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Changelog

Source: NEWS.md

photosynthesis 2.1.5

  • Added photoinhibition() to light response models. This allows users to estimate photoinhibitation at high light.

photosynthesis 2.1.4

CRAN release: 2023-08-15

  • Removed imports of unexported tealeaves functions using ::: operator
  • read_licor() removes lines where parameter settings are changed between logging

photosynthesis 2.1.3

CRAN release: 2023-05-11

photosynthesis 2.1.2

CRAN release: 2023-03-31

  • 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.

photosynthesis 2.1.1

CRAN release: 2022-11-19

  • 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()

photosynthesis 2.1.0

CRAN release: 2022-11-08

  • Commented out examples that took a long time to run
  • Added progress option to fit_many() to toggle progress bar
  • We removed large files from help subdirectory
  • Divided large vignette into smaller vignettes and removed figures to reduce file size
  • Updated CITATION
  • There is a new vignette on C3 photosynthesis modeling recommendations (modeling-recommendations)
  • Under the hood, many changes to photosynthesis(), but performance should be the same
  • Changed default C_air from 41 Pa to 420 umol/mol
  • Changed default O from 21.27565 kPa to 0.21 mol/mol
  • Added optional feature to calculate mesophyll conductance to CO2 (g_mc) as sum of internal airspace (g_iasc) and liquid-phase (g_liqc) conductances.
  • To avoid redundancy, photo_parameters is single source of truth for all input parameters to photo() and photosynthesis().
  • Fixed error in gc2gw() and gw2gc() and migrated to gunit version 1.0.2. Legacy version used version for still air in boundary layer conductance conversions. The corrected version includes modification for laminar flow in the boundary layer. Legacy version can be obtained with option use_legacy_version = TRUE.
  • Changed default conductance units from [umol / m ^ 2 / s / Pa] to [mol / m ^ 2 / s]
  • Changed <- to = in many instances
  • Changed %>% to |> in many instances

photosynthesis 2.0.3

CRAN release: 2022-08-12

  • In the DESCRIPTION file, rewrote references in the form authors (year) <doi:…>
  • In the DESCRIPTION file, added () behind all function names
  • Added to .Rd files regarding exported methods for bake.Rd, bake_par.Rd, constants.Rd, enviro_par.Rd, leaf_par.Rd, parameter_names.Rd
  • Changed print() to stop() or message() in R/compile_data.R; R/fit_gs_model.R; R/fit_t_response.R; R/print_graphs.R
  • In R/print_graphs.R, added code to restore users’ option for par()$mfrow
  • Removed “2020” from the field COPYRIGHT HOLDER in the LICENCE file
  • Updated link to Prometheus protocols in vignette
  • Stopped evaluating parallel example in vignette
  • Fixed tests that failed because of update to dependency units 0.8-0. (#7)

photosynthesis 2.0.1

CRAN release: 2021-07-01

  • for temp_resp1 and temp_resp2, corrected reference. (#6)

photosynthesis 2.0.0

CRAN release: 2020-09-12

  • Added analytical tools for plant ecophysiology, including fitting stomatal conductance models, photosynthetic responses to light, CO2, and temperature, light respiration, as well as tools for performing sensitivity analyses.

  • Added tests for new functions.

  • Added new vignette to include examples of new analytical functions.

photosynthesis 1.0.2

CRAN release: 2020-07-01

  • Fixed bug with crossing parameters in photosynthesis() that was introduced when use_tealeaves = TRUE because of changes in the tealeaves package. This led to crossing all parameter values with all unique values of calculated T_sky, which was incorrect. Added unit tests to ensuring that crossing is done correctly under tests/test-photosynthesis-crossing.R
  • Fixed bug in photosynthesis() caused by new version of dplyr.
  • In enviro_par(), “sky” temperature (T_sky) can now be provided directly as a values (in K) or as a function (the default).
  • If parallel = TRUE in photosynthesis(), future uses plan("multisession") rather than plan("multiprocess").
  • Added full URL for CONDUCT.md in README
  • Fixed cross-references in .Rd files

photosynthesis 1.0.1

Release to be archived with revision of “Is amphistomy an adaptation to high light? Optimality models of stomatal traits along light gradients.”

Blog post.

photosynthesis 1.0.0

CRAN release: 2019-05-09

Description: Simulate C3_3 photosynthesis using the Farquhar, von Caemmerer, Berry (1980) model as described in Buckley and Diaz-Espejo (2015). It uses units to ensure that parameters are properly specified and transformed before calculations. Temperature response functions get automatically “baked” into all parameters based on leaf temperature following Bernacchi et al. (2002). The package includes boundary layer, cuticular, stomatal, and mesophyll conductances to CO2_2, which each can vary on the upper and lower portions of the leaf. Use straightforward functions to simulate photosynthesis over environmental gradients such as Photosynthetic Photon Flux Density (PPFD) and leaf temperature, or over trait gradients such as CO2_2 conductance or photochemistry.

  • Added a NEWS.md file to track changes to the package.