-
Notifications
You must be signed in to change notification settings - Fork 4
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Release v0.11.0 #89
Merged
Merged
Release v0.11.0 #89
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Increment version number
Documentation is not complete and vignettes/examples need to be updated
Standardize guess boundaries Use alpha = 0.5 for guesses
Fix up aci fits
If they are are not numeric values, there must a corresponding column in a related exdf object Also added a unit dictionary This approach seems to be slow
This allows us to use columns for the values of fixed parameters, which was not possible before
More fit improvements
Added tests for the Warren function Renamed the `alpha` used in TPU calculations because there is a Licor column called `alpha` `check_required_variables` no longer throws an error if a column is NA
Rename alpha used for calculating Gamma_star Rename alpha used in C4 assimilation
Now we can distinguish between the process (triose phosphate utilization; TPU) and the maximum rate at which the process occurs (Tp)
More tweaks
Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## main #89 +/- ##
==========================================
+ Coverage 85.42% 86.11% +0.69%
==========================================
Files 64 74 +10
Lines 3018 3717 +699
==========================================
+ Hits 2578 3201 +623
- Misses 440 516 +76 ☔ View full report in Codecov by Sentry. |
Merged
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
CHANGES IN PhotoGEA VERSION 0.11.0 (2024-02-12)
fit_c3_aci
andfit_c3_variable_j
):alpha
(related to TPU) andGamma_star
.initial_guess_c3_aci
andinitial_guess_c3_variable_j
) can now accomodate user-supplied values ofalpha
.fit_c3_aci
,fit_c3_variable_j
, andfit_c4_aci
):error_function_c3_aci
,error_function_c3_variable_j
, anderror_function_c4_aci
.functions in the package namespace:
confidence_intervals_c3_aci
,confidence_intervals_c3_variable_j
, andconfidence_intervals_c4_aci
.calculate_c3_assimilation
).NA
for all results, along with a message explaining the issue.Rd
with the Laisk method:calculate_rd_laisk
alpha
, and several different "alphas" were used throughoutPhotoGEA
. To avoid confusion, the values inPhotoGEA
were renamed as follows:alpha_g
: used in C3 assimilation calculationsalpha_pr
: used in Gamma_star calculationsalpha_psii
: used in C4 assimilation calculationsTp
calculate_c3_assimilation
fit_c3_aci
fit_c3_variable_j
fit_c4_aci
calculate_c3_limitations_grassi
calculate_c3_limitations_warren
read_gasex_file
function now automatically includes the filename as a column in the resultingexdf
object; this helps with troubleshooting problematic curves or files.