Last updated on 2022-09-15 07:50:46 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2.0 | 37.82 | 310.97 | 348.79 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.2.0 | 28.34 | 229.28 | 257.62 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.2.0 | 429.28 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2.0 | 427.58 | ERROR | |||
| r-devel-windows-x86_64 | 0.2.0 | 53.00 | 301.00 | 354.00 | ERROR | |
| r-patched-linux-x86_64 | 0.2.0 | 33.66 | 289.10 | 322.76 | ERROR | |
| r-release-linux-x86_64 | 0.2.0 | 32.31 | 293.47 | 325.78 | ERROR | |
| r-release-macos-arm64 | 0.2.0 | 149.00 | NOTE | |||
| r-release-macos-x86_64 | 0.2.0 | 295.00 | NOTE | |||
| r-release-windows-x86_64 | 0.2.0 | 49.00 | 298.00 | 347.00 | ERROR | |
| r-oldrel-macos-arm64 | 0.2.0 | 189.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 0.2.0 | 303.00 | NOTE | |||
| r-oldrel-windows-ix86+x86_64 | 0.2.0 | 70.00 | 297.00 | 367.00 | ERROR |
Version: 0.2.0
Check: examples
Result: ERROR
Running examples in 'corncob-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HDIbetabinom
> ### Title: Get highest density interval of beta-binomial
> ### Aliases: HDIbetabinom
>
> ### ** Examples
>
> data(soil_phylum_small)
> mod <- bbdml(formula = OTU.1 ~ DayAmdmt,
+ phi.formula = ~ DayAmdmt,
+ data = soil_phylum_small)
Error in if (detectseparation::detect_separation(y = cbind(W, M - W), :
argument is of length zero
Calls: bbdml
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running 'testthat.R' [16s/20s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(corncob)
>
> test_check("corncob")
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
== Failed tests ================================================================
-- Error (test_bbdml.R:32:1): (code run outside of `test_that()`) --------------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_bbdml.R:32:0
-- Error (test_differentialTest.R:11:1): (code run outside of `test_that()`) ---
Error in `differentialTest(formula = ~Plants + DayAmdmt, phi.formula = ~Plants +
DayAmdmt, formula_null = ~1, phi.formula_null = ~1, data = subsoil,
boot = FALSE, test = "LRT", inits = rbind(rep(0.01, 6)),
inits_null = rbind(rep(0.01, 2)))`: All models failed to converge!
If you are seeing this, it is likely that your model is overspecified. This occurs when your sample size is not large enough to estimate all the parameters of your model. This is most commonly due to categorical variables that include many categories.
Alternatively, double-check your values for the arguments `link`, `phi.link`, and `method` to makes sure that they follow the specified options.
To confirm you have fixed the issue, try running a model for a single taxon with bbdml.
Backtrace:
x
1. \-corncob::differentialTest(...) at test_differentialTest.R:11:0
-- Error (test_getRestrictionTerms.R:12:1): (code run outside of `test_that()`) --
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_getRestrictionTerms.R:12:0
-- Error (test_lrtest.R:19:1): (code run outside of `test_that()`) -------------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_lrtest.R:19:0
-- Error (test_pb.R:14:1): (code run outside of `test_that()`) -----------------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_pb.R:14:0
-- Error (test_s3.R:12:1): (code run outside of `test_that()`) -----------------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_s3.R:12:0
-- Error (test_sandwich.R:12:1): (code run outside of `test_that()`) -----------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_sandwich.R:12:0
-- Error (test_scorehessian.R:12:1): (code run outside of `test_that()`) -------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_scorehessian.R:12:0
-- Error (test_simulate.R:12:1): (code run outside of `test_that()`) -----------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_simulate.R:12:0
-- Error (test_waldtest.R:18:1): (code run outside of `test_that()`) -----------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_waldtest.R:18:0
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [12s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(corncob)
>
> test_check("corncob")
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_bbdml.R:32:1): (code run outside of `test_that()`) ──────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_bbdml.R:32:0
── Error (test_differentialTest.R:11:1): (code run outside of `test_that()`) ───
Error in `differentialTest(formula = ~Plants + DayAmdmt, phi.formula = ~Plants +
DayAmdmt, formula_null = ~1, phi.formula_null = ~1, data = subsoil,
boot = FALSE, test = "LRT", inits = rbind(rep(0.01, 6)),
inits_null = rbind(rep(0.01, 2)))`: All models failed to converge!
If you are seeing this, it is likely that your model is overspecified. This occurs when your sample size is not large enough to estimate all the parameters of your model. This is most commonly due to categorical variables that include many categories.
Alternatively, double-check your values for the arguments `link`, `phi.link`, and `method` to makes sure that they follow the specified options.
To confirm you have fixed the issue, try running a model for a single taxon with bbdml.
Backtrace:
▆
1. └─corncob::differentialTest(...) at test_differentialTest.R:11:0
── Error (test_getRestrictionTerms.R:12:1): (code run outside of `test_that()`) ──
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_getRestrictionTerms.R:12:0
── Error (test_lrtest.R:19:1): (code run outside of `test_that()`) ─────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_lrtest.R:19:0
── Error (test_pb.R:14:1): (code run outside of `test_that()`) ─────────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_pb.R:14:0
── Error (test_s3.R:12:1): (code run outside of `test_that()`) ─────────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_s3.R:12:0
── Error (test_sandwich.R:12:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_sandwich.R:12:0
── Error (test_scorehessian.R:12:1): (code run outside of `test_that()`) ───────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_scorehessian.R:12:0
── Error (test_simulate.R:12:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_simulate.R:12:0
── Error (test_waldtest.R:18:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_waldtest.R:18:0
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.2.0
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘Matrix’ ‘rmutil’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 0.2.0
Check: examples
Result: ERROR
Running examples in ‘corncob-Ex.R’ failed
The error most likely occurred in:
> ### Name: HDIbetabinom
> ### Title: Get highest density interval of beta-binomial
> ### Aliases: HDIbetabinom
>
> ### ** Examples
>
> data(soil_phylum_small)
> mod <- bbdml(formula = OTU.1 ~ DayAmdmt,
+ phi.formula = ~ DayAmdmt,
+ data = soil_phylum_small)
Error in if (detectseparation::detect_separation(y = cbind(W, M - W), :
argument is of length zero
Calls: bbdml
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-ix86+x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/57s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(corncob)
>
> test_check("corncob")
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_bbdml.R:32:1): (code run outside of `test_that()`) ──────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_bbdml.R:32:0
── Error (test_differentialTest.R:11:1): (code run outside of `test_that()`) ───
Error in `differentialTest(formula = ~Plants + DayAmdmt, phi.formula = ~Plants +
DayAmdmt, formula_null = ~1, phi.formula_null = ~1, data = subsoil,
boot = FALSE, test = "LRT", inits = rbind(rep(0.01, 6)),
inits_null = rbind(rep(0.01, 2)))`: All models failed to converge!
If you are seeing this, it is likely that your model is overspecified. This occurs when your sample size is not large enough to estimate all the parameters of your model. This is most commonly due to categorical variables that include many categories.
Alternatively, double-check your values for the arguments `link`, `phi.link`, and `method` to makes sure that they follow the specified options.
To confirm you have fixed the issue, try running a model for a single taxon with bbdml.
Backtrace:
▆
1. └─corncob::differentialTest(...) at test_differentialTest.R:11:0
── Error (test_getRestrictionTerms.R:12:1): (code run outside of `test_that()`) ──
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_getRestrictionTerms.R:12:0
── Error (test_lrtest.R:19:1): (code run outside of `test_that()`) ─────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_lrtest.R:19:0
── Error (test_pb.R:14:1): (code run outside of `test_that()`) ─────────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_pb.R:14:0
── Error (test_s3.R:12:1): (code run outside of `test_that()`) ─────────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_s3.R:12:0
── Error (test_sandwich.R:12:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_sandwich.R:12:0
── Error (test_scorehessian.R:12:1): (code run outside of `test_that()`) ───────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_scorehessian.R:12:0
── Error (test_simulate.R:12:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_simulate.R:12:0
── Error (test_waldtest.R:18:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_waldtest.R:18:0
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [21s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(corncob)
>
> test_check("corncob")
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_bbdml.R:32:1): (code run outside of `test_that()`) ──────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_bbdml.R:32:0
── Error (test_differentialTest.R:11:1): (code run outside of `test_that()`) ───
Error in `differentialTest(formula = ~Plants + DayAmdmt, phi.formula = ~Plants +
DayAmdmt, formula_null = ~1, phi.formula_null = ~1, data = subsoil,
boot = FALSE, test = "LRT", inits = rbind(rep(0.01, 6)),
inits_null = rbind(rep(0.01, 2)))`: All models failed to converge!
If you are seeing this, it is likely that your model is overspecified. This occurs when your sample size is not large enough to estimate all the parameters of your model. This is most commonly due to categorical variables that include many categories.
Alternatively, double-check your values for the arguments `link`, `phi.link`, and `method` to makes sure that they follow the specified options.
To confirm you have fixed the issue, try running a model for a single taxon with bbdml.
Backtrace:
▆
1. └─corncob::differentialTest(...) at test_differentialTest.R:11:0
── Error (test_getRestrictionTerms.R:12:1): (code run outside of `test_that()`) ──
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_getRestrictionTerms.R:12:0
── Error (test_lrtest.R:19:1): (code run outside of `test_that()`) ─────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_lrtest.R:19:0
── Error (test_pb.R:14:1): (code run outside of `test_that()`) ─────────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_pb.R:14:0
── Error (test_s3.R:12:1): (code run outside of `test_that()`) ─────────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_s3.R:12:0
── Error (test_sandwich.R:12:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_sandwich.R:12:0
── Error (test_scorehessian.R:12:1): (code run outside of `test_that()`) ───────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_scorehessian.R:12:0
── Error (test_simulate.R:12:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_simulate.R:12:0
── Error (test_waldtest.R:18:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_waldtest.R:18:0
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.0
Check: tests
Result: ERROR
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(corncob)
>
> test_check("corncob")
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_bbdml.R:32:1): (code run outside of `test_that()`) ──────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_bbdml.R:32:0
── Error (test_differentialTest.R:11:1): (code run outside of `test_that()`) ───
Error in `differentialTest(formula = ~Plants + DayAmdmt, phi.formula = ~Plants +
DayAmdmt, formula_null = ~1, phi.formula_null = ~1, data = subsoil,
boot = FALSE, test = "LRT", inits = rbind(rep(0.01, 6)),
inits_null = rbind(rep(0.01, 2)))`: All models failed to converge!
If you are seeing this, it is likely that your model is overspecified. This occurs when your sample size is not large enough to estimate all the parameters of your model. This is most commonly due to categorical variables that include many categories.
Alternatively, double-check your values for the arguments `link`, `phi.link`, and `method` to makes sure that they follow the specified options.
To confirm you have fixed the issue, try running a model for a single taxon with bbdml.
Backtrace:
▆
1. └─corncob::differentialTest(...) at test_differentialTest.R:11:0
── Error (test_getRestrictionTerms.R:12:1): (code run outside of `test_that()`) ──
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_getRestrictionTerms.R:12:0
── Error (test_lrtest.R:19:1): (code run outside of `test_that()`) ─────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_lrtest.R:19:0
── Error (test_pb.R:14:1): (code run outside of `test_that()`) ─────────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_pb.R:14:0
── Error (test_s3.R:12:1): (code run outside of `test_that()`) ─────────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_s3.R:12:0
── Error (test_sandwich.R:12:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_sandwich.R:12:0
── Error (test_scorehessian.R:12:1): (code run outside of `test_that()`) ───────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_scorehessian.R:12:0
── Error (test_simulate.R:12:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_simulate.R:12:0
── Error (test_waldtest.R:18:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_waldtest.R:18:0
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [16s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(corncob)
>
> test_check("corncob")
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_bbdml.R:32:1): (code run outside of `test_that()`) ──────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_bbdml.R:32:0
── Error (test_differentialTest.R:11:1): (code run outside of `test_that()`) ───
Error in `differentialTest(formula = ~Plants + DayAmdmt, phi.formula = ~Plants +
DayAmdmt, formula_null = ~1, phi.formula_null = ~1, data = subsoil,
boot = FALSE, test = "LRT", inits = rbind(rep(0.01, 6)),
inits_null = rbind(rep(0.01, 2)))`: All models failed to converge!
If you are seeing this, it is likely that your model is overspecified. This occurs when your sample size is not large enough to estimate all the parameters of your model. This is most commonly due to categorical variables that include many categories.
Alternatively, double-check your values for the arguments `link`, `phi.link`, and `method` to makes sure that they follow the specified options.
To confirm you have fixed the issue, try running a model for a single taxon with bbdml.
Backtrace:
▆
1. └─corncob::differentialTest(...) at test_differentialTest.R:11:0
── Error (test_getRestrictionTerms.R:12:1): (code run outside of `test_that()`) ──
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_getRestrictionTerms.R:12:0
── Error (test_lrtest.R:19:1): (code run outside of `test_that()`) ─────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_lrtest.R:19:0
── Error (test_pb.R:14:1): (code run outside of `test_that()`) ─────────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_pb.R:14:0
── Error (test_s3.R:12:1): (code run outside of `test_that()`) ─────────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_s3.R:12:0
── Error (test_sandwich.R:12:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_sandwich.R:12:0
── Error (test_scorehessian.R:12:1): (code run outside of `test_that()`) ───────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_scorehessian.R:12:0
── Error (test_simulate.R:12:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_simulate.R:12:0
── Error (test_waldtest.R:18:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_waldtest.R:18:0
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
Error: Test failures
Execution halted
Flavors: r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(corncob)
>
> test_check("corncob")
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error (test_bbdml.R:32:1): (code run outside of `test_that()`) ──────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_bbdml.R:32:0
── Error (test_differentialTest.R:11:1): (code run outside of `test_that()`) ───
Error in `differentialTest(formula = ~Plants + DayAmdmt, phi.formula = ~Plants +
DayAmdmt, formula_null = ~1, phi.formula_null = ~1, data = subsoil,
boot = FALSE, test = "LRT", inits = rbind(rep(0.01, 6)),
inits_null = rbind(rep(0.01, 2)))`: All models failed to converge!
If you are seeing this, it is likely that your model is overspecified. This occurs when your sample size is not large enough to estimate all the parameters of your model. This is most commonly due to categorical variables that include many categories.
Alternatively, double-check your values for the arguments `link`, `phi.link`, and `method` to makes sure that they follow the specified options.
To confirm you have fixed the issue, try running a model for a single taxon with bbdml.
Backtrace:
▆
1. └─corncob::differentialTest(...) at test_differentialTest.R:11:0
── Error (test_getRestrictionTerms.R:12:1): (code run outside of `test_that()`) ──
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_getRestrictionTerms.R:12:0
── Error (test_lrtest.R:19:1): (code run outside of `test_that()`) ─────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_lrtest.R:19:0
── Error (test_pb.R:14:1): (code run outside of `test_that()`) ─────────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_pb.R:14:0
── Error (test_s3.R:12:1): (code run outside of `test_that()`) ─────────────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_s3.R:12:0
── Error (test_sandwich.R:12:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_sandwich.R:12:0
── Error (test_scorehessian.R:12:1): (code run outside of `test_that()`) ───────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_scorehessian.R:12:0
── Error (test_simulate.R:12:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_simulate.R:12:0
── Error (test_waldtest.R:18:1): (code run outside of `test_that()`) ───────────
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
▆
1. └─corncob::bbdml(...) at test_waldtest.R:18:0
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.2.0
Check: tests
Result: ERROR
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(corncob)
>
> test_check("corncob")
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
== Failed tests ================================================================
-- Error (test_bbdml.R:32:1): (code run outside of `test_that()`) --------------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_bbdml.R:32:0
-- Error (test_differentialTest.R:11:1): (code run outside of `test_that()`) ---
Error in `differentialTest(formula = ~Plants + DayAmdmt, phi.formula = ~Plants +
DayAmdmt, formula_null = ~1, phi.formula_null = ~1, data = subsoil,
boot = FALSE, test = "LRT", inits = rbind(rep(0.01, 6)),
inits_null = rbind(rep(0.01, 2)))`: All models failed to converge!
If you are seeing this, it is likely that your model is overspecified. This occurs when your sample size is not large enough to estimate all the parameters of your model. This is most commonly due to categorical variables that include many categories.
Alternatively, double-check your values for the arguments `link`, `phi.link`, and `method` to makes sure that they follow the specified options.
To confirm you have fixed the issue, try running a model for a single taxon with bbdml.
Backtrace:
x
1. \-corncob::differentialTest(...) at test_differentialTest.R:11:0
-- Error (test_getRestrictionTerms.R:12:1): (code run outside of `test_that()`) --
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_getRestrictionTerms.R:12:0
-- Error (test_lrtest.R:19:1): (code run outside of `test_that()`) -------------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_lrtest.R:19:0
-- Error (test_pb.R:14:1): (code run outside of `test_that()`) -----------------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_pb.R:14:0
-- Error (test_s3.R:12:1): (code run outside of `test_that()`) -----------------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_s3.R:12:0
-- Error (test_sandwich.R:12:1): (code run outside of `test_that()`) -----------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_sandwich.R:12:0
-- Error (test_scorehessian.R:12:1): (code run outside of `test_that()`) -------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_scorehessian.R:12:0
-- Error (test_simulate.R:12:1): (code run outside of `test_that()`) -----------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_simulate.R:12:0
-- Error (test_waldtest.R:18:1): (code run outside of `test_that()`) -----------
Error in `if (detectseparation::detect_separation(y = cbind(W, M - W),
x = X.b, family = stats::binomial("logit"), control = list(purpose = "test"))$separation) {
warning(paste("Separation detected in abundance model!",
"Likely, one of your covariates/experimental conditions is such that",
"there are all zero counts within a group. Consider identifying and removing",
"this covariate from your model. The results of this model are not to be",
"trusted because there is not enough data. \n", sep = "\n"),
immediate. = TRUE)
sep_da <- TRUE
}`: argument is of length zero
Backtrace:
x
1. \-corncob::bbdml(...) at test_waldtest.R:18:0
[ FAIL 10 | WARN 0 | SKIP 0 | PASS 17 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-ix86+x86_64