apaTables

Context

Reproducible research is research for which the numbers reported in the paper can obtained by others using the original data and analysis scripts. (Note that this differs from replicability - the extent to which findings are consistent across samples.) Recent research has revealed a problem with the reproducibility of analyses in many fields. For example, in psychology Nuijten et al. (2015) found that in 50% of articles there was at least once instance of a reported test statistic (e.g., t(24)=22.71) being inconsistent with the reported p-value. This inconsistency rate suggests there is a major problem with reproducibility in the psychological literature.

My objective in creating the apaTables package was to automate the process through which tables are created from analyses when using R. Using apaTables ensures that the tables in your manuscript are reproducible.

Although a number of table generation packages exist for R they are typically not useful for psychology researchers because of the need to report results in the style required by the American Psychological Association; that is, APA Style. Consequently, apaTables creates Microsoft Word documents (.doc files) that contain tables that conform to APA Style.

In many cases it would be necessary to execute additional R commands to obtain all of the statistics needed for an APA Style table. For example, if conducting a regression using the lm command the unstandardized regression (i.e., b) weights are reported. Additional commands are needed to obtain standardized (i.e., beta) weights. apaTables automatically executes these additional commands to create a table with the required information in Microsoft Word .doc format¹.

Additionally, the American Statistical Association recently released a position paper on the use of p-values in research. A component of that statement indicated that “Scientific conclusions and business or policy decisions should not be based only on whether a p-value passes a specific threshold.” The Executive Director of the ASA suggested that confidence intervals should be used to interpret data. This statement is consistent with the 1999 position paper from the APA Task Force on Statistical Inference. Consequently, the current version of apaTables indicates significance using stars but more importantly reports confidence intervals for the reported effect sizes.

Bugs and feature requests can be reported at: https://github.com/dstanley4/apaTables/issues

Correlation table

Correlation tables can be constructed using the apa.cor.table function. The constructed table includes descriptive statistics (i.e., mean and standard deviation) for each variable and a confidence interval for each correlation.

The apa.cor.table function creates a correlation table with confidence intervals based on a data frame; see Figure 1. The confidence intervals can be suppressed but are on by default.

library(apaTables)
apa.cor.table(attitude, filename="Table1_APA.doc", table.number=1)

The resulting table is illustrated in Table 1. If confidence intervals are not desired they can be omitted by using the argument show.conf.interval=FALSE in apa.cor.table calls.

Correlation table in MSWord

Regression table (1 block)

Regression tables can be constructed using the apa.reg.table function. The constructed table includes the unstandardized regression coefficient (b with CI), standardized regression coefficient (beta with CI), semi-partial correlation squared (\(sr^2\) with CI), the correlation (\(r\)), and the overall fit of the model (indexed by \(R^2\) with CI). The album sales data set from Field et al. (2012) is used to illustrate the apa.reg.table function.

Basic regression table

The apa.reg.table function creates a regression table with confidence intervals based on lm output; see Table 2.

library(apaTables)
basic.reg <- lm(sales ~ adverts + airplay, data=album)
apa.reg.table(basic.reg, filename="Table2_APA.doc", table.number=2)

Basic regression table in MSWord

Blocks regression table

In many cases, it is more useful for psychology researchers to compare the results of two regression models with common variables. This approach is known to many psychology researchers as block-based regression (likely due to the labeling used in popular software packages). Using regression to “control” for certain variables (e.g., demographic or socio-economic variables) is a common use case. In this scenario, the researcher conducts a regression with the “control” variables that is referred to as block 1. Following this, the researcher conducts a second regression with the “control” variables and the substantive variables that is referred to as block 2. If block 2 accounts for significant variance in the criterion above and beyond block 1 then substantive variables are deemed to be meaningful predictors.

A second common use of block-based regression in psychology is testing for continuous-variable interactions. Consider a scenario in which a researcher is testing for an interaction between two continuous variables and two regressions are conducted. The first regression includes the two predictors of interest (block 1). The second regression includes the two predictors of interest as well as their product term (block 2). If block 2 accounts for significant variance in the criterion above and beyond block 1 an interaction is deemed to be present. Admittedly interactions could be tested in a single regression; however, using a block-based regression for this analysis is common in psychology. The example below examines whether advertisements and amount of airplay for a song interact to predict album sales. The resulting table is presented in Figure 3. Although this example only uses two blocks, note that any number of blocks can be used with the apa.reg.table function. As well, if the predictors in any of the blocks are a product-term, the zero-order correlation will be omitted from the output to prevent interpretation errors common in psychology.

The apa.reg.table function allows for multiple (i.e., more 2 or more) blocks as per below; see Table 3.

library(apaTables)
block1 <- lm(sales ~ adverts + airplay, data=album)
block2 <- lm(sales ~ adverts + airplay + I(adverts*airplay), data=album)
apa.reg.table(block1, block2, filename="Table3_APA.doc", table.number=3)

Blocks regression table in MSWord

1-way ANOVA and d-value tables

There are three functions in apaTables that are helpful for 1-way ANOVA analyses within predictor variables that are independent (apa.aov.table, apa.1way.table, and apa.d.table). All three are illustrated below. First, however, the ANOVA must be conducted - I do so using the Viagra data set from Field et al. (2012). When conducting an ANOVA in R using the lm command you must ensure your independent variables are R factors and that contrasts are set correctly. Note: repeated measures designs are not currently supported.

options(contrasts = c("contr.sum", "contr.poly"))
lm_output <- lm(libido ~ dose, data=viagra)

The apa.aov.table function creates a 1-way ANOVA table based on lm_output; see Table 4.

library(apaTables)
apa.aov.table(lm_output,filename="Figure4_APA.doc",table.number = 4)

1-way ANOVA table in MSWord

The apa.1way.table function creates a table with the mean and sd for each cell; see Table 5.

apa.1way.table(iv=dose,dv=libido,data=viagra,filename="Figure5_APA.doc",table.number = 5)

1-way M/SD table in MSWord

The apa.d.table function show a d-value (with confidence interval) for each paired comparison; see Table 6.

apa.d.table(iv=dose,dv=libido,data=viagra,filename="Figure6_APA.doc",table.number = 6)

1-way Paired Comparison d-values (with CI) in MSWord

N-way ANOVA tables: 2-way Example

The 2-way example with independent variable predictors is based on the goggles data set from Field et al. (2012). As before, when conducting an ANOVA in R using the lm command you must ensure your independent variables are R factors and that contrasts are set correctly. Note: repeated measures designs are not currently supported.

options(contrasts = c("contr.sum", "contr.poly"))
lm_output <- lm(attractiveness ~ gender*alcohol, data=goggles)

The apa.aov.table function creates a 2-way ANOVA table based on lm_output; see Table 7.

library(apaTables)
apa.aov.table(lm_output,filename="Figure7_APA.doc",table.number = 7)

2-way ANOVA table in MSWord

The apa.2way.table function creates a table with the mean and sd for each cell; see Table 8. Marginal means can also be requested – see the help file (?apa.2way.table). For higher-order designs (i.e., 3-way or higher) use the filter command in the dplyr package to select the subset of rows and then use apa.2way.table to display cell statistics.

apa.2way.table(iv1=gender,iv2=alcohol,dv=attractiveness,data=goggles,filename="Figure8_APA.doc",table.number = 8)

2-way M/SD table in MSWord

You can use the dplyr package to conducted paired comparisons within each gender again using apa.d.table; see Tables 9 and 10.

library(apaTables)
library(dplyr)
goggles.men   <- filter(goggles,gender=="Male")
goggles.women <- filter(goggles,gender=="Female")

apa.d.table(iv=alcohol,dv=attractiveness,data=goggles.men,filename="Table9_APA.doc",table.number = 9)
apa.d.table(iv=alcohol,dv=attractiveness,data=goggles.women,filename="Table10_APA.doc",table.number = 10)

2-way Male Subgroup Paired Comparison d-values (with CI) in MSWord 2-way Female Subgroup Paired Comparison d-values (with CI) in MSWord

Technically the tables are in .rtf format. But you should end all files with .doc; this will ensure they are automatically loaded by Microsoft Word↩