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renamed etrmax_with_without_ratio to etrmax_without_with_ratio #8

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b92cfe9
renamed etrmax_with_without_ratio to etrmax_without_with_ratio
Phi-S Apr 11, 2026
29cc8e3
2.1.0
Phi-S Apr 11, 2026
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8 changes: 6 additions & 2 deletions CITATION.cff
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Expand Up @@ -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"
6 changes: 5 additions & 1 deletion Makefile
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Expand Up @@ -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)
14 changes: 7 additions & 7 deletions README.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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:

$${{etrmax\\_with\\_without\\_ratio}} = \frac{{etrmax\\_with\\_photoinhibition}}{{etrmax\\_without\\_photoinhibition}}$$

Expand Down Expand Up @@ -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

Expand All @@ -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()

Expand Down
2 changes: 1 addition & 1 deletion packages.txt
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Expand Up @@ -5,4 +5,4 @@ minpack.lm
ggthemes
gridExtra
cowplot
Metrics
Metrics
8 changes: 6 additions & 2 deletions src/DESCRIPTION
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@@ -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",
Expand All @@ -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,
Expand Down
2 changes: 1 addition & 1 deletion src/R/eilers_peeters.R
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Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions src/R/platt.R
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Expand Up @@ -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
Expand Down Expand Up @@ -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)
Expand Down
4 changes: 2 additions & 2 deletions src/R/util.R
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Expand Up @@ -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,
Expand All @@ -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)
Expand Down
6 changes: 3 additions & 3 deletions src/R/validation.R
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Expand Up @@ -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) {
Expand Down
4 changes: 2 additions & 2 deletions src/R/vollenweider.R
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Expand Up @@ -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
Expand Down Expand Up @@ -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)
Expand Down
4 changes: 2 additions & 2 deletions src/R/walsby.R
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Expand Up @@ -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
Expand Down Expand Up @@ -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)
Expand Down
8 changes: 6 additions & 2 deletions src/inst/CITATION
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Expand Up @@ -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"
)
2 changes: 1 addition & 1 deletion src/man/eilers_peeters_modified.Rd
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2 changes: 1 addition & 1 deletion src/man/platt_modified.Rd
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2 changes: 1 addition & 1 deletion src/man/vollenweider_modified.Rd
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2 changes: 1 addition & 1 deletion src/man/walsby_modified.Rd
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11 changes: 1 addition & 10 deletions src/tests/testthat/helper-os-detection.R
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Expand Up @@ -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)
}
2 changes: 1 addition & 1 deletion src/tests/testthat/test-eilers_peeters_etr_I.R
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Expand Up @@ -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", {
Expand Down
2 changes: 1 addition & 1 deletion src/tests/testthat/test-eilers_peeters_etr_II.R
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Expand Up @@ -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", {
Expand Down
2 changes: 1 addition & 1 deletion src/tests/testthat/test-eilers_peeters_junior_pam_etr_II.R
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Expand Up @@ -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", {
Expand Down
2 changes: 1 addition & 1 deletion src/tests/testthat/test-platt_etr_I.R
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Expand Up @@ -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", {
Expand Down
2 changes: 1 addition & 1 deletion src/tests/testthat/test-platt_etr_II.R
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Expand Up @@ -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", {
Expand Down
8 changes: 4 additions & 4 deletions src/tests/testthat/test-universal_data_etr_I.R
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Expand Up @@ -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)
Expand All @@ -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)
Expand All @@ -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)
Expand All @@ -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", {
Expand Down
2 changes: 1 addition & 1 deletion src/tests/testthat/test-vollenweider_etr_I.R
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Expand Up @@ -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", {
Expand Down
2 changes: 1 addition & 1 deletion src/tests/testthat/test-vollenweider_etr_II.R
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Expand Up @@ -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", {
Expand Down
2 changes: 1 addition & 1 deletion src/tests/testthat/test-walsby_etr_I.R
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Expand Up @@ -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", {
Expand Down
2 changes: 1 addition & 1 deletion src/tests/testthat/test-walsby_etr_II.R
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Expand Up @@ -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", {
Expand Down
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