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Add vignette and bump to 0.4.1
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‎CITATION.cff‎

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‎DESCRIPTION‎

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Package: REcoTox
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Type: Package
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Title: REcoTox - a workflow to process US EPA ECOTOX Knowledgebase ASCII files
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Version: 0.4.0
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Date: 2023-5-2
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Version: 0.4.1
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Date: 2023-4-11
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Authors@R:
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c(person(given = "Tobias",
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family = "Schulze",
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role = c("aut", "cre"),
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email = "tobias.schulze@ufz.de",
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email = "tsufz1@gmail.com",
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comment = c(ORCID = "0000-0002-9744-8914")),
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person(given = "Wibke",
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family = "Busch",
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Rdpack,
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readr,
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tibble,
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tidyr,
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tidyr,
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utils,
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webchem
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Suggests:
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knitr,
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markdown,
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rmarkdown,
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testthat
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testthat,
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kableExtra,
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tidyverse
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VignetteBuilder:
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knitr
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RdMacros:

‎inst/CHANGELOG.md‎

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# Changelog
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*Version 0.4.1 (4 November 2023)*
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- Add vignette
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*Version 0.4.0 (2 May 2023)*
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- Refactorization of the chemical list and the final results schemes

‎inst/extdata/database_folder/project.RData‎

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‎inst/extdata/database_folder/tests.txt‎

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test_id|reference_number|cas_number|test_grade|test_grade_comments|test_formulation|test_formulation_comments|test_radiolabel|test_radiolabel_comments|test_purity_mean_op|test_purity_mean|test_purity_min_op|test_purity_min|test_purity_max_op|test_purity_max|test_purity_comments|test_characteristics|species_number|organism_habitat|organism_source|organism_source_comments|organism_lifestage|organism_lifestage_comments|organism_age_mean_op|organism_age_mean|organism_age_min_op|organism_age_min|organism_age_max_op|organism_age_max|organism_age_unit|organism_init_wt_mean_op|organism_init_wt_mean|organism_init_wt_min_op|organism_init_wt_min|organism_init_wt_max_op|organism_init_wt_max|organism_init_wt_unit|organism_characteristics|organism_gender|experimental_design|study_duration_mean_op|study_duration_mean|study_duration_min_op|study_duration_min|study_duration_max_op|study_duration_max|study_duration_unit|study_duration_comments|exposure_duration_mean_op|exposure_duration_mean|exposure_duration_min_op|exposure_duration_min|exposure_duration_max_op|exposure_duration_max|exposure_duration_unit|exposure_duration_comments|study_type|study_type_comments|test_type|test_type_comments|test_location|test_location_comments|test_method|test_method_comments|exposure_type|exposure_type_comments|control_type|control_type_comments|media_type|media_type_comments|num_doses_mean_op|num_doses_mean|num_doses_min_op|num_doses_min|num_doses_max_op|num_doses_max|num_doses_comments|other_effect_comments|application_freq_mean_op|application_freq_mean|application_freq_min_op|application_freq_min|application_freq_max_op|application_freq_max|application_freq_unit|application_freq_comments|application_type|application_type_comments|application_rate|application_rate_unit|application_date|application_date_comments|application_season|application_season_comments|subhabitat|subhabitat_description|substrate|substrate_description|water_depth_mean_op|water_depth_mean|water_depth_min_op|water_depth_min|water_depth_max_op|water_depth_max|water_depth_unit|water_depth_comments|geographic_code|geographic_location|latitude|longitude|halflife_mean_op|halflife_mean|halflife_min_op|halflife_min|halflife_max_op|halflife_max|halflife_unit|halflife_comments|additional_comments|created_date|modified_date|published_date
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test_id|reference_number|test_cas|test_grade|test_grade_comments|test_formulation|test_formulation_comments|test_radiolabel|test_radiolabel_comments|test_purity_mean_op|test_purity_mean|test_purity_min_op|test_purity_min|test_purity_max_op|test_purity_max|test_purity_comments|test_characteristics|species_number|organism_habitat|organism_source|organism_source_comments|organism_lifestage|organism_lifestage_comments|organism_age_mean_op|organism_age_mean|organism_age_min_op|organism_age_min|organism_age_max_op|organism_age_max|organism_age_unit|organism_init_wt_mean_op|organism_init_wt_mean|organism_init_wt_min_op|organism_init_wt_min|organism_init_wt_max_op|organism_init_wt_max|organism_init_wt_unit|organism_characteristics|organism_gender|experimental_design|study_duration_mean_op|study_duration_mean|study_duration_min_op|study_duration_min|study_duration_max_op|study_duration_max|study_duration_unit|study_duration_comments|exposure_duration_mean_op|exposure_duration_mean|exposure_duration_min_op|exposure_duration_min|exposure_duration_max_op|exposure_duration_max|exposure_duration_unit|exposure_duration_comments|study_type|study_type_comments|test_type|test_type_comments|test_location|test_location_comments|test_method|test_method_comments|exposure_type|exposure_type_comments|control_type|control_type_comments|media_type|media_type_comments|num_doses_mean_op|num_doses_mean|num_doses_min_op|num_doses_min|num_doses_max_op|num_doses_max|num_doses_comments|other_effect_comments|application_freq_mean_op|application_freq_mean|application_freq_min_op|application_freq_min|application_freq_max_op|application_freq_max|application_freq_unit|application_freq_comments|application_type|application_type_comments|application_rate|application_rate_unit|application_date|application_date_comments|application_season|application_season_comments|subhabitat|subhabitat_description|substrate|substrate_description|water_depth_mean_op|water_depth_mean|water_depth_min_op|water_depth_min|water_depth_max_op|water_depth_max|water_depth_unit|water_depth_comments|geographic_code|geographic_location|latitude|longitude|halflife_mean_op|halflife_mean|halflife_min_op|halflife_min|halflife_max_op|halflife_max|halflife_unit|halflife_comments|additional_comments|created_date|modified_date|published_date
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1000494|95|1912249|||PU|||||99.9|||||||58471|Water|||EX|||||||||||||||||||||||||||||||||||||||LAB||||S||S||FW|||||||||RECOVERY||1|||||X|||||||||||||||||||||||||||||||||| |10/06/1992||
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1000495|95|1912249|||PU|||||99.9|||||||58471|Water|||EX|||||||||||||||||||||||||||||||||||||||LAB||||S||S||FW|||||||||RECOVERY||1|||||X|||||||||||||||||||||||||||||||||| |10/06/1992||
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1000496|95|1912249|||PU|||||99.9|||||||58471|Water|||EX|||||||||||||||||||||||||||||||||||||||LAB||||S||S||FW|||||||||RECOVERY||1|||||X|||||||||||||||||||||||||||||||||| |10/06/1992||

‎vignettes/REcoTox.R‎

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## ----biocstyle, echo = FALSE, messages = FALSE, results = "hide"--------------
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BiocStyle::markdown()
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## ----init, message = FALSE, echo = FALSE, results = "hide"--------------------
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## Silently loading all packages
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library(BiocStyle)
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library(desc)
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library(kableExtra)
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library(tidyverse)
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## ----load REcoTox package, eval = FALSE, echo = TRUE, message = FALSE, warning = FALSE----
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# # Load the REcoTox package
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# library(REcoTox)
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## ----R Documentation, echo = TRUE, eval = FALSE-------------------------------
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# # Documentation of REcoTox
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# help(package = "REcoTox")
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## ----initialize folders, echo = TRUE, message = FALSE, warning = FALSE, eval = TRUE----
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# Path of the project folder
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project_folder <- "REcoTox_demo"
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database_folder <- system.file("extdata/database_folder", package="REcoTox")
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# The project folder is created in the home directory
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project_path <- normalizePath(ifelse(.Platform$OS.type == "unix",
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paste0("~/", project_folder),
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paste0(
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Sys.getenv("HOMEPATH"),
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"\\",
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project_folder
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)
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))
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# An existing folder is deleted
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if (dir.exists(project_folder)) {
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unlink(project_folder, recursive = TRUE)
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}
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## ----create project, echo = TRUE, message = FALSE, warning = FALSE, eval = TRUE----
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project <- REcoTox::create_project(database_path = database_folder,
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project_path,
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initalise_database_project = TRUE, # create the basic project from current ASCII files in DB folder
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initalise_project = TRUE, # initializes the project folder
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load_default = FALSE) # loads the default project in the project folder in the memoryfault_example = TRUE
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file.copy(
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from = system.file(
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"extdata",
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"Query_EcoTox_DB.R",
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package = "REcoTox"
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),
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to = normalizePath(
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path = file.path(
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project_folder,
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"Query_EcoTox_DB.R"
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),
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winslash = "\\",
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mustWork = FALSE
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),
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overwrite = TRUE
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)
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## ----list project folder------------------------------------------------------
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# List files and directories in project_folder
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list.files(project_folder, recursive = TRUE, include.dirs = TRUE)
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## ----list database folder-----------------------------------------------------
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# List files and directories in project_folder
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list.files(database_folder, recursive = TRUE, include.dirs = TRUE)
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## ----view chemical_properties, echo = TRUE, eval = TRUE, message = TRUE-------
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# Review of the chemical properties
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chemical_properties <- readr::read_csv(file = normalizePath(path = file.path(
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database_folder,
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"chemical_properties.csv"
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), ), show_col_types = FALSE)
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kable(
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chemical_properties %>%
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head(5),
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format = "html",
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digits = 2
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) %>%
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kable_styling("striped", full_width = TRUE) %>%
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scroll_box(width = "700px", height = "300px")
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## ----view results, echo = TRUE, eval = TRUE, message = TRUE-------------------
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# Review of the result table
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results <-
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readr::read_delim(
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file = normalizePath(
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path = file.path(
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database_folder,
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"results.txt"
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),
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),
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show_col_types = FALSE,
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delim = "|"
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)
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kable(
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results %>%
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head(5),
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format = "html", digits = 2
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) %>%
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kable_styling("striped", full_width = TRUE) %>%
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scroll_box(width = "700px", height = "300px")
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## ----view chemicals, echo = TRUE, eval = TRUE, message = TRUE-----------------
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# Review of the substance_table
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substances <-
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readr::read_delim(
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file = normalizePath(
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path = file.path(
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database_folder,
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"validation",
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"chemicals.txt"
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),
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),
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show_col_types = FALSE,
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delim = "|"
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)
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kable(
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substances %>%
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head(5),
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format = "html", digits = 2
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) %>%
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kable_styling("striped", full_width = TRUE) %>%
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scroll_box(width = "700px", height = "300px")
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## ----view references, echo = TRUE, eval = TRUE, message = TRUE----------------
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# Review of the substance_table
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references <-
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readr::read_delim(
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file = normalizePath(
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path = file.path(
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database_folder,
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"validation",
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"references.txt"
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),
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),
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show_col_types = FALSE,
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delim = "|"
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)
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kable(
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references %>%
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head(5),
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format = "html", digits = 2
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) %>%
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kable_styling("striped", full_width = TRUE) %>%
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scroll_box(width = "700px", height = "300px")
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## ----view species, echo = TRUE, eval = TRUE, message = TRUE-------------------
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# Review of the substance_table
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species <-
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readr::read_delim(
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file = normalizePath(
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path = file.path(
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database_folder,
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"validation",
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"species.txt"
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),
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),
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show_col_types = FALSE,
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delim = "|"
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)
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kable(
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species %>%
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head(5),
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format = "html", digits = 2
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) %>%
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kable_styling("striped", full_width = TRUE) %>%
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scroll_box(width = "700px", height = "300px")
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## ----initialize databases, echo = TRUE, message = FALSE, warning = FALSE, eval = FALSE----
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# project <- REcoTox::create_project(database_path = database_folder,
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# project_path,
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# initalise_database_project = TRUE,
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# initalise_project = TRUE,
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# load_default = FALSE)
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## ----initialize project, echo = TRUE, message = FALSE, warning = FALSE, eval = FALSE----
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# project <- REcoTox::prepare_data(project = project,
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# load_initial_project = FALSE,
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# new_project_path = NA,
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# save_project = TRUE
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# )
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## ----view pivot tables, echo = FALSE, eval = TRUE, message = TRUE-------------
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# Review of the privot table
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pivot <-
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project$object$results_pivot
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kable(
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pivot %>%
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head(5),
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format = "html", digits = 2
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) %>%
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kable_styling("striped", full_width = TRUE) %>%
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scroll_box(width = "700px", height = "300px")
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## ----sessioninfo, echo = TRUE, eval = TRUE, message = FALSE-------------------
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sessionInfo()
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## ----clean_up, echo = FALSE, results = "asis", eval = FALSE-------------------
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# unlink(project_folder, recursive = TRUE)
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