v2.1.3

Merge branch 'experimental' into dev # Conflicts: # docs/404.html # docs/CONDUCT.html # docs/LICENSE-text.html # docs/LICENSE.html # docs/articles/co2-response.html # docs/articles/hydraulic-vulnerability.html # docs/articles/index.html # docs/articles/light-respiration.html # docs/articles/light-response.html # docs/articles/mesophyll-conductance.html # docs/articles/modeling-recommendations.html # docs/articles/photosynthesis-introduction.html # docs/articles/pressure-volume.html # docs/articles/sensitivity-analysis.html # docs/articles/stomatal-conductance.html # docs/articles/temperature-response.html # docs/authors.html # docs/index.html # docs/news/index.html # docs/pkgdown.yml # docs/reference/A_supply.html # docs/reference/CO2_conductance.html # docs/reference/FvCB.html # docs/reference/J.html # docs/reference/analyze_sensitivity.html # docs/reference/aq_response.html # docs/reference/bake.html # docs/reference/bake_par.html # docs/reference/baked-class.html # docs/reference/calculated-parameters.html # docs/reference/compile_data.html # docs/reference/compute_sensitivity.html # docs/reference/constants.html # docs/reference/enviro_par.html # docs/reference/fit_PV_curve.html # docs/reference/fit_aci_response.html # docs/reference/fit_aq_response.html # docs/reference/fit_aq_response2.html # docs/reference/fit_g_mc_variableJ.html # docs/reference/fit_gs_model.html # docs/reference/fit_hydra_vuln_curve.html # docs/reference/fit_many.html # docs/reference/fit_photosynthesis.html # docs/reference/fit_r_light.html # docs/reference/fit_r_light2.html # docs/reference/fit_t_response.html # docs/reference/gs_models.html # docs/reference/index.html # docs/reference/j_calculations.html # docs/reference/leaf_par.html # docs/reference/make_parameters.html # docs/reference/models.html # docs/reference/parameter_names.html # docs/reference/photo_parameters.html # docs/reference/photosynthesis-package.html # docs/reference/photosynthesis.html # docs/reference/ppm2pa.html # docs/reference/print_graphs.html # docs/reference/read_li6800.html # docs/reference/read_licor.html # docs/reference/required_variables.html # docs/reference/simulate_error.html # docs/reference/t_functions.html # man/simulate_error.Rd
cdmuir · May 11, 2023 · c8717f8 · c8717f8
2 parents a54be73 + 80e4117
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: photosynthesis
-Version: 2.1.2.9002
-Date: 2023-05-08
+Version: 2.1.3
+Date: 2023-05-11
 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 2.1.3
 
+* Added example LI6800 data set (inst/extdata/li6800_example) for unit testing `read_licor()`
 * Soft-deprecated `read_li6800()` in favor of `read_licor()`
 * Soft-deprecated `fit_many()` in favor of generic methods like `purrr::map()`
 

diff --git a/R/simulate_error.R b/R/simulate_error.R
@@ -4,21 +4,10 @@
 #' 
 #' `r lifecycle::badge("experimental")`
 #' 
-#' @param ph_out A data frame of output from [photo()] or [photosynthesis()] 
+#' @param ph_out A data frame of output from `photo()` or `photosynthesis()` 
 #' with units.
 #' @param chamber_pars A data frame with a single row of chamber parameters. 
-#' Required parameters are:
-#' 
-#' * `flow` (\eqn{\mu}mol / s): chamber flow rate
-#' * `leaf_area` \[cm ^ 2\]: leaf area in chamber
-#' * `sigma_CO2_s` \[\eqn{\mu}mol / mol\]: standard deviation of sample \[CO\eqn{_2}\] measurement error
-#' * `sigma_CO2_r` \[\eqn{\mu}mol / mol\]: standard deviation of reference [CO\eqn{_2}\]
-#' * `sigma_H2O_s` \[mmol / mol\]: standard deviation of sample \[H\eqn{_2}O\] measurement error
-#' * `sigma_H2O_r` \[mmol / mol\]: standard deviation of sample \[H\eqn{_2}O\] measurement error
-#' 
-#' Units for `flow` and `leaf_area` should be provided; units are implied for
-#' sigma's but not necessary to specify because `rnorm()` drop units.
-#' 
+#' See Note below for table of required parameters. 
 #' @param n Integer. Number of replicated simulations per row of `ph_out`.
 #' @param use_tealeaves Flag. The **tealeaves** package uses a slightly 
 #' different equation to calculate the saturating water content of air as a 
@@ -62,10 +51,21 @@
 #' | `C_i`           | derived             | Intercellular CO\eqn{_2} concentration (measured) \[\eqn{\mu}mol/mol\] |
 #' 
 #' @note 
+#' The required parameters for the `chamber_pars` argument are:
+#' 
+#' * `flow` \[\eqn{\mu}mol / s\]: chamber flow rate
+#' * `leaf_area` \[cm ^ 2\]: leaf area in chamber
+#' * `sigma_CO2_s` \[\eqn{\mu}mol / mol\]: standard deviation of sample \[CO\eqn{_2}\] measurement error
+#' * `sigma_CO2_r` \[\eqn{\mu}mol / mol\]: standard deviation of reference [CO\eqn{_2}\]
+#' * `sigma_H2O_s` \[mmol / mol\]: standard deviation of sample \[H\eqn{_2}O\] measurement error
+#' * `sigma_H2O_r` \[mmol / mol\]: standard deviation of sample \[H\eqn{_2}O\] measurement error
+#' 
+#' Units for `flow` and `leaf_area` should be provided; units are implied for sigma's but not necessary to specify because `rnorm()` drop units.
+#' 
 #' To evaluate the accuracy and precision of parameter estimation methods, it 
 #' may be useful to simulate data with realistic measurement error. This 
-#' function takes output from from [photo()] or [photosynthesis()] models, adds 
-#' measurement error in CO\eqn{_2} and H\eqn{_2}O concentrations, and calculates 
+#' function takes output from from `photo()` or `photosynthesis()` models, adds 
+#' measurement error in CO\eqn{_2} and H\eqn{_2}O concentrations, and calculates
 #' parameter estimates with synthetic data. Currently, the function assumes a 
 #' simplified 1-dimensional CO\eqn{_2} and H\eqn{_2}O conductance model: zero 
 #' cuticular conductance, infinite boundary layer conductance, and infinite 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,13 +1,8 @@
 ## Summary of new changes
 
-* 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.
+* Added example LI6800 data set (inst/extdata/li6800_example) for unit testing `read_licor()`
+* Soft-deprecated `read_li6800()` in favor of `read_licor()`
+* Soft-deprecated `fit_many()` in favor of generic methods like `purrr::map()`
 
 ## Test environments
 * local R installation, R 4.2.3
@@ -21,6 +16,6 @@
 ## R CMD check results
 
 ❯ checking installed package size ... NOTE
-    installed size is  7.1Mb
+    installed size is  7.2Mb
     sub-directories of 1Mb or more:
       doc   6.1Mb
diff --git a/data-raw/li6800_example.R b/data-raw/li6800_example.R
@@ -0,0 +1,8 @@
+## code to prepare `li6800_example` dataset goes here
+
+usethis::use_data(li6800_example, overwrite = TRUE)
+
+file.copy(
+  "/Users/cdmuir/Library/CloudStorage/GoogleDrive-cdmuir@hawaii.edu/Shared drives/muir-lab/adaptive-amphistomy/raw-data/licor/2023-04-23-0804_logdata",
+  "inst/extdata/li6800_example"
+)
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