Running 'testthat.R' [305s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > ################################################################################
  > # Use testthat to test that nothing important breaks
  > ################################################################################
  > 
  > library(testthat)
  > library(breakaway)
  > library(phyloseq)
  > library(magrittr)
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > 
  > test_check("breakaway")
  $estimate
  [1] 2319
  
  $error
  [1] 0
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Plug-in"
  
  $interval
  [1] 2319 2319
  
  $interval_type
  [1] NA
  
  $type
  [1] NA
  
  $model
  [1] "none"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] FALSE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 2319
  
  $seest
  [1] 0
  
  $ci
  [1] 2319 2319
  
  $estimate
  [1] 1000
  
  $error
  [1] 0
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Plug-in"
  
  $interval
  [1] 1000 1000
  
  $interval_type
  [1] NA
  
  $type
  [1] NA
  
  $model
  [1] "none"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] FALSE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 1000
  
  $seest
  [1] 0
  
  $ci
  [1] 1000 1000
  
  $estimate
  [1] 331
  
  $error
  [1] 0
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Plug-in"
  
  $interval
  [1] 331 331
  
  $interval_type
  [1] NA
  
  $type
  [1] NA
  
  $model
  [1] "none"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] FALSE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 331
  
  $seest
  [1] 0
  
  $ci
  [1] 331 331
  
  $estimate
  [1] 356
  
  $error
  [1] 0
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Plug-in"
  
  $interval
  [1] 356 356
  
  $interval_type
  [1] NA
  
  $type
  [1] NA
  
  $model
  [1] "none"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] FALSE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 356
  
  $seest
  [1] 0
  
  $ci
  [1] 356 356
  
  $estimate
  [1] 349
  
  $error
  [1] 0
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Plug-in"
  
  $interval
  [1] 349 349
  
  $interval_type
  [1] NA
  
  $type
  [1] NA
  
  $model
  [1] "none"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] FALSE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 349
  
  $seest
  [1] 0
  
  $ci
  [1] 349 349
  
  $estimate
  [1] 367
  
  $error
  [1] 0
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Plug-in"
  
  $interval
  [1] 367 367
  
  $interval_type
  [1] NA
  
  $type
  [1] NA
  
  $model
  [1] "none"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] FALSE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 367
  
  $seest
  [1] 0
  
  $ci
  [1] 367 367
  
  $estimate
  [1] 306
  
  $error
  [1] 0
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Plug-in"
  
  $interval
  [1] 306 306
  
  $interval_type
  [1] NA
  
  $type
  [1] NA
  
  $model
  [1] "none"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] FALSE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 306
  
  $seest
  [1] 0
  
  $ci
  [1] 306 306
  
  $estimate
  [1] 3181.5
  
  $error
  [1] 88.71478
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1"
  
  $interval
  [1]  2362.714 19336.617
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 3181.5
  
  $seest
  [1] 88.71478
  
  $ci
  [1]  2362.714 19336.617
  
  $estimate
  [1] 1241.286
  
  $error
  [1] 38.05458
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1"
  
  $interval
  [1] 1015.669 4715.556
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 1241.286
  
  $seest
  [1] 38.05458
  
  $ci
  [1] 1015.669 4715.556
  
  $estimate
  [1] 371.3333
  
  $error
  [1] 16.00014
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1"
  
  $interval
  [1] 333.5326 973.3283
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 371.3333
  
  $seest
  [1] 16.00014
  
  $ci
  [1] 333.5326 973.3283
  
  $estimate
  [1] 367.7647
  
  $error
  [1] 6.898408
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1"
  
  $interval
  [1] 356.9721 498.3858
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 367.7647
  
  $seest
  [1] 6.898408
  
  $ci
  [1] 356.9721 498.3858
  
  $estimate
  [1] 370.875
  
  $error
  [1] 9.677414
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1"
  
  $interval
  [1] 350.7452 623.1820
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 370.875
  
  $seest
  [1] 9.677414
  
  $ci
  [1] 350.7452 623.1820
  
  $estimate
  [1] 381.0192
  
  $error
  [1] 7.120062
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1"
  
  $interval
  [1] 368.2416 525.2956
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 381.0192
  
  $seest
  [1] 7.120062
  
  $ci
  [1] 368.2416 525.2956
  
  $estimate
  [1] 362.9412
  
  $error
  [1] 23.28989
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1"
  
  $interval
  [1]  308.8149 1457.8195
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 362.9412
  
  $seest
  [1] 23.28989
  
  $ci
  [1]  308.8149 1457.8195
  
  $estimate
  [1] 3177.141
  
  $error
  [1] 88.21714
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1]  2362.649 19189.923
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 3177.141
  
  $seest
  [1] 88.21714
  
  $ci
  [1]  2362.649 19189.923
  
  $estimate
  [1] 1238.912
  
  $error
  [1] 37.69171
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1] 1015.602 4658.503
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 1238.912
  
  $seest
  [1] 37.69171
  
  $ci
  [1] 1015.602 4658.503
  
  $estimate
  [1] 368.84
  
  $error
  [1] 15.03456
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1] 333.4643 912.0415
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 368.84
  
  $seest
  [1] 15.03456
  
  $ci
  [1] 333.4643 912.0415
  
  $estimate
  [1] 366.5556
  
  $error
  [1] 6.314576
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1] 356.9099 478.4579
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 366.5556
  
  $seest
  [1] 6.314576
  
  $ci
  [1] 356.9099 478.4579
  
  $estimate
  [1] 369.5172
  
  $error
  [1] 9.168819
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1] 350.6818 599.2976
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 369.5172
  
  $seest
  [1] 9.168819
  
  $ci
  [1] 350.6818 599.2976
  
  $estimate
  [1] 380
  
  $error
  [1] 6.710938
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1] 368.1824 509.9289
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 380
  
  $seest
  [1] 6.710938
  
  $ci
  [1] 368.1824 509.9289
  
  $estimate
  [1] 358.5556
  
  $error
  [1] 21.31788
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1]  308.7484 1310.9893
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 358.5556
  
  $seest
  [1] 21.31788
  
  $ci
  [1]  308.7484 1310.9893
  
  $estimate
  [1] 4152.555
  
  $error
  [1] 291.5206
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Chao-Bunge"
  
  $interval
  [1]  2358.034 88446.264
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  NULL
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] TRUE
  
  $other
  $other$cutoff
  [1] 10
  
  
  $est
  [1] 4152.555
  
  $seest
  [1] 291.5206
  
  $ci
  [1]  2358.034 88446.264
  
  $estimate
  [1] 1376.942
  
  $error
  [1] 64.43054
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Chao-Bunge"
  
  $interval
  [1] 1017.146 9286.904
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  NULL
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] TRUE
  
  $other
  $other$cutoff
  [1] 10
  
  
  $est
  [1] 1376.942
  
  $seest
  [1] 64.43054
  
  $ci
  [1] 1017.146 9286.904
  
  $estimate
  [1] 399.445
  
  $error
  [1] 32.91482
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Chao-Bunge"
  
  $interval
  [1]  333.5417 2174.1395
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  NULL
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] TRUE
  
  $other
  $other$cutoff
  [1] 10
  
  
  $est
  [1] 399.445
  
  $seest
  [1] 32.91482
  
  $ci
  [1]  333.5417 2174.1395
  
  $estimate
  [1] 366.037
  
  $error
  [1] 10.48092
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Chao-Bunge"
  
  $interval
  [1] 356.4582 575.8740
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  NULL
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] TRUE
  
  $other
  $other$cutoff
  [1] 10
  
  
  $est
  [1] 366.037
  
  $seest
  [1] 10.48092
  
  $ci
  [1] 356.4582 575.8740
  
  $estimate
  [1] 378.7363
  
  $error
  [1] 15.09051
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Chao-Bunge"
  
  $interval
  [1] 350.6699 878.5170
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  NULL
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] TRUE
  
  $other
  $other$cutoff
  [1] 10
  
  
  $est
  [1] 378.7363
  
  $seest
  [1] 15.09051
  
  $ci
  [1] 350.6699 878.5170
  
  $estimate
  [1] 384.8917
  
  $error
  [1] 12.15087
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Chao-Bunge"
  
  $interval
  [1] 367.9616 699.9053
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  NULL
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] TRUE
  
  $other
  $other$cutoff
  [1] 10
  
  
  $est
  [1] 384.8917
  
  $seest
  [1] 12.15087
  
  $ci
  [1] 367.9616 699.9053
  
  $estimate
  [1] 337.8483
  
  $error
  [1] 14.91761
  
  $estimand
  [1] "richness"
  
  $name
  [1] "Chao-Bunge"
  
  $interval
  [1] 307.8883 843.1520
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  NULL
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] TRUE
  
  $other
  $other$cutoff
  [1] 10
  
  
  $est
  [1] 337.8483
  
  $seest
  [1] 14.91761
  
  $ci
  [1] 307.8883 843.1520
  
  $estimate
  [1] 2691.593
  
  $error
  [1] 50.23337
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_transformed"
  
  $interval
  [1] 2341.506 8487.342
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
                Estimate  Std. Error
  (Intercept) 0.61620601 0.120062903
  xs          0.08651219 0.007555332
  
  $other$full
  
  Call:
  lm(formula = log(ys) ~ xs, weights = weights_trans)
  
  Coefficients:
  (Intercept)           xs  
      0.61621      0.08651  
  
  
  $other$cutoff
  [1] 63
  
  
  $est
  [1] 2691.593
  
  $seest
  [1] 50.23337
  
  $ci
  [1] 2341.506 8487.342
  
  $estimate
  [1] 1178.603
  
  $error
  [1] 28.17513
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_transformed"
  
  $interval
  [1] 1013.925 3290.816
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
               Estimate Std. Error
  (Intercept) 0.4388526 0.12855085
  xs          0.1382131 0.01625013
  
  $other$full
  
  Call:
  lm(formula = log(ys) ~ xs, weights = weights_trans)
  
  Coefficients:
  (Intercept)           xs  
       0.4389       0.1382  
  
  
  $other$cutoff
  [1] 33
  
  
  $est
  [1] 1178.603
  
  $seest
  [1] 28.17513
  
  $ci
  [1] 1013.925 3290.816
  
  $estimate
  [1] 358.6254
  
  $error
  [1] 9.335348
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_transformed"
  
  $interval
  [1] 333.6635 617.5239
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
               Estimate Std. Error
  (Intercept) 0.4654530 0.24094924
  xs          0.1351371 0.02153069
  
  $other$full
  
  Call:
  lm(formula = log(ys) ~ xs, weights = weights_trans)
  
  Coefficients:
  (Intercept)           xs  
       0.4655       0.1351  
  
  
  $other$cutoff
  [1] 28
  
  
  $est
  [1] 358.6254
  
  $seest
  [1] 9.335348
  
  $ci
  [1] 333.6635 617.5239
  
  $estimate
  [1] 363.7108
  
  $error
  [1] 3.55656
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_transformed"
  
  $interval
  [1] 357.1177 409.1938
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
               Estimate Std. Error
  (Intercept) 0.9531054  0.1892241
  xs          0.1134064  0.0170140
  
  $other$full
  
  Call:
  lm(formula = log(ys) ~ xs, weights = weights_trans)
  
  Coefficients:
  (Intercept)           xs  
       0.9531       0.1134  
  
  
  $other$cutoff
  [1] 26
  
  
  $est
  [1] 363.7108
  
  $seest
  [1] 3.55656
  
  $ci
  [1] 357.1177 409.1938
  
  $estimate
  [1] 363.2128
  
  $error
  [1] 5.061292
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_transformed"
  
  $interval
  [1] 350.9435 452.9358
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
                Estimate Std. Error
  (Intercept) 0.90120646  0.1750310
  xs          0.09149412  0.0103463
  
  $other$full
  
  Call:
  lm(formula = log(ys) ~ xs, weights = weights_trans)
  
  Coefficients:
  (Intercept)           xs  
      0.90121      0.09149  
  
  
  $other$cutoff
  [1] 41
  
  
  $est
  [1] 363.2128
  
  $seest
  [1] 5.061292
  
  $ci
  [1] 350.9435 452.9358
  
  $estimate
  [1] 377.768
  
  $error
  [1] 4.203355
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_transformed"
  
  $interval
  [1] 368.5607 441.2943
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
               Estimate Std. Error
  (Intercept) 0.9192573 0.15849327
  xs          0.1014363 0.01178144
  
  $other$full
  
  Call:
  lm(formula = log(ys) ~ xs, weights = weights_trans)
  
  Coefficients:
  (Intercept)           xs  
       0.9193       0.1014  
  
  
  $other$cutoff
  [1] 34
  
  
  $est
  [1] 377.768
  
  $seest
  [1] 4.203355
  
  $ci
  [1] 368.5607 441.2943
  
  $estimate
  [1] 326.1506
  
  $error
  [1] 6.568058
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_transformed"
  
  $interval
  [1] 308.4754 470.0321
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
               Estimate Std. Error
  (Intercept) 0.7809542 0.19223603
  xs          0.1137681 0.01622871
  
  $other$full
  
  Call:
  lm(formula = log(ys) ~ xs, weights = weights_trans)
  
  Coefficients:
  (Intercept)           xs  
       0.7810       0.1138  
  
  
  $other$cutoff
  [1] 31
  
  
  $est
  [1] 326.1506
  
  $seest
  [1] 6.568058
  
  $ci
  [1] 308.4754 470.0321
  
  $estimate
  [1] 17172.71
  
  $error
  [1] 25406.72
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_untransformed"
  
  $interval
  [1]    2343.552 8988555.243
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
                Estimate Std. Error
  (Intercept) 0.04645303 0.07944223
  xs          0.79539264 0.04466347
  
  $other$full
  
  Call:
  lm(formula = ys ~ xs, weights = weights_untrans)
  
  Coefficients:
  (Intercept)           xs  
      0.04645      0.79539  
  
  
  $other$cutoff
  [1] 63
  
  
  $est
  [1] 17172.71
  
  $seest
  [1] 25406.72
  
  $ci
  [1]    2343.552 8988555.243
  
  $estimate
  [1] 1329.659
  
  $error
  [1] 77.00265
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_untransformed"
  
  $interval
  [1]  1011.418 10517.510
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
               Estimate Std. Error
  (Intercept) 0.8402622 0.18726617
  xs          0.4302112 0.07963557
  
  $other$full
  
  Call:
  lm(formula = ys ~ xs, weights = weights_untrans)
  
  Coefficients:
  (Intercept)           xs  
       0.8403       0.4302  
  
  
  $other$cutoff
  [1] 33
  
  
  $est
  [1] 1329.659
  
  $seest
  [1] 77.00265
  
  $ci
  [1]  1011.418 10517.510
  
  $estimate
  [1] 454.3961
  
  $error
  [1] 90.41193
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_untransformed"
  
  $interval
  [1]  333.2136 7209.7238
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
               Estimate Std. Error
  (Intercept) 0.3565752  0.2549538
  xs          0.4224995  0.1016797
  
  $other$full
  
  Call:
  lm(formula = ys ~ xs, weights = weights_untrans)
  
  Coefficients:
  (Intercept)           xs  
       0.3566       0.4225  
  
  
  $other$cutoff
  [1] 28
  
  
  $est
  [1] 454.3961
  
  $seest
  [1] 90.41193
  
  $ci
  [1]  333.2136 7209.7238
  
  $estimate
  [1] 370.9951
  
  $error
  [1] 7.278956
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_untransformed"
  
  $interval
  [1] 357.3472 522.8973
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
               Estimate Std. Error
  (Intercept) 1.3337724  0.4705246
  xs          0.5083045  0.1057248
  
  $other$full
  
  Call:
  lm(formula = ys ~ xs, weights = weights_untrans)
  
  Coefficients:
  (Intercept)           xs  
       1.3338       0.5083  
  
  
  $other$cutoff
  [1] 26
  
  
  $est
  [1] 370.9951
  
  $seest
  [1] 7.278956
  
  $ci
  [1] 357.3472 522.8973
  
  $estimate
  [1] 377.421
  
  $error
  [1] 10.02023
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_untransformed"
  
  $interval
  [1] 351.5538 665.2963
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
               Estimate Std. Error
  (Intercept) 1.2314857 0.31651827
  xs          0.3904014 0.07329653
  
  $other$full
  
  Call:
  lm(formula = ys ~ xs, weights = weights_untrans)
  
  Coefficients:
  (Intercept)           xs  
       1.2315       0.3904  
  
  
  $other$cutoff
  [1] 41
  
  
  $est
  [1] 377.421
  
  $seest
  [1] 10.02023
  
  $ci
  [1] 351.5538 665.2963
  
  $estimate
  [1] 385.6043
  
  $error
  [1] 7.22905
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_untransformed"
  
  $interval
  [1] 368.9285 546.4727
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
               Estimate Std. Error
  (Intercept) 1.4512764 0.37146900
  xs          0.4437526 0.08545767
  
  $other$full
  
  Call:
  lm(formula = ys ~ xs, weights = weights_untrans)
  
  Coefficients:
  (Intercept)           xs  
       1.4513       0.4438  
  
  
  $other$cutoff
  [1] 34
  
  
  $est
  [1] 385.6043
  
  $seest
  [1] 7.22905
  
  $ci
  [1] 368.9285 546.4727
  
  $estimate
  [1] 450.7536
  
  $error
  [1] 109.5887
  
  $estimand
  [1] "richness"
  
  $name
  [1] "wlrm_untransformed"
  
  $interval
  [1]  308.3385 9266.2155
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Negative Binomial"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$para
               Estimate Std. Error
  (Intercept) 0.3039649 0.22522282
  xs          0.6353653 0.08851121
  
  $other$full
  
  Call:
  lm(formula = ys ~ xs, weights = weights_untrans)
  
  Coefficients:
  (Intercept)           xs  
       0.3040       0.6354  
  
  
  $other$cutoff
  [1] 31
  
  
  $est
  [1] 450.7536
  
  $seest
  [1] 109.5887
  
  $ci
  [1]  308.3385 9266.2155
  
  $estimate
  [1] 3177.141
  
  $error
  [1] 88.21714
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1]  2362.649 19189.923
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 3177.141
  
  $seest
  [1] 88.21714
  
  $ci
  [1]  2362.649 19189.923
  
  $estimate
  [1] 1238.912
  
  $error
  [1] 37.69171
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1] 1015.602 4658.503
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 1238.912
  
  $seest
  [1] 37.69171
  
  $ci
  [1] 1015.602 4658.503
  
  $estimate
  [1] 368.84
  
  $error
  [1] 15.03456
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1] 333.4643 912.0415
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 368.84
  
  $seest
  [1] 15.03456
  
  $ci
  [1] 333.4643 912.0415
  
  $estimate
  [1] 366.5556
  
  $error
  [1] 6.314576
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1] 356.9099 478.4579
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 366.5556
  
  $seest
  [1] 6.314576
  
  $ci
  [1] 356.9099 478.4579
  
  $estimate
  [1] 369.5172
  
  $error
  [1] 9.168819
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1] 350.6818 599.2976
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 369.5172
  
  $seest
  [1] 9.168819
  
  $ci
  [1] 350.6818 599.2976
  
  $estimate
  [1] 380
  
  $error
  [1] 6.710938
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1] 368.1824 509.9289
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 380
  
  $seest
  [1] 6.710938
  
  $ci
  [1] 368.1824 509.9289
  
  $estimate
  [1] 358.5556
  
  $error
  [1] 21.31788
  
  $estimand
  [1] "richness"
  
  $name
  [1] "chao1_bc"
  
  $interval
  [1]  308.7484 1310.9893
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson (homogeneous)"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  NULL
  
  $est
  [1] 358.5556
  
  $seest
  [1] 21.31788
  
  $ci
  [1]  308.7484 1310.9893
  
  $estimate
  [1] 3099.945
  
  $error
  [1] 2944.04
  
  $estimand
  [1] "richness"
  
  $name
  [1] "breakaway_nof1"
  
  $interval
       beta0      beta0 
    1631.675 363345.520 
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  NULL
  
  $model
  [1] "Kemp"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] TRUE
  
  $other
  $other$xbar
  [1] 31.5
  
  $other$code
  [1] 1
  
  $other$the_function
  [1] "f_{x+1}/f_{x} ~ (beta0+beta1*(x-xbar))/(1+alpha1*(x-xbar))"
  
  $other$name
  [1] "model_1_1"
  
  
  $est
  [1] 3099.945
  
  $seest
  [1] 2944.04
  
  $ci
       beta0      beta0 
    1631.675 363345.520 
  
  $para
         Coef estimates Coef std errors
  beta0      1.20274114      0.15475350
  beta1      0.03355936      0.01238761
  alpha1     0.02241446      0.01614515
  
  $full
  Nonlinear regression model
    model: y ~ structure_1_1(x, beta0, beta1, alpha1)
     data: lhs
    beta0   beta1  alpha1 
  1.20274 0.03356 0.02241 
   weighted residual sum-of-squares: 2.155
  
  Number of iterations to convergence: 5 
  Achieved convergence tolerance: 3.274e-06
  
  $estimate
  [1] 1500.401
  
  $error
  [1] 1341.351
  
  $estimand
  [1] "richness"
  
  $name
  [1] "breakaway_nof1"
  
  $interval
        beta0       beta0 
     724.8861 139032.6457 
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  NULL
  
  $model
  [1] "Kemp"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] TRUE
  
  $other
  $other$xbar
  [1] 16.5
  
  $other$code
  [1] 1
  
  $other$the_function
  [1] "f_{x+1}/f_{x} ~ (beta0+beta1*(x-xbar))/(1+alpha1*(x-xbar))"
  
  $other$name
  [1] "model_1_1"
  
  
  $est
  [1] 1500.401
  
  $seest
  [1] 1341.351
  
  $ci
        beta0       beta0 
     724.8861 139032.6457 
  
  $para
         Coef estimates Coef std errors
  beta0      1.20078845      0.18102489
  beta1      0.05614293      0.04800126
  alpha1     0.02874888      0.05381204
  
  $full
  Nonlinear regression model
    model: y ~ structure_1_1(x, beta0, beta1, alpha1)
     data: lhs
    beta0   beta1  alpha1 
  1.20079 0.05614 0.02875 
   weighted residual sum-of-squares: 1.274
  
  Number of iterations to convergence: 25 
  Achieved convergence tolerance: 8.431e-06
  
  $estimate
  [1] 131.0542
  
  $error
  [1] 0.06962563
  
  $estimand
  [1] "richness"
  
  $name
  [1] "PoissonModel"
  
  $interval
  [1] 131.0306 131.0962
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson"
  
  $warnings
  [1] "no kemp models converged"
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$outcome
  [1] 0
  
  $other$code
  [1] 1
  
  
  $est
  [1] 131.0542
  
  $seest
  [1] 0.06962563
  
  $ci
  [1] 131.0306 131.0962
  
  $estimate
  [1] 181.0752
  
  $error
  [1] 0.08198957
  
  $estimand
  [1] "richness"
  
  $name
  [1] "PoissonModel"
  
  $interval
  [1] 181.0424 181.1335
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson"
  
  $warnings
  [1] "no kemp models converged"
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$outcome
  [1] 0
  
  $other$code
  [1] 1
  
  
  $est
  [1] 181.0752
  
  $seest
  [1] 0.08198957
  
  $ci
  [1] 181.0424 181.1335
  
  $estimate
  [1] 226.0025
  
  $error
  [1] 0.01296301
  
  $estimand
  [1] "richness"
  
  $name
  [1] "PoissonModel"
  
  $interval
  [1] 226.0015 226.0042
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  [1] "parametric"
  
  $model
  [1] "Poisson"
  
  $warnings
  [1] "no kemp models converged"
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] FALSE
  
  $other
  $other$outcome
  [1] 0
  
  $other$code
  [1] 1
  
  
  $est
  [1] 226.0025
  
  $seest
  [1] 0.01296301
  
  $ci
  [1] 226.0015 226.0042
  
  $estimate
  [1] 438.3885
  
  $error
  [1] 170.5326
  
  $estimand
  [1] "richness"
  
  $name
  [1] "breakaway_nof1"
  
  $interval
      beta0     beta0 
   340.4654 8249.2646 
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  NULL
  
  $model
  [1] "Kemp"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] TRUE
  
  $other
  $other$xbar
  [1] 17
  
  $other$code
  [1] 1
  
  $other$the_function
  [1] "f_{x+1}/f_{x} ~ (beta0+beta1*(x-xbar))/(1+alpha1*(x-xbar))"
  
  $other$name
  [1] "model_1_1"
  
  
  $est
  [1] 438.3885
  
  $seest
  [1] 170.5326
  
  $ci
      beta0     beta0 
   340.4654 8249.2646 
  
  $para
         Coef estimates Coef std errors
  beta0      1.37045876      0.22197453
  beta1      0.05764483      0.06192103
  alpha1     0.02187070      0.05307755
  
  $full
  Nonlinear regression model
    model: y ~ structure_1_1(x, beta0, beta1, alpha1)
     data: lhs
    beta0   beta1  alpha1 
  1.37046 0.05764 0.02187 
   weighted residual sum-of-squares: 334.7
  
  Number of iterations to convergence: 4 
  Achieved convergence tolerance: 2.52e-06
  
  $estimate
  [1] 293.0844
  
  $error
  [1] 7.454846
  
  $estimand
  [1] "richness"
  
  $name
  [1] "breakaway_nof1"
  
  $interval
     beta0    beta0 
  263.3197 434.2805 
  
  $interval_type
  [1] "Approximate: log-normal"
  
  $type
  NULL
  
  $model
  [1] "Kemp"
  
  $warnings
  NULL
  
  $frequentist
  [1] TRUE
  
  $parametric
  [1] TRUE
  
  $reasonable
  [1] TRUE
  
  $other
  $other$xbar
  [1] 15.5
  
  $other$code
  [1] 1
  
  $other$the_function
  [1] "f_{x+1}/f_{x} ~ (beta0+beta1*(x-xbar))/(1+alpha1*(x-xbar))"
  
  $other$name
  [1] "model_1_1"
  
  
  $est
  [1] 293.0844
  
  $seest
  [1] 7.454846
  
  $ci
     beta0    beta0 
  263.3197 434.2805 
  
  $para
         Coef estimates Coef std errors
  beta0      1.07899737     0.130652854
  beta1     -0.07078637     0.014271665
  alpha1    -0.06774517     0.003805578
  
  $full
  Nonlinear regression model
    model: y ~ structure_1_1(x, beta0, beta1, alpha1)
     data: lhs
     beta0    beta1   alpha1 
   1.07900 -0.07079 -0.06775 
   weighted residual sum-of-squares: 1.312
  
  Number of iterations to convergence: 18 
  Achieved convergence tolerance: 6.196e-06
  
  Estimate of richness from method breakaway:
    Estimate is 1552
   with standard error 304.71
    Confidence interval: (1007, 47805)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 254 ]
  
  == Failed tests ================================================================
  -- Error ('test-q2.R:6'): Canonical QIIME2 Example Datasets Work ---------------
  <SSL_CONNECT_ERROR/GenericCurlError/error/condition>
  Error in `function (type, msg, asError = TRUE) 
  {
      if (!is.character(type)) {
          i = match(type, CURLcodeValues)
          typeName = if (is.na(i)) 
              character()
          else names(CURLcodeValues)[i]
      }
      typeName = gsub("^CURLE_", "", typeName)
      fun = (if (asError) 
          stop
      else warning)
      fun(structure(list(message = msg, call = sys.call()), class = c(typeName, 
          "GenericCurlError", "error", "condition")))
  }(35L, "error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version", 
      TRUE)`: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
  Backtrace:
      x
   1. +-RCurl::getURL("https://raw.githubusercontent.com/paulinetrinh/data/master/otu_table_atacama.txt") at test-q2.R:6:2
   2. | \-RCurl::curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
   3. \-RCurl (local) `<fn>`(...)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 254 ]
  Error: Test failures
  Execution halted