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fix warnings in tests #610

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Jun 30, 2023
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fix warnings in tests #610

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2 changes: 1 addition & 1 deletion vignettes/bayes_factors.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@
"rstanarm", "BayesFactor", "emmeans", "logspline", "lme4", "ggplot2",
"see", "insight", "knitr", "effectsize", "bayestestR"
)
if (!all(sapply(pkgs, require, quietly = TRUE, character.only = TRUE))) {

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file=vignettes/bayes_factors.Rmd,line=44,col=10,[undesirable_function_linter] Function "sapply" is undesirable.
knitr::opts_chunk$set(eval = FALSE)
}

Expand Down Expand Up @@ -251,9 +251,9 @@
theme_modern() +
theme(legend.position = c(0.2, 0.8))

My_first_BF <- bayesfactor_parameters(model, null = c(-1, 1), prior = model_prior)

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file=vignettes/bayes_factors.Rmd,line=254,col=1,[object_name_linter] Variable and function name style should match snake_case or symbols.

BF <- as.numeric(My_first_BF)[2]

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file=vignettes/bayes_factors.Rmd,line=256,col=1,[object_name_linter] Variable and function name style should match snake_case or symbols.
post_odds <- prior_odds * BF

med_post <- point_estimate(posterior)$Median
Expand All @@ -280,7 +280,7 @@
computes a Bayes factor for each of the model's parameters:

```{r, eval=FALSE}
My_first_BF <- bayesfactor_parameters(model, null = c(-1, 1))

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file=vignettes/bayes_factors.Rmd,line=283,col=1,[object_name_linter] Variable and function name style should match snake_case or symbols.
My_first_BF
```

Expand Down Expand Up @@ -323,12 +323,12 @@
the point of interest." [@wagenmakers2010bayesian]

```{r, eval=FALSE}
My_second_BF <- bayesfactor_parameters(model, null = 0)

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file=vignettes/bayes_factors.Rmd,line=326,col=1,[object_name_linter] Variable and function name style should match snake_case or symbols.
My_second_BF
```

```{r, echo=FALSE}
My_second_BF <- bayesfactor_parameters(

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file=vignettes/bayes_factors.Rmd,line=331,col=1,[object_name_linter] Variable and function name style should match snake_case or symbols.
data.frame(group2 = posterior),
data.frame(group2 = prior),
null = 0,
Expand Down Expand Up @@ -360,7 +360,7 @@
verbose = FALSE
)

BF <- as.numeric(test_group2_right)

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file=vignettes/bayes_factors.Rmd,line=363,col=1,[object_name_linter] Variable and function name style should match snake_case or symbols.

print(test_group2_right)
```
Expand Down Expand Up @@ -698,7 +698,7 @@
```{r}
model_prior <- unupdate(iris_model)

botanist_BFs <- bayesfactor_restricted(

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file=vignettes/bayes_factors.Rmd,line=701,col=1,[object_name_linter] Variable and function name style should match snake_case or symbols.
posterior = iris_model,
prior = model_prior,
hypothesis = botanist_hypotheses
Expand Down Expand Up @@ -799,9 +799,9 @@
```{r JASP_all}
library(BayesFactor)
data(ToothGrowth)
ToothGrowth$dose <- as.factor(ToothGrowth$dose)

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file=vignettes/bayes_factors.Rmd,line=802,col=1,[object_name_linter] Variable and function name style should match snake_case or symbols.

BF_ToothGrowth <- anovaBF(len ~ dose * supp, ToothGrowth, progress = FALSE)

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file=vignettes/bayes_factors.Rmd,line=804,col=1,[object_name_linter] Variable and function name style should match snake_case or symbols.

bayesfactor_inclusion(BF_ToothGrowth)
```
Expand Down Expand Up @@ -1185,7 +1185,7 @@
chains = 4, iter = 2000, warmup = 1000 # reduce build time
)

em_sum <- emmeans(fit_sum, ~Species) # the posterior marginal means
em_sum <- emmeans(fit_sum, ~Species, data = iris) # the posterior marginal means

bayesfactor_restricted(em_sum, fit_sum, hypothesis = hyp)
```
Expand Down
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