Restructuring of the package

DESCRIPTION

@@ -17,16 +17,15 @@ Depends:
 Imports: 
     assertthat,
     methods,
-    readr,
     jsonlite,
-    stringr,
     tidytree,
     utils,
     gh,
     curl,
     cli,
-    magrittr,
-    bnpsd
+    bnpsd,
+    rlang,
+    phangorn
 Suggests:
     devtools,
     ggplot2,
@@ -40,8 +39,7 @@ Suggests:
     treeio (>= 1.32.0),
     rmarkdown,
     pandoc,
-    dplyr,
-    rlang
+    dplyr
 VignetteBuilder: knitr
 Config/Needs/website: rmarkdown
 Remotes: 

NAMESPACE

@@ -1,26 +1,25 @@
 # Generated by roxygen2: do not edit by hand
 
-export("%>%")
 export(tp_compile)
 export(tp_data)
-export(tp_fp_fetch)
+export(tp_expected_input)
 export(tp_json_to_phylo)
-export(tp_list)
 export(tp_map_tree)
 export(tp_model)
-export(tp_model_names)
-export(tp_parse)
+export(tp_model_library)
 export(tp_parse_host_rep)
+export(tp_parse_mcmc)
+export(tp_parse_smc)
 export(tp_phylo_to_tpjson)
 export(tp_run)
+export(tp_run_options)
 export(tp_smc_convergence)
-export(tp_stored_compiled)
-export(tp_stored_data)
-export(tp_stored_model)
 export(tp_tempdir)
-export(tp_treeppl)
 export(tp_treeppl_json)
-export(tp_write)
+export(tp_write_data)
+export(tp_write_model)
 importFrom(bnpsd,tree_reorder)
-importFrom(magrittr,"%>%")
 importFrom(methods,is)
+importFrom(phangorn,add_edge_length)
+importFrom(phangorn,allCompat)
+importFrom(rlang,.data)

R/compile.R

@@ -0,0 +1,176 @@
+#' Options that can be passed to TreePPL compiler
+#'
+#' @returns A string with the output from the compiler's help <tpplc --help>
+#'
+tp_compile_options <- function() {
+
+  #### under development ####
+
+  # text from tpplc --help
+  return()
+
+}
+
+
+
+#' Compile a TreePPL model and create inference machinery
+#'
+#' @description
+#' `tp_compile` compile a TreePPL model and create inference machinery to be
+#' used by [treepplr::tp_run].
+#'
+#' @param model One of tree options:
+#'   * The full path of the model file that contains the TreePPL code, OR
+#'   * A string with the name of a model supported by treepplr
+#' (see [treepplr::tp_model_library()]), OR
+#'   * A string containing the entire TreePPL code.
+#' @param method Inference method to be used. See tp_compile_options()
+#' for all supported methods.
+#' @param iterations The number of MCMC iterations to be run.
+#' @param particles The number of SMC particles to be run.
+#' @param dir The directory where you want to save the executable. Default is
+#' [base::tempdir()]
+#' @param output Complete path to the compiled TreePPL program that will be
+#' created. Default is dir/<name of the model object>.exe
+#' @param ... See tp_compile_options() for all supported arguments.
+#'
+#' @return The path for the compiled TreePPL program.
+#' @export
+
+tp_compile <- function(model,
+                       method,
+                       iterations = NULL,
+                       particles = NULL,
+                       dir = NULL,
+                       output = NULL,
+                       ...) {
+
+  options(scipen=999)
+
+  if(is.null(dir)){
+    dir_path <- tp_tempdir()
+  } else {
+    dir_path <- dir
+  }
+
+  # check path, find or write model
+  model_file_name <- tp_model(model)
+
+  musts <- paste("-m", method)
+
+  if(is.null(iterations) & is.null(particles)){
+    stop("If using MCMC, please choose number of iterations.
+         If using SMC, please choose number of particles.")
+  }
+
+  if(!is.null(iterations)){
+    musts <- paste(musts, "--particles", iterations)
+  }
+
+  if(!is.null(particles)){
+    musts <- paste(musts, "--particles", particles)
+  }
+
+  # create string with other options to tpplc
+  args_list <- list(...)
+  args_vec <- unlist(args_list)
+
+  vec <- c()
+  for(i in seq_along(args_vec)) {
+    str <- paste0("--", names(args_vec[i]), " ", args_vec[[i]])
+    vec <- c(vec, str)
+  }
+
+  args_str <- paste(vec, collapse = " ")
+
+  # output
+  if(is.null(output)){
+    output_path <- paste0(dir_path, names(model_file_name), ".exe")
+  } else {
+    output_path <- output
+  }
+
+  options <- paste("--output", output_path, args_str)
+
+  # Preparing the command line program
+  tpplc_path <- installing_treeppl()   #### move this? ####
+  command <- paste(tpplc_path, model_file_name, musts, options)
+
+  # Compile program
+  # Empty LD_LIBRARY_PATH from R_env for this command specifically
+  # due to conflict with internal env from treeppl self-contained
+  system(paste0("LD_LIBRARY_PATH= MCORE_LIBS= ", command))
+
+  return(output_path)
+}
+
+
+
+#' Import a TreePPL model
+#'
+#' @description
+#' `tp_model` takes TreePPL code and prepares it to be used by
+#' [treepplr::tp_compile()].
+#'
+#' @param model_input One of tree options:
+#'   * The full path of the model file that contains the TreePPL code, OR
+#'   * A string with the name of a model supported by treepplr
+#' (see [treepplr::tp_model_library()]), OR
+#'   * A string containing the entire TreePPL code.
+#'
+#' @return The path to the TreePPL model file
+#' @export
+tp_model <- function(model_input) {
+
+  if (!assertthat::is.string(model_input)){
+    stop("Input has to be a sring.")
+  }
+
+  res <- try(file.exists(model_input), silent = TRUE)
+
+  # If path exists, it's all good
+  if (!is(res,"try-error") && res) {
+    model_path <- model_input
+    # name the model
+    if (is.null(names(model_path))){
+      names(model_path) <- "custom_model"
+    }
+
+    # If path doesn't exist
+  } else {
+    # It can be a model name in the library
+    res_lib <- try(tp_find_model(model_input), silent = TRUE)
+    # model_input has the name of a known model
+    if (!is(res_lib,"try-error") && length(res_lib) != 0) {
+      model_path <- res_lib
+      names(model_path) <- model_input
+      # OR model_input contains the model
+      #### (needs to be verified as an appropriate model later) ####
+    } else {
+      model_path <- tp_write_model(model_input)
+      names(model_path) <- "custom_model"
+    }
+  }
+  return(model_path)
+}
+
+
+
+
+#' Write out a custom model to tp_tempdir()
+#'
+#' @param model A string containing the entire TreePPL code.
+#' @param model_file_name An optional name to the file created
+#'
+#' @returns The path to the file created
+#' @export
+#'
+tp_write_model <- function(model, model_file_name = "tmp_model_file") {
+
+  path <- paste0(tp_tempdir(), model_file_name, ".tppl")
+  cat(model, file = path)
+
+  return(path)
+
+}
+