| context("fit_photosynthesis()") | |
| library(photosynthesis) | |
| test_that("'fit_photosynthesis()' accepts data.frames and tibbles", { | |
| df1 = data.frame( | |
| .A = c(10, 9.5, 8, 3.5, 2.5, 2.0, 1, 0.2), | |
| .Q = c(1500, 750, 375, 125, 100, 75, 50, 25) | |
| ) | |
| df2 = tibble::as_tibble(df1) | |
| f1 = suppressMessages(fit_photosynthesis(.data = df1, .photo_fun = "aq_response")) | |
| f2 = suppressMessages(fit_photosynthesis(.data = df2, .photo_fun = "aq_response")) | |
| expect_equal(coef(f1), coef(f2)) | |
| }) | |
| test_that(".vars argument renames variables", { | |
| df1 = data.frame( | |
| .A = c(10, 9.5, 8, 3.5, 2.5, 2.0, 1, 0.2), | |
| .Q = c(1500, 750, 375, 125, 100, 75, 50, 25) | |
| ) | |
| df2 = dplyr::rename(df1, Photo = .A) | |
| df3 = dplyr::rename(df1, PPFD = .Q) | |
| df4 = dplyr::rename(df1, Photo = .A, PPFD = .Q) | |
| expect_error({fit_photosynthesis(.data = df2, .photo_fun = "aq_response")}) | |
| expect_error({fit_photosynthesis(.data = df3, .photo_fun = "aq_response")}) | |
| expect_error({fit_photosynthesis(.data = df4, .photo_fun = "aq_response")}) | |
| f1 = suppressMessages( | |
| fit_photosynthesis(.data = df2, .photo_fun = "aq_response", | |
| .vars = list(.A = Photo)) | |
| ) | |
| f2 = suppressMessages(fit_photosynthesis(.data = df3, .photo_fun = "aq_response", | |
| .vars = list(.Q = PPFD)) | |
| ) | |
| f3 = suppressMessages( | |
| fit_photosynthesis(.data = df4, .photo_fun = "aq_response", | |
| .vars = list(.A = Photo, .Q = PPFD)) | |
| ) | |
| expect_equal(coef(f1), coef(f2)) | |
| expect_equal(coef(f2), coef(f3)) | |
| expect_error({fit_photosynthesis(.data = df2, .photo_fun = "aq_response", | |
| .vars = list(.A = foo))}) | |
| expect_error({fit_photosynthesis(.data = df3, .photo_fun = "aq_response", | |
| .vars = list(.Q = bar))}) | |
| f4 = suppressMessages( | |
| fit_photosynthesis(.data = dplyr::mutate(df4, A1 = Photo), | |
| .photo_fun = "aq_response", | |
| .vars = list(.A = Photo, .Q = PPFD)) | |
| ) | |
| expect_equal(coef(f3), coef(f4)) | |
| }) | |
| df1 = data.frame( | |
| .A = c(10, 9.5, 8, 3.5, 2.5, 2.0, 1, 0.2), | |
| .Q = c(1500, 750, 375, 125, 100, 75, 50, 25) | |
| ) | |
| fit = fit_photosynthesis( | |
| .data = df1, | |
| .photo_fun = "aq_response", | |
| .model = "marshall_biscoe_1980" | |
| ) | |
| test_that("marshall_biscoe_1980 output", { | |
| expect_is(object = fit, class = "nls") | |
| }) | |
| fit = fit_photosynthesis( | |
| .data = df1, | |
| .photo_fun = "aq_response", | |
| .model = "photoinhibition" | |
| ) | |
| test_that("photoinhibition output", { | |
| expect_is(object = fit, class = "nls") | |
| }) | |