Etrmax with without ratio rename

CITATION.cff

@@ -8,7 +8,7 @@ authors:
   given-names: "Philipp"
   orcid: "https://orcid.org/0009-0002-7697-5536"
 title: "pam"
-version: 2.0.2
-date-released: 2025-07-29
+version: 2.1.0
+date-released: 2026-04-11
 url: "https://github.com/biotoolbox/pam"
 doi: "10.32614/CRAN.package.pam"

Makefile

@@ -20,4 +20,9 @@ build:
 buildtest:
 	rm -rf src/tests/testthat/results
 	make build
-	R CMD check pam_2.0.2.tar.gz
+	R CMD check pam_2.1.0.tar.gz
+
+buildtestcran:
+	rm -rf src/tests/testthat/results
+	make build
+	R CMD check --as-cran pam_2.1.0.tar.gz

README.md

@@ -14,7 +14,9 @@ Generated control plots make it possible to check each individual regression fit
 
 ## Publications using this package
 
-- Böhm, J., Blindow, I., Gyllenstrand, N., Diewald, W., & Schubert, H. (2025). Sphaerochara canadensis (Charophyceae): A circumpolar species with a high temperature optimum. Journal of Phycology, 00, 1–11. https://doi.org/10.1111/jpy.70111
+- J. Böhm, J. Trossen, I. Blindow, and H. Schubert, ‘Impact of temperature and light on the physiology and morphology of *Chara hispida* L. (Charophyceae)’, Aquatic Botany, vol. 206, p. 104022, Sep. 2026, doi: [10.1016/j.aquabot.2026.104022]( https://doi.org/10.1016/j.aquabot.2026.104022).
+
+- J. Böhm, I. Blindow, N. Gyllenstrand, W. Diewald, and H. Schubert, ‘*Sphaerochara canadensis* (Charophyceae): A circumpolar species with a high temperature optimum’, Journal of Phycology, vol. 61, no. 6, pp. 1863–1873, Dec. 2025, doi: [10.1111/jpy.70111]( https://doi.org/10.1111/jpy.70111).
 
 ## Test coverage
 
@@ -87,7 +89,7 @@ fraction_photosystem_II = 0.5)
 
 #### References
 
-- Heinz Walz GmbH. (2024). *DUAL-PAM-100 DUAL-PAM/F MANUAL, 5th Edition, April 2024, Chapter 7 (pp. 162-172).* Heinz Walz GmbH, Effeltrich, Germany. Available at: [DUAL-PAM-100 Manual](https://www.walz.com/files/downloads/manuals/dual-pam-100/DualPamEd05.pdf)
+- Heinz Walz GmbH. (2024). *DUAL-PAM-100 DUAL-PAM/F MANUAL, 5th Edition, April 2024, Chapter 7 (pp. 162-172).* Heinz Walz GmbH, Effeltrich, Germany. Available at: [DUAL-PAM-100 Manual](https://www.walz.com/files/downloads/dualpamed05.pdf)
 
 
 ### read_dual_pam_data()
@@ -141,7 +143,7 @@ fraction_photosystem_II = 0.5)
 
 #### References
 
-- Heinz Walz GmbH. (2024). *DUAL-PAM-100 DUAL-PAM/F MANUAL, 5th Edition, April 2024, Chapter 7 (pp. 162-172).* Heinz Walz GmbH, Effeltrich, Germany. Available at: [DUAL-PAM-100 Manual](https://www.walz.com/files/downloads/manuals/dual-pam-100/DualPamEd05.pdf)
+- Heinz Walz GmbH. (2024). *DUAL-PAM-100 DUAL-PAM/F MANUAL, 5th Edition, April 2024, Chapter 7 (pp. 162-172).* Heinz Walz GmbH, Effeltrich, Germany. Available at: [DUAL-PAM-100 Manual](https://www.walz.com/files/downloads/dualpamed05.pdf)
 
 ### read_junior_pam_data()
 
@@ -193,7 +195,7 @@ fraction_photosystem_II = 0.5)
 
 #### References
 
-- Heinz Walz GmbH. (2024). *DUAL-PAM-100 DUAL-PAM/F MANUAL, 5th Edition, April 2024, Chapter 7 (pp. 162-172).* Heinz Walz GmbH, Effeltrich, Germany. Available at: [DUAL-PAM-100 Manual](https://www.walz.com/files/downloads/manuals/dual-pam-100/DualPamEd05.pdf)
+- Heinz Walz GmbH. (2024). *DUAL-PAM-100 DUAL-PAM/F MANUAL, 5th Edition, April 2024, Chapter 7 (pp. 162-172).* Heinz Walz GmbH, Effeltrich, Germany. Available at: [DUAL-PAM-100 Manual](https://www.walz.com/files/downloads/dualpamed05.pdf)
 
 ### vollenweider_generate_regression_ETR_I() and vollenweider_generate_regression_ETR_II()
 
@@ -477,7 +479,7 @@ $${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 +521,9 @@ 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:
 
-$${{etrmax\\_with\\_without\\_ratio}} = \frac{{etrmax\\_with\\_photoinhibition}}{{etrmax\\_without\\_photoinhibition}}$$
+$${{etrmax\\_without\\_with\\_ratio}} = \frac{{etrmax\\_without\\_photoinhibition}}{{etrmax\\_with\\_photoinhibition}}$$
 
 #### Details
 
@@ -563,7 +565,7 @@ 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
 
@@ -626,9 +628,9 @@ $$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:
 
-$${{etrmax\\_with\\_without\\_ratio}} = \frac{{etrmax\\_with\\_photoinhibition}}{{etrmax\\_without\\_photoinhibition}}$$
+$${{etrmax\\_without\\_with\\_ratio}} = \frac{{etrmax\\_without\\_photoinhibition}}{{etrmax\\_with\\_photoinhibition}}$$
 
 #### Details
 
@@ -662,7 +664,7 @@ 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 +686,7 @@ 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()
 

src/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pam
 Type: Package
 Title: Fast and Efficient Processing of PAM Data
-Version: 2.0.2
+Version: 2.1.0
 Authors@R: c(
     person(
         "Julien",
@@ -26,7 +26,7 @@ LazyData: true
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Imports: 
     rlang,
     data.table,

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

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_without_photoinhibition} / \code{etrmax_with_photoinhibition}, and \code{ik_without_photoinhibition} / \code{ik_with_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)

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)

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) {

src/R/vollenweider.R

@@ -33,14 +33,14 @@ vollenweider_default_start_value_n <- 100
 #'   \item \code{residual_sum_of_squares}: Difference between observed and predicted ETR values, expressed as the sum of squared residuals.
 #'   \item \code{root_mean_squared_error}: Difference between observed and predicted ETR values, expressed as the root mean squared error.
 #'   \item \code{relative_root_mean_squared_error}: Difference between observed and predicted ETR values, expressed as the relative root mean squared error, normalized by the mean.
-#'   \item \code{pmax}: Maximum electron transport rate (\eqn{p_{max}}).
+#'   \item \code{pmax}: Maximum electron transport rate without photoinhibition (\eqn{p_{max}}).
 #'   \item \code{a}: Parameter \eqn{a}.
 #'   \item \code{alpha}: Parameter \eqn{\alpha}.
 #'   \item \code{n}: Parameter \eqn{n}.
 #'   \item \code{popt}: Maximum electron transport rate with photoinhibition (\eqn{p_{opt}}).
 #'   \item \code{ik}: Transition point from light limitation to light saturation without photoinhibition (\eqn{I_k}).
 #'   \item \code{iik}: Transition point from light limitation to light saturation with photoinhibition (\eqn{I_k^\prime}).
-#'   \item \code{pmax_popt_and_ik_iik_ratio}: Ratio of \eqn{p_{max}} to \eqn{p_{opt}} and \eqn{I_k} to \eqn{I_k^\prime}.
+#'   \item \code{pmax_popt_and_ik_iik_ratio}: Ratio of \eqn{p_{max}} / \eqn{p_{opt}} and \eqn{I_k} / \eqn{I_k^\prime}.
 #' }
 #'
 #' @references{
@@ -91,14 +91,14 @@ vollenweider_generate_regression_ETR_I <- function(
 #'   \item \code{residual_sum_of_squares}: Difference between observed and predicted ETR values, expressed as the sum of squared residuals.
 #'   \item \code{root_mean_squared_error}: Difference between observed and predicted ETR values, expressed as the root mean squared error.
 #'   \item \code{relative_root_mean_squared_error}: Difference between observed and predicted ETR values, expressed as the relative root mean squared error, normalized by the mean.
-#'   \item \code{pmax}: Maximum electron transport rate (\eqn{p_{max}}).
+#'   \item \code{pmax}: Maximum electron transport rate without photoinhibition (\eqn{p_{max}}).
 #'   \item \code{a}: Parameter \eqn{a}.
 #'   \item \code{alpha}: Parameter \eqn{\alpha}.
 #'   \item \code{n}: Parameter \eqn{n}.
 #'   \item \code{popt}: Maximum electron transport rate with photoinhibition (\eqn{p_{opt}}).
 #'   \item \code{ik}: Transition point from light limitation to light saturation without photoinhibition (\eqn{I_k}).
 #'   \item \code{iik}: Transition point from light limitation to light saturation with photoinhibition (\eqn{I_k^\prime}).
-#'   \item \code{pmax_popt_and_ik_iik_ratio}: Ratio of \eqn{p_{max}} to \eqn{p_{opt}} and \eqn{I_k} to \eqn{I_k^\prime}.
+#'   \item \code{pmax_popt_and_ik_iik_ratio}: Ratio of \eqn{p_{max}} / \eqn{p_{opt}} and \eqn{I_k} / \eqn{I_k^\prime}.
 #' }
 #'
 #' @references{
@@ -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_without_photoinhibition} / \code{etrmax_with_photoinhibition} and \code{ik_without_photoinhibition} / \code{ik_with_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)

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_without_photoinhibition} / \code{etrmax_with_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)

src/inst/CITATION

@@ -2,8 +2,8 @@ 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,
+  note = "R package version 2.1.0",
   url = "https://CRAN.R-project.org/package=pam",
   doi = "10.32614/CRAN.package.pam"
 )