R Under development (unstable) (2024-03-19 r86153 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> library(testthat)
> library(o2geosocial)
Registered S3 methods overwritten by 'o2geosocial':
  method                    from       
  plot.outbreaker_chains    outbreaker2
  print.custom_likelihoods  outbreaker2
  print.custom_priors       outbreaker2
  print.outbreaker_chains   outbreaker2
  summary.outbreaker_chains outbreaker2
> 
> test_check("o2geosocial")


 ///// outbreaker custom likelihoods ///

class: custom_likelihoods list
number of items: 5 

/// custom likelihoods set to NULL (default used) //
$reporting
NULL

$timing_infections
NULL

$timing_sampling
NULL

$space
NULL

$age
NULL



 ///// outbreaker custom likelihoods ///

class: custom_likelihoods list
number of items: 5 

/// custom likelihoods //
$reporting
function(data, param, i) cpp_ll_reporting(data, param, i)
<environment: 0x0000023709d6ffb8>

$timing_infections
function(data, param, i) cpp_ll_timing_infections(data, param, i)
<environment: 0x0000023709d6ffb8>

$timing_sampling
function(data, param, i) cpp_ll_timing_sampling(data, param, i)
<environment: 0x0000023709d6ffb8>

$space
function(data, config, param, i) cpp_ll_space(data, config, param, i)
<environment: 0x0000023709d6ffb8>

$age
function(data, param, i) cpp_ll_age(data, param, i)
<environment: 0x0000023709d6ffb8>



 ///// outbreaker results ///

class:  outbreaker_chains data.frame
dimensions 21 rows,  22 columns
ancestries not shown: alpha_2 - alpha_5
infection dates not shown: t_inf_1 - t_inf_5
intermediate generations not shown: kappa_1 - kappa_5

/// head //
  step      post      like      prior   a   b        pi alpha_1
1    1 -32.88389 -33.28774  0.4038415 0.7 0.1 0.9103669      NA
2   50 -39.51264 -38.91464 -0.5980045 0.7 0.1 0.8051902       2
3  100 -34.21771 -35.52312  1.3054073 0.7 0.1 0.9948269       2

...
/// tail //
   step      post      like     prior   a   b        pi alpha_1
19  900 -32.02185 -33.24110 1.2192534 0.7 0.1 0.9853492       5
20  950 -33.65435 -34.66317 1.0088272 0.7 0.1 0.9625783       2
21 1000 -35.73840 -36.49890 0.7604945 0.7 0.1 0.9363814       2


 ///// outbreaker results ///

class:  outbreaker_chains data.frame
dimensions 21 rows,  22 columns
ancestries not shown: alpha_2 - alpha_5
infection dates not shown: t_inf_1 - t_inf_5
intermediate generations not shown: kappa_1 - kappa_5

/// head //
  step      post      like      prior   a   b        pi alpha_1
1    1 -32.88389 -33.28774  0.4038415 0.7 0.1 0.9103669      NA
2   50 -39.51264 -38.91464 -0.5980045 0.7 0.1 0.8051902       2

...
/// tail //
   step      post      like     prior   a   b        pi alpha_1
20  950 -33.65435 -34.66317 1.0088272 0.7 0.1 0.9625783       2
21 1000 -35.73840 -36.49890 0.7604945 0.7 0.1 0.9363814       2


 ///// outbreaker results ///

class:  outbreaker_chains data.frame
dimensions 21 rows,  22 columns
ancestries not shown: alpha_1 - alpha_5
infection dates not shown: t_inf_1 - t_inf_5
intermediate generations not shown: kappa_1 - kappa_5

/// head //
  step      post      like      prior
1    1 -32.88389 -33.28774  0.4038415
2   50 -39.51264 -38.91464 -0.5980045
3  100 -34.21771 -35.52312  1.3054073

...
/// tail //
   step      post      like     prior
19  900 -32.02185 -33.24110 1.2192534
20  950 -33.65435 -34.66317 1.0088272
21 1000 -35.73840 -36.49890 0.7604945


/// head //
  1 2 3 4 5
1 0 0 0 0 1
2 0 0 0 0 1
3 0 0 0 0 1

...
/// tail //
   1 2 3 4 5
19 0 0 0 0 1
20 0 0 0 0 1
21 0 0 0 0 1

 Biggest cluster: 5
 Cluster not shown: 2 to 5 


/// head //
  1 2
1 0 0
2 0 0
3 0 0

...
/// tail //
   1 2
19 0 0
20 0 0
21 0 0


/// head //
  1 2 3 4 5
1 0 0 0 0 1
2 0 0 0 0 1
3 0 0 0 0 1

...
/// tail //
   1 2 3 4 5
19 0 0 0 0 1
20 0 0 0 0 1
21 0 0 0 0 1


 ///// outbreaker custom priors ///

class: custom_priors list
number of items: 3 

/// custom priors set to NULL (default used) //
$pi
NULL

$a
NULL

$b
NULL



 ///// outbreaker custom priors ///

class: custom_priors list
number of items: 3 

/// custom priors //
$pi
function(param){
    return(dnorm(x = param$pi, mean = config$prior_pi[1], sd = config$prior_pi[2], log = T))
  }
<environment: 0x000002370ecb83f8>

$a
function(param){
    return(dnorm(x = param$a, mean = config$prior_a[1], sd = config$prior_a[2], log = T))
  }
<environment: 0x000002370ecb83f8>

$b
function(param){
    return(dnorm(x = param$b, mean = config$prior_b[1], sd = config$prior_b[2], log = T))
  }
<environment: 0x000002370ecb83f8>

[ FAIL 0 | WARN 3031 | SKIP 0 | PASS 197 ]

[ FAIL 0 | WARN 3031 | SKIP 0 | PASS 197 ]
> 
> proc.time()
   user  system elapsed 
  33.50    1.64   35.21