In mschmidty/AIMtools: Tools for working with AIM Data.

knitr::opts_chunk$set(echo = TRUE)

library(RODBC)
library(AIMtools)
library(tidyverse)
library(dplyr)

file_path<-list.files("test_data/DIMA_5_5", pattern=".mdb", full.names=TRUE)
connect<-odbcDriverConnect("Driver={Microsoft Access Driver (*.mdb, *.accdb)};DBQ=data/DIMA_5_5/DIMA_2020.mdb")
connect<-odbcConnectAccess(file_path)

sqlTables(connect)%>%
  View()

lpi_detail<-sqlFetch(connect, "tblLPIDetail")

sqlFetch(connect, "tblLines")%>%
  View()

Read DIMA function

Sys.getenv("R_ARCH")

read_dima<-function(file_path){

  read_table<-function(connection, name) as_tibble(sqlFetch(connection, name))

  if(Sys.getenv("R_ARCH") != "/i386"){

    stop('You are currently using a 64-bit version of R. Please change your R version to 32-bit in "Tools>Global Options" and in the dropdown change your R version to 32-bit. Microsoft Access Does not work with 64-bit R.')
  }
  con<-odbcConnectAccess(file_path)

  test<-list(
    plots = read_table(con, "tblPlots"),
    lines = read_table(con, "tblLines"),
    lpi_detail = read_table(con, "tblLPIDetail"),
    lpi_header = read_table(con, "tblLPIHeader"),
    sp_rich_detail = read_table(con, "tblSpecRichDetail"),
    sp_rich_header = read_table(con, "tblSpecRichHeader")
  )

  odbcClose(con)

  test
}

data<-read_dima(file_path)

[x] This was copied to R - into the

library(AIMtools)
file_path<-list.files("test_data/2018", pattern=".mdb", full.names=TRUE)
data<-read_dima(file_path)

names(data)

Species Richness Tests

header<-data$sp_rich_header

data$sp_rich_detail%>%
  select(-SpeciesCount)%>%
  tidyr::unnest(symbol = stringr::str_split(SpeciesList, ";"))%>%
  select(-SpeciesList)%>%
  filter(symbol!="")%>%
  left_join(select(data$sp_rich_header, LineKey, RecKey), by="RecKey" )%>%
  left_join(select(data$lines, LineKey, PlotKey ))%>%
  left_join(select(data$plots, PlotKey, PlotID))

names(data)

detail%>%
  count(RecKey)

detail%>%
  count(symbol)%>%
  View()

detail%>%
  filter(symbol=="CHER")

Test sp_rich_dima() function

data<-read_dima(file_path)

sp_richness<-sp_rich_dima(data)

mschmidty/AIMtools documentation built on Sept. 29, 2022, 7:40 p.m.