Jeff Stevens

2023-05-05

# Journal article templates

{rticles}

{papaja}

## APA template

{papaja}

• r_refs() and cite_r()

• APA 7

# Extracting statistics

## Extracting statistics

apa_print()

## Run a t-test

library(palmerpenguins)
library(tidyverse)
(penguin_ttest <- t.test(formula = bill_length_mm ~ sex, data = penguins))

Welch Two Sample t-test

data:  bill_length_mm by sex
t = -6.6725, df = 329.29, p-value = 1.066e-10
alternative hypothesis: true difference in means between group female and group male is not equal to 0
95 percent confidence interval:
-4.865676 -2.649908
sample estimates:
mean in group female   mean in group male
42.09697             45.85476 

## View structure of a t-test

str(penguin_ttest)
List of 10
$statistic : Named num -6.67 ..- attr(*, "names")= chr "t"$ parameter  : Named num 329
..- attr(*, "names")= chr "df"
$p.value : num 1.07e-10$ conf.int   : num [1:2] -4.87 -2.65
..- attr(*, "conf.level")= num 0.95
$estimate : Named num [1:2] 42.1 45.9 ..- attr(*, "names")= chr [1:2] "mean in group female" "mean in group male"$ null.value : Named num 0
..- attr(*, "names")= chr "difference in means between group female and group male"
$stderr : num 0.563$ alternative: chr "two.sided"
$method : chr "Welch Two Sample t-test"$ data.name  : chr "bill_length_mm by sex"
- attr(*, "class")= chr "htest"

## Extract information from t-test

library(papaja)
apa_print(penguin_ttest)
$estimate [1] "$\\Delta M = -3.76$, 95\\% CI$[-4.87, -2.65]$"$statistic
[1] "$t(329.29) = -6.67$, $p < .001$"

$full_result [1] "$\\Delta M = -3.76$, 95\\% CI$[-4.87, -2.65]$,$t(329.29) = -6.67$,$p < .001$"$table
A data.frame with 5 labelled columns:

estimate       conf.int statistic     df p.value
1    -3.76 [-4.87, -2.65]     -6.67 329.29  < .001

estimate : $\\Delta M$
conf.int : 95\\% CI
statistic: $t$
df       : $\\mathit{df}$
p.value  : $p$
attr(,"class")
[1] "apa_results" "list"       

apa_print(penguin_ttest)$full_result [1] "$\\Delta M = -3.76$, 95\\% CI$[-4.87, -2.65]$,$t(329.29) = -6.67$,$p < .001$" ## Insert statistics as inline code  Male and female penguins differ in their bill length (r apa_print(penguin_ttest)$full_result).

Male and female penguins differ in their bill length ($\Delta M = -3.76$, 95% CI $[-4.87, -2.65]$, $t(329.29) = -6.67$, $p < .001$).

## apa_print() objects

• Non-parametrics (wilcox.test())
• Correlations (cor.test())
• T-tests (t.test())
• ANOVA (aov(), Anova(), afex_aov())
• MANOVA (manova())
• Linear regressions (lm())
• Generalized linear models (glm())
• Mixed models (lmer(), glmer())
• Non-linear models (nlme())
• Estimated marginal means (emm())
• Within-subjects confidence intervals (wsci())
• Bayes factors (from BayesFactor package)

## Printing p-values

printp()

printp(0.23456)
[1] ".235"
printp(0.23456, add_equals = TRUE)
[1] "= .235"
printp(0.000000000000001)
[1] "< .001"

## Printing other numbers

printnum()

printnum(0.5555555)
[1] "0.56"
printnum(0.5555555, digits = 4)
[1] "0.5556"
printnum(0.5555555, gt1 = FALSE)
[1] ".56"
printnum(0.00000000000001)
[1] "0.00"
printnum(0.00000000000001, zero = FALSE)
[1] "< 0.01"

# Before and after journal articles

{prereg}

{preregr}

## Revision letter template

Friends don’t let friends copy-paste