{"action":"created","issue":{"url":"https://api.github.com/repos/bobmuscarella/ENMeval/issues/30","labels_url":"https://api.github.com/repos/bobmuscarella/ENMeval/issues/30/labels{/name}","comments_url":"https://api.github.com/repos/bobmuscarella/ENMeval/issues/30/comments","events_url":"https://api.github.com/repos/bobmuscarella/ENMeval/issues/30/events","html_url":"https://github.com/bobmuscarella/ENMeval/issues/30","id":110449568,"number":30,"title":"Allow all maxent args to be passed (e.g., prevelance)","user":{"login":"bobmuscarella","id":5683268,"avatar_url":"https://avatars.githubusercontent.com/u/5683268?v=3","gravatar_id":"","url":"https://api.github.com/users/bobmuscarella","html_url":"https://github.com/bobmuscarella","followers_url":"https://api.github.com/users/bobmuscarella/followers","following_url":"https://api.github.com/users/bobmuscarella/following{/other_user}","gists_url":"https://api.github.com/users/bobmuscarella/gists{/gist_id}","starred_url":"https://api.github.com/users/bobmuscarella/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bobmuscarella/subscriptions","organizations_url":"https://api.github.com/users/bobmuscarella/orgs","repos_url":"https://api.github.com/users/bobmuscarella/repos","events_url":"https://api.github.com/users/bobmuscarella/events{/privacy}","received_events_url":"https://api.github.com/users/bobmuscarella/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":3,"created_at":"2015-10-08T13:21:02Z","updated_at":"2015-10-21T15:52:30Z","closed_at":null,"body":"We should add a ... argument to the ENMevaluate function that allows other options to be passed to maxent (e.g. prevalence).  This will require changes to the ENMevaluate, tuning, and make.args functions.\r\n\r\n**From Xavier Rotllan-Puig:**\r\n\"I have modified ENMevaluate.R and make.args.R in order to be able to modify the parameter \"prevalence\" to be passed to maxent.\"\r\n\r\n**From Jamie:**\r\n\"...I think to avoid adding too many extra parameters, we might want to simply add a \"...\" parameter to allow users to input any maxent-related parameter they'd like.\"\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/bobmuscarella/ENMeval/issues/comments/149940691","html_url":"https://github.com/bobmuscarella/ENMeval/issues/30#issuecomment-149940691","issue_url":"https://api.github.com/repos/bobmuscarella/ENMeval/issues/30","id":149940691,"user":{"login":"bobmuscarella","id":5683268,"avatar_url":"https://avatars.githubusercontent.com/u/5683268?v=3","gravatar_id":"","url":"https://api.github.com/users/bobmuscarella","html_url":"https://github.com/bobmuscarella","followers_url":"https://api.github.com/users/bobmuscarella/followers","following_url":"https://api.github.com/users/bobmuscarella/following{/other_user}","gists_url":"https://api.github.com/users/bobmuscarella/gists{/gist_id}","starred_url":"https://api.github.com/users/bobmuscarella/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bobmuscarella/subscriptions","organizations_url":"https://api.github.com/users/bobmuscarella/orgs","repos_url":"https://api.github.com/users/bobmuscarella/repos","events_url":"https://api.github.com/users/bobmuscarella/events{/privacy}","received_events_url":"https://api.github.com/users/bobmuscarella/received_events","type":"User","site_admin":false},"created_at":"2015-10-21T15:52:30Z","updated_at":"2015-10-21T15:52:30Z","body":"It looks like arguments that take numeric values are okay but I ran into problems with things that require 'true'.  For instance, this seemed to work:\r\n```r\r\n> res <- ENMevaluate(occ, env, method='block', n.bg=500, RM=2, fc=c('L'), defaultprevalence=.9)\r\n```\r\nBut this didn't:\r\n```r\r\n> res <- ENMevaluate(occ, env, method='block', n.bg=500, RM=2, fc=c('L'), doclamp=true)\r\n\r\nError in ENMevaluate(occ, env, method = \"block\", n.bg = 500, RM = 2, fc = c(\"L\"),  : \r\n  object 'true' not found\r\n```\r\n\r\nCan think of a way around this? \r\n\r\nIn any case, some things are not relevant to what ENMeval does - like the option to draw response curves in the .html file is irrelevant unless we start allowing an option to save the html files somewhere.  Also, some of the arguments are duplicated by the ENMeval arguments (i.e., 'betamultiplier').  **I think we should make a more narrow list of arguments that are novel (to ENMeval) and then add those as explicit arguments.**\r\n\r\nBelow, I have separated arguments from the list you added into 2 categories (Should include + Would be nice but won't work right now).  The codes in parentheses stand for B=boolean, N=numeric, C=character.  The Numeric arguments appear to work in the way you already implemented but it seems we have to find a different solution to get the Boolean and Character arguments to work (like add them as explicit arguments).\r\n\r\n**These things seem relevant and good to include (although some more important than others):**\r\n- addallsamplestobackground (B)\r\n- addsamlpestobackground (B)\r\n- allowpartialdata (B)\r\n- beta_categorical (N)\r\n- beta_hinge (N)\r\n- beta_lqp (N)\r\n- beta_threshold (N)\r\n- defaultprevalence (N)\r\n- extrapolate (B)\r\n- fadebyclamping (B)\r\n- jackknife (B)\r\n- outputformat (C)\r\n- removeduplicates (B)\r\n- convergencethreshold (N)\r\n- maximumiterations (N)\r\n\r\n**These could be nice but won't work as things are currently implemented (either because of ENMeval or dismo):**\r\n- biasfile (C)\r\n- outputdirectory (C)\r\n- writeclampgrid (B)\r\n- writemess (B)\r\n\r\n*What do you think?*"}}