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eduardklap · Jun 14, 2024 · cfc8e4d · cfc8e4d
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-56305d0f
+11d694fa
diff --git a/_tex/index.tex b/_tex/index.tex
@@ -190,7 +190,7 @@
 using Bayesian updating}
 \author{Eduard T. Klapwijk \and Joran Jongerling \and Herbert
 Hoijtink \and Eveline A. Crone}
-\date{2024-06-13}
+\date{2024-06-14}
 
 \begin{document}
 \maketitle

diff --git a/index-meca.zip b/index-meca.zip
diff --git a/index.docx b/index.docx
diff --git a/index.html b/index.html
@@ -10,7 +10,7 @@
 <meta name="author" content="Joran Jongerling">
 <meta name="author" content="Herbert Hoijtink">
 <meta name="author" content="Eveline A. Crone">
-<meta name="dcterms.date" content="2024-06-13">
+<meta name="dcterms.date" content="2024-06-14">
 <meta name="keywords" content="power analysis, region of interest, effect size, R package, sample sizes, Bayesian updating">
 
 <title>Sample size estimation for task-related functional MRI studies using Bayesian updating</title>
@@ -107,10 +107,10 @@
 <meta name="citation_author" content="Joran Jongerling">
 <meta name="citation_author" content="Herbert Hoijtink">
 <meta name="citation_author" content="Eveline A. Crone">
-<meta name="citation_publication_date" content="2024-06-13">
-<meta name="citation_cover_date" content="2024-06-13">
+<meta name="citation_publication_date" content="2024-06-14">
+<meta name="citation_cover_date" content="2024-06-14">
 <meta name="citation_year" content="2024">
-<meta name="citation_online_date" content="2024-06-13">
+<meta name="citation_online_date" content="2024-06-14">
 <meta name="citation_language" content="en">
 <meta name="citation_reference" content="citation_title=Strategies for the development of volcanic hazard maps in monogenetic volcanic fields: The example of La Palma (Canary Islands);,citation_author=José Marrero;,citation_author=Alicia García;,citation_author=Manuel Berrocoso;,citation_author=Ángeles Llinares;,citation_author=Antonio Rodríguez-Losada;,citation_author=R. Ortiz;,citation_publication_date=2019-07;,citation_cover_date=2019-07;,citation_year=2019;,citation_doi=10.1186/s13617-019-0085-5;,citation_volume=8;,citation_journal_title=Journal of Applied Volcanology;">
 <meta name="citation_reference" content="citation_title=Rein in the four horsemen of irreproducibility;,citation_author=Dorothy Bishop;,citation_publication_date=2019-04;,citation_cover_date=2019-04;,citation_year=2019;,citation_fulltext_html_url=http://www.nature.com/articles/d41586-019-01307-2;,citation_issue=7753;,citation_doi=10.1038/d41586-019-01307-2;,citation_volume=568;,citation_language=en;,citation_journal_title=Nature;">
@@ -218,7 +218,7 @@ <h1 class="title">Sample size estimation for task-related functional MRI studies
                 <div>
             <div class="quarto-title-meta-heading">Published</div>
             <div class="quarto-title-meta-contents">
-              <p class="date">June 13, 2024</p>
+              <p class="date">June 14, 2024</p>
             </div>
           </div>
 
@@ -1232,7 +1232,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
 });
 </script>
 </div> <!-- /content -->
-<script>var lightboxQuarto = GLightbox({"loop":false,"selector":".lightbox","closeEffect":"zoom","descPosition":"bottom","openEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","selector":".lightbox","closeEffect":"zoom","descPosition":"bottom","loop":false});
 (function() {
   let previousOnload = window.onload;
   window.onload = () => {

diff --git a/index.pdf b/index.pdf
diff --git a/notebooks/figures-cohens_d.embed.ipynb b/notebooks/figures-cohens_d.embed.ipynb
@@ -10,7 +10,7 @@
     "\n",
     "Load libraries to produce figures:"
    ],
-   "id": "12f62f38-3caf-48de-b4d3-0f5c3c22325e"
+   "id": "965c58fd-f144-4302-8e4b-811784cb0724"
   },
   {
    "cell_type": "code",
@@ -26,15 +26,15 @@
     "install_github(\"eduardklap/neuroUp\")\n",
     "library(neuroUp)"
    ],
-   "id": "a9b6f287-225c-4a01-9d28-553836c3ab09"
+   "id": "d0eaae12-f3a3-456f-b11e-590e2d50bebc"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Set seed and create Figure 1A for the Feedback task DLPFC ROI:"
    ],
-   "id": "0fa61e97-ca75-4561-929a-0bc9785f1b10"
+   "id": "f0644099-4be1-45d4-9919-0e1a6c5f353c"
   },
   {
    "cell_type": "code",
@@ -53,15 +53,15 @@
     "                    k = 1000, \n",
     "                    name = \"A. Feedback DLPFC\")"
    ],
-   "id": "32a35652-1a16-459b-a6bb-917d8232761b"
+   "id": "1e61cfe1-4c1d-410f-9f0d-4c46849e41a5"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Set seed and create Figure 1B for the Gambling task NAcc ROI:"
    ],
-   "id": "370968a9-a8a4-4620-8537-6d54ce48b9cf"
+   "id": "17d6e9dc-d870-4c26-a5b3-fcfaca83470d"
   },
   {
    "cell_type": "code",
@@ -80,15 +80,15 @@
     "                    k = 1000, \n",
     "                    name = \"B. Gambling NAcc\")"
    ],
-   "id": "334beaa4-a9cd-4422-8890-a71e5c796311"
+   "id": "530c5043-ace6-4ce1-8795-1e940b3130df"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Set seed and create Figure 1C for the Self-evaluations task mPFC ROI:"
    ],
-   "id": "0f495a0c-02e5-45d6-a8db-0dcdf2422ae1"
+   "id": "bb78fa88-53bd-42bd-8337-b856462898fc"
   },
   {
    "cell_type": "code",
@@ -107,15 +107,15 @@
     "                    k = 10, \n",
     "                    name = \"C. Self-evaluations mPFC\")"
    ],
-   "id": "f2b98cdc-68ca-4b5e-9b39-00660ba12373"
+   "id": "699acff8-0cf8-4ca4-a111-9512c2c22777"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Set seed and create Figure 1D for the Gaining for self task NAcc ROI:"
    ],
-   "id": "b4e52e50-3169-4ef4-a66a-d846d0d87044"
+   "id": "a3a02ab8-1c48-4277-a469-760e232e3d39"
   },
   {
    "cell_type": "code",
@@ -134,15 +134,15 @@
     "                    k = 10, \n",
     "                    name = \"D. Gaining self NAcc\")"
    ],
-   "id": "2c1fc2d3-6a27-4f7e-b814-e99a82b71474"
+   "id": "8bfb19e4-ff16-46ee-a4b6-40dad4852768"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Combine figures 1A-D in one figure for Cohen’s d estimates:"
    ],
-   "id": "9716c865-0099-4e17-996b-4d408d674612"
+   "id": "39350bc2-7c73-4caa-a249-8df9f2f1485c"
   },
   {
    "cell_type": "code",
@@ -152,15 +152,15 @@
    "source": [
     "Fig1a$fig_cohens_d + Fig1b$fig_cohens_d + Fig1c$fig_cohens_d + Fig1d$fig_cohens_d"
    ],
-   "id": "d475a488-4dff-479a-bd3c-44ec49a12ecc"
+   "id": "f2a90480-c149-4a43-a15b-b136556a4baf"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Combine figures 1A-D in one figure for the proportion of intervals not containing the value 0:"
    ],
-   "id": "6117dbcf-0a42-4faf-96a4-6501e3bf5c84"
+   "id": "9b09048e-ea96-49ce-b863-0c6a1fa5f478"
   },
   {
    "cell_type": "code",
@@ -170,15 +170,15 @@
    "source": [
     "Fig1a$fig_d_nozero + Fig1b$fig_d_nozero + Fig1c$fig_d_nozero + Fig1d$fig_d_nozero"
    ],
-   "id": "b74ce21c-6fff-44a7-9ceb-06179a5c3185"
+   "id": "636ae763-78b6-45fb-81b8-6daa66874ce7"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Extract numbers to make table 2:"
    ],
-   "id": "8c266dbe-a6b5-4117-9d70-0616c092fb0f"
+   "id": "2865344b-e474-4fdf-97ae-929696edb81f"
   },
   {
    "cell_type": "code",
@@ -198,7 +198,7 @@
     "\n",
     "# use numbers to make a table in text"
    ],
-   "id": "87c637dd-d51f-42de-9657-675e5cb7ffcf"
+   "id": "3c50681d-f628-4c82-8dbb-3105ae0f20e0"
   }
  ],
  "nbformat": 4,

diff --git a/notebooks/figures-cohens_d.out.ipynb b/notebooks/figures-cohens_d.out.ipynb
@@ -10,7 +10,7 @@
     "\n",
     "Load libraries to produce figures:"
    ],
-   "id": "9de9b363-cc19-4bda-9996-ac63d9e294a4"
+   "id": "83eb5812-5a6d-4b3d-8056-87c0fd2620ca"
   },
   {
    "cell_type": "code",
@@ -26,15 +26,15 @@
     "install_github(\"eduardklap/neuroUp\")\n",
     "library(neuroUp)\n"
    ],
-   "id": "f95cc0a0-97f9-474e-8c4c-d0c6f8a51006"
+   "id": "dff4abd5-d346-4f2a-b82c-099dda20f65a"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Set seed and create Figure 1A for the Feedback task DLPFC ROI:"
    ],
-   "id": "f0a8104a-16b5-42c9-b6a0-324069d54fa6"
+   "id": "67a4fcac-6486-4349-979f-e38354327251"
   },
   {
    "cell_type": "code",
@@ -53,15 +53,15 @@
     "                    k = 1000, \n",
     "                    name = \"A. Feedback DLPFC\")\n"
    ],
-   "id": "dc6585c7-a185-4a59-8cfe-28e52ba8c060"
+   "id": "cae9d2c1-f332-42ee-8cfd-e7223368957e"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Set seed and create Figure 1B for the Gambling task NAcc ROI:"
    ],
-   "id": "b9f45310-01c1-49ac-a0ed-d877087a5473"
+   "id": "89f339aa-a071-4757-afc4-90a4fc96528d"
   },
   {
    "cell_type": "code",
@@ -80,15 +80,15 @@
     "                    k = 1000, \n",
     "                    name = \"B. Gambling NAcc\")\n"
    ],
-   "id": "38f6321d-6531-464c-994d-ba47d6bade05"
+   "id": "1e2fa765-a40a-460c-8899-bddc2d2e09bf"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Set seed and create Figure 1C for the Self-evaluations task mPFC ROI:"
    ],
-   "id": "848b1b8e-9c04-4be2-8d9a-bc2ffe893797"
+   "id": "eb400f59-c36c-4b9b-baf1-e07d028cf253"
   },
   {
    "cell_type": "code",
@@ -107,15 +107,15 @@
     "                    k = 10, \n",
     "                    name = \"C. Self-evaluations mPFC\")\n"
    ],
-   "id": "14913667-aed2-4da5-bba5-80ebb81e4df9"
+   "id": "c6004407-a8e5-44d7-85a1-0ce7b340df97"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Set seed and create Figure 1D for the Gaining for self task NAcc ROI:"
    ],
-   "id": "71fb6ce7-cbca-40c3-a0f3-a1bc15e50c60"
+   "id": "39263064-db9c-4153-8fe6-d3d4e617bff8"
   },
   {
    "cell_type": "code",
@@ -134,15 +134,15 @@
     "                    k = 10, \n",
     "                    name = \"D. Gaining self NAcc\")\n"
    ],
-   "id": "932addcb-f8b3-4c5a-b564-f53cfd58f136"
+   "id": "ac5a931b-1cc2-409e-8d47-f665a61ef0c8"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Combine figures 1A-D in one figure for Cohen’s d estimates:"
    ],
-   "id": "a7221330-16da-4c43-b831-a2e055125886"
+   "id": "07016677-583e-417f-a234-ceba8b6b8591"
   },
   {
    "cell_type": "code",
@@ -152,15 +152,15 @@
    "source": [
     "Fig1a$fig_cohens_d + Fig1b$fig_cohens_d + Fig1c$fig_cohens_d + Fig1d$fig_cohens_d\n"
    ],
-   "id": "66cd57be-95ed-4f89-9775-d2d0dd4b0ad7"
+   "id": "7ffa36ff-27c3-417c-af77-10b0bc4b7a81"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Combine figures 1A-D in one figure for the proportion of intervals not containing the value 0:"
    ],
-   "id": "d879e2ea-3265-4dae-a30c-75ace0513442"
+   "id": "c1461a0b-a49f-4472-90f6-d7ad2de535f5"
   },
   {
    "cell_type": "code",
@@ -170,15 +170,15 @@
    "source": [
     "Fig1a$fig_d_nozero + Fig1b$fig_d_nozero + Fig1c$fig_d_nozero + Fig1d$fig_d_nozero\n"
    ],
-   "id": "ea4f29da-7ef3-424f-aac8-f2d76785a98e"
+   "id": "52d1353b-a287-41a2-a4e2-bdcba2b9beb0"
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
     "Extract numbers to make table 2:"
    ],
-   "id": "8a483859-75c4-4e7b-b7be-8e896a1278e1"
+   "id": "02af453c-aaa1-416c-b326-d77953d60a93"
   },
   {
    "cell_type": "code",
@@ -198,7 +198,7 @@
     "\n",
     "# use numbers to make a table in text\n"
    ],
-   "id": "8b424f87-76dc-4bdd-8ee3-e8865decb028"
+   "id": "896699a2-b1b5-47af-a86d-afe2e95aff7c"
   }
  ],
  "nbformat": 4,