library(data.table)

library(Vpalmr)

library(dplyr)

library(lubridate)

library(ggplot2)

library(plotly)

parameters= fread("0-data/Archi/ParameterSimu.csv", data.table = F)

development=

fread("0-data/Archi/Development_Rep4_SMSE.csv", data.table = F, sep=';', dec=',', fill= T)%>%

mutate(Transplanting_Date= lubridate::dmy(.data$Transplanting_Date),

Observation_Date= lubridate::dmy(.data$Observation_Date))

development= Vpalmr::compute_MAP(x = development)

development2=

development%>%

group_by(.data$TreeNumber,.data$MonthAfterPlanting)%>%

summarise(Nb_frond_new= mean(.data$Nb_frond), LeafIndexRank1= max(.data$LeafIndexRank1))%>%

arrange(TreeNumber, MonthAfterPlanting)%>%

mutate(Nb_frond_new= ifelse(is.na(.data$Nb_frond_new),

.data$LeafIndexRank1-lag(.data$LeafIndexRank1),

.data$Nb_frond_new),

TotalEmitted= cumsum(.data$Nb_frond_new))%>%

select(-.data$LeafIndexRank1)%>%

merge(development,., by= c("TreeNumber","MonthAfterPlanting"),sort = F)%>%

mutate(Nb_frond= .data$Nb_frond_new)%>%select(-.data$Nb_frond_new)

development2%>%

group_by(.data$MonthAfterPlanting,.data$Progeny)%>%

summarise(TotalEmitted= mean(.data$TotalEmitted, na.rm= T))%>%

bind_rows(tibble::tibble(MonthAfterPlanting= 1,

Progeny= unique(development2$Progeny), TotalEmitted= 1),.)

expand.grid(Progeny= unique(MAP_average$Progeny),

MonthAfterPlanting= 1:max(MAP_average$MonthAfterPlanting))%>%

left_join(MAP_average,c("MonthAfterPlanting","Progeny"))%>%

group_by(.data$Progeny)%>%

mutate(nbLeaves= zoo::na.approx(.data$TotalEmitted,.data$MonthAfterPlanting))%>%

mutate(nbLeaves= round(.data$nbLeaves))%>%

select(-.data$TotalEmitted)%>%

rename(MAP= .data$MonthAfterPlanting)

ggplot(data = development2, aes(x = MonthAfterPlanting, y= TotalEmitted))+

facet_wrap(.~Progeny)+

geom_line(aes(group= TreeNumber))+

geom_point(data= df_MAP, aes(x = MAP, y= nbLeaves, color= "Fit"))

right_join(parameters%>%select(-.data$nbLeaves),df_MAP, by= c("MAP","Progeny"))%>%

mutate(Date= min(lubridate::dmy(.data$Date), na.rm = T) + months(.data$MAP))%>%

mutate(Year= lubridate::year(.data$Date), Month= lubridate::month(.data$Date))%>%

mutate(Date= format(.data$Date, '%d/%m/%Y'))

area_df= data.table::fread("0-data/Archi/LeafArea_monitoring_SMSE.csv", data.table = F, sep=';',

fill= T, dec=".")

is(area_df$Width)

area_df[is.na(as.numeric(area_df$Width)),]

area_df%>%

select(.data$TreeNumber,.data$FieldPlantingDate)%>%

na.omit()%>%

group_by(.data$TreeNumber)%>%

summarise(Transplanting_Date= unique(.data$FieldPlantingDate))

area_df=

area_df%>%

dplyr::left_join(Planting_date_area, by= "TreeNumber")%>%

dplyr::mutate(Obs_Date= lubridate::dmy(.data$Obs_Date),

FieldPlantingDate= lubridate::dmy(.data$FieldPlantingDate))%>%

dplyr::mutate(FieldPlantingDate= lubridate::dmy(.data$Transplanting_Date))%>%

dplyr::mutate(MAP= lubridate::interval(.data$FieldPlantingDate,.data$Obs_Date)%/%

months(1))%>%

dplyr::mutate(Obs_Date= format(.data$Obs_Date, "%d/%m/%Y"),

FieldPlantingDate= format(.data$FieldPlantingDate, "%d/%m/%Y"))%>%

select(-.data$Transplanting_Date)

path_data= '0-data/Archi'

test=

Vpalmr::import_data(parameter= file.path(path_data,'ParameterSimu.csv'),

development= file.path(path_data,'Development_Rep4_SMSE.csv'),

phylotaxy= file.path(path_data,'Stem_SMSE14.csv'),

declination= file.path(path_data,'AnglesC&A_SMSE_Nov14.csv'),

curvature= file.path(path_data,'LeafCurvature_SMSE14.csv'),

leaf_area= file.path(path_data,'LeafArea_monitoring_SMSE.csv'),

axial_angle= file.path(path_data,'LeafDispositionComp_SMSE14.csv'),

petiole_width= file.path(path_data,'Petiole_SMSE14.csv'),

twist= file.path(path_data,'Torsion_SMSE14.csv'), map = 60)

Vpalmr::test_Area(x = test$Area, path = "C:/Users/vezy/Desktop")

Palm_Param= compute_archi(map = 60, data_path = "0-data/Archi",

write_path = "../VPalm_Architecture")

Palm_Param= compute_archi(map = 60, data_path = "0-data/Archi",

write_path = "../VPalm_Architecture")

Palm_Param= readRDS(file = "../VPalm_Architecture/models_MAP_60.RData")

make_scene(data = Palm_Param, nleaves = 45, Progeny = NULL, ntrees= 0,

path = "C:/Users/vezy/Desktop",

AMAPStudio = "D:/OneDrive/Travail_AMAP/PalmStudio/VPalm_IDE",

overwrite = T)

ggplot(test$DataAll, aes(x= MonthAfterPlanting, y= PosB))+

facet_wrap(.~Progeny)+

geom_point(aes(group= TreeNumber))

plotly::ggplotly(test_plot)

OPFs= make_opf_all(parameter = "C:/Users/vezy/Desktop/VPalm_inputs",

opf = "C:/Users/vezy/Desktop/scenes/opf",

AMAPStudio = "vpalm.jar", overwrite = T)

make_opf(parameter = "C:/Users/vezy/Desktop/VPalm_inputs/DA1_Average_MAP_60_2.txt",

opf = "C:/Users/vezy/Desktop/scenes/opf/DA1_Average_MAP_60_2.opf",

AMAPStudio = "D:/OneDrive/Travail_AMAP/PalmStudio/VPalm_IDE",

overwrite = T)

test2= test_pos_on_leaflet_all(test$Area)

list(

nbLeafEmitted= "Total cumulative number of emitted leaves from planting",

rachisLengthIntercept= "Intercept of the rachis length equation (cm)",

rachisLengthSlope= "Slope of the rachis length equation (cm.leaves-1)",

Nbmax= "Maximum number of leaflets per leaf (-)",

nbSlope= "Slope of the number of leaflets per leaf ~ rachis length (leaflets.cm-1)",

nbInfl= "Inflexion point of the number of leaflets per leaf ~ rachis length (cm)",

lenfletLengthAtBIntercept = "Intercept of the leaflet length at B point ~ rachis length (cm)",

leafletLengthAtBSlope = "Slope of the allometry between leaflet length at B point and rachis length (cm.cm-1)",

bWidthIntercept= "Intercept of the leaflet width at B point ~ rachis length (cm)",

bWidthSlope= "Slope of the leaflet width at B point ~ rachis length (cm.cm-1)",

xm_intercept= "Intercept of the relative position of maximum width on leaflet ~ position on rachis (-)",

xm_slope= "Slope of the relative position of maximum width on leaflet ~ position on rachis (-)",

ym_intercept= "Intercept of leaflet shape ~ position on rachis (-)",

ym_slope= "Slope of the leaflet shape ~ position on rachis (-)",

petioleRachisRatio_M= "Ratio of the petiole length to rachis length (cm.cm-1)",

nbFronds_M= "Number of green leaves on the palm (leaves)",

decMaxA= "Maximum declination angle (i.e leaf curvature) at point A (degrees)",

decSlopeA= "Slope at inflexion point of the declination angle (i.e leaf curvature) at A point ~ at C point (degrees.degrees-1)",

decInflA= "Inflexion point of the declination angle at A point ~ at C point (degrees)"

)

Palm_Param= list(custom= VPalm_list$Average)

make_scene_custom(x = Palm_Param()$custom, path = parseDirPath(volumes, dir()),

AMAPStudio = getwd(),

planting_design= if(!isTruthy(input$planting_design)){

NULL

}else{

custom_design()

},

progress=function(x){

updateProgress(detail = x, progress_obj = progress_obj,

steps = 7)

})

Palm_Param= readRDS(file = "../VPalm_Architecture/models_MAP_60.RData")

VPalm_list = Vpalmr::extract_progeny(data = Palm_Param$input,

model = Palm_Param$model, n = 0, leaves = 45, seed = NULL,

average = T)

saveRDS(VPalm_list$DA1$Average,"0-data/VPalm_list/vpalm_template.rds")

scene= make_scene_custom(x = VPalm_list$DA1, path = "C:/Users/vezy/Desktop",

AMAPStudio = getwd(),plant_dist = 9.2)

test= default_params()

paste(test$value, collapse = "', '" )