cesabfunctionalwebsdata:

# read the dataset

library(dplyr)
library(readr)
library(tidyr)

# bromeliads --------------------------------------------------------------

summ_broms0 <- read.csv("data-raw/02_broms.csv")

broms01 <- read.csv("data-raw/01_broms.csv")
id_spp <- broms01 %>%
  select(bromeliad_id, species, actual_water, leaf_width) %>%
  distinct()

summ_broms0 <- summ_broms0 %>%
  left_join(id_spp)

summ_broms <- summ_broms0

## French Guiana, We used the Regis's equation ####
## ~/Dropbox/communityanalysis/CESAB\ trait\ working\ group/Max_Volume_models/


## FrenchGuianaAechmea2007,

# Equation= exp(0.611+1.09*log(diameter)) for Aechmea mertensii
volFrench2007<- function(a){exp(0.611+1.09*log(a))}
summ_broms <- summ_broms %>%
  mutate(max_water= ifelse(visit_id == 286,
                           volFrench2007(diameter),
                           NA))
## NA not max_water, this creates the column as all NA

#FrenchGuianaAechmea2008,

# PetitSaut, Aechmea mertensii,
#Vmax=exp(4.838+5.5888*log(diameter)-1.1649*(log(fg$diameter))^2 +
#     5.7181*log(fg$num_leaf)-1.7982*(log(fg$num_leaf)^2))

volFrench2008<- function(a,b){exp(0.0292 +0.339*log(a) + 1.3563*log(b))}
summ_broms <- summ_broms%>%
  mutate(max_water= ifelse(visit_id == 301,
                           volFrench2008(diameter,num_leaf),
                           max_water))

#FrenchGuianaAechmea2008,

# Kaw, Aechmea mertensii,
#Vmax= exp(0.0292 +0.339*log(fg$diameter) + 1.3563*log(fg$num_leaf))

volFrench2008_2<- function(a,b){exp(0.0292 +0.339*log(a) + 1.3563*log(b))}
summ_broms <- summ_broms%>%
  mutate(max_water= ifelse(visit_id == 296,
                           volFrench2008_2(diameter,num_leaf),
                           max_water))

#Nouragues2009,Sinnamary2011,
# Aechmea aquilega
# Vmax= exp(-0.4368 +0.735*log(fg1$diameter)+ 1.4260*log(fg1$num_leaf))

volNouragues2009<- function(a,b){exp(-0.4368 +0.735*log(a)+ 1.4260*log(b))}
summ_broms <- summ_broms%>%
  mutate(max_water= ifelse(visit_id == 336|visit_id==331,
                           volNouragues2009(diameter,num_leaf),
                           max_water))


#FrenchGuianaVriesea2007, Vriesea splendens No information of diameter and
#number of leaf, information about actual water select data set only Vriesea
#splendens and create an equation

# Equation vmax = 1.4144*actual vol + 39.343

volFrench2007Vrisea<- function(a){1.4144*a + 39.343}
summ_broms <-summ_broms%>%
  mutate(max_water= ifelse(visit_id == 341 & species=="Vriesea splendens",
                           volFrench2007Vrisea(actual_water),
                           max_water))

#### For the other sites ####

#how many species names are there for bromeliads
unique(summ_broms$species)
#select only Guzmania
guz_only = filter(summ_broms, grepl("^Gu|^G\\.", species))
unique(guz_only$species)
glimpse(guz_only)

# Model for Honduras and Colombia2000, 2001
# plot(log(guz_only$num_leaf),log(guz_only$max_water))
# summary(lm(log(max_water)~log(num_leaf) + log(actual_water +1),data=guz_only ))

#Equation for Honduras and Colombia2000 and 2001:
# Vmax=exp(0.78960 + 0.68576*log(Col$num_leaf) + 0.44664*log(Col$actual_water +1))
# Tillandsia

##Kurt and Paula
full <- fw_data("0.5.0")
full$bromeliads$max_water_imputed<-NA

#Cusuco 2006 and 2007; visit id 106, 111
# Tillandsia
til_only = filter(full$bromeliads, grepl("^Ti|^T\\.", species))
til2<-subset(til_only,!is.na(max_water))  #Saba

#look at Honduras data Cusuco2006 2007, Guasca2001, Sisga2000
Cusuco2006_2007<-subset(full$bromeliads,visit_id %in% c(111,106,91,96))
View(Cusuco2006_2007)

plot(log(til2$num_leaf),log(til2$max_water))
a<-summary(lm(log(max_water)~log(num_leaf),data=til2))  #Saba
int<-a$coefficients[1,1] #intercept
slope<-a$coefficients[2,1] #slope


volHonduras2000<- function(a){exp(int + slope*log(a) )}
til_only <- til_only%>%
  mutate(max_water_imputed= ifelse(visit_id == 106|visit_id==111|visit_id==91|visit_id==96,
                           volHonduras2000(num_leaf),
                           max_water))

plot(log(til_only$num_leaf),log(til_only$max_water_imputed),type='n')
abline(a)
points(log(til2$num_leaf),log(til2$max_water))


#Model for Colombia.Rioblanco 2012 (366) and ElVerde

# summary(lm(log(max_water)~log(num_leaf),data=guz_only))

# equation for Colombia.Rioblanco 2012 (366) and ElVerde
# Vol.max=exp(-2.3418 + 2.1025*log(Col2012$num_leaf))
# Guzmania

volColombia2012<- function(a){exp(-2.3418 + 2.1025*log(a))}
summ_broms <- summ_broms%>%
  mutate(max_water= ifelse(visit_id%in%c(131,146,151,156,161,166,171,176,181,351,356,361,366),
                           volColombia2012(num_leaf),
                           max_water))

# Model for Colombia. Rioblanco 2014(371)

# plot(log(guz_only$leaf_width),log(guz_only$max_water))
# summary(lm(log(max_water)~log(num_leaf) + log(leaf_width) ,data=guz_only))

#Equation for Colombia. Rioblanco 2014(371)
# Vol.max= exp(-4.18214 + 1.55894*log(Col2014$num_leaf) +
#          2.25906*log(Col2014$leaf_width))
# Guzmania
volColombia2014<- function(a,b){exp(-4.18214 + 1.55894*log(a) + 2.25906*log(b))}
summ_broms <- summ_broms %>%
  mutate(max_water= ifelse(visit_id==371,
                           volColombia2014(num_leaf,leaf_width),
                           max_water))

# Model Sonadora
# summary(lm(log(max_water)~log(actual_water+1),data=guz_only))

#Equation for Sonora,
# exp(2.412+ 0.619*log(actual_water+1))
#Vriesea or Guzmania
volSonora<- function(a){exp(2.412+ 0.619*log(a+1))}
summ_broms <- summ_broms%>%
  mutate(max_water= ifelse(visit_id%in%c(376,391,396,401,406,411,416,421,426,431,436,441,446),
                           volSonora(actual_water),
                           max_water))

stopifnot(nrow(summ_broms0) == nrow(summ_broms))

volume_final <- summ_broms %>%
  select(bromeliad_id, max_water)

write.csv(volume_final, "data-raw/24_volume.csv", row.names = FALSE)