Running 'testthat.R' [168s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ### to also run skip_on_cran() tests, uncomment:
  > Sys.setenv(NOT_CRAN="true")
  > 
  > library(testthat)
  > library(bumblebee)
  Welcome to bumblebee 
   see https://magosil86.github.io/bumblebee/ for examples and documentation
  > 
  > test_check("bumblebee")
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Executing function: prep_p_hat(). 
  
  'data.frame':	2 obs. of  3 variables:
   $ group                 : Factor w/ 2 levels "control","intervention": 2 1
   $ individuals_sampled   : num  2281 1551
   $ individuals_population: num  14263 13183
  'data.frame':	4 obs. of  2 variables:
   $ H1_group: chr  "control" "control" "intervention" "intervention"
   $ H2_group: chr  "control" "intervention" "control" "intervention"
  
  str(df_group_permutations): 
  
   Named chr [1:2] "control" "control"
   - attr(*, "names")= chr [1:2] "H1_group" "H2_group"
  str(df_number_hosts_per_group): 
  
  'data.frame':	2 obs. of  3 variables:
   $ group                 : Factor w/ 2 levels "control","intervention": 2 1
   $ individuals_sampled   : num  2281 1551
   $ individuals_population: num  14263 13183
  
  Number of hosts in group 1: control
  
  [1] 1551
  
  Number of hosts in group 2: control
  
  [1] 1551
  Max distinct possible linked pairs in sample for current group pairing i.e. individuals_sampled_group_1 * individuals_sampled_group_2: 
  
  [1] 1202025
  
  Estimated number of individuals in population group 1: 
  
  [1] 13182.92
  
  Estimated number of individuals in population group 2: 
  
  [1] 13182.92
  Max distinct possible linked pairs in population for current group pairing i.e. individuals_population_group_1 * individuals_population_group_2: 
  
  [1] 86888118
  
  str(df_group_permutations): 
  
   Named chr [1:2] "control" "intervention"
   - attr(*, "names")= chr [1:2] "H1_group" "H2_group"
  str(df_number_hosts_per_group): 
  
  'data.frame':	2 obs. of  3 variables:
   $ group                 : Factor w/ 2 levels "control","intervention": 2 1
   $ individuals_sampled   : num  2281 1551
   $ individuals_population: num  14263 13183
  
  Number of hosts in group 1: control
  
  [1] 1551
  
  Number of hosts in group 2: intervention
  
  [1] 2281
  Max distinct possible linked pairs in sample for current group pairing i.e. individuals_sampled_group_1 * individuals_sampled_group_2: 
  
  [1] 3537831
  
  Estimated number of individuals in population group 1: 
  
  [1] 13182.92
  
  Estimated number of individuals in population group 2: 
  
  [1] 14263.39
  Max distinct possible linked pairs in population for current group pairing i.e. individuals_population_group_1 * individuals_population_group_2: 
  
  [1] 188033179
  
  str(df_group_permutations): 
  
   Named chr [1:2] "intervention" "control"
   - attr(*, "names")= chr [1:2] "H1_group" "H2_group"
  str(df_number_hosts_per_group): 
  
  'data.frame':	2 obs. of  3 variables:
   $ group                 : Factor w/ 2 levels "control","intervention": 2 1
   $ individuals_sampled   : num  2281 1551
   $ individuals_population: num  14263 13183
  
  Number of hosts in group 1: intervention
  
  [1] 2281
  
  Number of hosts in group 2: control
  
  [1] 1551
  Max distinct possible linked pairs in sample for current group pairing i.e. individuals_sampled_group_1 * individuals_sampled_group_2: 
  
  [1] 3537831
  
  Estimated number of individuals in population group 1: 
  
  [1] 14263.39
  
  Estimated number of individuals in population group 2: 
  
  [1] 13182.92
  Max distinct possible linked pairs in population for current group pairing i.e. individuals_population_group_1 * individuals_population_group_2: 
  
  [1] 188033179
  
  str(df_group_permutations): 
  
   Named chr [1:2] "intervention" "intervention"
   - attr(*, "names")= chr [1:2] "H1_group" "H2_group"
  str(df_number_hosts_per_group): 
  
  'data.frame':	2 obs. of  3 variables:
   $ group                 : Factor w/ 2 levels "control","intervention": 2 1
   $ individuals_sampled   : num  2281 1551
   $ individuals_population: num  14263 13183
  
  Number of hosts in group 1: intervention
  
  [1] 2281
  
  Number of hosts in group 2: intervention
  
  [1] 2281
  Max distinct possible linked pairs in sample for current group pairing i.e. individuals_sampled_group_1 * individuals_sampled_group_2: 
  
  [1] 2600340
  
  Estimated number of individuals in population group 1: 
  
  [1] 14263.39
  
  Estimated number of individuals in population group 2: 
  
  [1] 14263.39
  Max distinct possible linked pairs in population for current group pairing i.e. individuals_population_group_1 * individuals_population_group_2: 
  
  [1] 101715045
  Executing function: estimate_p_hat(). 
  
  Executing function: estimate_prob_group_pairing_and_linked(). 
  
  'data.frame':	4 obs. of  10 variables:
   $ H1_group                        : chr  "control" "control" "intervention" "intervention"
   $ H2_group                        : chr  "control" "intervention" "control" "intervention"
   $ number_hosts_sampled_group_1    : num  1551 1551 2281 2281
   $ number_hosts_sampled_group_2    : num  1551 2281 1551 2281
   $ number_hosts_population_group_1 : num  13183 13183 14263 14263
   $ number_hosts_population_group_2 : num  13183 14263 13183 14263
   $ max_possible_pairs_in_sample    : num  1202025 3537831 3537831 2600340
   $ max_possible_pairs_in_population: num  8.69e+07 1.88e+08 1.88e+08 1.02e+08
   $ num_linked_pairs_observed       : num  32 13 4 33
   $ p_hat                           : num  2.66e-05 3.67e-06 1.13e-06 1.27e-05
  [1] 27446.31
  Executing function: estimate_theta_hat(). 
  
  Executing function: estimate_c_hat(). 
  
  Executing function: estimate_multinom_ci(). 
  
  [ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
  > 
  > proc.time()
     user  system elapsed 
     1.04    0.25    1.26