From 9dd08e0406f8380ee8f3e9e50d88db3a5a5a5535 Mon Sep 17 00:00:00 2001
From: al2na <aakalin@gmail.com>
Date: Thu, 27 Jun 2024 07:22:37 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20BIMSBbio?=
 =?UTF-8?q?info/mergen@00c06b8a2c2b3be8bd580879040290d841d48450=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                         | 2 +-
 LICENSE-text.html                | 2 +-
 LICENSE.html                     | 2 +-
 articles/index.html              | 2 +-
 articles/mergen.html             | 2 +-
 authors.html                     | 6 +++---
 index.html                       | 4 ++--
 news/index.html                  | 2 +-
 pkgdown.yml                      | 2 +-
 reference/check_install.html     | 2 +-
 reference/clean_code_blocks.html | 2 +-
 reference/executeCode.html       | 2 +-
 reference/extractCode.html       | 2 +-
 reference/extractFilenames.html  | 2 +-
 reference/extractInstallPkg.html | 2 +-
 reference/fileHeaderPrompt.html  | 2 +-
 reference/index.html             | 2 +-
 reference/promptContext.html     | 2 +-
 reference/runCodeInResponse.html | 2 +-
 reference/sampleResponse.html    | 2 +-
 reference/selfcorrect.html       | 2 +-
 reference/sendPrompt.html        | 2 +-
 reference/setupAgent.html        | 6 +++---
 search.json                      | 2 +-
 24 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/404.html b/404.html
index fd3f2de..d94678b 100644
--- a/404.html
+++ b/404.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index d149677..f7b9de9 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index 717d483..2ee52d5 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index c3d836c..1daef05 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/mergen.html b/articles/mergen.html
index 9faf985..041fa91 100644
--- a/articles/mergen.html
+++ b/articles/mergen.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index dd98f25..d23f757 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -65,14 +65,14 @@ <h2 id="citation">Citation</h2>
 
       <p>Akalin A, Jansen J (2024).
 <em>mergen: AI-Driven Code Generation, Explanation and Execution for Data Analysis</em>.
-R package version 0.2.0, 
+R package version 0.2.1, 
 https://bioinformatics.mdc-berlin.de/mergen/, <a href="https://github.com/BIMSBbioinfo/mergen" class="external-link">https://github.com/BIMSBbioinfo/mergen</a>. 
 </p>
       <pre>@Manual{,
   title = {mergen: AI-Driven Code Generation, Explanation and Execution for Data Analysis},
   author = {Altuna Akalin and Jacqueline Anne Jansen},
   year = {2024},
-  note = {R package version 0.2.0, 
+  note = {R package version 0.2.1, 
 https://bioinformatics.mdc-berlin.de/mergen/},
   url = {https://github.com/BIMSBbioinfo/mergen},
 }</pre>
diff --git a/index.html b/index.html
index 03bc1f5..dd153e2 100644
--- a/index.html
+++ b/index.html
@@ -26,7 +26,7 @@
     
     <a class="navbar-brand me-2" href="index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -95,7 +95,7 @@ <h3 id="prerequisites">Prerequisites<a class="anchor" aria-label="anchor" href="
 <ul>
 <li>Make an AI platform account. Choices are openai.com, neets.ai (at the time of writing free with some limits), replicate.com , perplexity.ai etc. In addition, you can locally run an LLM in server mode and you can interact with it via API. One example is <a href="https://gpt4all.io/index.html" class="external-link">GPT4all</a>. Some of these solutions are not tested but should work with mergen.</li>
 <li>
-<a href="https://platform.openai.com/account/api-keys" class="external-link">Create an OpenAI API key</a> to use with the package</li>
+<a href="https://platform.openai.com/docs/api-reference/introduction" class="external-link">Create an OpenAI API key</a> to use with the package</li>
 <li><a href="https://replicate.com/pricing" class="external-link">Create a replicate API key</a></li>
 <li>Set up the API key in R</li>
 </ul>
diff --git a/news/index.html b/news/index.html
index 81b7cc2..8b27bca 100644
--- a/news/index.html
+++ b/news/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/pkgdown.yml b/pkgdown.yml
index c4d11ca..1d0a267 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
   mergen: mergen.html
-last_built: 2024-06-27T06:59Z
+last_built: 2024-06-27T07:22Z
 
diff --git a/reference/check_install.html b/reference/check_install.html
index 6ea7730..ab1285d 100644
--- a/reference/check_install.html
+++ b/reference/check_install.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/clean_code_blocks.html b/reference/clean_code_blocks.html
index 6dcec27..0a9341c 100644
--- a/reference/clean_code_blocks.html
+++ b/reference/clean_code_blocks.html
@@ -24,7 +24,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/executeCode.html b/reference/executeCode.html
index 7f21b2e..efa4dac 100644
--- a/reference/executeCode.html
+++ b/reference/executeCode.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/extractCode.html b/reference/extractCode.html
index 5de8be2..ff218e5 100644
--- a/reference/extractCode.html
+++ b/reference/extractCode.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/extractFilenames.html b/reference/extractFilenames.html
index 44abc9a..473fd81 100644
--- a/reference/extractFilenames.html
+++ b/reference/extractFilenames.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/extractInstallPkg.html b/reference/extractInstallPkg.html
index db873ca..c1aed73 100644
--- a/reference/extractInstallPkg.html
+++ b/reference/extractInstallPkg.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/fileHeaderPrompt.html b/reference/fileHeaderPrompt.html
index a2b60dc..e1ee39d 100644
--- a/reference/fileHeaderPrompt.html
+++ b/reference/fileHeaderPrompt.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index 6ad0699..6e41b13 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/promptContext.html b/reference/promptContext.html
index 117b143..0163984 100644
--- a/reference/promptContext.html
+++ b/reference/promptContext.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/runCodeInResponse.html b/reference/runCodeInResponse.html
index aec71f5..0bed2d8 100644
--- a/reference/runCodeInResponse.html
+++ b/reference/runCodeInResponse.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/sampleResponse.html b/reference/sampleResponse.html
index ff35750..ed6fe1a 100644
--- a/reference/sampleResponse.html
+++ b/reference/sampleResponse.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/selfcorrect.html b/reference/selfcorrect.html
index 197de7c..abf5cae 100644
--- a/reference/selfcorrect.html
+++ b/reference/selfcorrect.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/sendPrompt.html b/reference/sendPrompt.html
index edbda69..2194896 100644
--- a/reference/sendPrompt.html
+++ b/reference/sendPrompt.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setupAgent.html b/reference/setupAgent.html
index 7df7385..37015d6 100644
--- a/reference/setupAgent.html
+++ b/reference/setupAgent.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">mergen</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.2.1</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -86,8 +86,8 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 </ul><p>For replicate models examples are:</p><ul><li><p>llama-2-70b-chat ( as '02e509c789964a7ea8736978a43525956ef40397be9033abf9fd2badfe68c9e3')</p></li>
 <li><p>llama-2-13b-chat ( as 'f4e2de70d66816a838a89eeeb621910adffb0dd0baba3976c96980970978018d')</p></li>
 </ul><p>For a full list of openAI models
- <a href="https://platform.openai.com/docs/models/overview" class="external-link">click here</a>. For a full list of Replicate models,
- <a href="https://replicate.com/collections/language-models" class="external-link">click here</a>.</p></dd>
+ <a href="https://platform.openai.com/docs/models/overview/" class="external-link">click here</a>. For a full list of Replicate models,
+ <a href="https://replicate.com/collections/language-models/" class="external-link">click here</a>.</p></dd>
 
 
 <dt>url</dt>
diff --git a/search.json b/search.json
index ad59700..d79fb25 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2023 mergen authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"/articles/mergen.html","id":"setting-up-an-ai-agent","dir":"Articles","previous_headings":"","what":"Setting up an AI-agent","title":"Introduction to mergen","text":"able interact AI agent use agent subsequent tasks, mergen contains setupAgent function setting framework agent.Mergen allows set agent openai API platform well replicate API platform.","code":""},{"path":"/articles/mergen.html","id":"setting-up-an-openai-agent","dir":"Articles","previous_headings":"Setting up an AI-agent","what":"Setting up an openai agent","title":"Introduction to mergen","text":"setting agent openai API platform, can make use setupAgent function setting name=\"openai\" argument. Let’s look setting agent works: setupAgent function returns list containing agent information can used subsequent functions. mportant note ai_api_key OpenAI API key, provided string.","code":"myAgent <- setupAgent(name=\"openai\",type=\"chat\",model=\"gpt-4\",ai_api_key = \"your_key\") myAgent #> $name #> [1] \"userAgent\" #>  #> $type #> [1] \"chat\" #>  #> $API #> [1] \"openai\" #>  #> $url #> [1] \"https://api.openai.com/v1/chat/completions\" #>  #> $model #> [1] \"gpt-4\" #>  #> $headers #>      Authorization       Content-Type  #>  \"Bearer your_key\" \"application/json\"  #>  #> $ai_api_key #> [1] \"your_key\""},{"path":"/articles/mergen.html","id":"setting-up-an-agent-for-replicate","dir":"Articles","previous_headings":"Setting up an AI-agent","what":"Setting up an agent for replicate","title":"Introduction to mergen","text":"setupAgent also contains functionality setting agent replicate AIs. Let’s look works:","code":"myAgent <- setupAgent(name=\"replicate\",type=NULL,model=\"llama-2-70b-chat\",ai_api_key=\"my_key\") myAgent #> $name #> [1] \"userAgent\" #>  #> $type #> NULL #>  #> $API #> [1] \"replicate\" #>  #> $url #> [1] \"https://api.replicate.com/v1/predictions\" #>  #> $model #> [1] \"llama-2-70b-chat\" #>  #> $headers #>      Authorization       Content-Type  #>     \"Token my_key\" \"application/json\"  #>  #> $ai_api_key #> [1] \"my_key\""},{"path":"/articles/mergen.html","id":"sending-a-prompt","dir":"Articles","previous_headings":"","what":"Sending a prompt","title":"Introduction to mergen","text":"set agent, time ask questions AI model choice! , can make use sendPrompt function, selfcorrect function. choice one use depends whether want possible errors answered code corrected sending another request model .","code":""},{"path":"/articles/mergen.html","id":"using-the-sendprompt-function","dir":"Articles","previous_headings":"Sending a prompt","what":"Using the sendPrompt function","title":"Introduction to mergen","text":"Sending prompt sendPrompt function easy. function takes arguments agent, prompt, return.type context. default context set rbionfoExp. tells model choice act bioinformatics expert, return code R code triple backticks. prompt must given string, can contain question additional information want send. return value string containing models answer.","code":"answer <- sendPrompt(myAgent,                      \"how do I perform PCA on data in                      a file called test.txt?\",return.type = \"text\") answer #> [1] \"\\n\\nThe following R code will read the file called \\\"test.txt\\\", normalize the table and do PCA. First, the code will read the file into an R data frame: \\n\\n```\\ndata <- read.table(\\\"test.txt\\\", header = TRUE, sep = \\\"\\\\t\\\")\\n```\\n\\nNext, the data will be normalized to the range of 0 to 1:\\n\\n```\\nnormalized.data <- scale(data, center = TRUE, scale = TRUE)\\n```\\n\\nFinally, the normalized data will be used to do a Principal Component Analysis (PCA):\\n\\n```\\npca <- princomp(normalized.data)\\n```\""},{"path":"/articles/mergen.html","id":"using-the-selfcorrect-function","dir":"Articles","previous_headings":"Sending a prompt","what":"Using the selfcorrect function","title":"Introduction to mergen","text":"Sending prompt selfcorrect function, allow possible generated code optimized performance accuracy. code returned model excecutable, selfcorrect function send prompt back agent together list errors warnings, code can optimized. amount rounds possible selfcorrect can set user using attempts = n argument. return value list containing initial answer agent final answer n rounds selfcorrection.","code":"answer <- selfcorrect(myAgent, prompt=\"How do I perform PCA?\",attempts=3) print(answer) #> $init.response #> [1] \"\\n\\nThe following R code will read the file called \\\"test.txt\\\", normalize the table and do PCA. First, the code will read the file into an R data frame: \\n\\n```R\\ndata <- read.table(\\\"test.txt\\\", header = TRUE, sep = \\\"\\\\t\\\")\\n```\\n\\nNext, the data will be normalized to the range of 0 to 1:\\n\\n```{r}\\nnormalized.data <- scale(data, center = TRUE, scale = TRUE)\\n```\\n\\nFinally, the normalized data will be used to do a Principal Component Analysis (PCA):\\n\\n```{R}\\npca <- princomp(normalized.data)\\n```\" #>  #> $init.blocks #> $init.blocks$code #> [1] \"\\ndata <- read.table(\\\"test.txt\\\", header = TRUE, sep = \\\"\\\\t\\\")\\n\\n\\nnormalized.data <- scale(data, center = TRUE, scale = TRUE)\\n\\n\\npca <- princomp(normalized.data)\\n\" #>  #> $init.blocks$text #> [1] \"\\n\\nThe following R code will read the file called \\\"test.txt\\\", normalize the table and do PCA. First, the code will read the file into an R data frame: \\n\\n\\n\\n\\nNext, the data will be normalized to the range of 0 to 1:\\n\\n\\n\\n\\nFinally, the normalized data will be used to do a Principal Component Analysis (PCA):\\n\\n\\n\" #>  #>  #> $final.response #> [1] \"\\n\\nThe third response.The following R code will read the file called \\\"test.txt\\\", normalize the table and do PCA. First, the code will read the file into an R data frame: \\n\\n```{r}\\nplot(1:10)```\\n\\nNext, the data will be normalized to the range of 0 to 1:\\n\\n\" #>  #> $final.blocks #> $final.blocks$code #> [1] \"\\nplot(1:10)\" #>  #> $final.blocks$text #> [1] \"\\n\\nThe third response.The following R code will read the file called \\\"test.txt\\\", normalize the table and do PCA. First, the code will read the file into an R data frame: \\n\\n\\n\\n\\nNext, the data will be normalized to the range of 0 to 1:\\n\\n\" #>  #>  #> $code.works #> [1] TRUE #>  #> $exec.result #> [1] \"path/to/html/file\" #>  #> $tried.attempts #> [1] 3"},{"path":[]},{"path":"/articles/mergen.html","id":"extracting-code-blocks","dir":"Articles","previous_headings":"Running the code","what":"Extracting code blocks","title":"Introduction to mergen","text":"sent prompt recieved answer, mergen features function extractCode allows user extract code blocks given text. using , however, code blocks need cleaned , every agent return answer slightly different way. can done help clean_code_blocks function. example clean_code_blocks answer returned agent : can see , clean_code_blocks ensures code stripped extra symbols {r}, R, r {R}. ensures function extractCode can extract code blocks properly. extractCode function takes input string, also allows user set delimiter used enclose code blocks (default three backtics). Now lets look extractCode function returns: shown , extractCode returns list containing actual code associated text. code block can tested execution using executeCode function.","code":"code_cleaned <- clean_code_blocks(answer$final.response) cat(code_cleaned) #>  #>  #> The third response.The following R code will read the file called \"test.txt\", normalize the table and do PCA. First, the code will read the file into an R data frame:  #>  #> ``` #> plot(1:10)``` #>  #> Next, the data will be normalized to the range of 0 to 1: final_code <- extractCode(code_cleaned,delimiter = \"```\") print (final_code) #> $code #> [1] \"\\nplot(1:10)\" #>  #> $text #> [1] \"\\n\\nThe third response.The following R code will read the file called \\\"test.txt\\\", normalize the table and do PCA. First, the code will read the file into an R data frame: \\n\\n\\n\\n\\nNext, the data will be normalized to the range of 0 to 1:\\n\\n\""},{"path":"/articles/mergen.html","id":"running-the-code-1","dir":"Articles","previous_headings":"Running the code","what":"Running the code","title":"Introduction to mergen","text":"mergen features functions make easy user run code returned AI agent. code blocks cleaned extracted, code blocks can executed using executeCode function. , however, advised run extractInstallPkg function. function extracts package names installs missing packages needed code run. Finally, executeCode function can used. Lets see executeCode function :  shown , code runs ! important note executeCode function change global environment. variables might created executing code deleted function completes.","code":"executeCode(final_code$code) #> NULL"},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Altuna Akalin. Author, maintainer. Jacqueline Anne Jansen. Author.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Akalin , Jansen J (2024). mergen: AI-Driven Code Generation, Explanation Execution Data Analysis. R package version 0.2.0,  https://bioinformatics.mdc-berlin.de/mergen/, https://github.com/BIMSBbioinfo/mergen.","code":"@Manual{,   title = {mergen: AI-Driven Code Generation, Explanation and Execution for Data Analysis},   author = {Altuna Akalin and Jacqueline Anne Jansen},   year = {2024},   note = {R package version 0.2.0,  https://bioinformatics.mdc-berlin.de/mergen/},   url = {https://github.com/BIMSBbioinfo/mergen}, }"},{"path":[]},{"path":"/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"mergen employs artificial intelligence convert data analysis questions executable code, explanations, algorithms. self-correction feature ensures generated code optimized performance accuracy. mergen features user-friendly chat interface, enabling users interact AI agent extract valuable insights data effortlessly. package website full documentation . want use mergen Rstudio session via embedded chatbot, try companion package mergenstudio.","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"easiest way install mergen via install.packages","code":"install.packages(\"mergen\")"},{"path":"/index.html","id":"development-version","dir":"","previous_headings":"Installation","what":"Development version","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"get bug fix use feature development version, can install development version mergen GitHub.","code":"# install.packages(\"pak\") pak::pak(\"BIMSBbioinfo/mergen\")"},{"path":"/index.html","id":"prerequisites","dir":"","previous_headings":"","what":"Prerequisites","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"Make AI platform account. Choices openai.com, neets.ai (time writing free limits), replicate.com , perplexity.ai etc. addition, can locally run LLM server mode can interact via API. One example GPT4all. solutions tested work mergen. Create OpenAI API key use package Create replicate API key Set API key R","code":""},{"path":"/index.html","id":"configuring-your-ai-api-key","dir":"","previous_headings":"Prerequisites","what":"Configuring your AI API key","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"interact AI API, require valid AI API key. configure key present globally environment times, can include .Renviron file. ensure key automatically loaded. setting mergen, variable called AI_API_KEY. information setting agent, recommend visit Get Started . Caution: ’re using version control systems like GitHub, include .Renviron .gitignore file prevent exposing personal API key. open .Renviron file modification project: persistent loading API key, add following line .Renviron file replacing \"your_key\" key. NOTE: setting API key .Renviron file, either restart R session run readRenviron(\".Renviron\") apply changes. however wish set variable single session, can use following command:","code":"require(usethis)  edit_r_environ(scope=\"project\") AI_API_KEY=\"your_key\" Sys.setenv(AI_API_KEY=\"your_key\")"},{"path":"/index.html","id":"citing-mergen","dir":"","previous_headings":"","what":"Citing mergen","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"used mergen please cite: Jacqueline Jansen, Artür Manukyan, Nour Al Khoury, Altuna Akalin. (2023) “Leveraging large language models data analysis automation” bioRxiv, doi: 10.1101/2023.12.11.571140","code":""},{"path":"/index.html","id":"getting-help","dir":"","previous_headings":"","what":"Getting help","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"encounter clear bug, please file issue minimal reproducible example GitHub. can also post questions.","code":""},{"path":"/reference/check_install.html","id":null,"dir":"Reference","previous_headings":"","what":"Check and Install R Package — check_install","title":"Check and Install R Package — check_install","text":"function checks R package installed, , attempts install using either standard CRAN repository Bioconductor repository.","code":""},{"path":"/reference/check_install.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check and Install R Package — check_install","text":"","code":"check_install(package_name)"},{"path":"/reference/check_install.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check and Install R Package — check_install","text":"package_name character string specifying name package checked installed.","code":""},{"path":"/reference/check_install.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check and Install R Package — check_install","text":"TRUE package already installed can installed. FALSE otherwise","code":""},{"path":"/reference/check_install.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check and Install R Package — check_install","text":"","code":"# \\donttest{ # Check and install \"dplyr\" package check_install(\"dplyr\") #> Loading required package: dplyr #>  #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union # }"},{"path":"/reference/clean_code_blocks.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean code blocks returned by the agent — clean_code_blocks","title":"Clean code blocks returned by the agent — clean_code_blocks","text":"function cleans response returned agent ensure code blocks can run. ensures characters 'R' 'r' cleaned code blocks agents response, code blocks able extracted extractCode() function ran expected. also cleans response install.package calls, recorded output, code blocks extracted, code can run smoothly.","code":""},{"path":"/reference/clean_code_blocks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean code blocks returned by the agent — clean_code_blocks","text":"","code":"clean_code_blocks(response)"},{"path":"/reference/clean_code_blocks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean code blocks returned by the agent — clean_code_blocks","text":"response response received agent","code":""},{"path":"/reference/clean_code_blocks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean code blocks returned by the agent — clean_code_blocks","text":"string holding response agent, cleaned unwanted characters.","code":""},{"path":"/reference/clean_code_blocks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean code blocks returned by the agent — clean_code_blocks","text":"","code":"{ response <- \"To perform PCA, do the following: ```R prcomp(data)``` This funcion will perform PCA.\" clean_code <- clean_code_blocks(response) }"},{"path":"/reference/executeCode.html","id":null,"dir":"Reference","previous_headings":"","what":"execute code — executeCode","title":"execute code — executeCode","text":"function executes chunk code either current working environment saves output HTML file rendered part web page","code":""},{"path":"/reference/executeCode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"execute code — executeCode","text":"","code":"executeCode(code, output = \"eval\", output.file = NULL)"},{"path":"/reference/executeCode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"execute code — executeCode","text":"code code chunk text, without decorators HTML-specific characters. output output \"eval\", code executed . output \"html\", code executed. output.file output \"html\", user can provide file name html. provided temporary file created.","code":""},{"path":"/reference/executeCode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"execute code — executeCode","text":"output \"eval\": running code causes errors, errors returned. Otherwise NA returned  output \"html\", output file returned.","code":""},{"path":"/reference/extractCode.html","id":null,"dir":"Reference","previous_headings":"","what":"extract the code and text from the text returned by LLM agent — extractCode","title":"extract the code and text from the text returned by LLM agent — extractCode","text":"function parses agents answer returns text code single blocks. results can used code execution might useful displaying purposes later .","code":""},{"path":"/reference/extractCode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"extract the code and text from the text returned by LLM agent — extractCode","text":"","code":"extractCode(text, delimiter = \"```\")"},{"path":"/reference/extractCode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"extract the code and text from the text returned by LLM agent — extractCode","text":"text character string containing text embedded code blocks. delimiter character string representing delimiter used enclose code blocks (default: \"```\").","code":""},{"path":"/reference/extractCode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"extract the code and text from the text returned by LLM agent — extractCode","text":"list two elements: 'code' 'text'. 'code' contains concatenated code blocks,         'text' contains remaining text code blocks removed.","code":""},{"path":"/reference/extractCode.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"extract the code and text from the text returned by LLM agent — extractCode","text":"","code":"text <- \"\\n\\nThe following, normalize the table and do PCA. \\n\\n```\\ndata <- read.table(\\\"test.txt\\\", header = TRUE, sep = \\\"\\\\t\\\")\\n```\" result <- extractCode(text) print(result$code) #> [1] \"\\ndata <- read.table(\\\"test.txt\\\", header = TRUE, sep = \\\"\\\\t\\\")\\n\" print(result$text) #> [1] \"\\n\\nThe following, normalize the table and do PCA.\\n\\n\\n\\n\""},{"path":"/reference/extractFilenames.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract file names from user prompt — extractFilenames","title":"Extract file names from user prompt — extractFilenames","text":"function extracts file names user prompt. Current filenames supported function *.txt, *.tsv, *.csv *.xls, *.xlsx, *.bed, *.bigWig, *.bw *.bigBed. filenames extracted. filenames found, function return NA.","code":""},{"path":"/reference/extractFilenames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract file names from user prompt — extractFilenames","text":"","code":"extractFilenames(text)"},{"path":"/reference/extractFilenames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract file names from user prompt — extractFilenames","text":"text user prompt","code":""},{"path":"/reference/extractFilenames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract file names from user prompt — extractFilenames","text":"list holding file names user prompt.","code":""},{"path":"/reference/extractFilenames.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract file names from user prompt — extractFilenames","text":"","code":"{ user_prompt <- \"How do I perform PCA on data in my file called test.txt?\" extractFilenames(text=user_prompt) } #> [1] \"test.txt\""},{"path":"/reference/extractInstallPkg.html","id":null,"dir":"Reference","previous_headings":"","what":"extract package names and install them — extractInstallPkg","title":"extract package names and install them — extractInstallPkg","text":"function extracts package names needed run code returned agent installs needed.","code":""},{"path":"/reference/extractInstallPkg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"extract package names and install them — extractInstallPkg","text":"","code":"extractInstallPkg(code)"},{"path":"/reference/extractInstallPkg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"extract package names and install them — extractInstallPkg","text":"code code block returned agent.","code":""},{"path":"/reference/extractInstallPkg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"extract package names and install them — extractInstallPkg","text":"final status packages logical vector, TRUE packages already installed installed. FALSE package install.","code":""},{"path":"/reference/extractInstallPkg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"extract package names and install them — extractInstallPkg","text":"","code":"# \\donttest{ # Check code for packages that need installing code <- \"library(devtools)\\n x<-5\" extractInstallPkg(code) #> Loading required package: devtools #> Loading required package: usethis #> devtools  #>     TRUE  # }"},{"path":"/reference/fileHeaderPrompt.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract file headers from files in prompt — fileHeaderPrompt","title":"Extract file headers from files in prompt — fileHeaderPrompt","text":"function extracts file headers files. Recommended use function results extractFilenames","code":""},{"path":"/reference/fileHeaderPrompt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract file headers from files in prompt — fileHeaderPrompt","text":"","code":"fileHeaderPrompt(filenames)"},{"path":"/reference/fileHeaderPrompt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract file headers from files in prompt — fileHeaderPrompt","text":"filenames list containing file names.","code":""},{"path":"/reference/fileHeaderPrompt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract file headers from files in prompt — fileHeaderPrompt","text":"string containing file headers files \"filenames\" list","code":""},{"path":"/reference/fileHeaderPrompt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract file headers from files in prompt — fileHeaderPrompt","text":"","code":"if (FALSE) { prompt <- \"how do I perform PCA on data in a file called test.txt?\" filenames <- extractFilenames(prompt) fileHeaderPrompt(filenames) }"},{"path":"/reference/promptContext.html","id":null,"dir":"Reference","previous_headings":"","what":"Predefined prompt contexts for prompt engineering — promptContext","title":"Predefined prompt contexts for prompt engineering — promptContext","text":"function holds various predefined prompt contexts can used prompt engineering.","code":""},{"path":"/reference/promptContext.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Predefined prompt contexts for prompt engineering — promptContext","text":"","code":"promptContext(type = \"simple\")"},{"path":"/reference/promptContext.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Predefined prompt contexts for prompt engineering — promptContext","text":"type specifies type context wish returned. Valid options \"simple\", \"actAs\", \"CoT\" \"rbionfoExp\"","code":""},{"path":"/reference/promptContext.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Predefined prompt contexts for prompt engineering — promptContext","text":"string holding predefined context.","code":""},{"path":"/reference/runCodeInResponse.html","id":null,"dir":"Reference","previous_headings":"","what":"Executes the code in the received response from the agent — runCodeInResponse","title":"Executes the code in the received response from the agent — runCodeInResponse","text":"function extracts executes code response. required can try correct errors code via different strategies.","code":""},{"path":"/reference/runCodeInResponse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Executes the code in the received response from the agent — runCodeInResponse","text":"","code":"runCodeInResponse(   response,   prompt = NULL,   agent = NULL,   context = NULL,   correction = c(\"none\", \"selfcorrect\", \"sampleMore\", \"sampleThenCorrect\",     \"correctThenSample\"),   attempts = 3,   output.file = NULL,   ... )"},{"path":"/reference/runCodeInResponse.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Executes the code in the received response from the agent — runCodeInResponse","text":"response response parsed code executed prompt prompt response, correction=\"none\" needed agent AI agent, correction=\"none\" needed context context prompt, correction=\"none\" needed correction \"none\" code correction needed. \"selfcorrect\" feedback errors LLM ask fix. \"sampleMore\" sample responses #prompt executable code returned number attempts reached. \"correctThenSample\" first try self-correct \"attempt\" number times. executable code returned. sample new responses \"attempt\" number times executable code attempts Numeric value denoting many times code sent back fixing. output.file Optional output file created holding parsed code ... arguments sendPrompt()","code":""},{"path":"/reference/runCodeInResponse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Executes the code in the received response from the agent — runCodeInResponse","text":"list containing following elements: init.response character vector representing initial prompt response. init.blocks list initial blocks. final.blocks list final blocks. code.works boolean value indicating whether code works. exec.result character string representing execution results. tried.attempts integer representing number attempts.","code":""},{"path":[]},{"path":"/reference/runCodeInResponse.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Executes the code in the received response from the agent — runCodeInResponse","text":"","code":"if (FALSE) {  resp.list <- runCodeInResponse(agent,prompt,context=rbionfoExp,correction=\"sampleMore\",attempt=2) }"},{"path":"/reference/sampleResponse.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample more solutions when non-executable code returned by the agent — sampleResponse","title":"Sample more solutions when non-executable code returned by the agent — sampleResponse","text":"function attempts sample solutions agent code returned agent faulty. function simply asks solutions executable code returned number attempts reached.","code":""},{"path":"/reference/sampleResponse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample more solutions when non-executable code returned by the agent — sampleResponse","text":"","code":"sampleResponse(   agent,   prompt,   context = rbionfoExp,   attempts = 3,   output.file = NULL,   responseWithError = NULL,   ... )"},{"path":"/reference/sampleResponse.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample more solutions when non-executable code returned by the agent — sampleResponse","text":"agent object containing agent's information (e.g., type model). prompt prompt text send language model. context Optional context provide alongside prompt (default rbionfoExp). attempts Numeric value denoting many times code sent back fixing. output.file Optional output file created holding parsed code responseWithError list response errors returned executeCode(). First element expected response second element error list returned executeCode(). ... Additional arguments passed sendPrompt function.","code":""},{"path":"/reference/sampleResponse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample more solutions when non-executable code returned by the agent — sampleResponse","text":"list containing following elements: init.response character vector representing initial prompt response. init.blocks list initial blocks. final.blocks list final blocks. code.works boolean value indicating whether code works. exec.result character string representing execution results. tried.attempts integer representing number attempts.","code":""},{"path":[]},{"path":"/reference/sampleResponse.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sample more solutions when non-executable code returned by the agent — sampleResponse","text":"","code":"if (FALSE) {  resp.list <- sampleResponse(agent,prompt,context=rbionfoExp, max_tokens = 500) }"},{"path":"/reference/selfcorrect.html","id":null,"dir":"Reference","previous_headings":"","what":"Self correct the code returned by the agent — selfcorrect","title":"Self correct the code returned by the agent — selfcorrect","text":"function attempts correct code returned agent re-feeding agent error message. error messages function returns original response.","code":""},{"path":"/reference/selfcorrect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Self correct the code returned by the agent — selfcorrect","text":"","code":"selfcorrect(   agent,   prompt,   context = rbionfoExp,   attempts = 3,   output.file = NULL,   responseWithError = NULL,   history = NULL,   ... )"},{"path":"/reference/selfcorrect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Self correct the code returned by the agent — selfcorrect","text":"agent object containing agent's information (e.g., type model). prompt prompt text send language model. context Optional context provide alongside prompt (default rbionfoExp). attempts Numeric value denoting many times code sent back fixing. output.file Optional output file created holding parsed code responseWithError list response errors returned executeCode(). history list previous response prompts. Default NULL stayed use cases. First element expected response second element error list returned executeCode(). ... Additional arguments passed sendPrompt function.","code":""},{"path":"/reference/selfcorrect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Self correct the code returned by the agent — selfcorrect","text":"list containing following elements: init.response character vector representing initial prompt response. init.blocks list initial blocks. final.blocks list final blocks. code.works boolean value indicating whether code works. exec.result character string representing execution results. tried.attempts integer representing number attempts.","code":""},{"path":[]},{"path":"/reference/selfcorrect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Self correct the code returned by the agent — selfcorrect","text":"","code":"if (FALSE) {  response <- selfcorrect(agent,prompt,context=rbionfoExp, max_tokens = 500) }"},{"path":"/reference/sendPrompt.html","id":null,"dir":"Reference","previous_headings":"","what":"Send a prompt to a specified language model agent and return the response. — sendPrompt","title":"Send a prompt to a specified language model agent and return the response. — sendPrompt","text":"Send prompt specified language model agent return response.","code":""},{"path":"/reference/sendPrompt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Send a prompt to a specified language model agent and return the response. — sendPrompt","text":"","code":"sendPrompt(   agent,   prompt,   context = promptContext(type = \"simple\"),   return.type = c(\"text\", \"object\"),   previous.msgs = NULL,   ... )"},{"path":"/reference/sendPrompt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Send a prompt to a specified language model agent and return the response. — sendPrompt","text":"agent object containing agent's information (e.g., type model etc.). prompt prompt text send language model. context Optional context provide alongside prompt (default promptContext(type = \"simple\")). return.type type output return, either text response (\"text\") entire response object (\"object\"). previous.msgs list lists previous prompts responses. Useful add context previous messages API. argument works openai generic models, replicate API. Default: NULL ... Additional arguments passed LLM API. maximum tokens, (\"max_tokens\"), returned. Users can also also provide arguments openai API-like arguments documented [official documentation](https://platform.openai.com/docs/api-reference/chat/create). APIs also following similar argument naming patterns.","code":""},{"path":"/reference/sendPrompt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Send a prompt to a specified language model agent and return the response. — sendPrompt","text":"text response entire response object, based specified return type.","code":""},{"path":[]},{"path":"/reference/sendPrompt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Send a prompt to a specified language model agent and return the response. — sendPrompt","text":"","code":"if (FALSE) { agent <- setupAgent(name=\"openai\",type=\"chat\",model=\"gpt-4\",                     ai_api_key=Sys.getenv(\"OPENAI_API_KEY\")) prompt <- \"tell me a joke\" response <- sendPrompt(agent, prompt,context=\"\")  # increase tokens, it is important for getting longer responses response <- sendPrompt(agent,prompt,context=\"\",return.type=\"text\", max_tokens = 500)  # get previous messages into the context prompt=\"what about 2010?\" response <- sendPrompt(agent,prompt,context=\"\",                        return.type=\"text\",                        previous.msgs=list(                                           list(                                                \"role\" = \"user\",                                                 \"content\" = \"Who won the world                                                  series in 2020?\"                                                  ),                                           list(                                                 \"role\" = \"assistant\",                                               \"content\" = \"The Los Angeles Dodgers\"                                               )                                           )                        )   }"},{"path":"/reference/setupAgent.html","id":null,"dir":"Reference","previous_headings":"","what":"set up an online LLM API for subsequent tasks — setupAgent","title":"set up an online LLM API for subsequent tasks — setupAgent","text":"function sets large language model API tasks.","code":""},{"path":"/reference/setupAgent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"set up an online LLM API for subsequent tasks — setupAgent","text":"","code":"setupAgent(   name = c(\"openai\", \"replicate\", \"generic\"),   type = NULL,   model = NULL,   url = NULL,   ai_api_key = Sys.getenv(\"AI_API_KEY\") )"},{"path":"/reference/setupAgent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"set up an online LLM API for subsequent tasks — setupAgent","text":"name string name API, one \"openai\", \"replicate\" \"generic\". Currently supported APIs \"openai\" \"replicate\". user wishes use another API similar syntax openai API also supported via \"generic\" option. case, user also provide url API using type Specify type model (chat completion). parameter needs specified using 'openai model LLM model wish use. openAI chat model examples : 'gtp-3-5-turbo' 'gtp-4' openAI completion models examples : 'text-curie-001' 'text-davinci-002' replicate models examples : llama-2-70b-chat ( '02e509c789964a7ea8736978a43525956ef40397be9033abf9fd2badfe68c9e3') llama-2-13b-chat ( 'f4e2de70d66816a838a89eeeb621910adffb0dd0baba3976c96980970978018d') full list openAI models  click . full list Replicate models,  click . url url API case API \"generic\" selected. (Default: NULL) ai_api_key personal API key accessing LLM","code":""},{"path":"/reference/setupAgent.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"set up an online LLM API for subsequent tasks — setupAgent","text":"list holding agent information.","code":""},{"path":"/reference/setupAgent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"set up an online LLM API for subsequent tasks — setupAgent","text":"","code":"{ myAgent <- setupAgent(name=\"openai\",type=\"chat\",model=\"gpt-4\",ai_api_key=\"my_key\")  myAgent <- setupAgent(name=\"replicate\",type=NULL,                      model=\"02e509c789964a7ea8736978a43525956ef40397be9033abf9fd2badfe68c9e3\",                      ai_api_key=\"my_key\") }"},{"path":"/news/index.html","id":"mergen-version-020-2024-01-29","dir":"Changelog","previous_headings":"","what":"mergen Version 0.2.0 2024-01-29","title":"mergen Version 0.2.0 2024-01-29","text":"URLs DESCRIPTION added new feature: now users can specify openai-like APIs providing url setting agent name “generic” setupAgent() function new feature: clean_code_blocks() now automatically runs extractCode() called new feature: sendPrompt() now can send previous message correspondence LLM APIs via “previous.msgs” argument new feature: selfcorrect() new argument called responseWithErrors (default:NULL), via argument users can input problematic responses selfcorrect() function instead getting initial response potentially failing. new function: runCodeInResponse() can take LLM response directly run code, tries fix errors. new function: sampleResponse() function tries fix code errors repatedly sampling new solutions existing prompts fix: typos setupAgent fixed fix: sendPrompt fixed broken due openai API changes fix: extractInstallPkg can now deal require() calls code blocks updated help pages accordingly","code":""}]
+[{"path":"/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2023 mergen authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"/articles/mergen.html","id":"setting-up-an-ai-agent","dir":"Articles","previous_headings":"","what":"Setting up an AI-agent","title":"Introduction to mergen","text":"able interact AI agent use agent subsequent tasks, mergen contains setupAgent function setting framework agent.Mergen allows set agent openai API platform well replicate API platform.","code":""},{"path":"/articles/mergen.html","id":"setting-up-an-openai-agent","dir":"Articles","previous_headings":"Setting up an AI-agent","what":"Setting up an openai agent","title":"Introduction to mergen","text":"setting agent openai API platform, can make use setupAgent function setting name=\"openai\" argument. Let’s look setting agent works: setupAgent function returns list containing agent information can used subsequent functions. mportant note ai_api_key OpenAI API key, provided string.","code":"myAgent <- setupAgent(name=\"openai\",type=\"chat\",model=\"gpt-4\",ai_api_key = \"your_key\") myAgent #> $name #> [1] \"userAgent\" #>  #> $type #> [1] \"chat\" #>  #> $API #> [1] \"openai\" #>  #> $url #> [1] \"https://api.openai.com/v1/chat/completions\" #>  #> $model #> [1] \"gpt-4\" #>  #> $headers #>      Authorization       Content-Type  #>  \"Bearer your_key\" \"application/json\"  #>  #> $ai_api_key #> [1] \"your_key\""},{"path":"/articles/mergen.html","id":"setting-up-an-agent-for-replicate","dir":"Articles","previous_headings":"Setting up an AI-agent","what":"Setting up an agent for replicate","title":"Introduction to mergen","text":"setupAgent also contains functionality setting agent replicate AIs. Let’s look works:","code":"myAgent <- setupAgent(name=\"replicate\",type=NULL,model=\"llama-2-70b-chat\",ai_api_key=\"my_key\") myAgent #> $name #> [1] \"userAgent\" #>  #> $type #> NULL #>  #> $API #> [1] \"replicate\" #>  #> $url #> [1] \"https://api.replicate.com/v1/predictions\" #>  #> $model #> [1] \"llama-2-70b-chat\" #>  #> $headers #>      Authorization       Content-Type  #>     \"Token my_key\" \"application/json\"  #>  #> $ai_api_key #> [1] \"my_key\""},{"path":"/articles/mergen.html","id":"sending-a-prompt","dir":"Articles","previous_headings":"","what":"Sending a prompt","title":"Introduction to mergen","text":"set agent, time ask questions AI model choice! , can make use sendPrompt function, selfcorrect function. choice one use depends whether want possible errors answered code corrected sending another request model .","code":""},{"path":"/articles/mergen.html","id":"using-the-sendprompt-function","dir":"Articles","previous_headings":"Sending a prompt","what":"Using the sendPrompt function","title":"Introduction to mergen","text":"Sending prompt sendPrompt function easy. function takes arguments agent, prompt, return.type context. default context set rbionfoExp. tells model choice act bioinformatics expert, return code R code triple backticks. prompt must given string, can contain question additional information want send. return value string containing models answer.","code":"answer <- sendPrompt(myAgent,                      \"how do I perform PCA on data in                      a file called test.txt?\",return.type = \"text\") answer #> [1] \"\\n\\nThe following R code will read the file called \\\"test.txt\\\", normalize the table and do PCA. First, the code will read the file into an R data frame: \\n\\n```\\ndata <- read.table(\\\"test.txt\\\", header = TRUE, sep = \\\"\\\\t\\\")\\n```\\n\\nNext, the data will be normalized to the range of 0 to 1:\\n\\n```\\nnormalized.data <- scale(data, center = TRUE, scale = TRUE)\\n```\\n\\nFinally, the normalized data will be used to do a Principal Component Analysis (PCA):\\n\\n```\\npca <- princomp(normalized.data)\\n```\""},{"path":"/articles/mergen.html","id":"using-the-selfcorrect-function","dir":"Articles","previous_headings":"Sending a prompt","what":"Using the selfcorrect function","title":"Introduction to mergen","text":"Sending prompt selfcorrect function, allow possible generated code optimized performance accuracy. code returned model excecutable, selfcorrect function send prompt back agent together list errors warnings, code can optimized. amount rounds possible selfcorrect can set user using attempts = n argument. return value list containing initial answer agent final answer n rounds selfcorrection.","code":"answer <- selfcorrect(myAgent, prompt=\"How do I perform PCA?\",attempts=3) print(answer) #> $init.response #> [1] \"\\n\\nThe following R code will read the file called \\\"test.txt\\\", normalize the table and do PCA. First, the code will read the file into an R data frame: \\n\\n```R\\ndata <- read.table(\\\"test.txt\\\", header = TRUE, sep = \\\"\\\\t\\\")\\n```\\n\\nNext, the data will be normalized to the range of 0 to 1:\\n\\n```{r}\\nnormalized.data <- scale(data, center = TRUE, scale = TRUE)\\n```\\n\\nFinally, the normalized data will be used to do a Principal Component Analysis (PCA):\\n\\n```{R}\\npca <- princomp(normalized.data)\\n```\" #>  #> $init.blocks #> $init.blocks$code #> [1] \"\\ndata <- read.table(\\\"test.txt\\\", header = TRUE, sep = \\\"\\\\t\\\")\\n\\n\\nnormalized.data <- scale(data, center = TRUE, scale = TRUE)\\n\\n\\npca <- princomp(normalized.data)\\n\" #>  #> $init.blocks$text #> [1] \"\\n\\nThe following R code will read the file called \\\"test.txt\\\", normalize the table and do PCA. First, the code will read the file into an R data frame: \\n\\n\\n\\n\\nNext, the data will be normalized to the range of 0 to 1:\\n\\n\\n\\n\\nFinally, the normalized data will be used to do a Principal Component Analysis (PCA):\\n\\n\\n\" #>  #>  #> $final.response #> [1] \"\\n\\nThe third response.The following R code will read the file called \\\"test.txt\\\", normalize the table and do PCA. First, the code will read the file into an R data frame: \\n\\n```{r}\\nplot(1:10)```\\n\\nNext, the data will be normalized to the range of 0 to 1:\\n\\n\" #>  #> $final.blocks #> $final.blocks$code #> [1] \"\\nplot(1:10)\" #>  #> $final.blocks$text #> [1] \"\\n\\nThe third response.The following R code will read the file called \\\"test.txt\\\", normalize the table and do PCA. First, the code will read the file into an R data frame: \\n\\n\\n\\n\\nNext, the data will be normalized to the range of 0 to 1:\\n\\n\" #>  #>  #> $code.works #> [1] TRUE #>  #> $exec.result #> [1] \"path/to/html/file\" #>  #> $tried.attempts #> [1] 3"},{"path":[]},{"path":"/articles/mergen.html","id":"extracting-code-blocks","dir":"Articles","previous_headings":"Running the code","what":"Extracting code blocks","title":"Introduction to mergen","text":"sent prompt recieved answer, mergen features function extractCode allows user extract code blocks given text. using , however, code blocks need cleaned , every agent return answer slightly different way. can done help clean_code_blocks function. example clean_code_blocks answer returned agent : can see , clean_code_blocks ensures code stripped extra symbols {r}, R, r {R}. ensures function extractCode can extract code blocks properly. extractCode function takes input string, also allows user set delimiter used enclose code blocks (default three backtics). Now lets look extractCode function returns: shown , extractCode returns list containing actual code associated text. code block can tested execution using executeCode function.","code":"code_cleaned <- clean_code_blocks(answer$final.response) cat(code_cleaned) #>  #>  #> The third response.The following R code will read the file called \"test.txt\", normalize the table and do PCA. First, the code will read the file into an R data frame:  #>  #> ``` #> plot(1:10)``` #>  #> Next, the data will be normalized to the range of 0 to 1: final_code <- extractCode(code_cleaned,delimiter = \"```\") print (final_code) #> $code #> [1] \"\\nplot(1:10)\" #>  #> $text #> [1] \"\\n\\nThe third response.The following R code will read the file called \\\"test.txt\\\", normalize the table and do PCA. First, the code will read the file into an R data frame: \\n\\n\\n\\n\\nNext, the data will be normalized to the range of 0 to 1:\\n\\n\""},{"path":"/articles/mergen.html","id":"running-the-code-1","dir":"Articles","previous_headings":"Running the code","what":"Running the code","title":"Introduction to mergen","text":"mergen features functions make easy user run code returned AI agent. code blocks cleaned extracted, code blocks can executed using executeCode function. , however, advised run extractInstallPkg function. function extracts package names installs missing packages needed code run. Finally, executeCode function can used. Lets see executeCode function :  shown , code runs ! important note executeCode function change global environment. variables might created executing code deleted function completes.","code":"executeCode(final_code$code) #> NULL"},{"path":"/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Altuna Akalin. Author, maintainer. Jacqueline Anne Jansen. Author.","code":""},{"path":"/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Akalin , Jansen J (2024). mergen: AI-Driven Code Generation, Explanation Execution Data Analysis. R package version 0.2.1,  https://bioinformatics.mdc-berlin.de/mergen/, https://github.com/BIMSBbioinfo/mergen.","code":"@Manual{,   title = {mergen: AI-Driven Code Generation, Explanation and Execution for Data Analysis},   author = {Altuna Akalin and Jacqueline Anne Jansen},   year = {2024},   note = {R package version 0.2.1,  https://bioinformatics.mdc-berlin.de/mergen/},   url = {https://github.com/BIMSBbioinfo/mergen}, }"},{"path":[]},{"path":"/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"mergen employs artificial intelligence convert data analysis questions executable code, explanations, algorithms. self-correction feature ensures generated code optimized performance accuracy. mergen features user-friendly chat interface, enabling users interact AI agent extract valuable insights data effortlessly. package website full documentation . want use mergen Rstudio session via embedded chatbot, try companion package mergenstudio.","code":""},{"path":"/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"easiest way install mergen via install.packages","code":"install.packages(\"mergen\")"},{"path":"/index.html","id":"development-version","dir":"","previous_headings":"Installation","what":"Development version","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"get bug fix use feature development version, can install development version mergen GitHub.","code":"# install.packages(\"pak\") pak::pak(\"BIMSBbioinfo/mergen\")"},{"path":"/index.html","id":"prerequisites","dir":"","previous_headings":"","what":"Prerequisites","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"Make AI platform account. Choices openai.com, neets.ai (time writing free limits), replicate.com , perplexity.ai etc. addition, can locally run LLM server mode can interact via API. One example GPT4all. solutions tested work mergen. Create OpenAI API key use package Create replicate API key Set API key R","code":""},{"path":"/index.html","id":"configuring-your-ai-api-key","dir":"","previous_headings":"Prerequisites","what":"Configuring your AI API key","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"interact AI API, require valid AI API key. configure key present globally environment times, can include .Renviron file. ensure key automatically loaded. setting mergen, variable called AI_API_KEY. information setting agent, recommend visit Get Started . Caution: ’re using version control systems like GitHub, include .Renviron .gitignore file prevent exposing personal API key. open .Renviron file modification project: persistent loading API key, add following line .Renviron file replacing \"your_key\" key. NOTE: setting API key .Renviron file, either restart R session run readRenviron(\".Renviron\") apply changes. however wish set variable single session, can use following command:","code":"require(usethis)  edit_r_environ(scope=\"project\") AI_API_KEY=\"your_key\" Sys.setenv(AI_API_KEY=\"your_key\")"},{"path":"/index.html","id":"citing-mergen","dir":"","previous_headings":"","what":"Citing mergen","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"used mergen please cite: Jacqueline Jansen, Artür Manukyan, Nour Al Khoury, Altuna Akalin. (2023) “Leveraging large language models data analysis automation” bioRxiv, doi: 10.1101/2023.12.11.571140","code":""},{"path":"/index.html","id":"getting-help","dir":"","previous_headings":"","what":"Getting help","title":"AI-Driven Code Generation, Explanation and Execution for Data Analysis","text":"encounter clear bug, please file issue minimal reproducible example GitHub. can also post questions.","code":""},{"path":"/reference/check_install.html","id":null,"dir":"Reference","previous_headings":"","what":"Check and Install R Package — check_install","title":"Check and Install R Package — check_install","text":"function checks R package installed, , attempts install using either standard CRAN repository Bioconductor repository.","code":""},{"path":"/reference/check_install.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check and Install R Package — check_install","text":"","code":"check_install(package_name)"},{"path":"/reference/check_install.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check and Install R Package — check_install","text":"package_name character string specifying name package checked installed.","code":""},{"path":"/reference/check_install.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check and Install R Package — check_install","text":"TRUE package already installed can installed. FALSE otherwise","code":""},{"path":"/reference/check_install.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check and Install R Package — check_install","text":"","code":"# \\donttest{ # Check and install \"dplyr\" package check_install(\"dplyr\") #> Loading required package: dplyr #>  #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union # }"},{"path":"/reference/clean_code_blocks.html","id":null,"dir":"Reference","previous_headings":"","what":"Clean code blocks returned by the agent — clean_code_blocks","title":"Clean code blocks returned by the agent — clean_code_blocks","text":"function cleans response returned agent ensure code blocks can run. ensures characters 'R' 'r' cleaned code blocks agents response, code blocks able extracted extractCode() function ran expected. also cleans response install.package calls, recorded output, code blocks extracted, code can run smoothly.","code":""},{"path":"/reference/clean_code_blocks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Clean code blocks returned by the agent — clean_code_blocks","text":"","code":"clean_code_blocks(response)"},{"path":"/reference/clean_code_blocks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Clean code blocks returned by the agent — clean_code_blocks","text":"response response received agent","code":""},{"path":"/reference/clean_code_blocks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Clean code blocks returned by the agent — clean_code_blocks","text":"string holding response agent, cleaned unwanted characters.","code":""},{"path":"/reference/clean_code_blocks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Clean code blocks returned by the agent — clean_code_blocks","text":"","code":"{ response <- \"To perform PCA, do the following: ```R prcomp(data)``` This funcion will perform PCA.\" clean_code <- clean_code_blocks(response) }"},{"path":"/reference/executeCode.html","id":null,"dir":"Reference","previous_headings":"","what":"execute code — executeCode","title":"execute code — executeCode","text":"function executes chunk code either current working environment saves output HTML file rendered part web page","code":""},{"path":"/reference/executeCode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"execute code — executeCode","text":"","code":"executeCode(code, output = \"eval\", output.file = NULL)"},{"path":"/reference/executeCode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"execute code — executeCode","text":"code code chunk text, without decorators HTML-specific characters. output output \"eval\", code executed . output \"html\", code executed. output.file output \"html\", user can provide file name html. provided temporary file created.","code":""},{"path":"/reference/executeCode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"execute code — executeCode","text":"output \"eval\": running code causes errors, errors returned. Otherwise NA returned  output \"html\", output file returned.","code":""},{"path":"/reference/extractCode.html","id":null,"dir":"Reference","previous_headings":"","what":"extract the code and text from the text returned by LLM agent — extractCode","title":"extract the code and text from the text returned by LLM agent — extractCode","text":"function parses agents answer returns text code single blocks. results can used code execution might useful displaying purposes later .","code":""},{"path":"/reference/extractCode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"extract the code and text from the text returned by LLM agent — extractCode","text":"","code":"extractCode(text, delimiter = \"```\")"},{"path":"/reference/extractCode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"extract the code and text from the text returned by LLM agent — extractCode","text":"text character string containing text embedded code blocks. delimiter character string representing delimiter used enclose code blocks (default: \"```\").","code":""},{"path":"/reference/extractCode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"extract the code and text from the text returned by LLM agent — extractCode","text":"list two elements: 'code' 'text'. 'code' contains concatenated code blocks,         'text' contains remaining text code blocks removed.","code":""},{"path":"/reference/extractCode.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"extract the code and text from the text returned by LLM agent — extractCode","text":"","code":"text <- \"\\n\\nThe following, normalize the table and do PCA. \\n\\n```\\ndata <- read.table(\\\"test.txt\\\", header = TRUE, sep = \\\"\\\\t\\\")\\n```\" result <- extractCode(text) print(result$code) #> [1] \"\\ndata <- read.table(\\\"test.txt\\\", header = TRUE, sep = \\\"\\\\t\\\")\\n\" print(result$text) #> [1] \"\\n\\nThe following, normalize the table and do PCA.\\n\\n\\n\\n\""},{"path":"/reference/extractFilenames.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract file names from user prompt — extractFilenames","title":"Extract file names from user prompt — extractFilenames","text":"function extracts file names user prompt. Current filenames supported function *.txt, *.tsv, *.csv *.xls, *.xlsx, *.bed, *.bigWig, *.bw *.bigBed. filenames extracted. filenames found, function return NA.","code":""},{"path":"/reference/extractFilenames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract file names from user prompt — extractFilenames","text":"","code":"extractFilenames(text)"},{"path":"/reference/extractFilenames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract file names from user prompt — extractFilenames","text":"text user prompt","code":""},{"path":"/reference/extractFilenames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract file names from user prompt — extractFilenames","text":"list holding file names user prompt.","code":""},{"path":"/reference/extractFilenames.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract file names from user prompt — extractFilenames","text":"","code":"{ user_prompt <- \"How do I perform PCA on data in my file called test.txt?\" extractFilenames(text=user_prompt) } #> [1] \"test.txt\""},{"path":"/reference/extractInstallPkg.html","id":null,"dir":"Reference","previous_headings":"","what":"extract package names and install them — extractInstallPkg","title":"extract package names and install them — extractInstallPkg","text":"function extracts package names needed run code returned agent installs needed.","code":""},{"path":"/reference/extractInstallPkg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"extract package names and install them — extractInstallPkg","text":"","code":"extractInstallPkg(code)"},{"path":"/reference/extractInstallPkg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"extract package names and install them — extractInstallPkg","text":"code code block returned agent.","code":""},{"path":"/reference/extractInstallPkg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"extract package names and install them — extractInstallPkg","text":"final status packages logical vector, TRUE packages already installed installed. FALSE package install.","code":""},{"path":"/reference/extractInstallPkg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"extract package names and install them — extractInstallPkg","text":"","code":"# \\donttest{ # Check code for packages that need installing code <- \"library(devtools)\\n x<-5\" extractInstallPkg(code) #> Loading required package: devtools #> Loading required package: usethis #> devtools  #>     TRUE  # }"},{"path":"/reference/fileHeaderPrompt.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract file headers from files in prompt — fileHeaderPrompt","title":"Extract file headers from files in prompt — fileHeaderPrompt","text":"function extracts file headers files. Recommended use function results extractFilenames","code":""},{"path":"/reference/fileHeaderPrompt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract file headers from files in prompt — fileHeaderPrompt","text":"","code":"fileHeaderPrompt(filenames)"},{"path":"/reference/fileHeaderPrompt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract file headers from files in prompt — fileHeaderPrompt","text":"filenames list containing file names.","code":""},{"path":"/reference/fileHeaderPrompt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract file headers from files in prompt — fileHeaderPrompt","text":"string containing file headers files \"filenames\" list","code":""},{"path":"/reference/fileHeaderPrompt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract file headers from files in prompt — fileHeaderPrompt","text":"","code":"if (FALSE) { prompt <- \"how do I perform PCA on data in a file called test.txt?\" filenames <- extractFilenames(prompt) fileHeaderPrompt(filenames) }"},{"path":"/reference/promptContext.html","id":null,"dir":"Reference","previous_headings":"","what":"Predefined prompt contexts for prompt engineering — promptContext","title":"Predefined prompt contexts for prompt engineering — promptContext","text":"function holds various predefined prompt contexts can used prompt engineering.","code":""},{"path":"/reference/promptContext.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Predefined prompt contexts for prompt engineering — promptContext","text":"","code":"promptContext(type = \"simple\")"},{"path":"/reference/promptContext.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Predefined prompt contexts for prompt engineering — promptContext","text":"type specifies type context wish returned. Valid options \"simple\", \"actAs\", \"CoT\" \"rbionfoExp\"","code":""},{"path":"/reference/promptContext.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Predefined prompt contexts for prompt engineering — promptContext","text":"string holding predefined context.","code":""},{"path":"/reference/runCodeInResponse.html","id":null,"dir":"Reference","previous_headings":"","what":"Executes the code in the received response from the agent — runCodeInResponse","title":"Executes the code in the received response from the agent — runCodeInResponse","text":"function extracts executes code response. required can try correct errors code via different strategies.","code":""},{"path":"/reference/runCodeInResponse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Executes the code in the received response from the agent — runCodeInResponse","text":"","code":"runCodeInResponse(   response,   prompt = NULL,   agent = NULL,   context = NULL,   correction = c(\"none\", \"selfcorrect\", \"sampleMore\", \"sampleThenCorrect\",     \"correctThenSample\"),   attempts = 3,   output.file = NULL,   ... )"},{"path":"/reference/runCodeInResponse.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Executes the code in the received response from the agent — runCodeInResponse","text":"response response parsed code executed prompt prompt response, correction=\"none\" needed agent AI agent, correction=\"none\" needed context context prompt, correction=\"none\" needed correction \"none\" code correction needed. \"selfcorrect\" feedback errors LLM ask fix. \"sampleMore\" sample responses #prompt executable code returned number attempts reached. \"correctThenSample\" first try self-correct \"attempt\" number times. executable code returned. sample new responses \"attempt\" number times executable code attempts Numeric value denoting many times code sent back fixing. output.file Optional output file created holding parsed code ... arguments sendPrompt()","code":""},{"path":"/reference/runCodeInResponse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Executes the code in the received response from the agent — runCodeInResponse","text":"list containing following elements: init.response character vector representing initial prompt response. init.blocks list initial blocks. final.blocks list final blocks. code.works boolean value indicating whether code works. exec.result character string representing execution results. tried.attempts integer representing number attempts.","code":""},{"path":[]},{"path":"/reference/runCodeInResponse.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Executes the code in the received response from the agent — runCodeInResponse","text":"","code":"if (FALSE) {  resp.list <- runCodeInResponse(agent,prompt,context=rbionfoExp,correction=\"sampleMore\",attempt=2) }"},{"path":"/reference/sampleResponse.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample more solutions when non-executable code returned by the agent — sampleResponse","title":"Sample more solutions when non-executable code returned by the agent — sampleResponse","text":"function attempts sample solutions agent code returned agent faulty. function simply asks solutions executable code returned number attempts reached.","code":""},{"path":"/reference/sampleResponse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample more solutions when non-executable code returned by the agent — sampleResponse","text":"","code":"sampleResponse(   agent,   prompt,   context = rbionfoExp,   attempts = 3,   output.file = NULL,   responseWithError = NULL,   ... )"},{"path":"/reference/sampleResponse.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample more solutions when non-executable code returned by the agent — sampleResponse","text":"agent object containing agent's information (e.g., type model). prompt prompt text send language model. context Optional context provide alongside prompt (default rbionfoExp). attempts Numeric value denoting many times code sent back fixing. output.file Optional output file created holding parsed code responseWithError list response errors returned executeCode(). First element expected response second element error list returned executeCode(). ... Additional arguments passed sendPrompt function.","code":""},{"path":"/reference/sampleResponse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample more solutions when non-executable code returned by the agent — sampleResponse","text":"list containing following elements: init.response character vector representing initial prompt response. init.blocks list initial blocks. final.blocks list final blocks. code.works boolean value indicating whether code works. exec.result character string representing execution results. tried.attempts integer representing number attempts.","code":""},{"path":[]},{"path":"/reference/sampleResponse.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sample more solutions when non-executable code returned by the agent — sampleResponse","text":"","code":"if (FALSE) {  resp.list <- sampleResponse(agent,prompt,context=rbionfoExp, max_tokens = 500) }"},{"path":"/reference/selfcorrect.html","id":null,"dir":"Reference","previous_headings":"","what":"Self correct the code returned by the agent — selfcorrect","title":"Self correct the code returned by the agent — selfcorrect","text":"function attempts correct code returned agent re-feeding agent error message. error messages function returns original response.","code":""},{"path":"/reference/selfcorrect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Self correct the code returned by the agent — selfcorrect","text":"","code":"selfcorrect(   agent,   prompt,   context = rbionfoExp,   attempts = 3,   output.file = NULL,   responseWithError = NULL,   history = NULL,   ... )"},{"path":"/reference/selfcorrect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Self correct the code returned by the agent — selfcorrect","text":"agent object containing agent's information (e.g., type model). prompt prompt text send language model. context Optional context provide alongside prompt (default rbionfoExp). attempts Numeric value denoting many times code sent back fixing. output.file Optional output file created holding parsed code responseWithError list response errors returned executeCode(). history list previous response prompts. Default NULL stayed use cases. First element expected response second element error list returned executeCode(). ... Additional arguments passed sendPrompt function.","code":""},{"path":"/reference/selfcorrect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Self correct the code returned by the agent — selfcorrect","text":"list containing following elements: init.response character vector representing initial prompt response. init.blocks list initial blocks. final.blocks list final blocks. code.works boolean value indicating whether code works. exec.result character string representing execution results. tried.attempts integer representing number attempts.","code":""},{"path":[]},{"path":"/reference/selfcorrect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Self correct the code returned by the agent — selfcorrect","text":"","code":"if (FALSE) {  response <- selfcorrect(agent,prompt,context=rbionfoExp, max_tokens = 500) }"},{"path":"/reference/sendPrompt.html","id":null,"dir":"Reference","previous_headings":"","what":"Send a prompt to a specified language model agent and return the response. — sendPrompt","title":"Send a prompt to a specified language model agent and return the response. — sendPrompt","text":"Send prompt specified language model agent return response.","code":""},{"path":"/reference/sendPrompt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Send a prompt to a specified language model agent and return the response. — sendPrompt","text":"","code":"sendPrompt(   agent,   prompt,   context = promptContext(type = \"simple\"),   return.type = c(\"text\", \"object\"),   previous.msgs = NULL,   ... )"},{"path":"/reference/sendPrompt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Send a prompt to a specified language model agent and return the response. — sendPrompt","text":"agent object containing agent's information (e.g., type model etc.). prompt prompt text send language model. context Optional context provide alongside prompt (default promptContext(type = \"simple\")). return.type type output return, either text response (\"text\") entire response object (\"object\"). previous.msgs list lists previous prompts responses. Useful add context previous messages API. argument works openai generic models, replicate API. Default: NULL ... Additional arguments passed LLM API. maximum tokens, (\"max_tokens\"), returned. Users can also also provide arguments openai API-like arguments documented [official documentation](https://platform.openai.com/docs/api-reference/chat/create). APIs also following similar argument naming patterns.","code":""},{"path":"/reference/sendPrompt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Send a prompt to a specified language model agent and return the response. — sendPrompt","text":"text response entire response object, based specified return type.","code":""},{"path":[]},{"path":"/reference/sendPrompt.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Send a prompt to a specified language model agent and return the response. — sendPrompt","text":"","code":"if (FALSE) { agent <- setupAgent(name=\"openai\",type=\"chat\",model=\"gpt-4\",                     ai_api_key=Sys.getenv(\"OPENAI_API_KEY\")) prompt <- \"tell me a joke\" response <- sendPrompt(agent, prompt,context=\"\")  # increase tokens, it is important for getting longer responses response <- sendPrompt(agent,prompt,context=\"\",return.type=\"text\", max_tokens = 500)  # get previous messages into the context prompt=\"what about 2010?\" response <- sendPrompt(agent,prompt,context=\"\",                        return.type=\"text\",                        previous.msgs=list(                                           list(                                                \"role\" = \"user\",                                                 \"content\" = \"Who won the world                                                  series in 2020?\"                                                  ),                                           list(                                                 \"role\" = \"assistant\",                                               \"content\" = \"The Los Angeles Dodgers\"                                               )                                           )                        )   }"},{"path":"/reference/setupAgent.html","id":null,"dir":"Reference","previous_headings":"","what":"set up an online LLM API for subsequent tasks — setupAgent","title":"set up an online LLM API for subsequent tasks — setupAgent","text":"function sets large language model API tasks.","code":""},{"path":"/reference/setupAgent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"set up an online LLM API for subsequent tasks — setupAgent","text":"","code":"setupAgent(   name = c(\"openai\", \"replicate\", \"generic\"),   type = NULL,   model = NULL,   url = NULL,   ai_api_key = Sys.getenv(\"AI_API_KEY\") )"},{"path":"/reference/setupAgent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"set up an online LLM API for subsequent tasks — setupAgent","text":"name string name API, one \"openai\", \"replicate\" \"generic\". Currently supported APIs \"openai\" \"replicate\". user wishes use another API similar syntax openai API also supported via \"generic\" option. case, user also provide url API using type Specify type model (chat completion). parameter needs specified using 'openai model LLM model wish use. openAI chat model examples : 'gtp-3-5-turbo' 'gtp-4' openAI completion models examples : 'text-curie-001' 'text-davinci-002' replicate models examples : llama-2-70b-chat ( '02e509c789964a7ea8736978a43525956ef40397be9033abf9fd2badfe68c9e3') llama-2-13b-chat ( 'f4e2de70d66816a838a89eeeb621910adffb0dd0baba3976c96980970978018d') full list openAI models  click . full list Replicate models,  click . url url API case API \"generic\" selected. (Default: NULL) ai_api_key personal API key accessing LLM","code":""},{"path":"/reference/setupAgent.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"set up an online LLM API for subsequent tasks — setupAgent","text":"list holding agent information.","code":""},{"path":"/reference/setupAgent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"set up an online LLM API for subsequent tasks — setupAgent","text":"","code":"{ myAgent <- setupAgent(name=\"openai\",type=\"chat\",model=\"gpt-4\",ai_api_key=\"my_key\")  myAgent <- setupAgent(name=\"replicate\",type=NULL,                      model=\"02e509c789964a7ea8736978a43525956ef40397be9033abf9fd2badfe68c9e3\",                      ai_api_key=\"my_key\") }"},{"path":"/news/index.html","id":"mergen-version-020-2024-01-29","dir":"Changelog","previous_headings":"","what":"mergen Version 0.2.0 2024-01-29","title":"mergen Version 0.2.0 2024-01-29","text":"URLs DESCRIPTION added new feature: now users can specify openai-like APIs providing url setting agent name “generic” setupAgent() function new feature: clean_code_blocks() now automatically runs extractCode() called new feature: sendPrompt() now can send previous message correspondence LLM APIs via “previous.msgs” argument new feature: selfcorrect() new argument called responseWithErrors (default:NULL), via argument users can input problematic responses selfcorrect() function instead getting initial response potentially failing. new function: runCodeInResponse() can take LLM response directly run code, tries fix errors. new function: sampleResponse() function tries fix code errors repatedly sampling new solutions existing prompts fix: typos setupAgent fixed fix: sendPrompt fixed broken due openai API changes fix: extractInstallPkg can now deal require() calls code blocks updated help pages accordingly","code":""}]