adding rough draft of plotting functions

R/00_shared-functions.R

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+## basic functions that will be shared and called by other functions
+
+## function to fitler by common arguments and throw errors if filtering parameters are wrongly specified 
+filter_by_arguments <- function(.fishbase_names = NULL, 
+                                .taxo_level = NULL,
+                                .taxo_levels = NULL,
+                                .datasets = NULL,
+                                .realms = NULL, 
+                                .taxo_scale_observation = NULL,
+                                .trait_names = NULL,
+                                .trait_types = NULL,
+                                .geographic_region = NULL, 
+                                .data = data) {
+
+  ## filter the full Phenofish dataset according to arguments passed to function
+  ## if taxonomic level AND species names are specified, throw error:
+  if(!is.null(.fishbase_names) & !is.null(.taxo_level)) {
+    print("Error: either a taxonomic level OR a vector of species names can be specified, not both.")
+    return()
+  }
+  ## if trait names AND trait types are specified, throw error:
+  if(!is.null(.trait_names) & !is.null(.trait_types)) {
+    print("Error: either a vector of trait names OR a vector of trait types can be specified, not both.")
+    return()
+  }
+
+  data_sub = data
+
+  ## filter to species list
+  if(!is.null(.fishbase_names)) {
+    data_sub <- data[which(data$fishbase_names %in% .fishbase_names),]
+  }
+  ## filter by taxonomic levels requested
+  else if(!is.null(.taxo_level)) {
+    if(taxo_level == "genus") {
+      if(length(which(!data_sub$genus %in% .taxo_levels)) == nrow(data_sub)) {
+        print("Error: no requested genus is in dataset")
+        return()
+      }
+      else {
+        data_sub <- data_sub[which(data_sub$genus %in% .taxo_levels),]
+      }
+    }
+    else if(.taxo_level == "family") {
+      if(length(which(!data_sub$family %in% taxo_levels)) == nrow(data_sub)) {
+        print("Error: no requested family is in dataset")
+        return()
+      }
+      else {
+        data_sub <- data_sub[which(data_sub$family %in% .taxo_levels),]
+      }
+    }
+    else if(.taxo_level == "order") {
+      if(length(which(!data_sub$order %in% .taxo_levels)) == nrow(data_sub)) {
+        print("Error: no requested order is in dataset")
+        return()
+      }
+      else {
+        data_sub <- data_sub[which(data_sub$order %in% .taxo_levels),]
+      }
+    }
+    else if(length(which(!data_sub$class %in% .taxo_levels)) == nrow(data_sub)) {
+      if(!data_sub$class %in% .taxo_levels) {
+        print("Error: no requested class is in dataset")
+        return()
+      }
+      else {
+        data_sub <- data_sub[which(data_sub$class %in% .taxo_levels),]
+      }
+    }
+
+    ## filter by datasets
+    if(!is.null(.datasets)) {
+      data_sub <- data_sub[which(data_sub$dataset %in% .datasets),]
+    }
+    ## filter by realms
+    if(!is.null(.realms)) {
+      data_sub <- data_sub[which(data_sub$realm %in% .realms),]
+    }
+    ## filter by the taxonomic scale of observation
+    if(!is.null(.taxo_scale_observation)) {
+      data_sub <- data_sub[which(data_sub$taxo_scale_observation %in% .taxo_scale_observation),]
+    }
+    ## filter to traits of interest
+    if(!is.null(.trait_names)) {
+      data_sub <- data_sub[which(data_sub$trait_name %in% .trait_names),]
+    }
+    ## filter to traits of interest
+    if(!is.null(.trait_types)) {
+      data_sub <- data_sub[which(data_sub$trait_types %in% .trait_types),]
+    }
+
+    ## filter to geographic region 
+    if(.geographic_region != "global") {
+      ## make sure specified coordinates make sense
+      ## check lat min < lat max, within -90 to 90
+      ## check lon min < lon max, within -180 to 180
+    }
+
+  }
+  return(data_sub)
+}

R/01_plotting-functions.R

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+## writing functions to map the data 
+library(tidyverse)
+
+## source shared functions 
+source("R/00_shared-functions.R")
+
+## read in the test data 
+load("data-raw/test_phenofish.RData")
+data <- test_phenofish
+
+## convert lat lon to numeric 
+data$latitude <- as.numeric(as.character(data$latitude))
+data$longitude <- as.numeric(as.character(data$longitude))
+
+## add fake classification info
+data$genus = c("Bloops")
+data$family = c("Bloopidae")
+data$order = c("Fisherii")
+data$class = c("Swimmyfishii")
+data$realm = rep(c("Freshwater", "Marine"), 1000)[1:nrow(data)]
+
+
+## set all arguments to NULL by default
+fishbase_names = NULL 
+taxo_level = NULL
+taxo_levels = NULL
+datasets = NULL
+realms = NULL
+taxo_scale_observation = NULL
+trait_names = NULL
+trait_types = NULL
+geographic_region = NULL
+
+## set arguments to different things to test
+fishbase_names <- unique(data$fishbase_name)[1:10]
+taxo_level = "family"
+taxo_levels = "Bloopidae"
+realms <- c("Freshwater")
+geographic_region = "global"
+
+
+## test the filter by arguments function 
+test <- filter_by_arguments(fishbase_names = NULL, 
+                    taxo_level = taxo_level,
+                    taxo_levels = taxo_levels,
+                    datasets = datasets,
+                    realms = realms, 
+                    taxo_scale_observation = taxo_scale_observation,
+                    trait_names = trait_names,
+                    trait_types = trait_types,
+                    geographic_region = geographic_region, 
+                    data = data)
+
+plot_observations <- function(fishbase_names = NULL, 
+                              taxo_level = NULL,
+                              taxo_levels = NULL,
+                              datasets = NULL,
+                              realms = NULL, 
+                              taxo_scale_observation = NULL,
+                              trait_names = NULL,
+                              trait_types = NULL,
+                              geographic_region = geographic_region, 
+                              data = data) {
+
+  ## filter Phenofish data by arguments:
+  data_sub <- filter_by_arguments(.fishbase_names = fishbase_names, 
+                      .taxo_level = taxo_level,
+                      .taxo_levels = taxo_levels,
+                      .datasets = datasets,
+                      .realms = realms, 
+                      .taxo_scale_observation = taxo_scale_observation,
+                      .trait_names = trait_names,
+                      .trait_types = trait_types,
+                      .geographic_region = geographic_region, 
+                      .data = data)
+
+  ## if dataset is null
+  if(is.null(data_sub)) {
+    print("Cannot plot observations! Error in data filtering")
+    return()
+  }
+  ## or if filtering resulted in dataset with no geo referenced data  
+  else if(length(which(is.na(data_sub$latitude))) == nrow(data_sub)) {
+    print("Cannot plot observations! No observations in filtered dataset contain geographic coordinates")
+    return()
+  }
+
+  ## otherwise, make the ggplot
+  library(ggplot2)
+  countries <- map_data("world")
+
+  ## remove missing points 
+  data_sub <- data_sub[which(!is.na(data_sub$latitude)) & which(!is.na(data_sub$longitude)), ]
+
+  map <- ggplot(countries, aes(x=long, y=lat, group = group)) + theme_minimal() + 
+    geom_polygon(fill = "grey") + 
+    coord_fixed() + 
+    geom_point(data = data_sub, aes(y = latitude, x = longitude), size = 1, 
+               inherit.aes = F) + 
+    labs(x =  "Latitude", y = "Longitude") +
+    theme(legend.title = element_text(size = 9))
+
+ return(map) 
+}
+
+
+## test it 
+plot_observations(fishbase_names = fishbase_names, 
+                            taxo_level = NULL,
+                            taxo_levels = NULL,
+                            datasets = datasets,
+                            realms = realms, 
+                            taxo_scale_observation = taxo_scale_observation,
+                            trait_names = trait_names,
+                            trait_types = trait_types,
+                            geographic_region = geographic_region, 
+                            data = data)
+
+plot_observations(fishbase_names = fishbase_names, 
+                  taxo_level = NULL,
+                  taxo_levels = NULL,
+                  datasets = c("fishmorph"),
+                  realms = realms, 
+                  taxo_scale_observation = taxo_scale_observation,
+                  trait_names = trait_names,
+                  trait_types = trait_types,
+                  geographic_region = geographic_region, 
+                  data = data)
+
+
+
+
+
+
+
+plot_phylo <- function() {}
+
+plot_diagnostics <- function() {}
+
+plot_by_ecoregion <- function() {}
+
+
+
+## add "save" as a parameter
+
+