppExports.o:RcppExports.cpp:(.text+0x296): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x2b4): undefined reference to `Rf_isNull'
RcppExports.o:RcppExports.cpp:(.text+0x2d2): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x2f3): undefined reference to `R_GetCCallable'
RcppExports.o:RcppExports.cpp:(.text+0x306): undefined reference to `__cxa_guard_release'
RcppExports.o:RcppExports.cpp:(.text+0x31d): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x33d): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x351): undefined reference to `__cxa_guard_abort'
RcppExports.o:RcppExports.cpp:(.text+0x35e): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x371): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x379): undefined reference to `_Unwind_Resume'
RcppExports.o:RcppExports.cpp:(.text+0x38b): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x393): undefined reference to `_Unwind_Resume'
RcppExports.o:RcppExports.cpp:(.text+0x3a2): undefined reference to `__cxa_guard_abort'
RcppExports.o:RcppExports.cpp:(.text+0x3c2): undefined reference to `__imp_R_NilValue'
RcppExports.o:RcppExports.cpp:(.text+0x3e3): undefined reference to `__cxa_guard_acquire'
RcppExports.o:RcppExports.cpp:(.text+0x407): undefined reference to `Rf_isNull'
RcppExports.o:RcppExports.cpp:(.text+0x41c): undefined reference to `R_PreserveObject'
RcppExports.o:RcppExports.cpp:(.text+0x431): undefined reference to `__cxa_guard_acquire'
RcppExports.o:RcppExports.cpp:(.text+0x45b): undefined reference to `Rf_isNull'
RcppExports.o:RcppExports.cpp:(.text+0x470): undefined reference to `R_PreserveObject'
RcppExports.o:RcppExports.cpp:(.text+0x48a): undefined reference to `__cxa_guard_acquire'
RcppExports.o:RcppExports.cpp:(.text+0x4ad): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x4ef): undefined reference to `Rf_isNull'
RcppExports.o:RcppExports.cpp:(.text+0x507): undefined reference to `R_PreserveObject'
RcppExports.o:RcppExports.cpp:(.text+0x519): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x52b): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x53d): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x54f): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x564): undefined reference to `__cxa_guard_acquire'
RcppExports.o:RcppExports.cpp:(.text+0x582): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x5af): undefined reference to `R_GetCCallable'
RcppExports.o:RcppExports.cpp:(.text+0x5c2): undefined reference to `__cxa_guard_release'
RcppExports.o:RcppExports.cpp:(.text+0x5df): undefined reference to `R_GetCCallable'
RcppExports.o:RcppExports.cpp:(.text+0x5f2): undefined reference to `__cxa_guard_release'
RcppExports.o:RcppExports.cpp:(.text+0x60f): undefined reference to `R_GetCCallable'
RcppExports.o:RcppExports.cpp:(.text+0x622): undefined reference to `__cxa_guard_release'
RcppExports.o:RcppExports.cpp:(.text+0x634): undefined reference to `Rf_isNull'
RcppExports.o:RcppExports.cpp:(.text+0x656): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x674): undefined reference to `Rf_isNull'
RcppExports.o:RcppExports.cpp:(.text+0x696): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x6a4): undefined reference to `Rf_isNull'
RcppExports.o:RcppExports.cpp:(.text+0x6c6): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x6ef): undefined reference to `R_GetCCallable'
RcppExports.o:RcppExports.cpp:(.text+0x702): undefined reference to `__cxa_guard_release'
RcppExports.o:RcppExports.cpp:(.text+0x720): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x73d): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x75d): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x774): undefined reference to `__cxa_guard_abort'
RcppExports.o:RcppExports.cpp:(.text+0x783): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x790): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x7a2): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x7c1): undefined reference to `__cxa_begin_catch'
RcppExports.o:RcppExports.cpp:(.text+0x7d1): undefined reference to `Rf_protect'
RcppExports.o:RcppExports.cpp:(.text+0x7d9): undefined reference to `__cxa_end_catch'
RcppExports.o:RcppExports.cpp:(.text+0x7e5): undefined reference to `Rf_install'
RcppExports.o:RcppExports.cpp:(.text+0x7f0): undefined reference to `Rf_lang2'
RcppExports.o:RcppExports.cpp:(.text+0x7f8): undefined reference to `Rf_protect'
RcppExports.o:RcppExports.cpp:(.text+0x7ff): undefined reference to `__imp_R_GlobalEnv'
RcppExports.o:RcppExports.cpp:(.text+0x80a): undefined reference to `Rf_eval'
RcppExports.o:RcppExports.cpp:(.text+0x825): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x843): undefined reference to `__cxa_end_catch'
RcppExports.o:RcppExports.cpp:(.text+0x84b): undefined reference to `_Unwind_Resume'
RcppExports.o:RcppExports.cpp:(.text+0x850): undefined reference to `__cxa_begin_catch'
RcppExports.o:RcppExports.cpp:(.text+0x869): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
RcppExports.o:RcppExports.cpp:(.text+0x879): undefined reference to `Rf_protect'
RcppExports.o:RcppExports.cpp:(.text+0x88f): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
RcppExports.o:RcppExports.cpp:(.text+0x894): undefined reference to `__cxa_end_catch'
RcppExports.o:RcppExports.cpp:(.text+0x89e): undefined reference to `__cxa_begin_catch'
RcppExports.o:RcppExports.cpp:(.text+0x8a3): undefined reference to `__cxa_end_catch'
RcppExports.o:RcppExports.cpp:(.text+0x8a8): undefined reference to `Rf_onintr'
RcppExports.o:RcppExports.cpp:(.text+0x8c3): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
RcppExports.o:RcppExports.cpp:(.text+0x8c8): undefined reference to `__cxa_end_catch'
RcppExports.o:RcppExports.cpp:(.text+0x8d0): undefined reference to `_Unwind_Resume'
RcppExports.o:RcppExports.cpp:(.text+0x92e): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x948): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x957): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x99f): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0x9b3): undefined reference to `__cxa_guard_abort'
RcppExports.o:RcppExports.cpp:(.text+0x9cd): undefined reference to `__cxa_guard_abort'
RcppExports.o:RcppExports.cpp:(.text+0x9ea): undefined reference to `__cxa_guard_abort'
RcppExports.o:RcppExports.cpp:(.text+0xa43): undefined reference to `__imp_R_NilValue'
RcppExports.o:RcppExports.cpp:(.text+0xa67): undefined reference to `__cxa_guard_acquire'
RcppExports.o:RcppExports.cpp:(.text+0xb15): undefined reference to `Rf_isNull'
RcppExports.o:RcppExports.cpp:(.text+0xb2d): undefined reference to `R_PreserveObject'
RcppExports.o:RcppExports.cpp:(.text+0xb3f): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0xb54): undefined reference to `__cxa_guard_acquire'
RcppExports.o:RcppExports.cpp:(.text+0xb6e): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0xbcf): undefined reference to `R_GetCCallable'
RcppExports.o:RcppExports.cpp:(.text+0xbe2): undefined reference to `__cxa_guard_release'
RcppExports.o:RcppExports.cpp:(.text+0xbff): undefined reference to `R_GetCCallable'
RcppExports.o:RcppExports.cpp:(.text+0xc12): undefined reference to `__cxa_guard_release'
RcppExports.o:RcppExports.cpp:(.text+0xc24): undefined reference to `Rf_isNull'
RcppExports.o:RcppExports.cpp:(.text+0xc42): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0xc60): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0xc77): undefined reference to `__cxa_guard_abort'
RcppExports.o:RcppExports.cpp:(.text+0xc84): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0xc9f): undefined reference to `__cxa_begin_catch'
RcppExports.o:RcppExports.cpp:(.text+0xcaf): undefined reference to `Rf_protect'
RcppExports.o:RcppExports.cpp:(.text+0xcb7): undefined reference to `__cxa_end_catch'
RcppExports.o:RcppExports.cpp:(.text+0xcc3): undefined reference to `Rf_install'
RcppExports.o:RcppExports.cpp:(.text+0xcce): undefined reference to `Rf_lang2'
RcppExports.o:RcppExports.cpp:(.text+0xcd6): undefined reference to `Rf_protect'
RcppExports.o:RcppExports.cpp:(.text+0xcdd): undefined reference to `__imp_R_GlobalEnv'
RcppExports.o:RcppExports.cpp:(.text+0xce8): undefined reference to `Rf_eval'
RcppExports.o:RcppExports.cpp:(.text+0xcfd): undefined reference to `__cxa_end_catch'
RcppExports.o:RcppExports.cpp:(.text+0xd05): undefined reference to `_Unwind_Resume'
RcppExports.o:RcppExports.cpp:(.text+0xd0a): undefined reference to `__cxa_begin_catch'
RcppExports.o:RcppExports.cpp:(.text+0xd23): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
RcppExports.o:RcppExports.cpp:(.text+0xd33): undefined reference to `Rf_protect'
RcppExports.o:RcppExports.cpp:(.text+0xd49): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
RcppExports.o:RcppExports.cpp:(.text+0xd4e): undefined reference to `__cxa_end_catch'
RcppExports.o:RcppExports.cpp:(.text+0xd58): undefined reference to `__cxa_begin_catch'
RcppExports.o:RcppExports.cpp:(.text+0xd5d): undefined reference to `__cxa_end_catch'
RcppExports.o:RcppExports.cpp:(.text+0xd62): undefined reference to `Rf_onintr'
RcppExports.o:RcppExports.cpp:(.text+0xd7a): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
RcppExports.o:RcppExports.cpp:(.text+0xd7f): undefined reference to `__cxa_end_catch'
RcppExports.o:RcppExports.cpp:(.text+0xd87): undefined reference to `_Unwind_Resume'
RcppExports.o:RcppExports.cpp:(.text+0xdcd): undefined reference to `R_ReleaseObject'
RcppExports.o:RcppExports.cpp:(.text+0xde9): undefined reference to `__cxa_guard_abort'
RcppExports.o:RcppExports.cpp:(.text+0x18): undefined reference to `std::ios_base::Init::~Init()'
RcppExports.o:RcppExports.cpp:(.text+0x7d): undefined reference to `std::ios_base::~ios_base()'
RcppExports.o:RcppExports.cpp:(.text+0x10d): undefined reference to `std::ios_base::~ios_base()'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x9e): undefined reference to `std::ios_base::~ios_base()'
SAC_spatial.o:SAC_spatial.cpp:(.text+0xa6): undefined reference to `_Unwind_Resume'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x12e): undefined reference to `std::ios_base::~ios_base()'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x136): undefined reference to `_Unwind_Resume'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x16c): undefined reference to `sqrt'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x3e3): undefined reference to `Rf_xlength'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x3ff): undefined reference to `__imp_R_NilValue'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x411): undefined reference to `Rf_allocVector'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x420): undefined reference to `Rf_isNull'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x42f): undefined reference to `__imp_R_NilValue'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x43c): undefined reference to `R_PreserveObject'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x455): undefined reference to `__cxa_guard_acquire'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x483): undefined reference to `__cxa_guard_acquire'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x49f): undefined reference to `Rf_xlength'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x4dc): undefined reference to `operator new[](unsigned long long)'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x87b): undefined reference to `sqrt'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x892): undefined reference to `Rf_isNull'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x89d): undefined reference to `__imp_R_NilValue'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x8ae): undefined reference to `R_ReleaseObject'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x8bd): undefined reference to `__imp_R_NilValue'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x8ce): undefined reference to `R_ReleaseObject'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x8d5): undefined reference to `__imp_R_NilValue'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x8e4): undefined reference to `_Unwind_Resume'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x8f4): undefined reference to `__imp_R_NilValue'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x905): undefined reference to `R_ReleaseObject'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x924): undefined reference to `__imp_R_NilValue'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x935): undefined reference to `R_ReleaseObject'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x93c): undefined reference to `__imp_R_NilValue'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x959): undefined reference to `R_GetCCallable'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x96c): undefined reference to `__cxa_guard_release'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x984): undefined reference to `R_GetCCallable'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x997): undefined reference to `__cxa_guard_release'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x9ab): undefined reference to `__cxa_guard_abort'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x18): undefined reference to `std::ios_base::Init::~Init()'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x7d): undefined reference to `std::ios_base::~ios_base()'
SAC_spatial.o:SAC_spatial.cpp:(.text+0x10d): undefined reference to `std::ios_base::~ios_base()'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x9e): undefined reference to `std::ios_base::~ios_base()'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xa6): undefined reference to `_Unwind_Resume'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x12e): undefined reference to `std::ios_base::~ios_base()'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x136): undefined reference to `_Unwind_Resume'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1a9): undefined reference to `__imp_R_NilValue'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x22d): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x240): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x255): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x272): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x2bc): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x2cf): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x2e4): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x301): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x336): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x341): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x356): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x36b): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x393): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x39e): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x3b3): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x3c8): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x3f6): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x419): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x439): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x444): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x459): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x46e): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x48a): undefined reference to `Rf_xlength'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x4a0): undefined reference to `Rf_rpois'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x4c1): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x4e7): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x51a): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x52f): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x544): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x56a): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x5a4): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x5bb): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x5d0): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x5fd): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x60f): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x61a): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x62f): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x644): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x6a8): undefined reference to `R_finite'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x6c2): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x6cd): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x6e2): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x6f7): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x712): undefined reference to `__imp_R_NaN'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x71f): undefined reference to `Rf_xlength'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x754): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x75d): undefined reference to `R_isnancpp'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x777): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x782): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x797): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x7ac): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x7c7): undefined reference to `__imp_R_NaN'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x7d4): undefined reference to `Rf_xlength'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x7f3): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x808): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x81d): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x83e): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x8c4): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x8e5): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x8f5): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x911): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x91e): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x944): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x957): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x96c): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x993): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x9a3): undefined reference to `Rf_protect'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x9c5): undefined reference to `SET_VECTOR_ELT'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x9d7): undefined reference to `Rf_mkChar'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x9ec): undefined reference to `SET_STRING_ELT'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xa09): undefined reference to `SET_VECTOR_ELT'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xa1e): undefined reference to `Rf_mkChar'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xa36): undefined reference to `SET_STRING_ELT'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xa55): undefined reference to `std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(char const*, std::allocator<char> const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xa62): undefined reference to `Rf_install'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xa75): undefined reference to `Rf_setAttrib'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xa9c): undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xaab): undefined reference to `Rf_unprotect'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xacd): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xaec): undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xb0b): undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xb2d): undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xb4c): undefined reference to `std::string::_Rep::_M_destroy(std::allocator<char> const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xb61): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xb7f): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xb8f): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xba4): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xbb9): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xc37): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xc4a): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xc62): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xc7c): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xc8f): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xca4): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xcb9): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xcc1): undefined reference to `_Unwind_Resume'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xcc9): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xce2): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xcf1): undefined reference to `R_finite'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xd2b): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xd36): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xd4b): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xd60): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xd7c): undefined reference to `Rf_xlength'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xdab): undefined reference to `R_finite'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xde0): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xe00): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xe0b): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xe20): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xe35): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xe51): undefined reference to `Rf_xlength'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xe65): undefined reference to `unif_rand'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xe99): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xebe): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xec9): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xede): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xef3): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xf0f): undefined reference to `Rf_xlength'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xf44): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xf57): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xf65): undefined reference to `R_finite'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xf93): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xfb3): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xfbe): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xfd3): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0xfe8): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1004): undefined reference to `Rf_xlength'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1016): undefined reference to `norm_rand'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x103a): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1062): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1082): undefined reference to `Rf_allocVector'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x108d): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x10a2): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x10b7): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x10d3): undefined reference to `Rf_xlength'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x10e5): undefined reference to `norm_rand'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1104): undefined reference to `__cxa_guard_acquire'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x111f): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1138): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1153): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1164): undefined reference to `R_PreserveObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x117c): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x118f): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x11a7): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x11ba): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x11d2): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x11e5): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x11f2): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x120b): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1223): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1236): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1255): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1262): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x127b): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1288): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x12a1): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x12ae): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x12c7): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x12df): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x12f2): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x130a): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x131d): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1335): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1348): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1360): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1373): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1380): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1399): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x13a6): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x13bf): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x13de): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x13ff): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1412): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x142a): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x143d): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1455): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1468): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1480): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1493): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x14ab): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x14be): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x14dd): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x14fc): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1524): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1543): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x156b): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1583): more undefined references to `R_ReleaseObject' follow
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x15c8): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x15e7): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x15f4): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1618): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x162e): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1664): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1680): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x16a6): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x16cc): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x16f2): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1717): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x173d): more undefined references to `R_ReleaseObject' follow
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x176b): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x179e): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x17c6): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x17ef): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1819): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x183f): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x186e): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1896): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x18ae): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x18c1): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x18da): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x18eb): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1900): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x192c): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1958): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x196f): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1984): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x199c): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x19af): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x19ce): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x19e2): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1a18): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1a2d): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1a47): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1a60): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1a71): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1a85): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1a96): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1ab5): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1b15): undefined reference to `std::string::_Rep::_M_dispose(std::allocator<char> const&)'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1b27): undefined reference to `Rf_unprotect'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1b3c): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1b8c): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1ba4): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1bb7): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1bd4): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1bf6): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1c0b): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1c32): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1c5f): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1c72): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1cb7): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1cfa): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1d25): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1d43): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1d50): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1d65): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1d8c): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1da4): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1db7): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1dd3): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1dea): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1e02): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1e15): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1e2e): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1e42): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1e56): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1e63): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1e78): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1e92): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1ebc): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1ec9): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1ede): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1ef6): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1f09): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1f28): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1f3c): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1f55): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1f75): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1f88): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1f95): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1faa): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1fc8): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1fdc): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x1ff8): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x201f): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x2032): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x203f): undefined reference to `Rf_isNull'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x2058): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x2070): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x2083): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x209b): undefined reference to `R_GetCCallable'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x20ae): undefined reference to `__cxa_guard_release'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x20c2): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x20d6): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x20ed): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x210c): undefined reference to `R_ReleaseObject'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x2120): undefined reference to `__cxa_guard_abort'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x18): undefined reference to `std::ios_base::Init::~Init()'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x7d): undefined reference to `std::ios_base::~ios_base()'
rThomas_rcpp.o:rThomas_rcpp.cpp:(.text+0x10d): undefined reference to `std::ios_base::~ios_base()'
make: *** [MoBspatial.so] Error 1
ERROR: compilation failed for package ‘MoBspatial’
* removing ‘/home/mcglinnd/R/x86_64-pc-linux-gnu-library/3.2/MoBspatial’
Error: Command failed (1)

Reintegrate volkov from sads

Error installing mobsim

Hi Felix - I tried to install mobsim but encountered the following error:

Error: processing vignette 'Biodiversity_Changes.Rmd' failed with diagnostics:
there is no package called 'GUILDS'

When I turned off build_vignettes, it worked fine.

Update vignettes

Remove the dependency of untb in the introductory vignettes!

Simulation of SADs

Question by @dmcglinn: Is it necessary to specify if we are drawing S species from an infinite or truncated to N log-normal? This was relevant when working with the log-series distribution with Harte’s METE where we input the size of the pool and the number of individuals. In other words the normalization of the pdf is across 1 to N and not 1 to infinity.

code for generating function times

nperm = 20
S = c(1e1, 1e2, 1e3)
N = c(1e3, 1e4, 1e5)
times = array(NA, dim = c(length(S), length(N)))
dimnames(times) = list(S, N)

for(i in seq_along(S)) {
    for(j in seq_along(N)) {
        times[i, j] = system.time(replicate(nperm, spec_sample_curve(
            sim_thomas_community(S[i], N[j], 'lnorm'), method='rarefaction')))[1] / nperm
    }
}

The above averages over 20 runs (nperm value) for a given S and N value. Probably its a good idea to test this for a different pattern as well.

Packages missing when running from a default R version

Hey Felix,
Valentin got the code working on my PC today.
The packages "RandomFields" and "SpadeR" (could only be installed with install_github('AnneChao/SpadeR')) where missing. So if John wants to teach with this package, maybe a load & install function should take care of that.
Thanks anyway, it's a great project you have there.

moving the Rshiny to the package (see SSDM example)

Hey @FelixMay and @KatharinaGerstner

I recently saw this R package which was published in MEE: https://github.com/sylvainschmitt/SSDM

The thing I found interesting with regard to mobsim and mobsim_app is that they created a function called gui() which called the shiny app when the SSDM package is loaded. I thought this was a pretty cool implementation and something to think about if you guys decide to develop and update the shiny app further.

Add continuous integration

Hey @FelixMay I just added continuous integration on the mobr repo it was pretty easy. If you'd like I can set this up for this repo as well. See the .travis.yml file: https://github.com/MoBiodiv/mobr/blob/master/.travis.yml
and linked tag on README.md: https://github.com/MoBiodiv/mobr/blob/master/README.md

need to run spell check on package

I just pushed a very minor commit 46bdd88 that removed a special character so that the function spelling::spell_check_package() would run. This package can be found here: https://github.com/ropensci/spelling/
There does appear to be some spelling errors.

ToDo MoBspatial development

Need a "Date" field in the DESCRIPTION file

This is minor but needed for citation(mobsim) to not issue warnings.

Require removing prior version of Rcpp

Downloading the latest version of MoBspatial gives me the following error message:

install_github('MoBiodiv/MoBspatial')
Downloading GitHub repo MoBiodiv/MoBspatial@master
from URL https://api.github.com/repos/MoBiodiv/MoBspatial/zipball/master
Installing MoBspatial
Installing 1 package: Rcpp
package ‘Rcpp’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘Rcpp’
[...]
ERROR: dependency 'Rcpp' is not available for package 'MoBspatial'
[...]

I remember installing 'Rcpp' is not the easiest task. So what about skipping if not yet installed and creating a warning.

Methods to specify species covariance

Currently the package distributes species independently of one another. I think it would be very cool if the user could specify if species are on average positively or negative associated with one another (i.e., specify the degree and directly of interspecific species associations). Basically I'm thinking about like a correlation parameter that would bias the location of the parent points in the clustering algorithm. @FelixMay @jmchase do you think something like this would be cool. I started thinking about this because mobr really ignores covariance patterns for the most part (some of it is captured in the metrics because intra- and inter-specific clustering influence one another) and in our framework they seem to represent a missing piece of information on community structure.

Bug in sample_quadrats

There seems to be a bug when in sample_quadrats the quadrat_area = 1.

need to remove mobsim.Rproj

Once I deleted this file I was able to open the repo as a project in Rstudio but it seems that this file was blocking me from doing that otherwise.

example for sim_poisson_community does not work

In the example the code is sim_poisson_community(S = 20, N = 500, cv = 1) but since variable names changed it should be sim_poisson_community(s_pool = 20, n_sim = 500, cv_abund = 1)

preparing for publication

Hey @FelixMay it is probably a good idea to create a software release in github once the manuscript is accepted so there is a clear time-stamped version of the repo showing the version of the code at time of publication. This is easy to do just click releases at the project home page and create a new one.

Trouble with install on Windows

I'm having a different problem than in #2 on my Windows machine. It appears that the .dll file is causing some trouble - I don't think you typically include pre-compiled files in packages so I guess not knowing any of the details I would suggest dropping the file MoBspatial.dll from the package. But again I'm really not sure.

 R.version
               _                           
platform       x86_64-w64-mingw32          
arch           x86_64                      
os             mingw32                     
system         x86_64, mingw32             
status                                     
major          3                           
minor          3.1                         
year           2016                        
month          06                          
day            21                          
svn rev        70800                       
language       R                           
version.string R version 3.3.1 (2016-06-21)
nickname       Bug in Your Hair         

install_github('MoBiodiv/MoBspatial')
Downloading GitHub repo MoBiodiv/MoBspatial@master
from URL https://api.github.com/repos/MoBiodiv/MoBspatial/zipball/master
Installing MoBspatial
"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" --no-site-file  \
  --no-environ --no-save --no-restore --quiet CMD  \
  INSTALL  \
  "C:/Users/Daniel/AppData/Local/Temp/RtmpCmydMy/devtools172c22b255bc/MoBiodiv-MoBspatial-4bd41e1"  \
  --library="C:/Users/Daniel/Documents/R/win-library/3.3"  \
  --install-tests 

* installing *source* package 'MoBspatial' ...
** libs

*** arch - i386
make: Nothing to be done for `all'.
installing to C:/Users/Daniel/Documents/R/win-library/3.3/MoBspatial/libs/i386

*** arch - x64
make: Nothing to be done for `all'.
installing to C:/Users/Daniel/Documents/R/win-library/3.3/MoBspatial/libs/x64
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
*** arch - i386
Error in inDL(x, as.logical(local), as.logical(now), ...) : 
  unable to load shared object 'C:/Users/Daniel/Documents/R/win-library/3.3/MoBspatial/libs/i386/MoBspatial.dll':
  LoadLibrary failure:  %1 is not a valid Win32 application.

Error: loading failed
Execution halted
*** arch - x64
ERROR: loading failed for 'i386'
* removing 'C:/Users/Daniel/Documents/R/win-library/3.3/MoBspatial'
Error: Command failed (1)

test files missing

it seems that the files ./tests/testthat/test_patterns.R and ./test/testthat/test_sampling.R are empty files still. We should replace these with actual test cases.