v2024.12.12

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: wallace
-Version: 2024.11.18
-Date: 2024-11-18
+Version: 2024.12.12
+Date: 2024-12-12
 Title: A Modular Platform for Reproducible Modeling of Species Niches 
     and Distributions
 Description: The 'shiny' application Wallace is a modular platform for 

README.md

@@ -1,6 +1,6 @@
 [![R-CMD-check](https://github.com/wallaceEcoMod/wallace/workflows/R-CMD-check/badge.svg)](https://github.com/wallaceEcoMod/wallace/actions) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) [![CRAN version](http://www.r-pkg.org/badges/version/wallace)](https://CRAN.R-project.org/package=wallace) [![downloads](https://cranlogs.r-pkg.org:443/badges/grand-total/wallace?color=orange)](https://cranlogs.r-pkg.org:443/badges/grand-total/wallace?color=orange)
 
-# Wallace (v2024.11.18)
+# Wallace (v2024.12.12)
 *Wallace* is a modular platform for reproducible modeling of species niches and distributions, written in R. The application guides users through a complete analysis, from the acquisition of data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.
 
 Developmental versions (such as this branch) can be downloaded from Github with the following R code.

inst/shiny/Rmd/text_about.Rmd

@@ -6,7 +6,7 @@ output: html_document
 ### **What is *Wallace*?**  
 
 <img src="logo.png" alt="logo" style="width: 150px; float:right; padding:10px;"/>
-Welcome to *Wallace*, a flexible application for reproducible ecological modeling, built for community expansion. The current version of *Wallace* (v2024.09.18) steps the user through a full niche/distribution modeling analysis, from data acquisition to visualizing results.
+Welcome to *Wallace*, a flexible application for reproducible ecological modeling, built for community expansion. The current version of *Wallace* (v2024.12.12) steps the user through a full niche/distribution modeling analysis, from data acquisition to visualizing results.
 
 The application is written in `R` with the web app development package `shiny`. Please find the stable version of *Wallace* on <a href="https://CRAN.R-project.org/package=wallace" target="_blank">CRAN</a>, and the development version on <a href="https://github.com/wallaceEcoMod/wallace" target="_blank">Github</a>. We also maintain a *Wallace* <a href="https://wallaceecomod.github.io/" target="_blank">website</a> that has some basic info, links, and will be updated with tutorial materials in the near future.
 

inst/shiny/Rmd/text_intro_tab.Rmd

@@ -5,7 +5,7 @@ output: html_document
 
 #### WORKFLOW
 
-*Wallace* (v2024.11.18) currently includes ten components, or steps of a possible workflow. Each component includes two or more modules, which are possible analyses for that step.  
+*Wallace* (v2024.12.12) currently includes thirteen components, or steps of a possible workflow. Each component includes two or more modules, which are possible analyses for that step.  
 
 **Components:**  
 

inst/shiny/Rmd/text_team.Rmd

@@ -28,13 +28,13 @@ output: html_document
 <a href="https://andrepazv.github.io" target="_blank">Andrea Paz</a> (developer) received her PhD at CUNY Graduate Center and City College of New York, after which she was a Postdoctoral Researcher at the Crowther Lab in ETH Zürich. She is now an Assistant Professor at the Biological Sciences Department, University of Montréal.  
 <br>
 
-<img src="img/daniel.jpeg" alt="dani" style="width: 100px;"/>
-
 <img src="img/beth.png" alt="beth" style="width: 100px;"/>
 
 <a href="https://bethgerstner.weebly.com/research.html" target="_blank">Beth E. Gerstner</a> (developer, Wallace Fellow) received her PhD from Michigan State University, is a NASA FINESST Award winner, and a Wallace fellow. She currently works for Map of Life at the Center for Biodiversity and Global Change at Yale University.  
 <br>
 
+<img src="img/daniel.jpeg" alt="dani" style="width: 100px;"/>
+
 <a href="https://www.amnh.org/research/staff-directory/daniel-lopez-lozano" target="_blank">Daniel López Lozano</a> (developer) is a Biodiversity Informatics Specialist at the American Museum of Natural History's Center for Biodiversity & Conservation.   
 <br>
 

inst/shiny/Rmd/userReport_intro.Rmd

@@ -10,7 +10,7 @@ knit_engines$set(asis = function(options) {
 knitr::opts_chunk$set(message = FALSE, warning = FALSE, eval = FALSE)
 ```
 
-Please find below the R code history from your *Wallace* v2024.11.18 session. 
+Please find below the R code history from your *Wallace* v2024.12.12 session. 
 
 You can reproduce your session results by running this R Markdown file in RStudio. 
 

inst/shiny/custom_modules/rep_biomodelos.R

@@ -60,72 +60,128 @@ rep_biomodelos_module_server <- function(input, output, session, common) {
   })
 
   observeEvent(input$pushBiomod, {
-    if (is.null(spp[[curSp()]]$visualization$mapPred)) {
+    if (is.null(spp[[curSp()]]$occs)) {
       #add warning
       shinyalert::shinyalert(
-        "You need a map prediction built on Wallace in order to push payload to BioModelos. ",
+        "You need occurrence data loaded in order to push payload to BioModelos. ",
         type = "error")
       return()
     } else {
 
     if (spp[[bioSp()]]$rmm$data$occurrence$sources != "Biomodelos") {
       shinyalert::shinyalert(
-        "You must submit a model built with occurrences from BioModelos. ",
+        "Your model may not be built with occurrences from BioModelos. ",
         type = "error")
-      return()
-    }
-    if (is.null(spp[[bioSp()]]$biomodelos$prediction)) {
-      shinyalert::shinyalert(
-        "You need a map prediction built on Wallace before pushing to BioModelos. ",
-        type = "error")
-      return()
+      #return()
     }
+    # if (is.null(spp[[bioSp()]]$biomodelos$prediction)) {
+    #   shinyalert::shinyalert(
+    #     "You need a map prediction built on Wallace before pushing to BioModelos. ",
+    #     type = "error")
+    #  # return()
+    # }
 
     URL <- 'https://api-biomodelos.humboldt.org.co/v2/models'
 
-
+  ### Create Manifest
     manifest <- list(
-      edited_occurrences = paste0(bioSp(), '_occs.csv'),
-      raster_model_prediction = paste0(bioSp(), '_pred.tif'),
-      raster_model_threshold = paste0(bioSp(), '_thr.csv'),
+      edited_occurrences =
+        if (is.null(spp[[bioSp()]]$occData$occsOrig)) {
+          "No occurrences uploaded. "
+        } else {
+        paste0(bioSp(), '_occs.csv')
+          },
+      raster_model_prediction =
+        if (is.null(spp[[bioSp()]]$biomodelos$prediction)) {
+          "No prediction. "
+        } else {
+        paste0(bioSp(), '_pred.tif')
+          },
+      raster_model_threshold =
+        if (is.null(spp[[bioSp()]]$biomodelos$thrs)) {
+          "No threshold values. "
+        } else {
+        paste0(bioSp(), '_thr.csv')
+          },
+      raster_user_prediction =
+        if (is.null(spp[[bioSp()]]$biomodelos$mask$userSDM)) {
+          "No user-specified SDM. "
+        } else {
+          paste0(bioSp(), '_userSDM.tif')
+        },
       raster_model_modified_expert =
         if (is.null(spp[[bioSp()]]$biomodelos$predExpert)) {
           "No model prediction modified by expert."
         } else {
           paste0(bioSp(), '_pred_expert.tif')
         },
       shape_file_expert =
-        if (is.null(spp[[bioSp()]]$mask$expertPoly)) {
+        if (is.null(spp[[bioSp()]]$mask$removePoly)) {
         "No model prediction modified by expert."
       } else {
-        paste0(bioSp(), '_expertPolygonsShp.zip')
+        paste0(bioSp(), '_expertPolygonShp.zip')
       },
-      shape_file_extent = paste0(bioSp(), '_projectionExtentShp.zip'),
-      biomodelos_metadata = paste0(bioSp(), '_metadata.csv'),
-      model_metadata = paste0(bioSp(), '_rmms.csv'),
-      wallace_session = paste0(bioSp(), '_session.Rmd')
+      shape_file_extent =
+        if (is.null(spp[[bioSp()]]$procEnvs$bgExt)) {
+          "No background extent. "
+        } else {
+        paste0(bioSp(), '_bgExtentShp.zip')
+          },
+      userSDM_extent =
+        if (is.null(spp[[bioSp()]]$biomodelos$mask$userPolyExt)) {
+          "No userSDM background extent. "
+        } else {
+          paste0(bioSp(), '_userSDM_ExtentShp.zip')
+        },
+      biomodelos_metadata =
+        paste0(bioSp(), '_metadata.csv'),
+      model_metadata =
+        paste0(bioSp(), '_rmms.csv'),
+      wallace_session =
+        paste0(bioSp(), '_session.Rmd')
+      # to add something else to the manifest
+      # new_thing =
+      #   if (is.null(spp[[bioSp()]]$biomodelos$check$here$to$see$if$null)) {
+      #     "Paste statement saying it is null. "
+      #   } else {
+      #     paste0(bioSp(), '_whatever.filetype')
+      #   },
     )
 
-    ### Create files
+  ### Create Files
     tmpdir <- tempdir()
     # Create occs
     # add req occs
+    if (!is.null(spp[[bioSp()]]$occData$occsOrig)) {
     tmpOccs <- file.path(tmpdir, paste0(bioSp(), '_occs.csv'))
     occsBio <- spp[[bioSp()]]$occData$occsOrig
     usedOccs <- occsBio$occID %in% spp[[bioSp()]]$occs$occID
     occsBio <- cbind(occsBio, use = usedOccs)
     write.csv(occsBio, tmpOccs, row.names = FALSE)
+    }
 
     # Create mapPrediction
     # add req pred
+    if (!is.null(spp[[bioSp()]]$biomodelos$prediction)) {
     tmpPred <- file.path(tmpdir, paste0(bioSp(), '_pred.tif'))
     raster::writeRaster(spp[[bioSp()]]$biomodelos$prediction, tmpPred,
                         overwrite = TRUE)
+    }
 
     # Create thr
     # add req occs
+    if (!is.null(spp[[bioSp()]]$biomodelos$thrs)) {
     tmpThrs <- file.path(tmpdir, paste0(bioSp(), '_thr.csv'))
     write.csv(spp[[bioSp()]]$biomodelos$thrs, tmpThrs, row.names = TRUE)
+    }
+
+    # Create userSDM prediction
+    # add req pred
+    if (!is.null(spp[[bioSp()]]$biomodelos$mask$userSDM)) {
+      tmpUserSDM <- file.path(tmpdir, paste0(bioSp(), '_userSDM.tif'))
+      raster::writeRaster(spp[[bioSp()]]$biomodelos$mask$userSDM, tmpUserSDM,
+                          overwrite = TRUE)
+    }
 
     # Create raster model modified by expert
     if (!is.null(spp[[bioSp()]]$biomodelos$predExpert)) {
@@ -135,25 +191,26 @@ rep_biomodelos_module_server <- function(input, output, session, common) {
     }
 
     # Create shapefile of expert polygons
-    if (!is.null(spp[[bioSp()]]$mask$expertPoly)) {
-      tmpExpPoly <- file.path(tmpdir, paste0(bioSp(), '_expertPolygonsShp.zip'))
+    if (!is.null(spp[[bioSp()]]$mask$removePoly)) {
+      tmpExpPoly <- file.path(tmpdir, paste0(bioSp(), '_expertPolygonShp.zip'))
       expertPolys <- do.call("rbind",
                              c(args = lapply(seq_along(spp[[bioSp()]]$mask$expertPoly),
                                              function(i){spp[[bioSp()]]$mask$expertPoly[i][[1]]}),
                                makeUniqueIDs = TRUE))
       sf::st_write(obj = sf::st_as_sf(expertPolys),
                       dsn = tmpdir,
-                      layer = paste0(bioSp(), '_expertPolygonsShp'),
+                      layer = paste0(bioSp(), '_expertPolygonShp'),
                       driver = "ESRI Shapefile",
                       append = FALSE)
       extsExpPoly <- c('dbf', 'shp', 'shx')
-      fsExpPoly <- file.path(tmpdir, paste0(bioSp(), '_expertPolygonsShp.', extsExpPoly))
+      fsExpPoly <- file.path(tmpdir, paste0(bioSp(), '_expertPolygonShp.', extsExpPoly))
       zip::zipr(zipfile = tmpExpPoly , files = fsExpPoly)
     }
 
     # Create extent shapefile
     # add req ext
-    tmpExt <- file.path(tmpdir, paste0(bioSp(), '_projectionExtentShp.zip'))
+    if (!is.null(spp[[bioSp()]]$procEnvs$bgExt)) {
+    tmpExt <- file.path(tmpdir, paste0(bioSp(), '_bgExtentShp.zip'))
     sf::st_write(obj = sf::st_as_sf(spp[[bioSp()]]$procEnvs$bgExt),
                     dsn = tmpdir,
                     layer = paste0(bioSp(), '_bgShp'),
@@ -162,8 +219,24 @@ rep_biomodelos_module_server <- function(input, output, session, common) {
     exts <- c('dbf', 'shp', 'shx')
     fsExt <- file.path(tmpdir, paste0(bioSp(), '_bgShp.', exts))
     zip::zipr(zipfile = tmpExt, files = fsExt)
+    }
+
+    # Create userSDM extent shapefile
+    # add req ext
+    if (!is.null(spp[[bioSp()]]$biomodelos$mask$userPolyExt)) {
+      tmpUserSDMExt <- file.path(tmpdir, paste0(bioSp(), '_userSDM_ExtentShp.zip'))
+      sf::st_write(obj = sf::st_as_sf(spp[[bioSp()]]$biomodelos$mask$userPolyExt),
+                   dsn = tmpdir,
+                   layer = paste0(bioSp(), '_userSDM_bgShp'),
+                   driver = "ESRI Shapefile",
+                   append = FALSE)
+      exts <- c('dbf', 'shp', 'shx')
+      fsExt <- file.path(tmpdir, paste0(bioSp(), '_userSDM_bgShp.', exts))
+      zip::zipr(zipfile = tmpUserSDMExt, files = fsExt)
+    }
 
     # Create Metadata
+    if (!is.null(spp[[bioSp()]]$evalOut)) {
     evalTbl <- spp[[bioSp()]]$evalOut@results
     if (grepl("Maxent", spp[[bioSp()]]$biomodelos$modelingMethod, fixed = TRUE)) {
       evalTbl <- evalTbl[evalTbl$tune.args == spp[[bioSp()]]$rmd$vis_curModel, ]
@@ -229,6 +302,7 @@ rep_biomodelos_module_server <- function(input, output, session, common) {
                                 '.zip'))
     names(bioMet) <- c("name", "value")
     write.csv(bioMet, tmpBioMeta, row.names = FALSE)
+    }
 
     # add req metadata
     tmpRMM <- file.path(tmpdir, paste0(bioSp(), '_rmms.csv'))
@@ -299,19 +373,53 @@ rep_biomodelos_module_server <- function(input, output, session, common) {
     combined_rmd <- gsub('``` r', '```{r}', combined_md)
     writeLines(combined_rmd, tmpRMD, useBytes = TRUE)
 
-    # Create ZIP file
-    tmpZIP <- file.path(tmpdir, paste0(spp[[bioSp()]]$rmm$code$wallace$biomodelosTaxID, '.zip'))
-    filesZIP <- c(tmpOccs, tmpBioMeta, tmpPred, tmpThrs, tmpExt, tmpRMM, tmpRMD)
+    # create file for new item added to manifest
+    # if (!is.null(spp[[bioSp()]]$biomodelos$check$here$to$see$if$null)) {
+    #   name_of_created_file <- file.path(tmpdir, paste0(bioSp(), '_whatever.filetype'))
+    #   write_function(spp[[bioSp()]]$biomodelos$NEWTHING, name_of_created_file,
+    #                       overwrite = TRUE)
+    # }
+
+
+  ### Create ZIP File
+    tmpZIP <- file.path(tmpdir, paste0(spp[[bioSp()]], '.zip'))
+    filesZIP <- c(tmpRMM, tmpRMD)
+    if (!is.null(spp[[bioSp()]]$occData$occsOrig)) {
+      filesZIP <- c(filesZIP, tmpOccs)
+    }
+    if (!is.null(spp[[bioSp()]]$evalOut)) {
+      filesZIP <- c(filesZIP, tmpBioMeta)
+    }
+    if (!is.null(spp[[bioSp()]]$biomodelos$prediction)) {
+      filesZIP <- c(filesZIP, tmpPred)
+    }
+    if (!is.null(spp[[bioSp()]]$biomodelos$thrs)) {
+      filesZIP <- c(filesZIP, tmpThrs)
+    }
+    if (!is.null(spp[[bioSp()]]$procEnvs$bgExt)) {
+      filesZIP <- c(filesZIP, tmpExt)
+    }
+    if (!is.null(spp[[bioSp()]]$biomodelos$mask$userSDM)) {
+      filesZIP <- c(filesZIP, tmpUserSDM)
+    }
+    if (!is.null(spp[[bioSp()]]$biomodelos$mask$userPolyExt)) {
+      filesZIP <- c(filesZIP, tmpUserSDMExt)
+    }
     if (!is.null(spp[[bioSp()]]$biomodelos$predExpert)) {
       filesZIP <- c(filesZIP, tmpPredExp)
     }
-    if (!is.null(spp[[bioSp()]]$mask$expertPolyt)) {
+    if (!is.null(spp[[bioSp()]]$mask$expertPoly)) {
       filesZIP <- c(filesZIP, tmpExpPoly)
     }
+    # to add something to the zip
+    #if (!is.null(spp[[bioSp()]]$check$if$null)) {
+    #   filesZIP <- c(filesZIP, name_of_created_file)
+    # }
 
     zip::zipr(zipfile = tmpZIP,
               files = filesZIP)
 
+  ### Create Payload
     PAYLOAD <- list(
       taxID = spp[[bioSp()]]$rmm$code$wallace$biomodelosTaxID,
       biomodelos_user = input$userBio,
@@ -321,10 +429,13 @@ rep_biomodelos_module_server <- function(input, output, session, common) {
       model = httr::upload_file(tmpZIP,
                                type = "application/zip")
     )
+
+
     response <- httr::content(httr::POST(URL, body = PAYLOAD, encode = "multipart",
                                          httr::add_headers(host = 'api-biomodelos.humboldt.org.co',
                                          authorization = paste0('apiKey ', input$keyPost))),
                         as = 'parsed')
+
     if (is.null(response)) {
       shinyalert::shinyalert(
         "Pushed to BioModelos (**)",