rebase

Merge branch 'main' of https://github.com/BIMSBbioinfo/mergen

# Conflicts:
#	R/selfcorrect.R
#	man/selfcorrect.Rd

.gitignore

@@ -7,5 +7,6 @@
 .Rdata
 .httr-oauth
 .quarto
+.Rproj
 docs
 inst/doc

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: mergen
 Type: Package
 Title: AI-Driven Code Generation, Explanation and Execution for Data Analysis
-Version: 0.2.0
+Version: 0.2.1
 Authors@R: c(
     person("Altuna", "Akalin", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-0468-0117")),

R/selfcorrect.R

@@ -10,7 +10,7 @@
 #' @param attempts Numeric value denoting how many times the code should be sent back for fixing.
 #' @param output.file Optional output file created holding parsed code
 #' @param responseWithError a list of response and errors returned from executeCode().
-#' @param history parameter to send history of the chat.
+#' @param history a list of previous response and prompts. Default is NULL and should be stayed as is for most use cases.
 #' First element is expected to be the response and the second element is the error list returned by executeCode().
 #' @param ... Additional arguments to be passed to the \code{\link{sendPrompt}} function.
 #' @return A list containing the following elements:

R/setupAgent.R

@@ -53,9 +53,9 @@ setupopenaiAgent<-function(model,type=c("chat","completion"),
 #' For replicate models examples are:\itemize{
 #'  \item llama-2-70b-chat ( as '02e509c789964a7ea8736978a43525956ef40397be9033abf9fd2badfe68c9e3')
 #'  \item llama-2-13b-chat ( as 'f4e2de70d66816a838a89eeeb621910adffb0dd0baba3976c96980970978018d')}
-#'  For a full list of openAI models
-#'  \href{https://platform.openai.com/docs/models/overview}{click here}. For a full list of Replicate models,
-#'  \href{https://replicate.com/collections/language-models}{click here}.
+#'  For a full list of openAI models see
+#'  https://platform.openai.com/docs/models/overview/. For a full list of Replicate models,
+#'  see https://replicate.com/collections/language-models.
 #' @param url the url for the API in case the API "generic" is selected. (Default: NULL)
 #' @param ai_api_key personal API key for accessing LLM
 #' @return A list holding agent information.

README.md

@@ -12,7 +12,7 @@ performance and accuracy. mergen features a user-friendly chat
 interface, enabling users to interact with the AI agent and extract
 valuable insights from their data effortlessly.
 
-The package website with full documentation is [here](http://bioinformatics.mdc-berlin.de/mergen).
+The package website with full documentation is [here](http://bioinformatics.mdc-berlin.de/mergen/).
 
 If you want to use **mergen** in your Rstudio session via an embedded chatbot, try out our companion package [mergenstudio](https://github.com/BIMSBbioinfo/mergenstudio/).
 
@@ -37,9 +37,9 @@ pak::pak("BIMSBbioinfo/mergen")
 ### Prerequisites
 
 - 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 [GPT4all](https://gpt4all.io/). Some of these solutions are not tested but should work with mergen. 
+  In addition, you can locally run an LLM in server mode and you can interact with it via API. One example is [GPT4all](https://gpt4all.io/index.html). Some of these solutions are not tested but should work with mergen. 
 - [Create an OpenAI API
-  key](https://platform.openai.com/account/api-keys) to use with the
+  key](https://platform.openai.com/docs/api-reference/introduction) to use with the
   package
 - [Create a replicate API key](https://replicate.com/pricing)
 - Set up the API key in R

mergen.Rproj

@@ -18,4 +18,5 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace