diff --git a/CITATION.cff b/CITATION.cff index e278fdc..8d9232c 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -8,7 +8,11 @@ authors: given-names: "Philipp" orcid: "https://orcid.org/0009-0002-7697-5536" title: "pam" -version: 2.0.2 -date-released: 2025-07-29 +<<<<<<< HEAD +version: 2.0.3 +======= +version: 2.1.0 +>>>>>>> a691a6c (renamed etrmax_with_without_ratio to etrmax_without_with_ratio) +date-released: 2026-04-11 url: "https://github.com/biotoolbox/pam" doi: "10.32614/CRAN.package.pam" diff --git a/Makefile b/Makefile index b923345..ac8b9d7 100644 --- a/Makefile +++ b/Makefile @@ -20,4 +20,8 @@ build: buildtest: rm -rf src/tests/testthat/results make build - R CMD check pam_2.0.2.tar.gz +<<<<<<< HEAD + R CMD check pam_2.0.3.tar.gz +======= + R CMD check pam_2.1.0.tar.gz +>>>>>>> a691a6c (renamed etrmax_with_without_ratio to etrmax_without_with_ratio) diff --git a/README.md b/README.md index 38c81de..e1b49ce 100644 --- a/README.md +++ b/README.md @@ -477,7 +477,7 @@ $${alpha} = \frac{{etrmax\\_with\\_photoinhibition}}{{ik\\_with\\_photoinhibitio - **w**: Not available, here set to `NA_real_` - **ib**: Not available, here set to `NA_real_` -- **etrmax_with_without_ratio**: Ratio of `etrmax_with_photoinhibition` to `etrmax_without_photoinhibition` and `ik_with_photoinhibition` to `ik_without_photoinhibition`, transfered as: `pmax_popt_and_ik_iik_ratio` +- **etrmax_without_with_ratio**: Ratio of `etrmax_without_photoinhibition` / `etrmax_with_photoinhibition` and `ik_without_photoinhibition` / `ik_with_photoinhibition`, transfered as: `pmax_popt_and_ik_iik_ratio` #### Details @@ -519,9 +519,9 @@ Returns a modified model result as a list with the following elements: - **im_with_photoinhibition**: The PAR at which the maximum electron transport rate is achieved by taking photoinhibition into account, transfered as: `im` - **w**: Not available, here set to `NA_real_` - **ib**: Transfered unchange as: `ib` -- **etrmax_with_without_ratio**: Ratio of `etrmax_with_photoinhibition` to `etrmax_without_photoinhibition` and `ik_with_photoinhibition` to `ik_without_photoinhibition`. Calculated as: +- **etrmax_without_with_ratio**: Ratio of `etrmax_without_photoinhibition` / `etrmax_with_photoinhibition` and `ik_without_photoinhibition` / `ik_with_photoinhibition`. Calculated as: -$${{etrmax\\_with\\_without\\_ratio}} = \frac{{etrmax\\_with\\_photoinhibition}}{{etrmax\\_without\\_photoinhibition}}$$ +$${{etrmax\\_with\\_without\\_ratio}} = \frac{{etrmax\\_without\\_photoinhibition}}{{etrmax\\_with\\_photoinhibition}}$$ #### Details @@ -563,7 +563,7 @@ Returns a modified model result as a list with the following elements: - **im_with_photoinhibition**: The PAR at which the maximum electron transport rate is achieved by taking photoinhibition into account, transfered as`im` - **w**: The sharpness of the peak, transfered as `w` - **ib**: Not available, here set to `NA_real_` -- **etrmax_with_without_ratio**: Not available, here set to `NA_real_` +- **etrmax_without_with_ratio**: Not available, here set to `NA_real_` #### Details @@ -626,7 +626,7 @@ $$ik\\_without\\_photoinhibition = \frac{etrmax\\_without\\_photoinhibition}{alp - **w**: Not available, here set to `NA_real_` - **ib**: Not available, here set to `NA_real_` -- **etrmax_with_without_ratio**: Ratio of `etrmax_with_photoinhibition` to `etrmax_without_photoinhibition` and `ik_with_photoinhibition` to `ik_without_photoinhibition`. Calculated as: +- **etrmax_without_with_ratio**: Ratio of `etrmax_without_photoinhibition` / `etrmax_with_photoinhibition` and `ik_without_photoinhibition` / `ik_with_photoinhibition`. Calculated as: $${{etrmax\\_with\\_without\\_ratio}} = \frac{{etrmax\\_with\\_photoinhibition}}{{etrmax\\_without\\_photoinhibition}}$$ @@ -662,7 +662,7 @@ modified |Eilers and Peeters |Platt |Walsby |Vollenweider |im_with_photoinhibition |im |im |NA |NA | |w |w |NA |NA |NA | |ib |NA |ib |NA |NA | -|etrmax_with_without_ratio |NA |NA |NA |pmax_popt_and_ik_iik_ratio | +|etrmax_without_with_ratio |NA |NA |NA |pmax_popt_and_ik_iik_ratio | #### Publication-accurate naming and the respective modified naming with additional calculations not included in the original publication @@ -684,7 +684,7 @@ modified |Eilers and Peeters |Platt |Walsby |Vollenweider |im_with_photoinhibition |im |im |im_with_photoinhibition |im_with_photoinhibition | |w |w |NA |NA |NA | |ib |NA |ib |NA |NA | -|etrmax_with_without_ratio |NA |etrmax_with_without_ratio |etrmax_with_without_ratio |pmax_popt_and_ik_iik_ratio | +|etrmax_without_with_ratio |NA |etrmax_without_with_ratio |etrmax_without_with_ratio |pmax_popt_and_ik_iik_ratio | ### compare_regression_models_ETR_I() and compare_regression_models_ETR_II() diff --git a/packages.txt b/packages.txt index b1fcd06..d486f1c 100644 --- a/packages.txt +++ b/packages.txt @@ -5,4 +5,4 @@ minpack.lm ggthemes gridExtra cowplot -Metrics \ No newline at end of file +Metrics diff --git a/src/DESCRIPTION b/src/DESCRIPTION index c0e70f5..b2ec71b 100644 --- a/src/DESCRIPTION +++ b/src/DESCRIPTION @@ -1,7 +1,11 @@ Package: pam Type: Package Title: Fast and Efficient Processing of PAM Data -Version: 2.0.2 +<<<<<<< HEAD +Version: 2.0.3 +======= +Version: 2.1.0 +>>>>>>> a691a6c (renamed etrmax_with_without_ratio to etrmax_without_with_ratio) Authors@R: c( person( "Julien", @@ -26,7 +30,7 @@ LazyData: true Suggests: testthat (>= 3.0.0) Config/testthat/edition: 3 -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 Imports: rlang, data.table, diff --git a/src/R/eilers_peeters.R b/src/R/eilers_peeters.R index a5b374f..83e3310 100644 --- a/src/R/eilers_peeters.R +++ b/src/R/eilers_peeters.R @@ -291,7 +291,7 @@ eilers_peeters_generate_regression_internal <- function( #' \item \code{im_with_photoinhibition}: The PAR at which the maximum electron transport rate is achieved with photoinhibition, transferred as \code{im}. #' \item \code{w}: The sharpness of the peak, transferred as \code{w}. #' \item \code{ib}: Not available, set to \code{NA_real_}. -#' \item \code{etrmax_with_without_ratio}: Not available, set to \code{NA_real_}. +#' \item \code{etrmax_without_with_ratio}: Not available, set to \code{NA_real_}. #' } #' #' @details diff --git a/src/R/platt.R b/src/R/platt.R index ed4cd3d..47c8c2a 100644 --- a/src/R/platt.R +++ b/src/R/platt.R @@ -299,7 +299,7 @@ platt_generate_regression_internal <- function( #' \item \code{im_with_photoinhibition}: The PAR at which the maximum electron transport rate is achieved with photoinhibition, transferred as \code{im}. #' \item \code{w}: Not available, set to \code{NA_real_}. #' \item \code{ib}: Transferred unchanged as \code{ib}. -#' \item \code{etrmax_with_without_ratio}: Ratio of \code{etrmax_with_photoinhibition} to \code{etrmax_without_photoinhibition}, and \code{ik_with_photoinhibition} to \code{ik_without_photoinhibition}. +#' \item \code{etrmax_without_with_ratio}: Ratio of \code{etrmax_with_photoinhibition} to \code{etrmax_without_photoinhibition}, and \code{ik_with_photoinhibition} to \code{ik_without_photoinhibition}. #' } #' #' @details @@ -334,7 +334,7 @@ platt_modified <- function(model_result) { im_with_photoinhibition = model_result[["im"]], w = NA_real_, ib = model_result[["ib"]], - etrmax_with_without_ratio = model_result[["ps"]] / model_result[["pm"]] + etrmax_without_with_ratio = model_result[["ps"]] / model_result[["pm"]] ) return(result) diff --git a/src/R/util.R b/src/R/util.R index 891da5e..931a7b6 100644 --- a/src/R/util.R +++ b/src/R/util.R @@ -211,7 +211,7 @@ create_modified_model_result <- function( im_with_photoinhibition, w, ib, - etrmax_with_without_ratio) { + etrmax_without_with_ratio) { result <- list( etr_type = etr_type, etr_regression_data = etr_regression_data, @@ -231,7 +231,7 @@ create_modified_model_result <- function( im_with_photoinhibition = im_with_photoinhibition, w = w, ib = ib, - etrmax_with_without_ratio = etrmax_with_without_ratio + etrmax_without_with_ratio = etrmax_without_with_ratio ) validate_modified_model_result(result) return(result) diff --git a/src/R/validation.R b/src/R/validation.R index 609e543..d47d394 100644 --- a/src/R/validation.R +++ b/src/R/validation.R @@ -259,9 +259,9 @@ validate_modified_model_result <- function(model_result) { stop("ib is null or not a valid number") } - if (is.null(model_result[["etrmax_with_without_ratio"]]) || - !is.numeric(model_result[["etrmax_with_without_ratio"]])) { - stop("etrmax_with_without_ratio is null or not a valid number") + if (is.null(model_result[["etrmax_without_with_ratio"]]) || + !is.numeric(model_result[["etrmax_without_with_ratio"]])) { + stop("etrmax_without_with_ratio is null or not a valid number") } }, error = function(e) { diff --git a/src/R/vollenweider.R b/src/R/vollenweider.R index e4a4149..4497b0f 100644 --- a/src/R/vollenweider.R +++ b/src/R/vollenweider.R @@ -301,7 +301,7 @@ vollenweider_generate_regression_internal <- function( #' \item \code{im_with_photoinhibition}: The PAR at which the maximum electron transport rate is achieved by taking photoinhibition into account, determined using the regression data from the model. #' \item \code{w}: Not available, here set to \code{NA_real_}. #' \item \code{ib}: Transferred unchanged as \code{ib}. -#' \item \code{etrmax_with_without_ratio}: Ratio of \code{etrmax_with_photoinhibition} to \code{etrmax_without_photoinhibition} and \code{ik_with_photoinhibition} to \code{ik_without_photoinhibition}. +#' \item \code{etrmax_without_with_ratio}: Ratio of \code{etrmax_with_photoinhibition} to \code{etrmax_without_photoinhibition} and \code{ik_with_photoinhibition} to \code{ik_without_photoinhibition}. #' } #' #' @details @@ -340,7 +340,7 @@ vollenweider_modified <- function(model_result) { im_with_photoinhibition = im_with_photoinhibition, w = NA_real_, ib = NA_real_, - etrmax_with_without_ratio = model_result[["pmax_popt_and_ik_iik_ratio"]] + etrmax_without_with_ratio = model_result[["pmax_popt_and_ik_iik_ratio"]] ) return(result) diff --git a/src/R/walsby.R b/src/R/walsby.R index 4e6df6b..da8e33f 100644 --- a/src/R/walsby.R +++ b/src/R/walsby.R @@ -232,7 +232,7 @@ walsby_generate_regression_internal <- function( #' \item \code{im_with_photoinhibition}: PAR at the maximum ETR with photoinhibition. #' \item \code{w}: Not available, set to \code{NA_real_}. #' \item \code{ib}: Not available, set to \code{NA_real_}. -#' \item \code{etrmax_with_without_ratio}: Ratio of \code{etrmax_with_photoinhibition} to \code{etrmax_without_photoinhibition}. +#' \item \code{etrmax_without_with_ratio}: Ratio of \code{etrmax_with_photoinhibition} to \code{etrmax_without_photoinhibition}. #' } #' #' @details @@ -273,7 +273,7 @@ walsby_modified <- function(model_result) { im_with_photoinhibition = im_with_photoinhibition, w = NA_real_, ib = NA_real_, - etrmax_with_without_ratio = model_result[["etr_max"]] / etrmax_with_photoinhibition + etrmax_without_with_ratio = model_result[["etr_max"]] / etrmax_with_photoinhibition ) return(result) diff --git a/src/inst/CITATION b/src/inst/CITATION index 27dcbec..bd9f208 100644 --- a/src/inst/CITATION +++ b/src/inst/CITATION @@ -2,8 +2,12 @@ citation <- bibentry( bibtype = "Manual", title = "pam: Fast and Efficient Processing of PAM Data", author = c(person("Julien", "Böhm"), person("Philipp", "Schrag")), - year = 2025, - note = "R package version 2.0.2", + year = 2026, +<<<<<<< HEAD + note = "R package version 2.0.3", +======= + note = "R package version 2.1.0", +>>>>>>> a691a6c (renamed etrmax_with_without_ratio to etrmax_without_with_ratio) url = "https://CRAN.R-project.org/package=pam", doi = "10.32614/CRAN.package.pam" ) diff --git a/src/man/eilers_peeters_modified.Rd b/src/man/eilers_peeters_modified.Rd index 5a0553f..8e18b1d 100644 --- a/src/man/eilers_peeters_modified.Rd +++ b/src/man/eilers_peeters_modified.Rd @@ -30,7 +30,7 @@ A modified model result as a list with the following elements: \item \code{im_with_photoinhibition}: The PAR at which the maximum electron transport rate is achieved with photoinhibition, transferred as \code{im}. \item \code{w}: The sharpness of the peak, transferred as \code{w}. \item \code{ib}: Not available, set to \code{NA_real_}. - \item \code{etrmax_with_without_ratio}: Not available, set to \code{NA_real_}. + \item \code{etrmax_without_with_ratio}: Not available, set to \code{NA_real_}. } } \description{ diff --git a/src/man/platt_modified.Rd b/src/man/platt_modified.Rd index f2d79d7..9c14648 100644 --- a/src/man/platt_modified.Rd +++ b/src/man/platt_modified.Rd @@ -30,7 +30,7 @@ A modified model result as a list with the following elements: \item \code{im_with_photoinhibition}: The PAR at which the maximum electron transport rate is achieved with photoinhibition, transferred as \code{im}. \item \code{w}: Not available, set to \code{NA_real_}. \item \code{ib}: Transferred unchanged as \code{ib}. - \item \code{etrmax_with_without_ratio}: Ratio of \code{etrmax_with_photoinhibition} to \code{etrmax_without_photoinhibition}, and \code{ik_with_photoinhibition} to \code{ik_without_photoinhibition}. + \item \code{etrmax_without_with_ratio}: Ratio of \code{etrmax_with_photoinhibition} to \code{etrmax_without_photoinhibition}, and \code{ik_with_photoinhibition} to \code{ik_without_photoinhibition}. } } \description{ diff --git a/src/man/vollenweider_modified.Rd b/src/man/vollenweider_modified.Rd index 24b10f1..2cfe5c4 100644 --- a/src/man/vollenweider_modified.Rd +++ b/src/man/vollenweider_modified.Rd @@ -30,7 +30,7 @@ A modified model result as a list containing the following elements: \item \code{im_with_photoinhibition}: The PAR at which the maximum electron transport rate is achieved by taking photoinhibition into account, determined using the regression data from the model. \item \code{w}: Not available, here set to \code{NA_real_}. \item \code{ib}: Transferred unchanged as \code{ib}. - \item \code{etrmax_with_without_ratio}: Ratio of \code{etrmax_with_photoinhibition} to \code{etrmax_without_photoinhibition} and \code{ik_with_photoinhibition} to \code{ik_without_photoinhibition}. + \item \code{etrmax_without_with_ratio}: Ratio of \code{etrmax_with_photoinhibition} to \code{etrmax_without_photoinhibition} and \code{ik_with_photoinhibition} to \code{ik_without_photoinhibition}. } } \description{ diff --git a/src/man/walsby_modified.Rd b/src/man/walsby_modified.Rd index 317cff2..56bb2d3 100644 --- a/src/man/walsby_modified.Rd +++ b/src/man/walsby_modified.Rd @@ -30,7 +30,7 @@ A list containing: \item \code{im_with_photoinhibition}: PAR at the maximum ETR with photoinhibition. \item \code{w}: Not available, set to \code{NA_real_}. \item \code{ib}: Not available, set to \code{NA_real_}. - \item \code{etrmax_with_without_ratio}: Ratio of \code{etrmax_with_photoinhibition} to \code{etrmax_without_photoinhibition}. + \item \code{etrmax_without_with_ratio}: Ratio of \code{etrmax_with_photoinhibition} to \code{etrmax_without_photoinhibition}. } } \description{ diff --git a/src/tests/testthat/helper-os-detection.R b/src/tests/testthat/helper-os-detection.R index 4dd8f18..d66c5c1 100644 --- a/src/tests/testthat/helper-os-detection.R +++ b/src/tests/testthat/helper-os-detection.R @@ -45,16 +45,7 @@ get_os_distro <- function() { return(tolower(sys_name)) } -is_supported_os <- function() { - os <- get_os_distro() - grepl("\\b(ubuntu|debian|windows)\\b", os, ignore.case = TRUE) -} - -is_windows <- function() { - tolower(Sys.info()[["sysname"]]) == "windows" -} - is_debian_or_ubuntu <- function() { os <- get_os_distro() - grepl("\\b(debian|ubuntu)\\b", os, ignore.case = TRUE) + grepl("\\b(debian|ubuntu|fedora)\\b", os, ignore.case = TRUE) } diff --git a/src/tests/testthat/test-eilers_peeters_etr_I.R b/src/tests/testthat/test-eilers_peeters_etr_I.R index b3cf615..b8d0fe2 100644 --- a/src/tests/testthat/test-eilers_peeters_etr_I.R +++ b/src/tests/testthat/test-eilers_peeters_etr_I.R @@ -63,7 +63,7 @@ test_that("test-eilers_peeters_etr_I generate regression modified 20240925.csv - expect_equal(model_result[["im_with_photoinhibition"]], 1399.769662) expect_equal(model_result[["w"]], 1.18036237) expect_equal(model_result[["ib"]], NA_real_) - expect_equal(model_result[["etrmax_with_without_ratio"]], NA_real_) + expect_equal(model_result[["etrmax_without_with_ratio"]], NA_real_) }) test_that("test-eilers_peeters_etr_I generate regression modified 20240925.csv", { diff --git a/src/tests/testthat/test-eilers_peeters_etr_II.R b/src/tests/testthat/test-eilers_peeters_etr_II.R index 3d722db..0dc92b6 100644 --- a/src/tests/testthat/test-eilers_peeters_etr_II.R +++ b/src/tests/testthat/test-eilers_peeters_etr_II.R @@ -44,7 +44,7 @@ test_that("test-eilers_peeters_etr_II modified 20240925.csv - linux", { expect_equal(model_result[["im_with_photoinhibition"]], 731.801311) expect_equal(model_result[["w"]], 0.69061233) expect_equal(model_result[["ib"]], NA_real_) - expect_equal(model_result[["etrmax_with_without_ratio"]], NA_real_) + expect_equal(model_result[["etrmax_without_with_ratio"]], NA_real_) }) test_that("test-eilers_peeters_etr_II modified 20240925.csv", { diff --git a/src/tests/testthat/test-eilers_peeters_junior_pam_etr_II.R b/src/tests/testthat/test-eilers_peeters_junior_pam_etr_II.R index eb9d39c..f5143e8 100644 --- a/src/tests/testthat/test-eilers_peeters_junior_pam_etr_II.R +++ b/src/tests/testthat/test-eilers_peeters_junior_pam_etr_II.R @@ -44,7 +44,7 @@ test_that("test-eilers_peeters_etr_II modified junior_pam_20250613.csv.csv - lin expect_equal(model_result[["im_with_photoinhibition"]], 1320.307821) expect_equal(model_result[["w"]], 5.7674788) expect_equal(model_result[["ib"]], NA_real_) - expect_equal(model_result[["etrmax_with_without_ratio"]], NA_real_) + expect_equal(model_result[["etrmax_without_with_ratio"]], NA_real_) }) test_that("test-eilers_peeters_etr_II modified junior_pam_20250613.csv.csv", { diff --git a/src/tests/testthat/test-platt_etr_I.R b/src/tests/testthat/test-platt_etr_I.R index 75cf0da..dded5b9 100644 --- a/src/tests/testthat/test-platt_etr_I.R +++ b/src/tests/testthat/test-platt_etr_I.R @@ -45,7 +45,7 @@ test_that("test-platt_etr_I generate regression modified 20240925.csv - linux", expect_equal(model_result[["im_with_photoinhibition"]], 1365.39202) expect_equal(model_result[["w"]], NA_real_) expect_equal(model_result[["ib"]], 4302.0636) - expect_equal(model_result[["etrmax_with_without_ratio"]], 1.59380602) + expect_equal(model_result[["etrmax_without_with_ratio"]], 1.59380602) }) test_that("test-platt_etr_I generate regression modified 20240925.csv", { diff --git a/src/tests/testthat/test-platt_etr_II.R b/src/tests/testthat/test-platt_etr_II.R index 88401b6..f5d7c93 100644 --- a/src/tests/testthat/test-platt_etr_II.R +++ b/src/tests/testthat/test-platt_etr_II.R @@ -64,7 +64,7 @@ test_that("test-platt_etr_II generate regression modified 20240925.csv - linux", expect_equal(model_result[["im_with_photoinhibition"]], 769.889813) expect_equal(model_result[["w"]], NA_real_) expect_equal(model_result[["ib"]], 2149.3914) - expect_equal(model_result[["etrmax_with_without_ratio"]], 1.7166423) + expect_equal(model_result[["etrmax_without_with_ratio"]], 1.7166423) }) test_that("test-platt_etr_II generate regression modified 20240925.csv", { diff --git a/src/tests/testthat/test-universal_data_etr_I.R b/src/tests/testthat/test-universal_data_etr_I.R index 8205632..e1ac1e3 100644 --- a/src/tests/testthat/test-universal_data_etr_I.R +++ b/src/tests/testthat/test-universal_data_etr_I.R @@ -23,7 +23,7 @@ test_that("test-universal_data_etr_I - linux", { expect_equal(eilers_peeters[["im_with_photoinhibition"]], 1399.769662) expect_equal(eilers_peeters[["w"]], 1.18036237) expect_equal(eilers_peeters[["ib"]], NA_real_) - expect_equal(eilers_peeters[["etrmax_with_without_ratio"]], NA_real_) + expect_equal(eilers_peeters[["etrmax_without_with_ratio"]], NA_real_) expect_equal(platt[["residual_sum_of_squares"]], 55.4812913) expect_equal(platt[["a"]], 242.02858) @@ -39,7 +39,7 @@ test_that("test-universal_data_etr_I - linux", { expect_equal(platt[["im_with_photoinhibition"]], 1365.39202) expect_equal(platt[["w"]], NA_real_) expect_equal(platt[["ib"]], 4302.0636) - expect_equal(platt[["etrmax_with_without_ratio"]], 1.59380602) + expect_equal(platt[["etrmax_without_with_ratio"]], 1.59380602) expect_equal(walsby[["residual_sum_of_squares"]], 55.5823146) expect_equal(walsby[["a"]], 221.237842) @@ -55,7 +55,7 @@ test_that("test-universal_data_etr_I - linux", { expect_equal(walsby[["im_with_photoinhibition"]], 1358.0) expect_equal(walsby[["w"]], NA_real_) expect_equal(walsby[["ib"]], NA_real_) - expect_equal(walsby[["etrmax_with_without_ratio"]], 1.456840082) + expect_equal(walsby[["etrmax_without_with_ratio"]], 1.456840082) expect_equal(vollenweider[["residual_sum_of_squares"]], 57.4443325) expect_equal(vollenweider[["a"]], 165.4671070) @@ -71,7 +71,7 @@ test_that("test-universal_data_etr_I - linux", { expect_equal(vollenweider[["im_with_photoinhibition"]], 1420) expect_equal(vollenweider[["w"]], NA_real_) expect_equal(vollenweider[["ib"]], NA_real_) - expect_equal(vollenweider[["etrmax_with_without_ratio"]], 1.08078520) + expect_equal(vollenweider[["etrmax_without_with_ratio"]], 1.08078520) }) test_that("test-universal_data_etr_I", { diff --git a/src/tests/testthat/test-vollenweider_etr_I.R b/src/tests/testthat/test-vollenweider_etr_I.R index ae57533..0c7bda5 100644 --- a/src/tests/testthat/test-vollenweider_etr_I.R +++ b/src/tests/testthat/test-vollenweider_etr_I.R @@ -64,7 +64,7 @@ test_that("test-vollenweider_etr_I generate regression modified 20240925.csv - l expect_equal(model_result[["im_with_photoinhibition"]], 1420) expect_equal(model_result[["w"]], NA_real_) expect_equal(model_result[["ib"]], NA_real_) - expect_equal(model_result[["etrmax_with_without_ratio"]], 1.08078520) + expect_equal(model_result[["etrmax_without_with_ratio"]], 1.08078520) }) test_that("test-vollenweider_etr_I generate regression modified 20240925.csv", { diff --git a/src/tests/testthat/test-vollenweider_etr_II.R b/src/tests/testthat/test-vollenweider_etr_II.R index f3836a4..ad71827 100644 --- a/src/tests/testthat/test-vollenweider_etr_II.R +++ b/src/tests/testthat/test-vollenweider_etr_II.R @@ -64,7 +64,7 @@ test_that("test-vollenweider_etr_II generate regression modified 20240925.csv - expect_equal(model_result[["im_with_photoinhibition"]], 767.0) expect_equal(model_result[["w"]], NA_real_) expect_equal(model_result[["ib"]], NA_real_) - expect_equal(model_result[["etrmax_with_without_ratio"]], 1.194065095) + expect_equal(model_result[["etrmax_without_with_ratio"]], 1.194065095) }) test_that("test-vollenweider_etr_II generate regression modified 20240925.csv", { diff --git a/src/tests/testthat/test-walsby_etr_I.R b/src/tests/testthat/test-walsby_etr_I.R index 15852b5..6da7dad 100644 --- a/src/tests/testthat/test-walsby_etr_I.R +++ b/src/tests/testthat/test-walsby_etr_I.R @@ -59,7 +59,7 @@ test_that("test-walsby_etr_I generate regression modified 20240925.csv - linux", expect_equal(model_result[["im_with_photoinhibition"]], 1358.0) expect_equal(model_result[["w"]], NA_real_) expect_equal(model_result[["ib"]], NA_real_) - expect_equal(model_result[["etrmax_with_without_ratio"]], 1.456840082) + expect_equal(model_result[["etrmax_without_with_ratio"]], 1.456840082) }) test_that("test-walsby_etr_I generate regression modified 20240925.csv", { diff --git a/src/tests/testthat/test-walsby_etr_II.R b/src/tests/testthat/test-walsby_etr_II.R index 067549c..55d94c5 100644 --- a/src/tests/testthat/test-walsby_etr_II.R +++ b/src/tests/testthat/test-walsby_etr_II.R @@ -59,7 +59,7 @@ test_that("test-walsby_etr_II generate regression modified 20240925.csv - linux" expect_equal(model_result[["im_with_photoinhibition"]], 781.0) expect_equal(model_result[["w"]], NA_real_) expect_equal(model_result[["ib"]], NA_real_) - expect_equal(model_result[["etrmax_with_without_ratio"]], 1.44981217) + expect_equal(model_result[["etrmax_without_with_ratio"]], 1.44981217) }) test_that("test-walsby_etr_II generate regression modified 20240925.csv", { diff --git a/src/tests/testthat/test-write_model_result_csv.R b/src/tests/testthat/test-write_model_result_csv.R index ba54203..a968478 100644 --- a/src/tests/testthat/test-write_model_result_csv.R +++ b/src/tests/testthat/test-write_model_result_csv.R @@ -36,7 +36,7 @@ test_that("test-write_model_result_csv - walsby_modified - 20240925.csv", { expect_equal(model_result_csv$im_with_photoinhibition, model_result$im_with_photoinhibition) expect_equal(model_result_csv$w, model_result$w) expect_equal(model_result_csv$ib, model_result$ib) - expect_equal(model_result_csv$etrmax_with_without_ratio, model_result$etrmax_with_without_ratio) + expect_equal(model_result_csv$etrmax_without_with_ratio, model_result$etrmax_without_with_ratio) raw_data_csv <- read.csv( file = raw_data_csv_path, @@ -88,7 +88,7 @@ test_that("test-write_model_result_csv - walsby - 20240925.csv", { expect_equal(model_result_csv$im_with_photoinhibition, model_result$im_with_photoinhibition) expect_equal(model_result_csv$w, model_result$w) expect_equal(model_result_csv$ib, model_result$ib) - expect_equal(model_result_csv$etrmax_with_without_ratio, model_result$etrmax_with_without_ratio) + expect_equal(model_result_csv$etrmax_without_with_ratio, model_result$etrmax_without_with_ratio) raw_data_csv <- read.csv( file = raw_data_csv_path, diff --git a/test-eilers_peeters_etr_II_modified_control_plot_20240925.jpg b/test-eilers_peeters_etr_II_modified_control_plot_20240925.jpg index 158d940..d138413 100644 Binary files a/test-eilers_peeters_etr_II_modified_control_plot_20240925.jpg and b/test-eilers_peeters_etr_II_modified_control_plot_20240925.jpg differ diff --git a/test_combo_plot_control_etr_II.jpg b/test_combo_plot_control_etr_II.jpg index af880d9..27258ad 100644 Binary files a/test_combo_plot_control_etr_II.jpg and b/test_combo_plot_control_etr_II.jpg differ