filter(study_id=="Finbarr_G_Horgan_Cucumis_sativus_Philippines_2015")
field_level_data_Lagenaria <- field_level_data %>%
filter(study_id=="Finbarr_G_Horgan_Lagenaria_siceraria_Philippines_2015")
field_level_data_Luffa <- field_level_data %>%
filter(study_id=="Finbarr_G_Horgan_Luffa_acutangula_Philippines_2015")
field_level_data_Momordica <- field_level_data %>%
filter(study_id=="Finbarr_G_Horgan_Momordica_charantia_Philippines_2015")
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data_Abelmoschus,
"field_level_data_Finbarr_G_Horgan_Abelmoschus_esculentus_Philippines_2015.csv")
write_csv(field_level_data_Cucumis,
"field_level_data_Finbarr_G_Horgan_Cucumis_sativus_Philippines_2015.csv")
write_csv(field_level_data_Lagenaria,
"field_level_data_Finbarr_G_Horgan_Lagenaria_siceraria_Philippines_2015.csv")
write_csv(field_level_data_Luffa,
"field_level_data_Finbarr_G_Horgan_Luffa_acutangula_Philippines_2015.csv")
write_csv(field_level_data_Momordica,
"field_level_data_Finbarr_G_Horgan_Momordica_charantia_Philippines_2015.csv")
setwd(dir_ini)
View(field_level_data_Momordica)
View(field_level_data_Abelmoschus)
View(field_level_data_Luffa)
View(field_level_data_Lagenaria)
field_level_data %>% group
field_level_data %>% group_by(study_id) %>% count()
# load libraries
library(tidyverse)
library("iNEXT")
library(parzer)
library(readxl)
library(openxlsx)
dir_ini <- getwd()
data.site <- read_excel("Crop pollinators.xlsx", sheet = "field_level_data")
data.site <- as_tibble(data.site)
data.site %>% group_by(site_id,sampling_year) %>% count()
data.site %>% group_by(crop,sampling_year) %>% count()
data.site %>% group_by(crop,site_id) %>% count() %>% filter(n>1)
data.site$crop[data.site$crop=="Ampalaya - Bitter melon (Momordica charantia)"] <- "Momordica charantia"
data.site$crop[data.site$crop=="Cucumber (Cucumis sativus)"] <- "Cucumis sativus"
data.site$crop[data.site$crop=="Okra (Abelmoschus esculentus)"] <- "Abelmoschus esculentus"
data.site$crop[data.site$crop=="Patola - Luffa gourd (Luffa acutangula)"] <- "Luffa acutangula"
data.site$crop[data.site$crop=="Upo - Bottle gourd (Lagenaria siceraria)"] <- "Lagenaria siceraria"
# New study ID
data.site <- data.site %>% mutate(new_study_id=
paste0("Finbarr_G_Horgan_",crop,"_Philippines_2015"))
data.site$new_study_id <- str_replace(data.site$new_study_id," ","_")
# New study ID
data.site <- data.site %>% mutate(new_site_id=study_id) %>%
separate(new_site_id,c("site","crops_informal","season"),"_") %>%
mutate(new_site_id=paste0(site,"_",season))
labeling <- data.site %>% select(study_id,site_id,new_study_id,new_site_id)
# Rename management
data.site$management <- "conventional"
# Fix latitude and longitude
data.site$latitude <- parse_lat(data.site$latitude)
data.site$longitude <- parse_lon(data.site$longitude)
insect_sampling <- read_excel("Crop pollinators.xlsx", sheet = "insect_sampling")
insect_sampling$site_id[insect_sampling$site_id=="Bukidnon1"] <- "Bukidnon 1"
insect_sampling$site_id[insect_sampling$site_id=="Bukidnon2"] <- "Bukidnon 2"
insect_sampling <- insect_sampling %>%
left_join(labeling,by=c("study_id","site_id"))
insect_sampling %>% group_by(guild) %>% count()
insect_sampling$guild[insect_sampling$guild=="honeybee"] <-"honeybees"
insect_sampling$guild[insect_sampling$guild=="moths"] <-"lepidoptera"
insect_sampling$guild[insect_sampling$guild=="butterflies"] <-"lepidoptera"
insect_sampling$guild[insect_sampling$guild=="other wild bees"] <-"other_wild_bees"
insect_sampling %>% group_by(guild) %>% count()
insect_sampling_new <- tibble(
study_id=insect_sampling$new_study_id,
site_id=insect_sampling$new_site_id,
pollinator=insect_sampling$pollinator,
guild=insect_sampling$guild,
sampling_method=insect_sampling$sampling_method,
abundance=insect_sampling$abundance,
total_sampled_area=insect_sampling$total_sampled_area,
total_sampled_time=insect_sampling$total_sampled_time,
total_sampled_flowers=insect_sampling$total_sampled_flowers,
Description=insect_sampling$`Description_(fee_text)`
)
# Save new insect sampling templates
insect_sampling_new %>% group_by(study_id) %>% count()
insect_sampling_Abelmoschus <- insect_sampling_new %>%
filter(study_id=="Finbarr_G_Horgan_Abelmoschus_esculentus_Philippines_2015")
insect_sampling_Cucumis <- insect_sampling_new %>%
filter(study_id=="Finbarr_G_Horgan_Cucumis_sativus_Philippines_2015")
insect_sampling_Lagenaria <- insect_sampling_new %>%
filter(study_id=="Finbarr_G_Horgan_Lagenaria_siceraria_Philippines_2015")
insect_sampling_Luffa <- insect_sampling_new %>%
filter(study_id=="Finbarr_G_Horgan_Luffa_acutangula_Philippines_2015")
insect_sampling_Momordica <- insect_sampling_new %>%
filter(study_id=="Finbarr_G_Horgan_Momordica_charantia_Philippines_2015")
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(insect_sampling_Abelmoschus,
"insect_sampling_Finbarr_G_Horgan_Abelmoschus_esculentus_Philippines_2015.csv")
write_csv(insect_sampling_Cucumis,
"insect_sampling_Finbarr_G_Horgan_Cucumis_sativus_Philippines_2015.csv")
write_csv(insect_sampling_Lagenaria,
"insect_sampling_Finbarr_G_Horgan_Lagenaria_siceraria_Philippines_2015.csv")
write_csv(insect_sampling_Luffa,
"insect_sampling_Finbarr_G_Horgan_Luffa_acutangula_Philippines_2015.csv")
write_csv(insect_sampling_Momordica,
"insect_sampling_Finbarr_G_Horgan_Momordica_charantia_Philippines_2015.csv")
setwd(dir_ini)
abundance_aux <- insect_sampling_new %>% select(study_id,site_id,guild,abundance) %>%
group_by(study_id,site_id,guild) %>% count(wt=abundance) %>%
spread(key=guild, value=n)
names(abundance_aux)
abundance_aux <- abundance_aux %>% mutate(bumblebees=0,
syrphids=0,
humbleflies=0,
other_flies=0,
beetles=0,
non_bee_hymenoptera=0,
other=0,
total=0)
abundance_aux[is.na(abundance_aux)] <- 0
abundance_aux$total <- rowSums(abundance_aux[,c(3:ncol(abundance_aux))])
abundance_aux <- abundance_aux %>%
rename(new_study_id=study_id,new_site_id=site_id)
data.site <- data.site %>% left_join(abundance_aux, by = c("new_study_id","new_site_id"))
abundace_field <- insect_sampling_new %>%
select(study_id, site_id,pollinator,abundance)%>%
group_by(study_id,site_id,pollinator) %>% count(wt=abundance)
abundace_field <- abundace_field %>% spread(key=pollinator,value=n)
abundace_field[is.na(abundace_field)] <- 0
abundace_field$r_obser <-  0
abundace_field$r_chao <-  0
for (i in 1:nrow(abundace_field)) {
x <- as.numeric(abundace_field[i,3:(ncol(abundace_field)-2)])
if (sum(x)>0){
chao  <-  ChaoRichness(x, datatype = "abundance", conf = 0.95)
abundace_field$r_obser[i] <-  chao$Observed
abundace_field$r_chao[i] <-  chao$Estimator
}else{
abundace_field$r_obser[i] <-  0
abundace_field$r_chao[i] <-  0.0
}
}
# Load our estimation for taxonomic resolution
percentage_species_morphos <- 1
richness_aux <- abundace_field %>% select(study_id,site_id,r_obser,r_chao)
richness_aux <- richness_aux %>% dplyr::rename(observed_pollinator_richness=r_obser,
other_pollinator_richness=r_chao) %>%
mutate(other_richness_estimator_method="Chao1",richness_restriction="Bees, including honeybees; butterflies and diurnal moths")
if (percentage_species_morphos < 0.8){
richness_aux[,3:ncol(richness_aux)] <- NA
}
richness_aux <- richness_aux %>%
rename(new_study_id=study_id,new_site_id=site_id)
data.site <- data.site %>% left_join(richness_aux, by = c("new_study_id","new_site_id"))
##################
# VISITATION RATES
##################
insect_sampling_new$total_sampled_flowers <- as.numeric(insect_sampling_new$total_sampled_flowers)
sampling <- insect_sampling_new %>% group_by(study_id,site_id) %>% summarise(flowers=mean(total_sampled_flowers,na.rm = T),
area=mean(total_sampled_area),
time=mean(total_sampled_time)) %>%
rename(new_study_id=study_id,new_site_id=site_id)
View(sampling)
visit_aux <- abundance_aux %>% left_join(sampling,by=c("new_study_id","new_site_id")) %>%
mutate(
vist_beetles = 60*beetles/time,
vist_bumblebees = 60*bumblebees/time,
vist_honeybees = 60*honeybees/time,
vist_humbleflies = 60*humbleflies/time,
vist_lepidoptera = 60*lepidoptera/time,
vist_non_bee_hymenoptera = 60*non_bee_hymenoptera/time,
vist_other_flies = 60*other_flies/time,
vist_other_wild_bees = 60*other_wild_bees/time,
vist_others = 60*other/time,
vist_syrphids =  60*syrphids/time,
vist_total = vist_beetles + vist_bumblebees +
vist_honeybees + vist_humbleflies +
vist_lepidoptera + vist_non_bee_hymenoptera +
vist_other_flies + vist_other_wild_bees + vist_others + vist_syrphids
) %>%
select(new_study_id,new_site_id,vist_beetles,vist_bumblebees,vist_honeybees, vist_humbleflies,
vist_lepidoptera,vist_non_bee_hymenoptera,vist_other_flies,
vist_other_wild_bees,vist_others,vist_syrphids,vist_total
)
data.site <- data.site %>% left_join(visit_aux,by=c("new_study_id","new_site_id"))
data.site <- data.site %>% left_join(sampling,by=c("new_study_id","new_site_id"))
field_level_data <- tibble(
study_id = data.site$new_study_id,
site_id = data.site$new_site_id,
crop = data.site$crop,
variety = data.site$variety,
management = data.site$management,
country = data.site$country,
latitude = data.site$latitude,
longitude = data.site$longitude,
X_UTM=NA,
Y_UTM=NA,
zone_UTM=NA,
sampling_start_month = data.site$sampling_start_month,
sampling_end_month = data.site$sampling_end_month,
sampling_year = data.site$sampling_year,
field_size = data.site$field_size,
yield=data.site$yield,
yield_units=data.site$yield_units,
yield2=data.site$yield2,
yield2_units=data.site$yield2_units,
yield_treatments_no_pollinators=data.site$yield_treatments_no_pollinators,
yield_treatments_pollen_supplement=data.site$yield_treatments_pollen_supplement,
yield_treatments_no_pollinators2=data.site$yield_treatments_no_pollinators2,
yield_treatments_pollen_supplement2=data.site$yield_treatments_pollen_supplement2,
fruits_per_plant=data.site$mean_fruits_per_plant,
fruit_weight= data.site$fruit_weight,
plant_density=data.site$plant_density,
seeds_per_fruit=data.site$seeds_per_fruit,
seeds_per_plant=data.site$seeds_per_plant,
seed_weight=data.site$seed_weight,
observed_pollinator_richness=data.site$observed_pollinator_richness.y,
other_pollinator_richness=data.site$other_pollinator_richness.y,
other_richness_estimator_method=data.site$other_richness_estimator_method.y,
richness_restriction = data.site$richness_restriction.y,
abundance = data.site$total,
ab_honeybee = data.site$honeybees,
ab_bombus = data.site$bumblebees,
ab_wildbees = data.site$other_wild_bees,
ab_syrphids = data.site$syrphids,
ab_humbleflies= data.site$humbleflies,
ab_other_flies= data.site$other_flies,
ab_beetles=data.site$beetles,
ab_lepidoptera=data.site$lepidoptera,
ab_nonbee_hymenoptera=data.site$non_bee_hymenoptera,
ab_others = data.site$other,
total_sampled_area = data.site$area,
total_sampled_time = data.site$time,
visitation_rate_units = "visits per hour",
visitation_rate = data.site$vist_total,
visit_honeybee = data.site$vist_honeybees,
visit_bombus = data.site$vist_bumblebees,
visit_wildbees = data.site$vist_other_wild_bees,
visit_syrphids = data.site$vist_syrphids,
visit_humbleflies = data.site$vist_humbleflies,
visit_other_flies = data.site$vist_other_flies,
visit_beetles = data.site$vist_beetles,
visit_lepidoptera = data.site$vist_lepidoptera,
visit_nonbee_hymenoptera = data.site$vist_non_bee_hymenoptera,
visit_others = data.site$vist_others,
Publication = data.site$Publication,
Credit = data.site$Credit,
Email_contact = data.site$email
)
field_level_data_Abelmoschus <- field_level_data %>%
filter(study_id=="Finbarr_G_Horgan_Abelmoschus_esculentus_Philippines_2015")
field_level_data_Cucumis <- field_level_data %>%
filter(study_id=="Finbarr_G_Horgan_Cucumis_sativus_Philippines_2015")
field_level_data_Lagenaria <- field_level_data %>%
filter(study_id=="Finbarr_G_Horgan_Lagenaria_siceraria_Philippines_2015")
field_level_data_Luffa <- field_level_data %>%
filter(study_id=="Finbarr_G_Horgan_Luffa_acutangula_Philippines_2015")
field_level_data_Momordica <- field_level_data %>%
filter(study_id=="Finbarr_G_Horgan_Momordica_charantia_Philippines_2015")
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data_Abelmoschus,
"field_level_data_Finbarr_G_Horgan_Abelmoschus_esculentus_Philippines_2015.csv")
write_csv(field_level_data_Cucumis,
"field_level_data_Finbarr_G_Horgan_Cucumis_sativus_Philippines_2015.csv")
write_csv(field_level_data_Lagenaria,
"field_level_data_Finbarr_G_Horgan_Lagenaria_siceraria_Philippines_2015.csv")
write_csv(field_level_data_Luffa,
"field_level_data_Finbarr_G_Horgan_Luffa_acutangula_Philippines_2015.csv")
write_csv(field_level_data_Momordica,
"field_level_data_Finbarr_G_Horgan_Momordica_charantia_Philippines_2015.csv")
setwd(dir_ini)
View(field_level_data_Momordica)
View(insect_sampling_Momordica)
View(field_level_data_Momordica)
View(field_level_data_Luffa)
# load libraries
library(tidyverse)
library("iNEXT")
library(parzer)
library(readxl)
library(openxlsx)
dir_ini <- getwd()
data.site <- read_excel("Crop pollinators.xlsx", sheet = "field_level_data")
data.site <- as_tibble(data.site)
data.site %>% group_by(site_id,sampling_year) %>% count()
data.site %>% group_by(crop,sampling_year) %>% count()
data.site %>% group_by(crop,site_id) %>% count() %>% filter(n>1)
data.site$crop[data.site$crop=="Ampalaya - Bitter melon (Momordica charantia)"] <- "Momordica charantia"
data.site$crop[data.site$crop=="Cucumber (Cucumis sativus)"] <- "Cucumis sativus"
data.site$crop[data.site$crop=="Okra (Abelmoschus esculentus)"] <- "Abelmoschus esculentus"
data.site$crop[data.site$crop=="Patola - Luffa gourd (Luffa acutangula)"] <- "Luffa acutangula"
data.site$crop[data.site$crop=="Upo - Bottle gourd (Lagenaria siceraria)"] <- "Lagenaria siceraria"
# New study ID
data.site <- data.site %>% mutate(new_study_id=
paste0("Finbarr_G_Horgan_",crop,"_Philippines_2015"))
data.site$new_study_id <- str_replace(data.site$new_study_id," ","_")
# New study ID
data.site <- data.site %>% mutate(new_site_id=study_id) %>%
separate(new_site_id,c("site","crops_informal","season"),"_") %>%
mutate(new_site_id=paste0(site,"_",season))
labeling <- data.site %>% select(study_id,site_id,new_study_id,new_site_id)
# Rename management
data.site$management <- "conventional"
# Fix latitude and longitude
data.site$latitude <- parse_lat(data.site$latitude)
data.site$longitude <- parse_lon(data.site$longitude)
insect_sampling <- read_excel("Crop pollinators.xlsx", sheet = "insect_sampling")
insect_sampling$site_id[insect_sampling$site_id=="Bukidnon1"] <- "Bukidnon 1"
insect_sampling$site_id[insect_sampling$site_id=="Bukidnon2"] <- "Bukidnon 2"
insect_sampling <- insect_sampling %>%
left_join(labeling,by=c("study_id","site_id"))
insect_sampling %>% group_by(guild) %>% count()
insect_sampling$guild[insect_sampling$guild=="honeybee"] <-"honeybees"
insect_sampling$guild[insect_sampling$guild=="moths"] <-"lepidoptera"
insect_sampling$guild[insect_sampling$guild=="butterflies"] <-"lepidoptera"
insect_sampling$guild[insect_sampling$guild=="other wild bees"] <-"other_wild_bees"
insect_sampling %>% group_by(guild) %>% count()
insect_sampling_new <- tibble(
study_id=insect_sampling$new_study_id,
site_id=insect_sampling$new_site_id,
pollinator=insect_sampling$pollinator,
guild=insect_sampling$guild,
sampling_method=insect_sampling$sampling_method,
abundance=insect_sampling$abundance,
total_sampled_area=insect_sampling$total_sampled_area,
total_sampled_time=insect_sampling$total_sampled_time,
total_sampled_flowers=insect_sampling$total_sampled_flowers,
Description=insect_sampling$`Description_(fee_text)`
)
# Save new insect sampling templates
insect_sampling_new %>% group_by(study_id) %>% count()
insect_sampling_Abelmoschus <- insect_sampling_new %>%
filter(study_id=="Finbarr_G_Horgan_Abelmoschus_esculentus_Philippines_2015")
insect_sampling_Cucumis <- insect_sampling_new %>%
filter(study_id=="Finbarr_G_Horgan_Cucumis_sativus_Philippines_2015")
insect_sampling_Lagenaria <- insect_sampling_new %>%
filter(study_id=="Finbarr_G_Horgan_Lagenaria_siceraria_Philippines_2015")
insect_sampling_Luffa <- insect_sampling_new %>%
filter(study_id=="Finbarr_G_Horgan_Luffa_acutangula_Philippines_2015")
insect_sampling_Momordica <- insect_sampling_new %>%
filter(study_id=="Finbarr_G_Horgan_Momordica_charantia_Philippines_2015")
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(insect_sampling_Abelmoschus,
"insect_sampling_Finbarr_G_Horgan_Abelmoschus_esculentus_Philippines_2015.csv")
write_csv(insect_sampling_Cucumis,
"insect_sampling_Finbarr_G_Horgan_Cucumis_sativus_Philippines_2015.csv")
write_csv(insect_sampling_Lagenaria,
"insect_sampling_Finbarr_G_Horgan_Lagenaria_siceraria_Philippines_2015.csv")
write_csv(insect_sampling_Luffa,
"insect_sampling_Finbarr_G_Horgan_Luffa_acutangula_Philippines_2015.csv")
write_csv(insect_sampling_Momordica,
"insect_sampling_Finbarr_G_Horgan_Momordica_charantia_Philippines_2015.csv")
setwd(dir_ini)
abundance_aux <- insect_sampling_new %>% select(study_id,site_id,guild,abundance) %>%
group_by(study_id,site_id,guild) %>% count(wt=abundance) %>%
spread(key=guild, value=n)
names(abundance_aux)
abundance_aux <- abundance_aux %>% mutate(bumblebees=0,
syrphids=0,
humbleflies=0,
other_flies=0,
beetles=0,
non_bee_hymenoptera=0,
other=0,
total=0)
abundance_aux[is.na(abundance_aux)] <- 0
abundance_aux$total <- rowSums(abundance_aux[,c(3:ncol(abundance_aux))])
abundance_aux <- abundance_aux %>%
rename(new_study_id=study_id,new_site_id=site_id)
data.site <- data.site %>% left_join(abundance_aux, by = c("new_study_id","new_site_id"))
abundace_field <- insect_sampling_new %>%
select(study_id, site_id,pollinator,abundance)%>%
group_by(study_id,site_id,pollinator) %>% count(wt=abundance)
abundace_field <- abundace_field %>% spread(key=pollinator,value=n)
abundace_field[is.na(abundace_field)] <- 0
abundace_field$r_obser <-  0
abundace_field$r_chao <-  0
for (i in 1:nrow(abundace_field)) {
x <- as.numeric(abundace_field[i,3:(ncol(abundace_field)-2)])
if (sum(x)>0){
chao  <-  ChaoRichness(x, datatype = "abundance", conf = 0.95)
abundace_field$r_obser[i] <-  chao$Observed
abundace_field$r_chao[i] <-  chao$Estimator
}else{
abundace_field$r_obser[i] <-  0
abundace_field$r_chao[i] <-  0.0
}
}
# Load our estimation for taxonomic resolution
percentage_species_morphos <- 1
richness_aux <- abundace_field %>% select(study_id,site_id,r_obser,r_chao)
richness_aux <- richness_aux %>% dplyr::rename(observed_pollinator_richness=r_obser,
other_pollinator_richness=r_chao) %>%
mutate(other_richness_estimator_method="Chao1",richness_restriction="Bees, including honeybees; butterflies and diurnal moths")
if (percentage_species_morphos < 0.8){
richness_aux[,3:ncol(richness_aux)] <- NA
}
richness_aux <- richness_aux %>%
rename(new_study_id=study_id,new_site_id=site_id)
data.site <- data.site %>% left_join(richness_aux, by = c("new_study_id","new_site_id"))
##################
# VISITATION RATES
##################
insect_sampling_new$total_sampled_flowers <- as.numeric(insect_sampling_new$total_sampled_flowers)
sampling <- insect_sampling_new %>% group_by(study_id,site_id) %>% summarise(flowers=mean(total_sampled_flowers,na.rm = T),
area=mean(total_sampled_area),
time=mean(total_sampled_time)) %>%
rename(new_study_id=study_id,new_site_id=site_id)
visit_aux <- abundance_aux %>% left_join(sampling,by=c("new_study_id","new_site_id")) %>%
mutate(
vist_beetles = 60*beetles/time,
vist_bumblebees = 60*bumblebees/time,
vist_honeybees = 60*honeybees/time,
vist_humbleflies = 60*humbleflies/time,
vist_lepidoptera = 60*lepidoptera/time,
vist_non_bee_hymenoptera = 60*non_bee_hymenoptera/time,
vist_other_flies = 60*other_flies/time,
vist_other_wild_bees = 60*other_wild_bees/time,
vist_others = 60*other/time,
vist_syrphids =  60*syrphids/time,
vist_total = vist_beetles + vist_bumblebees +
vist_honeybees + vist_humbleflies +
vist_lepidoptera + vist_non_bee_hymenoptera +
vist_other_flies + vist_other_wild_bees + vist_others + vist_syrphids
) %>%
select(new_study_id,new_site_id,vist_beetles,vist_bumblebees,vist_honeybees, vist_humbleflies,
vist_lepidoptera,vist_non_bee_hymenoptera,vist_other_flies,
vist_other_wild_bees,vist_others,vist_syrphids,vist_total
)
data.site <- data.site %>% left_join(visit_aux,by=c("new_study_id","new_site_id"))
data.site <- data.site %>% left_join(sampling,by=c("new_study_id","new_site_id"))
field_level_data <- tibble(
study_id = data.site$new_study_id,
site_id = data.site$new_site_id,
crop = data.site$crop,
variety = data.site$variety,
management = data.site$management,
country = data.site$country,
latitude = data.site$latitude,
longitude = data.site$longitude,
X_UTM=NA,
Y_UTM=NA,
zone_UTM=NA,
sampling_start_month = data.site$sampling_start_month,
sampling_end_month = data.site$sampling_end_month,
sampling_year = data.site$sampling_year,
field_size = data.site$field_size,
yield=data.site$yield,
yield_units=data.site$yield_units,
yield2=data.site$yield2,
yield2_units=data.site$yield2_units,
yield_treatments_no_pollinators=data.site$yield_treatments_no_pollinators,
yield_treatments_pollen_supplement=data.site$yield_treatments_pollen_supplement,
yield_treatments_no_pollinators2=data.site$yield_treatments_no_pollinators2,
yield_treatments_pollen_supplement2=data.site$yield_treatments_pollen_supplement2,
fruits_per_plant=data.site$mean_fruits_per_plant,
fruit_weight= data.site$fruit_weight,
plant_density=data.site$plant_density,
seeds_per_fruit=data.site$seeds_per_fruit,
seeds_per_plant=data.site$seeds_per_plant,
seed_weight=data.site$seed_weight,
observed_pollinator_richness=data.site$observed_pollinator_richness.y,
other_pollinator_richness=data.site$other_pollinator_richness.y,
other_richness_estimator_method=data.site$other_richness_estimator_method.y,
richness_restriction = data.site$richness_restriction.y,
abundance = data.site$total,
ab_honeybee = data.site$honeybees,
ab_bombus = data.site$bumblebees,
ab_wildbees = data.site$other_wild_bees,
ab_syrphids = data.site$syrphids,
ab_humbleflies= data.site$humbleflies,
ab_other_flies= data.site$other_flies,
ab_beetles=data.site$beetles,
ab_lepidoptera=data.site$lepidoptera,
ab_nonbee_hymenoptera=data.site$non_bee_hymenoptera,
ab_others = data.site$other,
total_sampled_area = data.site$area,
total_sampled_time = data.site$time,
visitation_rate_units = NA,#"visits per hour",
visitation_rate = NA,#data.site$vist_total,
visit_honeybee = NA,#data.site$vist_honeybees,
visit_bombus = NA,#data.site$vist_bumblebees,
visit_wildbees = NA,#data.site$vist_other_wild_bees,
visit_syrphids = NA,#data.site$vist_syrphids,
visit_humbleflies = NA,#data.site$vist_humbleflies,
visit_other_flies = NA,#data.site$vist_other_flies,
visit_beetles = NA,#data.site$vist_beetles,
visit_lepidoptera = NA,#data.site$vist_lepidoptera,
visit_nonbee_hymenoptera = NA,#data.site$vist_non_bee_hymenoptera,
visit_others = NA,#data.site$vist_others,
Publication = data.site$Publication,
Credit = data.site$Credit,
Email_contact = data.site$email
)
field_level_data_Abelmoschus <- field_level_data %>%
filter(study_id=="Finbarr_G_Horgan_Abelmoschus_esculentus_Philippines_2015")
field_level_data_Cucumis <- field_level_data %>%
filter(study_id=="Finbarr_G_Horgan_Cucumis_sativus_Philippines_2015")
field_level_data_Lagenaria <- field_level_data %>%
filter(study_id=="Finbarr_G_Horgan_Lagenaria_siceraria_Philippines_2015")
field_level_data_Luffa <- field_level_data %>%
filter(study_id=="Finbarr_G_Horgan_Luffa_acutangula_Philippines_2015")
field_level_data_Momordica <- field_level_data %>%
filter(study_id=="Finbarr_G_Horgan_Momordica_charantia_Philippines_2015")
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data_Abelmoschus,
"field_level_data_Finbarr_G_Horgan_Abelmoschus_esculentus_Philippines_2015.csv")
write_csv(field_level_data_Cucumis,
"field_level_data_Finbarr_G_Horgan_Cucumis_sativus_Philippines_2015.csv")
write_csv(field_level_data_Lagenaria,
"field_level_data_Finbarr_G_Horgan_Lagenaria_siceraria_Philippines_2015.csv")
write_csv(field_level_data_Luffa,
"field_level_data_Finbarr_G_Horgan_Luffa_acutangula_Philippines_2015.csv")
write_csv(field_level_data_Momordica,
"field_level_data_Finbarr_G_Horgan_Momordica_charantia_Philippines_2015.csv")
setwd(dir_ini)
