v2.1.2

cdmuir · Mar 31, 2023 · 07edf85 · 07edf85
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: photosynthesis
-Version: 2.1.1.9003
-Date: 2023-03-30
+Version: 2.1.2
+Date: 2023-03-31
 Title: Tools for Plant Ecophysiology & Modeling
 Authors@R: c(
     person("Joseph", "Stinziano", email = "josephstinziano@gmail.com", role = "aut", comment = c(ORCID = "0000-0002-7628-4201")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,6 @@
-# photosynthesis (development version)
+# photosynthesis 2.1.2
 
+* Updated CITATION using `bibentry()` instead of `citEntry()`
 * Resolved **purrr** deprecations
 * removed `expect_no_condition()` from unit tests to resolved issue #12
 * Replaced `dplyr::progress_estimated()` with `progress::progress_bar()`

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,22 +1,21 @@
 ## Summary of new changes
 
-* Added Bayesian options to fit light-response and light respiration models via `fit_photosynthesis(..., .method = "brms")`
-* Preferred method for fitting data to models is `fit_photosynthesis()` which performs all checks and manipulations prior to passing arguments to various `fit_` functions.
-* Deprecated `fit_r_light_kok()`, `fit_r_light_WalkerOrt()`, `fit_r_light_yin()` in favor of `fit_r_light2()`. The new function uses non-standard evaluation to replace variable names as in `dplyr::rename()`. It will also extend functionality to enable Bayesian fitting using **brms** and does not output a plot.
-* Added Bayesian fitting method to `fit_aq_response2()` using **brms** package.
-* Deprecated `fit_aq_response()` in favor of `fit_aq_response2()`. The new function uses non-standard evaluation to replace variable names as in `dplyr::rename()`. It will also extend functionality to enable Bayesian fitting using **brms** and does not output a plot.
-* Fixed bug with setting upper bound for search in `find_A()`
-* Addressed warnings about deprecated arguments in **tidyselect** and **ggplot2**
-* Added `C_i` (intercellular CO2 concentration) to output from `photo()` and `photosynthesis()`
+* Updated CITATION using `bibentry()` instead of `citEntry()`
+* Resolved **purrr** deprecations
+* removed `expect_no_condition()` from unit tests to resolved issue #12
+* Replaced `dplyr::progress_estimated()` with `progress::progress_bar()`
+* Fixed error in `photo(..., use_tealeaves = TRUE)`. User-defined changes in stomatal conductance ratio were not being passed to **tealeaves**.
+* Added evaporation (E) to `photo()` and `photosynthesis()` output when `use_tealeaves = TRUE`
+* Fixed issue with **lifecycle** badges
+* Added new function `simulate_error()` to simulate measurement error in gas exchange measurements.
 
 ## Test environments
-* local R installation, R 4.2.2
-* ubuntu 20.04.1 (on Github actions), R 4.2.2
+* local R installation, R 4.2.3
+* ubuntu 22.04.2 (on Github actions), R 4.2.3
 * win-builder (release)
 * win-builder (devel)
 * win-builder (oldrelease)
 * R-hub builder: Windows Server 2022, R-devel, 64 bit
-* R-hub builder: Ubuntu Linux 20.04.1 LTS, R-release, GCC
 * R-hub builder: Fedora Linux, R-devel, clang, gfortran
 
 ## R CMD check results

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CONDUCT.html b/docs/CONDUCT.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/co2-response.html b/docs/articles/co2-response.html
diff --git a/docs/articles/hydraulic-vulnerability.html b/docs/articles/hydraulic-vulnerability.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/light-respiration.html b/docs/articles/light-respiration.html
diff --git a/docs/articles/light-response.html b/docs/articles/light-response.html
diff --git a/docs/articles/mesophyll-conductance.html b/docs/articles/mesophyll-conductance.html
diff --git a/docs/articles/modeling-recommendations.html b/docs/articles/modeling-recommendations.html
diff --git a/docs/articles/photosynthesis-introduction.html b/docs/articles/photosynthesis-introduction.html
diff --git a/docs/articles/pressure-volume.html b/docs/articles/pressure-volume.html
diff --git a/docs/articles/sensitivity-analysis.html b/docs/articles/sensitivity-analysis.html
diff --git a/docs/articles/stomatal-conductance.html b/docs/articles/stomatal-conductance.html
diff --git a/docs/articles/temperature-response.html b/docs/articles/temperature-response.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -13,5 +13,5 @@ articles:
   sensitivity-analysis: sensitivity-analysis.html
   stomatal-conductance: stomatal-conductance.html
   temperature-response: temperature-response.html
-last_built: 2023-03-31T10:03Z
+last_built: 2023-03-31T17:57Z
 
diff --git a/docs/reference/A_supply.html b/docs/reference/A_supply.html
diff --git a/docs/reference/CO2_conductance.html b/docs/reference/CO2_conductance.html
diff --git a/docs/reference/FvCB.html b/docs/reference/FvCB.html
diff --git a/docs/reference/J.html b/docs/reference/J.html
diff --git a/docs/reference/analyze_sensitivity.html b/docs/reference/analyze_sensitivity.html
diff --git a/docs/reference/aq_response.html b/docs/reference/aq_response.html
diff --git a/docs/reference/bake.html b/docs/reference/bake.html
diff --git a/docs/reference/bake_par.html b/docs/reference/bake_par.html
diff --git a/docs/reference/baked-class.html b/docs/reference/baked-class.html
diff --git a/docs/reference/calculated-parameters.html b/docs/reference/calculated-parameters.html
diff --git a/docs/reference/compile_data.html b/docs/reference/compile_data.html
diff --git a/docs/reference/compute_sensitivity.html b/docs/reference/compute_sensitivity.html
diff --git a/docs/reference/constants.html b/docs/reference/constants.html
diff --git a/docs/reference/enviro_par.html b/docs/reference/enviro_par.html
diff --git a/docs/reference/fit_PV_curve.html b/docs/reference/fit_PV_curve.html