diff --git a/paper/paper.Rmd b/paper/paper.Rmd index 54503444..600f8d93 100644 --- a/paper/paper.Rmd +++ b/paper/paper.Rmd @@ -63,7 +63,7 @@ knitr::opts_chunk$set( comment = "#>", message = FALSE, warning = FALSE, - results="asis" + results = "asis" ) options(width = 60) @@ -99,17 +99,25 @@ data <- data.frame( "Age" = c(22, 23, 54, 21, 8, 42, 18, 32, 24, 27, 45), "Sex" = c("Intersex", "F", "F", "M", "M", "M", "F", "F", "F", "F", "F"), "Gender" = c("N", "W", "W", "M", "M", "M", "W", "W", "W", "W", "W"), - "Race" = c("Black", NA, "White", "Asian", "Black", "Arab", "Black", - "White", "Asian", "Southeast Asian", "Mixed"), - "Education" = c("Bachelor", "PhD", "Highschool", "Master", "Bachelor", - "Highschool", "Highschool", "Bachelor", "Bachelor", - "Highschool", "Master"), - "Country" = c("USA", NA, "Canada", "Canada", "India", "Germany", "USA", - "USA", "USA", "USA", "Canada") + "Race" = c( + "Black", NA, "White", "Asian", "Black", "Arab", "Black", + "White", "Asian", "Southeast Asian", "Mixed" + ), + "Education" = c( + "Bachelor", "PhD", "Highschool", "Master", "Bachelor", + "Highschool", "Highschool", "Bachelor", "Bachelor", + "Highschool", "Master" + ), + "Country" = c( + "USA", NA, "Canada", "Canada", "India", "Germany", "USA", + "USA", "USA", "USA", "Canada" + ) ) -cat(paste0("This study includes data from ", - report_participants(data), ".")) +cat(paste0( + "This study includes data from ", + report_participants(data), "." +)) ``` ## Models diff --git a/paper/paper.log b/paper/paper.log new file mode 100644 index 00000000..1a556f9d --- /dev/null +++ b/paper/paper.log @@ -0,0 +1,1328 @@ +This is XeTeX, Version 3.141592653-2.6-0.999995 (TeX Live 2023) (preloaded format=xelatex 2023.12.2) 4 MAR 2024 06:58 +entering extended mode + restricted \write18 enabled. + %&-line parsing enabled. +**paper.tex +(./paper.tex +LaTeX2e <2023-11-01> +L3 programming layer <2023-11-09> +(/Users/indrajeetpatil/Library/TinyTeX/texmf-dist/tex/latex/base/article.cls +Document Class: 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+(biblatex) paper +(biblatex) and rerun LaTeX afterwards. + +Package logreq Info: Writing requests to 'paper.run.xml'. +\openout1 = `paper.run.xml'. + + ) +Here is how much of TeX's memory you used: + 37241 strings out of 474924 + 763301 string characters out of 5755242 + 1963186 words of memory out of 5000000 + 58679 multiletter control sequences out of 15000+600000 + 564941 words of font info for 84 fonts, out of 8000000 for 9000 + 1348 hyphenation exceptions out of 8191 + 84i,12n,87p,1194b,1159s stack positions out of 10000i,1000n,20000p,200000b,200000s + +Output written on paper.pdf (6 pages). diff --git a/paper/paper.md b/paper/paper.md index b1f32238..043dd3bf 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -45,7 +45,7 @@ affiliations: - index: 7 name: Université du Québec à Montréal, Montréal, Canada -date: "2023-02-26" +date: "2024-03-04" bibliography: paper.bib output: rticles::joss_article: @@ -85,17 +85,25 @@ data <- data.frame( "Age" = c(22, 23, 54, 21, 8, 42, 18, 32, 24, 27, 45), "Sex" = c("Intersex", "F", "F", "M", "M", "M", "F", "F", "F", "F", "F"), "Gender" = c("N", "W", "W", "M", "M", "M", "W", "W", "W", "W", "W"), - "Race" = c("Black", NA, "White", "Asian", "Black", "Arab", "Black", - "White", "Asian", "Southeast Asian", "Mixed"), - "Education" = c("Bachelor", "PhD", "Highschool", "Master", "Bachelor", - "Highschool", "Highschool", "Bachelor", "Bachelor", - "Highschool", "Master"), - "Country" = c("USA", NA, "Canada", "Canada", "India", "Germany", "USA", - "USA", "USA", "USA", "Canada") + "Race" = c( + "Black", NA, "White", "Asian", "Black", "Arab", "Black", + "White", "Asian", "Southeast Asian", "Mixed" + ), + "Education" = c( + "Bachelor", "PhD", "Highschool", "Master", "Bachelor", + "Highschool", "Highschool", "Bachelor", "Bachelor", + "Highschool", "Master" + ), + "Country" = c( + "USA", NA, "Canada", "Canada", "India", "Germany", "USA", + "USA", "USA", "USA", "Canada" + ) ) -cat(paste0("This study includes data from ", - report_participants(data), ".")) +cat(paste0( + "This study includes data from ", + report_participants(data), "." +)) ``` This study includes data from 11 participants (Mean age = 28.7, SD = 13.4, range: [8, 54]; Sex: 63.6% females, 27.3% males, 9.1% other; Gender: 63.6% women, 27.3% men, 9.09% non-binary; Education: Bachelor, 36.36%; Highschool, 36.36%; Master, 18.18%; PhD, 9.09%; Country: 45.45% USA, 27.27% Canada, 27.27% other; Race: 27.27% Black, 18.18% Asian, 18.18% White, 36.36% other). @@ -175,41 +183,8 @@ report(m_rstan) We fitted a Bayesian linear model (estimated using MCMC sampling with 4 chains of 1000 iterations and a warmup of 500) to predict mpg with qsec and wt (formula: mpg ~ qsec + -wt). Priors over parameters were set as normal (mean = -0.00, SD = 8.43) distributions. The model's explanatory -power is substantial (R2 = 0.81, 95% CI [0.69, 0.89], adj. -R2 = 0.79). The model's intercept, corresponding to qsec = -0 and wt = 0, is at 19.59 (95% CI [8.71, 30.63]). Within -this model: - - - The effect of qsec (Median = 0.93, 95% CI [0.38, 1.50]) -has a 99.85% probability of being positive (> 0), 98.65% of -being significant (> 0.30), and 0.10% of being large (> -1.81). The estimation successfully converged (Rhat = 1.001) -and the indices are reliable (ESS = 2048) - - The effect of wt (Median = -5.05, 95% CI [-6.07, -4.05]) -has a 100.00% probability of being negative (< 0), 100.00% -of being significant (< -0.30), and 100.00% of being large -(< -1.81). The estimation successfully converged (Rhat = -0.999) and the indices are reliable (ESS = 1744) - -Following the Sequential Effect eXistence and sIgnificance -Testing (SEXIT) framework, we report the median of the -posterior distribution and its 95% CI (Highest Density -Interval), along the probability of direction (pd), the -probability of significance and the probability of being -large. The thresholds beyond which the effect is considered -as significant (i.e., non-negligible) and large are |0.30| -and |1.81| (corresponding respectively to 0.05 and 0.30 of -the outcome's SD). Convergence and stability of the -Bayesian sampling has been assessed using R-hat, which -should be below 1.01 (Vehtari et al., 2019), and Effective -Sample Size (ESS), which should be greater than 1000 -(Burkner, 2017). and We fitted a Bayesian linear model -(estimated using MCMC sampling with 4 chains of 1000 -iterations and a warmup of 500) to predict mpg with qsec -and wt (formula: mpg ~ qsec + wt). Priors over parameters -were set as normal (mean = 0.00, SD = 15.40) distributions. +wt). Priors over parameters were all set as normal (mean = +0.00, SD = 8.43; mean = 0.00, SD = 15.40) distributions. The model's explanatory power is substantial (R2 = 0.81, 95% CI [0.69, 0.89], adj. R2 = 0.79). The model's intercept, corresponding to qsec = 0 and wt = 0, is at @@ -257,7 +232,7 @@ export_table(format_table(report_table(m_lm)), format = "markdown") |Parameter | Coefficient| 95% CI | t(29)| p | Std. Coef.| Std. Coef. 95% CI| Fit| |:-----------|-----------:|:--------------|------:|:------|----------:|-----------------:|------:| -|(Intercept) | 19.75|[ 9.00, 30.49] | 3.76|< .001 | -5.21e-17| [-0.16, 0.16]| | +|(Intercept) | 19.75|[ 9.00, 30.49] | 3.76|< .001 | -1.36e-17| [-0.16, 0.16]| | |qsec | 0.93|[ 0.39, 1.47] | 3.51|0.001 | 0.28| [ 0.11, 0.44]| | |wt | -5.05|[-6.04, -4.06] | -10.43|< .001 | -0.82| [-0.98, -0.66]| | | | | | | | | | | @@ -268,6 +243,8 @@ export_table(format_table(report_table(m_lm)), format = "markdown") |R2 (adj.) | | | | | | | 0.81| |Sigma | | | | | | | 2.60| + + ```r export_table(format_table(report_table(m_lmer)), format = "markdown") @@ -277,7 +254,7 @@ export_table(format_table(report_table(m_lmer)), format = "markdown") |Parameter | Coefficient| 95% CI | t(146)| p | Effects| Group| Std. Coef.| Std. Coef. 95% CI| Fit| |:----------------|-----------:|:------------|------:|:------|-------:|--------:|----------:|-----------------:|------:| -|(Intercept) | 2.50|[1.19, 3.82] | 3.75|< .001 | fixed| | -1.46e-13| [-1.49, 1.49]| | +|(Intercept) | 2.50|[1.19, 3.82] | 3.75|< .001 | fixed| | -5.11e-13| [-1.49, 1.49]| | |Petal Length | 0.89|[0.76, 1.01] | 13.93|< .001 | fixed| | 1.89| [ 1.63, 2.16]| | | | 1.08| | | | random| Species| | | | | | 0.34| | | | random| Residual| | | | @@ -289,6 +266,8 @@ export_table(format_table(report_table(m_lmer)), format = "markdown") |R2 (marginal) | | | | | | | | | 0.66| |Sigma | | | | | | | | | 0.34| + + ```r export_table(format_table(report_table(m_rstan)), format = "markdown") @@ -309,6 +288,8 @@ export_table(format_table(report_table(m_rstan)), format = "markdown") |R2 (adj.) | | | | | | | | | 0.79| |Sigma | | | | | | | | | 2.65| + + ## Grouped Data You can also seamlessly integrate `{report}` with *tidyverse* workflows: diff --git a/paper/paper.pdf b/paper/paper.pdf index e8de12d1..ab448a9e 100644 Binary files a/paper/paper.pdf and b/paper/paper.pdf differ