Skip to content

add effect of temperature on plant growth with variable FTEMP and add… #7

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.

Sign up for GitHub

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

Merged
sbuis merged 8 commits into from
Oct 9, 2026
Merged

add effect of temperature on plant growth with variable FTEMP and add… #7

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
c60d180
add effect of temperature on plant growth with variable FTEMP and add…
Jul 18, 2026
33de8e9
Merge branch 'main' into meije
sbuis Jul 20, 2026
e2aff2b
Test: Add temperature params to valid_plant() fixture
sbuis Jul 20, 2026
d21f00a
doc: updated doc
sbuis Jul 20, 2026
e546c34
fix: address Benjamin's review comments in miniSTICS
sbuis Oct 9, 2026
a610d20
test: update reference after adding new parameters and equations
sbuis Oct 9, 2026
a52b25c
Merge branch 'main' into meije
sbuis Oct 9, 2026
825062b
test: update reference following merge from main
sbuis Oct 9, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 21 additions & 2 deletions R/miniSTICS.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,10 @@
#' \item parsurg: PAR fraction
#' \item extin: Light extinction coefficient
#' \item rue: Radiation use efficiency (g MJ-1)
#' \item temin: minimal temperature for plant growth (°C)
#' \item teopt: minimum range of optimal temperature for plant growth (°C)
#' \item teoptbis: maximum range of optimal temperature for plant growth (°C)
#' \item temax: Maximal temperature above which plant growth stops (°C)
#' }
#'
#' Water stress:
Expand Down Expand Up @@ -243,6 +247,7 @@ miniSTICS <- function(soil, weather_station, practices, plant, weather) {
practices = c("sowing_year", "doy_sowing", "doy_stop_sim", "zrac0", "density"),
plant = c(
"tcmin", "tcopt", "tcxstop",
"temin","teopt","teoptbis","temax",
"flag_vern", "jvc", "tfroid", "ampfroid",
"flag_photo", "phobase", "phosat",
"st2germinate", "st2emerge", "stlevamf", "stamflax", "stlevdrp", "stdrpmat",
Expand Down Expand Up @@ -516,6 +521,7 @@ miniSTICS <- function(soil, weather_station, practices, plant, weather) {
ministics$HUR1 <- vector("numeric", sz)
ministics$HUR2 <- vector("numeric", sz)
ministics$SWFAC <- vector("numeric", sz)
ministics$FTEMP <- vector("numeric",sz)

ministics$DELTAMS <- vector("numeric", sz)
ministics$DELTAMS_unstressed <- vector("numeric", sz)
Expand Down Expand Up @@ -766,10 +772,23 @@ miniSTICS <- function(soil, weather_station, practices, plant, weather) {

# TOTAL BIOMASS GROWTH
# --------------------
if (i==1){
ministics$FTEMP[i] <- 1
}else{
if (ministics$Temp[i] < teopt){
ministics$FTEMP[i] <- 1 - ((ministics$UDEVCULT[i-1]-teopt)/(temin-teopt))^2
}else if (teopt <= ministics$UDEVCULT[i-1] & ministics$UDEVCULT[i-1] <= teoptbis){
ministics$FTEMP[i] <- 1
}else{
ministics$FTEMP[i] <- 1-((ministics$UDEVCULT[i-1]-teoptbis)/(temax-teoptbis))^2
}

}
# ministics$FTEMP[i] <- 1

if (ministics$DOY_2EMERG[i] == 1 & ministics$DOY_2Z89[i] == 0) {
ministics$DELTAMS[i] <- 0.95 * parsurg * ministics$Radiation[i] * rue * (1 - exp(-extin * ministics$LAI[i]))
ministics$DELTAMS_unstressed[i] <- 0.95 * parsurg * ministics$Radiation[i] * rue * (1 - exp(-extin * ministics$LAI_unstressed[i]))
ministics$DELTAMS[i] <- 0.95 * parsurg * ministics$Radiation[i] * rue * (1 - exp(-extin * ministics$LAI[i])) * ministics$FTEMP[i]
ministics$DELTAMS_unstressed[i] <- 0.95 * parsurg * ministics$Radiation[i] * rue * (1 - exp(-extin * ministics$LAI_unstressed[i])) * ministics$FTEMP[i]
} else {
ministics$DELTAMS[i] <- 0
ministics$DELTAMS_unstressed[i] <- 0
Expand Down
9 changes: 8 additions & 1 deletion R/plant_parameters.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,10 @@
#' \item parsurg: PAR fraction
#' \item extin: Light extinction coefficient
#' \item rue: Radiation use efficiency (g MJ-1)
#' \item temin: minimal temperature for plant growth (°C)
#' \item teopt: minimum range of optimal temperature for plant growth (°C)
#' \item teoptbis: maximum range of optimal temperature for plant growth (°C)
#' \item temax: Maximal temperature above which plant growth stops (°C)
#' }
#'
#' Water stress:
Expand Down Expand Up @@ -102,6 +106,10 @@ plant_parameters <- function(...) {
params <- list(
tcmin = 0,
tcopt = 35,
temin=0,
teopt=12,
teoptbis=17,
temax=40,
tcxstop = 45,
flag_vern = TRUE,
jvc = 45,
Expand Down Expand Up @@ -148,7 +156,6 @@ plant_parameters <- function(...) {
tminremp = 0,
tmaxremp = 38
)

overrides <- list(...)

if (length(overrides) > 0) {
Expand Down
4 changes: 4 additions & 0 deletions man/miniSTICS.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 4 additions & 0 deletions man/plant_parameters.Rd
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Binary file modified tests/testthat/fixtures/miniSTICS_example_reference.rds
View file
Open in desktop
Binary file not shown.
4 changes: 4 additions & 0 deletions tests/testthat/test-parameter-validation.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,10 @@ valid_plant <- function() {
extin = 1,
rue = 1,
tetstomate = 1,
temin = 1,
teopt = 1,
teoptbis = 1,
temax = 1,
nbjgrain = 1,
cgrain = 1,
nbgrainmax = 1,
Expand Down
Loading