From b17dbd861e5fe245acffa24ae63346eb381369c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?R=C3=A9mi=20Th=C3=A9riault?= <13123390+rempsyc@users.noreply.github.com> Date: Mon, 1 Apr 2024 13:05:50 +0200 Subject: [PATCH] update snapshots, document --- man/report.BFBayesFactor.Rd | 4 +-- .../testthat/_snaps/windows/report.brmsfit.md | 35 ------------------- .../_snaps/windows/report_performance.md | 24 ------------- 3 files changed, 2 insertions(+), 61 deletions(-) diff --git a/man/report.BFBayesFactor.Rd b/man/report.BFBayesFactor.Rd index 31261d76..871c7ece 100644 --- a/man/report.BFBayesFactor.Rd +++ b/man/report.BFBayesFactor.Rd @@ -27,8 +27,8 @@ Interpretation of the Bayes factor output from the \code{BayesFactor} package. library(BayesFactor) rez <- BayesFactor::ttestBF(iris$Sepal.Width, iris$Sepal.Length) -report_statistics(rez, exact=TRUE) # Print exact BF -report(rez, h0="the null hypothesis", h1="the alternative") +report_statistics(rez, exact = TRUE) # Print exact BF +report(rez, h0 = "the null hypothesis", h1 = "the alternative") rez <- BayesFactor::correlationBF(iris$Sepal.Width, iris$Sepal.Length) report(rez) diff --git a/tests/testthat/_snaps/windows/report.brmsfit.md b/tests/testthat/_snaps/windows/report.brmsfit.md index 4f8894dd..35e5ea49 100644 --- a/tests/testthat/_snaps/windows/report.brmsfit.md +++ b/tests/testthat/_snaps/windows/report.brmsfit.md @@ -4,41 +4,6 @@ report(model, verbose = FALSE) Message Start sampling - Chain 1 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue: - Chain 1 Exception: normal_id_glm_lpdf: Scale vector is 0, but must be positive finite! (in 'C:/Users/DL/AppData/Local/Temp/RtmpERRA9z/model-12d437f47a61.stan', line 35, column 4 to column 62) - Chain 1 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine, - Chain 1 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified. - Chain 1 - Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue: - Chain 2 Exception: normal_id_glm_lpdf: Scale vector is inf, but must be positive finite! (in 'C:/Users/DL/AppData/Local/Temp/RtmpERRA9z/model-12d437f47a61.stan', line 35, column 4 to column 62) - Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine, - Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified. - Chain 2 - Chain 2 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue: - Chain 2 Exception: normal_id_glm_lpdf: Scale vector is inf, but must be positive finite! (in 'C:/Users/DL/AppData/Local/Temp/RtmpERRA9z/model-12d437f47a61.stan', line 35, column 4 to column 62) - Chain 2 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine, - Chain 2 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified. - Chain 2 - Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue: - Chain 3 Exception: normal_id_glm_lpdf: Scale vector is inf, but must be positive finite! (in 'C:/Users/DL/AppData/Local/Temp/RtmpERRA9z/model-12d437f47a61.stan', line 35, column 4 to column 62) - Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine, - Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified. - Chain 3 - Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue: - Chain 3 Exception: normal_id_glm_lpdf: Scale vector is inf, but must be positive finite! (in 'C:/Users/DL/AppData/Local/Temp/RtmpERRA9z/model-12d437f47a61.stan', line 35, column 4 to column 62) - Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine, - Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified. - Chain 3 - Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue: - Chain 3 Exception: normal_id_glm_lpdf: Scale vector is inf, but must be positive finite! (in 'C:/Users/DL/AppData/Local/Temp/RtmpERRA9z/model-12d437f47a61.stan', line 35, column 4 to column 62) - Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine, - Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified. - Chain 3 - Chain 3 Informational Message: The current Metropolis proposal is about to be rejected because of the following issue: - Chain 3 Exception: normal_id_glm_lpdf: Scale vector is inf, but must be positive finite! (in 'C:/Users/DL/AppData/Local/Temp/RtmpERRA9z/model-12d437f47a61.stan', line 35, column 4 to column 62) - Chain 3 If this warning occurs sporadically, such as for highly constrained variable types like covariance matrices, then the sampler is fine, - Chain 3 but if this warning occurs often then your model may be either severely ill-conditioned or misspecified. - Chain 3 Output We fitted a Bayesian linear model (estimated using MCMC sampling with 4 chains of 300 iterations and a warmup of 150) to predict mpg with qsec and wt diff --git a/tests/testthat/_snaps/windows/report_performance.md b/tests/testthat/_snaps/windows/report_performance.md index 0e669f03..76bd46c4 100644 --- a/tests/testthat/_snaps/windows/report_performance.md +++ b/tests/testthat/_snaps/windows/report_performance.md @@ -2,10 +2,6 @@ Code report_performance(x5) - Message - VSCode WebView has restricted access to local file. - Opening in external browser... - Browsing file:///C:/Users/DL/AppData/Local/Temp/RtmpERRA9z/file12d47a7090f_StanProgress.html Output The model's explanatory power is substantial (R2 = 0.62, 95% CI [0.53, 0.69], adj. R2 = 0.61) @@ -14,10 +10,6 @@ Code summary(report_performance(x5)) - Message - VSCode WebView has restricted access to local file. - Opening in external browser... - Browsing file:///C:/Users/DL/AppData/Local/Temp/RtmpERRA9z/file12d465985229_StanProgress.html Output [1] "The model's explanatory power is substantial (R2 = 0.62, adj. R2 = 0.61)" @@ -25,10 +17,6 @@ Code report_performance(x6) - Message - VSCode WebView has restricted access to local file. - Opening in external browser... - Browsing file:///C:/Users/DL/AppData/Local/Temp/RtmpERRA9z/file12d4560a39d2_StanProgress.html Output The model's explanatory power is substantial (R2 = 0.54, 95% CI [0.27, 0.77]) @@ -36,10 +24,6 @@ Code summary(report_performance(x6)) - Message - VSCode WebView has restricted access to local file. - Opening in external browser... - Browsing file:///C:/Users/DL/AppData/Local/Temp/RtmpERRA9z/file12d452f95d46_StanProgress.html Output [1] "The model's explanatory power is substantial (R2 = 0.54)" @@ -47,10 +31,6 @@ Code report_performance(x7) - Message - VSCode WebView has restricted access to local file. - Opening in external browser... - Browsing file:///C:/Users/DL/AppData/Local/Temp/RtmpERRA9z/file12d412fbc1_StanProgress.html Output The model's explanatory power is substantial (R2 = 0.83, 95% CI [0.79, 0.86], adj. R2 = 0.83) and the part related to the fixed effects alone (marginal R2) @@ -60,10 +40,6 @@ Code summary(report_performance(x7)) - Message - VSCode WebView has restricted access to local file. - Opening in external browser... - Browsing file:///C:/Users/DL/AppData/Local/Temp/RtmpERRA9z/file12d426713848_StanProgress.html Output [1] "The model's explanatory power is substantial (R2 = 0.83, adj. R2 = 0.83) and the part related to the fixed effects alone (marginal R2) is of 0.95"