## ----rmd_setup, include = FALSE----------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----data, echo=FALSE--------------------------------------------------------- # Packages #library(BioMonTools) #library(knitr) # Data df_obs <- BioMonTools::data_Taxa_MA # Show knitr::kable(head(df_obs)) ## ----Ex_gg, fig.width = 6----------------------------------------------------- # Packages #library(BioMonTools) #library(ggplot2) #library(knitr) # df_obs <- BioMonTools::data_Taxa_MA TaxaID <- "TaxaName" TaxaCount <- "Count" Lat <- "Latitude" Long <- "Longitude" myTaxa <- "ALEWIFE, ADULTS, 0.5-25 ppt" df_map <- subset(df_obs, df_obs[, TaxaID] == myTaxa) myDB <- "state" myRegion <- "massachusetts" Lat <- "Latitude" Long <- "Longitude" # Base Map m1 <- ggplot2::ggplot(data=subset(ggplot2::map_data(myDB) , region %in% c(myRegion))) + ggplot2::geom_polygon(ggplot2::aes(x = long , y = lat , group = group) , fill = "light gray", color = "black") + ggplot2::coord_fixed(1.3) + ggplot2::theme_void() # Add points (all) m1 <- m1 + ggplot2::geom_point(data=df_obs , ggplot2::aes(df_obs[, Long] , df_obs[, Lat]) , fill=NA , color="gray") # Add points (Taxa) m1 <- m1 + ggplot2::geom_point(data=df_map , ggplot2::aes(df_map[,Long] , df_map[,Lat]) , color="blue") # Map Title (center) m1 <- m1 + ggplot2::labs(title = myTaxa) + ggplot2::theme(plot.title = ggplot2::element_text(hjust = 0.5)) # Caption (left justified) m1 <- m1 + ggplot2::labs(caption = "caption1 \n caption2") + ggplot2::theme(plot.caption = ggplot2::element_text(hjust = 0)) # Show Results knitr::kable(head(df_obs)) m1 ## ----Ex_PDF, eval=FALSE------------------------------------------------------- # df_obs <- data_Taxa_MA # SampID <- "estuary" # TaxaID <- "TaxaName" # TaxaCount <- "Count" # Lat <- "Latitude" # Long <- "Longitude" # output_dir <- tempdir() # output_prefix <- "maps.taxa." # output_type <- "pdf" # # myDB <- "state" # myRegion <- "massachusetts" # myXlim <- c(-(73 + (30/60)), -(69 + (56/60))) # myYlim <- c((41 + (14/60)), (42 + (53/60))) # # # Run function with extra arguments for map # BioMonTools::MapTaxaObs(df_obs, # SampID, # TaxaID, # TaxaCount, # Lat, # Long, # output_dir, # output_prefix, # output_type, # database = "state", # regions = "massachusetts", # xlim = myXlim, # ylim = myYlim) #