## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) library('dplyr') ## ----eval = FALSE------------------------------------------------------------- # ### Load packages # library("pestr") ## ----eval = FALSE------------------------------------------------------------- # eppo_token <- create_eppo_token('<>') ## ----eval = FALSE------------------------------------------------------------- # eppo_database_download() ## ----eval = F----------------------------------------------------------------- # eppo_SQLite <- eppo_database_connect() ## ----eval = FALSE------------------------------------------------------------- # ### Create vector of names that you are looking for # pests_query <- c('Cydia', "Triticum aestivum", "abcdef", "cadang") ## ----eval = FALSE------------------------------------------------------------- # pest_names <- eppo_names_tables(pests_query, eppo_SQLite) # names(pest_names) # ### names that exist in database # head(pest_example[[1]], 5) # ### names that were not found # head(pest_example[[2]], 5) # ### preferred names for eppocodes from first table # head(pest_example[[3]], 5) # ### all names that are associated to eppocodes from first data frame # head(pest_example[[4]], 5) ## ----eval = TRUE, echo = FALSE------------------------------------------------ names_example <- readRDS("vignette_mock_names.RDS") names(names_example) names_example[[1]] %>% head(5) %>% knitr::kable(caption = "Names that exist in database", format = "html", table.attr = "style='width:80%;'") names_example[[3]] %>% head(5) %>% knitr::kable(caption = 'Preferred names for eppocodes from first table',format = "html", table.attr = "style='width:80%;'") names_example[[4]] %>% head(5) %>% knitr::kable(caption = 'All names that are associated to eppocodes from first data frame',format = "html", table.attr = "style='width:80%;'") ## ----eval = FALSE------------------------------------------------------------- # pests_cat <- eppo_tabletools_cat(pest_names, eppo_token) # ### long format table # head(pests_cat[[1]], 5) # ### comapct table with information for each eppocode condensed into one cell # head(pests_cat[[2]],5) ## ----eval = TRUE, echo = FALSE------------------------------------------------ cat_example <- readRDS("vignette_mock_cat.RDS") cat_example[[1]] %>% head(5) %>% knitr::kable(caption = "Long format table with pests categorization") cat_example[[2]] %>% head(5) %>% knitr::kable(caption = "Compact table with condensed information on categorization") ## ----eval = FALSE------------------------------------------------------------- # pests_cat <- eppo_tabletools_cat(token = eppo_token, # raw_eppocodes = c("LASPPA", "TRZAX", "CCCVD0"), # use_raw_codes = TRUE) # pest_cat[[2]] ## ----eval = TRUE, echo = FALSE------------------------------------------------ cat_raw_example <- readRDS("vignette_raw_cat.RDS") cat_raw_example[[2]] %>% knitr::kable(caption = "Limited results of using eppocodes LASPPA, TRZAX, CCCVD0") ## ----eval = FALSE------------------------------------------------------------- # pests_hosts <- eppo_tabletools_hosts(pest_names, eppo_token) # # head(pests_hosts[[1]], 5) # head(pests_hosts[[2]], 5) ## ----eval = TRUE, echo = FALSE------------------------------------------------ hosts_example <- readRDS("vignette_mock_hosts.RDS") hosts_example[[1]] %>% head(5) %>% knitr::kable(caption = "Long format table with pests hosts") hosts_example[[2]] %>% head(5) %>% knitr::kable(caption = "Compact table with condensed information on hosts") ## ----eval = FALSE------------------------------------------------------------- # virs_eppocodes <- pest_names$all_associated_names %>% # dplyr::filter(grepl("viroid", fullname) | grepl("virus", fullname)) %>% # .[,5] %>% ## eppocodes are in 5th column # unique() ## ----eval = FALSE------------------------------------------------------------- # virs_taxonomy <- eppo_tabletools_taxo(token = eppo_token, # raw_eppocodes = virs_eppocodes, # use_raw_codes = TRUE) # virs_taxonomy$long_table ## you can also access list elements by their names # virs_taxonomy$compact_table ## ----eval = TRUE, echo = FALSE------------------------------------------------ example_taxo <- readRDS("vignette_viroid_taxo.RDS") example_taxo$long_table %>% knitr::kable(caption = "Long table of viruses and viroids taxonomy") example_taxo$compact_table %>% knitr::kable(caption = "Compact table of viruses and viroids taxonomy") ## ----eval = FALSE------------------------------------------------------------- # abies_pests <- eppo_tabletools_pests(token = eppo_token, # raw_eppocodes = "ABIAL", # use_raw_codes = TRUE) # head(abies_pests[[1]], 5) # head(abies_pests[[2]], 5) ## ----eval = TRUE, echo = FALSE------------------------------------------------ example_pests <- readRDS("vignette_mock_pests.RDS") example_pests$long_table %>% head(5) %>% knitr::kable(caption = "Long table of Abies alba pests") example_pests$compact_table %>% head(5) %>% knitr::kable(caption = "Compact table of Abies alba pests") ## ----eval = FALSE------------------------------------------------------------- # pest_distri <- eppo_tabletools_distri(pest_names) # head(pestr_distri[[1]], 5) # head(pestr_distri[[2]], 5) ## ----evel = TRUE, echo = FALSE------------------------------------------------ example_distri <- readRDS("vignette_mock_distri.RDS") example_distri$long_table %>% head(5) %>% knitr::kable(caption = "Long table with distribution of pests") example_distri$compact_table %>% head(5) %>% knitr::kable(caption = "Compact table with distribution of pests") ## ----eval = FALSE------------------------------------------------------------- # eppo_fulltable <- eppo_table_full(c("Meloidogyne ethiopica", "Crataegus mexicana"), # eppo_SQLite, # eppo_token) # # eppo_fulltable ## ----eval = TRUE, echo = FALSE------------------------------------------------ example_full_table <- readRDS("vignette_mock_full_table.RDS") example_full_table %>% knitr::kable(caption = "Full table with names, hosts, distribution, taxonomy and categorizatio of pests")