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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,13 +1,13 @@ | ||
| Package: REcoTox | ||
| Type: Package | ||
| Title: REcoTox - a workflow to process US EPA ECOTOX Knowledgebase ASCII files | ||
| Version: 0.4.0 | ||
| Date: 2023-5-2 | ||
| Version: 0.4.1 | ||
| Date: 2023-4-11 | ||
| Authors@R: | ||
| c(person(given = "Tobias", | ||
| family = "Schulze", | ||
| role = c("aut", "cre"), | ||
| email = "[email protected]", | ||
| email = "[email protected]", | ||
| comment = c(ORCID = "0000-0002-9744-8914")), | ||
| person(given = "Wibke", | ||
| family = "Busch", | ||
|
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@@ -34,7 +34,7 @@ Imports: | |
| Rdpack, | ||
| readr, | ||
| tibble, | ||
| tidyr, | ||
| tidyr, | ||
| utils, | ||
| webchem | ||
| Suggests: | ||
|
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@@ -43,7 +43,9 @@ Suggests: | |
| knitr, | ||
| markdown, | ||
| rmarkdown, | ||
| testthat | ||
| testthat, | ||
| kableExtra, | ||
| tidyverse | ||
| VignetteBuilder: | ||
| knitr | ||
| RdMacros: | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,215 @@ | ||
| ## ----biocstyle, echo = FALSE, messages = FALSE, results = "hide"-------------- | ||
| BiocStyle::markdown() | ||
|
|
||
| ## ----init, message = FALSE, echo = FALSE, results = "hide"-------------------- | ||
| ## Silently loading all packages | ||
| library(BiocStyle) | ||
| library(desc) | ||
| library(kableExtra) | ||
| library(tidyverse) | ||
|
|
||
| ## ----load REcoTox package, eval = FALSE, echo = TRUE, message = FALSE, warning = FALSE---- | ||
| # # Load the REcoTox package | ||
| # library(REcoTox) | ||
|
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||
| ## ----R Documentation, echo = TRUE, eval = FALSE------------------------------- | ||
| # # Documentation of REcoTox | ||
| # help(package = "REcoTox") | ||
|
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| ## ----initialize folders, echo = TRUE, message = FALSE, warning = FALSE, eval = TRUE---- | ||
| # Path of the project folder | ||
| project_folder <- "REcoTox_demo" | ||
|
|
||
| database_folder <- system.file("extdata/database_folder", package="REcoTox") | ||
| # The project folder is created in the home directory | ||
| project_path <- normalizePath(ifelse(.Platform$OS.type == "unix", | ||
| paste0("~/", project_folder), | ||
| paste0( | ||
| Sys.getenv("HOMEPATH"), | ||
| "\\", | ||
| project_folder | ||
| ) | ||
| )) | ||
|
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||
| # An existing folder is deleted | ||
| if (dir.exists(project_folder)) { | ||
| unlink(project_folder, recursive = TRUE) | ||
| } | ||
|
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||
| ## ----create project, echo = TRUE, message = FALSE, warning = FALSE, eval = TRUE---- | ||
| project <- REcoTox::create_project(database_path = database_folder, | ||
| project_path, | ||
| initalise_database_project = TRUE, # create the basic project from current ASCII files in DB folder | ||
| initalise_project = TRUE, # initializes the project folder | ||
| load_default = FALSE) # loads the default project in the project folder in the memoryfault_example = TRUE | ||
|
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||
| file.copy( | ||
| from = system.file( | ||
| "extdata", | ||
| "Query_EcoTox_DB.R", | ||
| package = "REcoTox" | ||
| ), | ||
| to = normalizePath( | ||
| path = file.path( | ||
| project_folder, | ||
| "Query_EcoTox_DB.R" | ||
| ), | ||
| winslash = "\\", | ||
| mustWork = FALSE | ||
| ), | ||
| overwrite = TRUE | ||
| ) | ||
|
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||
|
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| ## ----list project folder------------------------------------------------------ | ||
| # List files and directories in project_folder | ||
| list.files(project_folder, recursive = TRUE, include.dirs = TRUE) | ||
|
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||
| ## ----list database folder----------------------------------------------------- | ||
| # List files and directories in project_folder | ||
| list.files(database_folder, recursive = TRUE, include.dirs = TRUE) | ||
|
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||
| ## ----view chemical_properties, echo = TRUE, eval = TRUE, message = TRUE------- | ||
| # Review of the chemical properties | ||
| chemical_properties <- readr::read_csv(file = normalizePath(path = file.path( | ||
| database_folder, | ||
| "chemical_properties.csv" | ||
| ), ), show_col_types = FALSE) | ||
|
|
||
| kable( | ||
| chemical_properties %>% | ||
| head(5), | ||
| format = "html", | ||
| digits = 2 | ||
| ) %>% | ||
| kable_styling("striped", full_width = TRUE) %>% | ||
| scroll_box(width = "700px", height = "300px") | ||
|
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||
| ## ----view results, echo = TRUE, eval = TRUE, message = TRUE------------------- | ||
| # Review of the result table | ||
| results <- | ||
| readr::read_delim( | ||
| file = normalizePath( | ||
| path = file.path( | ||
| database_folder, | ||
| "results.txt" | ||
| ), | ||
| ), | ||
| show_col_types = FALSE, | ||
| delim = "|" | ||
|
|
||
| ) | ||
|
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| kable( | ||
| results %>% | ||
| head(5), | ||
| format = "html", digits = 2 | ||
| ) %>% | ||
| kable_styling("striped", full_width = TRUE) %>% | ||
| scroll_box(width = "700px", height = "300px") | ||
|
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||
| ## ----view chemicals, echo = TRUE, eval = TRUE, message = TRUE----------------- | ||
| # Review of the substance_table | ||
| substances <- | ||
| readr::read_delim( | ||
| file = normalizePath( | ||
| path = file.path( | ||
| database_folder, | ||
| "validation", | ||
| "chemicals.txt" | ||
| ), | ||
| ), | ||
| show_col_types = FALSE, | ||
| delim = "|" | ||
|
|
||
| ) | ||
|
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| kable( | ||
| substances %>% | ||
| head(5), | ||
| format = "html", digits = 2 | ||
| ) %>% | ||
| kable_styling("striped", full_width = TRUE) %>% | ||
| scroll_box(width = "700px", height = "300px") | ||
|
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||
| ## ----view references, echo = TRUE, eval = TRUE, message = TRUE---------------- | ||
| # Review of the substance_table | ||
| references <- | ||
| readr::read_delim( | ||
| file = normalizePath( | ||
| path = file.path( | ||
| database_folder, | ||
| "validation", | ||
| "references.txt" | ||
| ), | ||
| ), | ||
| show_col_types = FALSE, | ||
| delim = "|" | ||
|
|
||
| ) | ||
|
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| kable( | ||
| references %>% | ||
| head(5), | ||
| format = "html", digits = 2 | ||
| ) %>% | ||
| kable_styling("striped", full_width = TRUE) %>% | ||
| scroll_box(width = "700px", height = "300px") | ||
|
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||
| ## ----view species, echo = TRUE, eval = TRUE, message = TRUE------------------- | ||
| # Review of the substance_table | ||
| species <- | ||
| readr::read_delim( | ||
| file = normalizePath( | ||
| path = file.path( | ||
| database_folder, | ||
| "validation", | ||
| "species.txt" | ||
| ), | ||
| ), | ||
| show_col_types = FALSE, | ||
| delim = "|" | ||
|
|
||
| ) | ||
|
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| kable( | ||
| species %>% | ||
| head(5), | ||
| format = "html", digits = 2 | ||
| ) %>% | ||
| kable_styling("striped", full_width = TRUE) %>% | ||
| scroll_box(width = "700px", height = "300px") | ||
|
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||
| ## ----initialize databases, echo = TRUE, message = FALSE, warning = FALSE, eval = FALSE---- | ||
| # project <- REcoTox::create_project(database_path = database_folder, | ||
| # project_path, | ||
| # initalise_database_project = TRUE, | ||
| # initalise_project = TRUE, | ||
| # load_default = FALSE) | ||
|
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||
| ## ----initialize project, echo = TRUE, message = FALSE, warning = FALSE, eval = FALSE---- | ||
| # project <- REcoTox::prepare_data(project = project, | ||
| # load_initial_project = FALSE, | ||
| # new_project_path = NA, | ||
| # save_project = TRUE | ||
| # ) | ||
|
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||
| ## ----view pivot tables, echo = FALSE, eval = TRUE, message = TRUE------------- | ||
| # Review of the privot table | ||
| pivot <- | ||
| project$object$results_pivot | ||
|
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||
| kable( | ||
| pivot %>% | ||
| head(5), | ||
| format = "html", digits = 2 | ||
| ) %>% | ||
| kable_styling("striped", full_width = TRUE) %>% | ||
| scroll_box(width = "700px", height = "300px") | ||
|
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||
| ## ----sessioninfo, echo = TRUE, eval = TRUE, message = FALSE------------------- | ||
| sessionInfo() | ||
|
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||
| ## ----clean_up, echo = FALSE, results = "asis", eval = FALSE------------------- | ||
| # unlink(project_folder, recursive = TRUE) | ||
|
|
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