README.md

Statistical analysis of stratified benchmarks

This repository contains R scripts allowing for statistical analysis of benchmark results obtained by a stratified approach.

Regression with a single categorical variable

The method called regression_single_variable runs a cumulative logit model over data explained by a single variable. The input data can take two formats: a contingency table or a dataframe with one trial per row.

Data as a contingency table

The dataframe should represent the contingency table, i.e. should contain the number of occurrences of each outcome (column) for each level of the explanatory variable (rows). If we assume that we have 3 levels to compare based on 4 outcomes, the dataframe (let's call it dataframe_example) should be formatted as follow (make sure to have levels set a factor):

levels	outcome 1	outcome 2	outcome 3	outcome 4
level 1	n11	n12	n13	n14
level 2	n21	n22	n23	n24
level 3	n31	n32	n33	n34

In this case, the formula needs to contain indicator variables that we can manually define

level1 <- ifelse(dataframe_example$levels=="level 1",1,0)
level2 <- ifelse(dataframe_example$levels=="level 2",1,0)
level3 <- ifelse(dataframe_example$levels=="level 3",1,0)

Then running

res <- regression_single_variable(cbind(outcome 1, outcome 2, outcome 3, outcome 4) ~ level1 + level2, dataframe_example, pod_assumption=TRUE)

would return all the pairwise comparisons (with level 3 as reference) with the corresponding p-values allowing you to rank the three levels over the entire distribution. Using pod_assumption=FALSE will return the pairwise comparisons values and p-values for each outcome separately.

Note that if you want to have level 1 set as reference, you should call the function as follows:

res <- regression_single_variable(cbind(outcome 1, outcome 2, outcome 3, outcome 4) ~ level2 + level3, dataframe_example, pod_assumption=TRUE)

Data with one trial per row

If the dataframe follows this format:

levels	outcome
level 1	outcome 1
level 1	outcome 2
level 1	outcome 1
...	...
level 2	outcome 4
...	...

then you need to be careful with the format of each column of your dataframe (let's call it second_dataframe). Indeed, levels must be a factor (the first provided level will set as a reference), and outcome should be an ordered factor. If the data follow these conditions, then you can call the same function as follows:

res <- regression_single_variable(outcome ~ levels, second_dataframe, pod_assumption=TRUE)

Feel free to compare the output with the one obtained with a contingency table and it will be the same!

Regression with several categorical variables

The method called regression_multi_variables runs a cumulative logit model over data explained by the joint effect of two variables. The input data can take two formats: a contingency-like table or a dataframe with one trial per row.

Data as a contingency-like table

If we assume that we have two variables, one with 3 levels and a second with 4 levels that we want to analyse based on 4 outcomes, the dataframe (let's call it dataframe_multi_example) should be formatted as follow (make sure to have either levels and second_variable set as factors if you want them to be treated as categorical variables):

levels	second_variable	outcome 1	outcome 2	outcome 3	outcome 4
level 1	var1	n111	n112	n113	n114
level 1	var2	n121	n122	n123	n124
level 1	var3	n131	n132	n133	n134
level 1	var4	n141	n142	n143	n144
level 2	var1	n211	n212	n213	n214
level 2	var2	n221	n222	n223	n224
level 2	var3	n231	n232	n233	n234
level 2	var4	n241	n242	n243	n244
level 3	var1	n311	n312	n313	n314
level 3	var2	n321	n322	n323	n324
level 3	var3	n331	n332	n333	n334
level 3	var4	n341	n342	n343	n344

In this case, the formula needs to contain indicator variables that we can manually define

level1 <- ifelse(dataframe_multi_example$levels=="level 1",1,0)
level2 <- ifelse(dataframe_multi_example$levels=="level 2",1,0)
level3 <- ifelse(dataframe_multi_example$levels=="level 3",1,0)
second_var1 <- ifelse(dataframe_multi_example$second_variable=="var1",1,0)
second_var2 <- ifelse(dataframe_multi_example$second_variable=="var2",1,0)
second_var3 <- ifelse(dataframe_multi_example$second_variable=="var3",1,0)
second_var4 <- ifelse(dataframe_multi_example$second_variable=="var4",1,0)

Then running

res <- regression_multi_variables(cbind(outcome 1, outcome 2, outcome 3, outcome 4) ~ (level1 + level2)*(second_var1 + second_var2 +second_var3), dataframe_multi_example)

would return all the pairwise comparisons (with level 3 as reference for levels and var4 as reference for second_variable) with the corresponding p-values allowing you to account for the interaction between the two variables. Note that if second_variable is numerical you don't need to use the corresponding set of indicators and use directly

res <- regression_multi_variables(cbind(outcome 1, outcome 2, outcome 3, outcome 4) ~ (level1 + level2)*(second_var)

Data with one trial per row

If the dataframe follows this format:

levels	second_variable	outcome
level 1	var1	outcome 1
level 1	var3	outcome 2
level 1	var2	outcome 1
...	...	...
level 2	var4	outcome 4
...	...	...

then you need to be careful with the format of each column of your dataframe (let's call it second_dataframe_multi). Indeed, levels and second_variable must be set as factors (the first level will set as a reference), and outcome should be an ordered factor. If the data follow these conditions, then you can call the same function as follows:

res <- regression_single_variable(outcome ~ levels*second_variable, second_dataframe_multi)

Please note that if second_variable is not categorical, you can use the same function here!

Feel free to compare the output with the one obtained with a contingency table and it will be the same!