diff --git a/notebooks/figures-cohens_d.subarticle.xml b/notebooks/figures-cohens_d.subarticle.xml deleted file mode 100644 index baa7d50..0000000 --- a/notebooks/figures-cohens_d.subarticle.xml +++ /dev/null @@ -1,122 +0,0 @@ - - - -Code for Figures 1-2 based on Cohen’s d - - - - -Klapwijk -Eduard - -Eduard Klapwijk - - - - - - -

Load libraries to produce figures:

- -# load libraries -library(dplyr) -library(patchwork) -# load devtools library and load neuro-up package from github repo -library(devtools) -install_github("eduardklap/neuroUp") -library(neuroUp) - - -

Set seed and create Figure 1A for the Feedback task DLPFC ROI:

- -# set seed -set.seed(1234) - -# Estimate differences (unstandardized and Cohen's d) -Fig1a <- estim_diff(data = feedback, - vars_of_interest = c("mfg_learning", - "mfg_application"), - sample_size = 20:271, - k = 1000, - name = "A. Feedback DLPFC") - - -

Set seed and create Figure 1B for the Gambling task NAcc ROI:

- -# set seed -set.seed(1234) - -# Estimate differences (unstandardized and Cohen's d) -Fig1b <- estim_diff(data = gambling, - vars_of_interest = c("lnacc_self_win", - "lnacc_self_loss"), - sample_size = 20:221, - k = 1000, - name = "B. Gambling NAcc") - - -

Set seed and create Figure 1C for the Self-evaluations task mPFC -ROI:

- -# set seed -set.seed(1234) - -# Estimate differences (unstandardized and Cohen's d) -Fig1c <- estim_diff(data = self_eval, - vars_of_interest = c("mpfc_self", - "mpfc_control"), - sample_size = 20:149, - k = 10, - name = "C. Self-evaluations mPFC") - - -

Set seed and create Figure 1D for the Gaining for self task NAcc -ROI:

- -# set seed -set.seed(1234) - -# Estimate differences (unstandardized and Cohen's d) -Fig1d <- estim_diff(data = vicar_char, - vars_of_interest = c("nacc_selfgain", - "nacc_bothnogain"), - sample_size = 20:156, - k = 10, - name = "D. Gaining self NAcc") - - -

Combine figures 1A-D in one figure for Cohen’s d estimates:

- -Fig1a$fig_cohens_d + Fig1b$fig_cohens_d + Fig1c$fig_cohens_d + Fig1d$fig_cohens_d - - -

Combine figures 1A-D in one figure for the proportion of intervals -not containing the value 0:

- -Fig1a$fig_d_nozero + Fig1b$fig_d_nozero + Fig1c$fig_d_nozero + Fig1d$fig_d_nozero - - -

Extract numbers to make table 2:

- -# first extract tibble from results (select mean only) -feedback <- as_tibble(Fig1a$tbl_select) %>% - dplyr::filter(permutation == "Overall") -gambling <- as_tibble(Fig1b$tbl_select) %>% - dplyr::filter(permutation == "Overall") -selfeval <- as_tibble(Fig1c$tbl_select) %>% - dplyr::filter(permutation == "Overall") -gaining <- as_tibble(Fig1d$tbl_select) %>% - dplyr::filter(permutation == "Overall") - -# use numbers to make a table in text - - - - - - - - - - - \ No newline at end of file