update dependecies, documentation and name functions (#2)

* arreglo carpetas R/stanmodels

* Funciones finales pendientes a modificación

* Delete Funciones eliminadas.docx

* Delete Explicación del código del paquete SEROFOI.docx

* Documentación en inglés y español

* Documentación lista

* modify package structure

* modify package structure

* modify names and folder test

* Creation of general modules and revision of functions

* refactoring visualization functions and define some general pck structure

* update readme file

* update readme file

* general settings

* modify dependecies, document and name functions

Co-authored-by: Zulma M. Cucunubá <[email protected]>
Co-authored-by: megamezl <[email protected]>
Co-authored-by: megamezl <[email protected]>

DESCRIPTION

@@ -1,11 +1,30 @@
-Package: serologypkg
+Package: serofoi
 Type: Package
-Title: What the Package Does (Title Case)
+Title:  Estimates the Force-of-Infection of a given pathogen from population based sero-prevalence studies.
 Version: 0.1.0
-Author: Who wrote it
-Maintainer: The package maintainer <[email protected]>
-Description: More about what it does (maybe more than one line)
-    Use four spaces when indenting paragraphs within the Description.
-License: What license is it under?
+Author: Zulma M. Cucunubá and Miguel Gamez
+Maintainer: The package maintainer <[email protected]>
+Description: Provides functions for estimate the Force-of-Infection of a given pathogen from population based sero-prevalence studies on a bayesian framework.
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
+RoxygenNote: 7.2.1
+Imports:
+    config,
+    rstan,
+    tidyverse,
+    reshape2,
+    bayesplot,
+    loo,
+    pracma,
+    cowplot,
+    grid,
+    gridExtra,
+    Hmisc,
+    dplyr,
+    epitrix,
+    gsubfn
+Suggests: 
+    knitr,
+    rmarkdown
+VignetteBuilder: knitr

NAMESPACE

@@ -1 +1,22 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(compare_and_save_best_model)
+export(dir_results)
+export(extract_and_save)
+export(extract_summary_mod)
+export(fit_model)
+export(fit_model_log)
+export(generate_combined_plots)
+export(get_exposure_matrix)
+export(get_posterior_summary)
+export(get_prev_expanded)
+export(get_residuals)
+export(get_table_rhats)
+export(make_thin_chain)
+export(make_yexpo)
+export(obtain_prevalence_extended)
+export(plot_info_table)
+export(run_save_models)
+export(vertical_plot_arrange_per_model)
+import(dplyr)
+importFrom(dplyr,"%>%")