total_sampled_time=data.site_i_mod$total_sampled_time,
visitation_rate_units=data.site_i_mod$visitation_rate_units,
visitation_rate=data.site_i_mod$visitation_rate,
visit_honeybee=data.site_i_mod$visit_honeybee,
visit_bombus=data.site_i_mod$visit_bombus,
visit_wildbees=data.site_i_mod$visit_wildbees,
visit_syrphids=data.site_i_mod$visit_syrphids,
visit_humbleflies=data.site_i_mod$visit_humbleflies,
visit_other_flies=data.site_i_mod$visit_other_flies,
visit_beetles=data.site_i_mod$visit_beetles,
visit_lepidoptera=data.site_i_mod$visit_lepidoptera,
visit_nonbee_hymenoptera=data.site_i_mod$visit_nonbee_hymenoptera,
visit_others=data.site_i_mod$visit_others,
Publication=data.site_i_mod$Publication,
Credit=data.site_i_mod$Credit,
Email_contact=data.site_i_mod$email
)
field_level_data_i <- tibble(
study_id=data.site_i_mod$study_id,
site_id=data.site_i_mod$site_id,
crop=data.site_i_mod$crop,
variety=data.site_i_mod$variety,
management=data.site_i_mod$management,
country=data.site_i_mod$country,
latitude=data.site_i_mod$latitude,
longitude=data.site_i_mod$longitude,
X_UTM=NA,
Y_UTM=NA,
zone_UTM=NA,
sampling_start_month=data.site_i_mod$sampling_start_month,
sampling_end_month=data.site_i_mod$sampling_end_month,
sampling_year=data.site_i_mod$sampling_year,
field_size=data.site_i_mod$field_size,
yield=data.site_i_mod$yield,
yield_units=data.site_i_mod$yield_units,
yield2=data.site_i_mod$yield2,
yield2_units=data.site_i_mod$yield2_units,
yield_treatments_no_pollinators=data.site_i_mod$yield_treatments_no_pollinators,
yield_treatments_pollen_supplement=data.site_i_mod$yield_treatments_pollen_supplement,
yield_treatments_no_pollinators2=data.site_i_mod$yield_treatments_no_pollinators2,
yield_treatments_pollen_supplement2=data.site_i_mod$yield_treatments_pollen_supplement2,
fruits_per_plant=data.site_i_mod$mean_fruits_per_plant,
fruit_weight=data.site_i_mod$fruit_weight,
plant_density=data.site_i_mod$plant_density,
seeds_per_fruit=data.site_i_mod$seeds_per_fruit,
seeds_per_plant=data.site_i_mod$seeds_per_plant,
seed_weight=data.site_i_mod$seed_weight,
observed_pollinator_richness=data.site_i_mod$observed_pollinator_richness,
other_pollinator_richness=data.site_i_mod$other_pollinator_richness,
other_richness_estimator_method=data.site_i_mod$other_richness_estimator_method,
richness_restriction=data.site_i_mod$richness_restriction,
abundance=data.site_i_mod$abundance,
ab_honeybee=data.site_i_mod$ab_honeybee,
ab_bombus=data.site_i_mod$ab_bombus,
ab_wildbees=data.site_i_mod$ab_wildbees,
ab_syrphids=data.site_i_mod$ab_syrphids,
ab_humbleflies=data.site_i_mod$ab_humbleflies,
ab_other_flies=data.site_i_mod$ab_other_flies,
ab_beetles=data.site_i_mod$ab_beetles,
ab_lepidoptera=data.site_i_mod$ab_lepidoptera,
ab_nonbee_hymenoptera=data.site_i_mod$ab_nonbee_hymenoptera,
ab_others=data.site_i_mod$ab_others,
total_sampled_area=data.site_i_mod$total_sampled_area,
total_sampled_time=data.site_i_mod$total_sampled_time,
visitation_rate_units=data.site_i_mod$visitation_rate_units,
visitation_rate=data.site_i_mod$visitation_rate,
visit_honeybee=data.site_i_mod$visit_honeybee,
visit_bombus=data.site_i_mod$visit_bombus,
visit_wildbees=data.site_i_mod$visit_wildbees,
visit_syrphids=data.site_i_mod$visit_syrphids,
visit_humbleflies=data.site_i_mod$visit_humbleflies,
visit_other_flies=data.site_i_mod$visit_other_flies,
visit_beetles=data.site_i_mod$visit_beetles,
visit_lepidoptera=data.site_i_mod$visit_lepidoptera,
visit_nonbee_hymenoptera=data.site_i_mod$visit_nonbee_hymenoptera,
visit_others=data.site_i_mod$visit_others,
Publication=data.site_i_mod$Publication,
Credit=data.site_i_mod$Credit,
Email_contact=data.site_i_mod$email
)
View(field_level_data_i)
field_level_data_i <- tibble(
study_id=data.site_i_mod$study_id,
site_id=data.site_i_mod$site_id,
crop=data.site_i_mod$crop,
variety=data.site_i_mod$variety,
management=data.site_i_mod$management,
country=data.site_i_mod$country,
latitude=data.site_i_mod$latitude,
longitude=data.site_i_mod$longitude,
X_UTM=NA,
Y_UTM=NA,
zone_UTM=NA,
sampling_start_month=data.site_i_mod$sampling_start_month,
sampling_end_month=data.site_i_mod$sampling_end_month,
sampling_year=data.site_i_mod$sampling_year,
field_size=data.site_i_mod$field_size,
yield=data.site_i_mod$yield,
yield_units=data.site_i_mod$yield_units,
yield2=data.site_i_mod$yield2,
yield2_units=data.site_i_mod$yield2_units,
yield_treatments_no_pollinators=data.site_i_mod$yield_treatments_no_pollinators,
yield_treatments_pollen_supplement=data.site_i_mod$yield_treatments_pollen_supplement,
yield_treatments_no_pollinators2=data.site_i_mod$yield_treatments_no_pollinators2,
yield_treatments_pollen_supplement2=data.site_i_mod$yield_treatments_pollen_supplement2,
fruits_per_plant=data.site_i_mod$mean_fruits_per_plant,
fruit_weight=data.site_i_mod$fruit_weight,
plant_density=data.site_i_mod$plant_density,
seeds_per_fruit=data.site_i_mod$seeds_per_fruit,
seeds_per_plant=data.site_i_mod$seeds_per_plant,
seed_weight=data.site_i_mod$seed_weight,
observed_pollinator_richness=data.site_i_mod$observed_pollinator_richness,
other_pollinator_richness=data.site_i_mod$other_pollinator_richness,
other_richness_estimator_method=data.site_i_mod$other_richness_estimator_method,
richness_restriction=data.site_i_mod$richness_restriction,
abundance=data.site_i_mod$abundance,
ab_honeybee=data.site_i_mod$ab_honeybee,
ab_bombus=data.site_i_mod$ab_bombus,
ab_wildbees=data.site_i_mod$ab_wildbees,
ab_syrphids=data.site_i_mod$ab_syrphids,
ab_humbleflies=data.site_i_mod$ab_humbleflies,
ab_other_flies=data.site_i_mod$ab_other_flies,
ab_beetles=data.site_i_mod$ab_beetles,
ab_lepidoptera=data.site_i_mod$ab_lepidoptera,
ab_nonbee_hymenoptera=data.site_i_mod$ab_nonbee_hymenoptera,
ab_others=data.site_i_mod$ab_others,
total_sampled_area=data.site_i_mod$total_sampled_area,
total_sampled_time=data.site_i_mod$total_sampled_time,
visitation_rate_units=data.site_i_mod$visitation_rate_units,
visitation_rate=data.site_i_mod$visitation_rate,
visit_honeybee=data.site_i_mod$visit_honeybee,
visit_bombus=data.site_i_mod$visit_bombus,
visit_wildbees=data.site_i_mod$visit_wildbees,
visit_syrphids=data.site_i_mod$visit_syrphids,
visit_humbleflies=data.site_i_mod$visit_humbleflies,
visit_other_flies=data.site_i_mod$visit_other_flies,
visit_beetles=data.site_i_mod$visit_beetles,
visit_lepidoptera=data.site_i_mod$visit_lepidoptera,
visit_nonbee_hymenoptera=data.site_i_mod$visit_nonbee_hymenoptera,
visit_others=data.site_i_mod$visit_others,
Publication=data.site_i_mod$Publication,
Credit=data.site_i_mod$Credit,
Email_contact=data.site_i_mod$email
)
field_level_data_i <- tibble(
study_id=data.site_i_mod$study_id,
site_id=data.site_i_mod$site_id,
crop=data.site_i_mod$crop,
variety=data.site_i_mod$variety,
management=data.site_i_mod$management,
country=data.site_i_mod$country,
latitude=data.site_i_mod$latitude,
longitude=data.site_i_mod$longitude,
X_UTM=NA,
Y_UTM=NA,
zone_UTM=NA,
sampling_start_month=data.site_i_mod$sampling_start_month,
sampling_end_month=data.site_i_mod$sampling_end_month,
sampling_year=data.site_i_mod$sampling_year,
field_size=data.site_i_mod$field_size,
yield=data.site_i_mod$yield,
yield_units=data.site_i_mod$yield_units,
yield2=data.site_i_mod$yield2,
yield2_units=data.site_i_mod$yield2_units,
yield_treatments_no_pollinators=data.site_i_mod$yield_treatments_no_pollinators,
yield_treatments_pollen_supplement=data.site_i_mod$yield_treatments_pollen_supplement,
yield_treatments_no_pollinators2=data.site_i_mod$yield_treatments_no_pollinators2,
yield_treatments_pollen_supplement2=data.site_i_mod$yield_treatments_pollen_supplement2,
fruits_per_plant=data.site_i_mod$fruits_per_plant,
fruit_weight=data.site_i_mod$fruit_weight,
plant_density=data.site_i_mod$plant_density,
seeds_per_fruit=data.site_i_mod$seeds_per_fruit,
seeds_per_plant=data.site_i_mod$seeds_per_plant,
seed_weight=data.site_i_mod$seed_weight,
observed_pollinator_richness=data.site_i_mod$observed_pollinator_richness,
other_pollinator_richness=data.site_i_mod$other_pollinator_richness,
other_richness_estimator_method=data.site_i_mod$other_richness_estimator_method,
richness_restriction=data.site_i_mod$richness_restriction,
abundance=data.site_i_mod$abundance,
ab_honeybee=data.site_i_mod$ab_honeybee,
ab_bombus=data.site_i_mod$ab_bombus,
ab_wildbees=data.site_i_mod$ab_wildbees,
ab_syrphids=data.site_i_mod$ab_syrphids,
ab_humbleflies=data.site_i_mod$ab_humbleflies,
ab_other_flies=data.site_i_mod$ab_other_flies,
ab_beetles=data.site_i_mod$ab_beetles,
ab_lepidoptera=data.site_i_mod$ab_lepidoptera,
ab_nonbee_hymenoptera=data.site_i_mod$ab_nonbee_hymenoptera,
ab_others=data.site_i_mod$ab_others,
total_sampled_area=data.site_i_mod$total_sampled_area,
total_sampled_time=data.site_i_mod$total_sampled_time,
visitation_rate_units=data.site_i_mod$visitation_rate_units,
visitation_rate=data.site_i_mod$visitation_rate,
visit_honeybee=data.site_i_mod$visit_honeybee,
visit_bombus=data.site_i_mod$visit_bombus,
visit_wildbees=data.site_i_mod$visit_wildbees,
visit_syrphids=data.site_i_mod$visit_syrphids,
visit_humbleflies=data.site_i_mod$visit_humbleflies,
visit_other_flies=data.site_i_mod$visit_other_flies,
visit_beetles=data.site_i_mod$visit_beetles,
visit_lepidoptera=data.site_i_mod$visit_lepidoptera,
visit_nonbee_hymenoptera=data.site_i_mod$visit_nonbee_hymenoptera,
visit_others=data.site_i_mod$visit_others,
Publication=data.site_i_mod$Publication,
Credit=data.site_i_mod$Credit,
Email_contact=data.site_i_mod$Email_contact
)
View(data.site_i_mod)
row_avo_5_2016$study_id[i]
data.site_i <- data.site_new %>% filter(study_id==row_avo_5_2016$study_id[i],
crop==row_avo_5_2016$crop[i],
country==row_avo_5_2016$country[i],
sampling_year==row_avo_5_2016$sampling_year[i])
data.insect_i <- data.insect %>% filter(study_id==row_avo_5_2016$study_id[i])
abundance_aux <- data.insect_i %>% group_by(site_id,guild) %>%
summarise(total_guild=sum(abundance)) %>% spread(guild,total_guild)
abundance_aux[is.na(abundance_aux)] <- 0
abundance_aux$total <- rowSums(abundance_aux[,c(2:ncol(abundance_aux))])
# Add missing guilds
guilds <- c("honeybees", "bumblebees", "other_wild_bees", "syrphids", "humbleflies",
"other_flies", "beetles", "non_bee_hymenoptera", "lepidoptera", "others")
for (j in 1:length(guilds)){
if (!guilds[j] %in% names(abundance_aux)){
abundance_aux$aux <- 0
names(abundance_aux)[names(abundance_aux)=="aux"] <- guilds[j]
}
}
abundance_aux <- abundance_aux %>%
rename(abundance = total, ab_bombus = bumblebees,
ab_honeybee = honeybees, ab_wildbees = other_wild_bees,
ab_syrphids = syrphids,	ab_humbleflies = humbleflies,
ab_other_flies = other_flies,	ab_beetles = beetles,
ab_lepidoptera = lepidoptera,	ab_nonbee_hymenoptera = non_bee_hymenoptera,
ab_others = others)
col_order <- c("site_id","ab_honeybee","ab_bombus","ab_wildbees","ab_humbleflies",
"ab_beetles","ab_nonbee_hymenoptera", "ab_other_flies",
"ab_syrphids", "ab_lepidoptera","ab_others","abundance")
abundance_aux <- abundance_aux[,col_order]
data.site_i_mod <- data.site_i %>% select(-abundance, -ab_bombus, -ab_honeybee, -ab_wildbees,
-ab_syrphids,-ab_humbleflies, -ab_other_flies,-ab_beetles,-ab_lepidoptera,
-ab_nonbee_hymenoptera,-ab_others)%>%
left_join(abundance_aux, by = "site_id")
richness_aux <- data.insect_i %>% group_by(site_id,pollinator) %>%
summarise(total_pollinator=sum(abundance)) %>% spread(pollinator,total_pollinator)
richness_aux[is.na(richness_aux)] <- 0
richness_aux$r_obser <-  0
richness_aux$r_chao <-  0
for (j in 1:nrow(richness_aux)) {
x <- as.numeric(richness_aux[j,2:(ncol(richness_aux)-2)])
chao  <-  ChaoRichness(x, datatype = "abundance", conf = 0.95)
richness_aux$r_obser[j] <-  chao$Observed
richness_aux$r_chao[j] <-  chao$Estimator
}
abundance_non_bee <- rowSums(abundance_aux[,5:11],na.rm = TRUE)
if (sum(abundance_non_bee)>0){richness_restriction=NA}else{richness_restriction="Only bees"}
richness_aux <- richness_aux %>% select(site_id,r_obser,r_chao)
richness_aux <- richness_aux %>% rename(observed_pollinator_richness=r_obser,
other_pollinator_richness=r_chao) %>%
mutate(other_richness_estimator_method="Chao1",richness_restriction=richness_restriction)
data.site_i_mod <- data.site_i_mod %>%
select(-observed_pollinator_richness,-other_pollinator_richness,-other_richness_estimator_method,
-richness_restriction)%>%
left_join(richness_aux, by = "site_id")
sampling_aux <- data.insect_i %>% select(site_id,total_sampled_area,total_sampled_time) %>%
mutate(total_sampled_area=as.numeric(total_sampled_area)) %>%
group_by(site_id) %>% summarise_all(mean,na.rm=T)
data.site_i_mod <- data.site_i_mod %>%
select(-total_sampled_area,-total_sampled_time)%>%
left_join(sampling_aux, by = "site_id")
field_level_data_i <- tibble(
study_id=data.site_i_mod$study_id,
site_id=data.site_i_mod$site_id,
crop=data.site_i_mod$crop,
variety=data.site_i_mod$variety,
management=data.site_i_mod$management,
country=data.site_i_mod$country,
latitude=data.site_i_mod$latitude,
longitude=data.site_i_mod$longitude,
X_UTM=NA,
Y_UTM=NA,
zone_UTM=NA,
sampling_start_month=data.site_i_mod$sampling_start_month,
sampling_end_month=data.site_i_mod$sampling_end_month,
sampling_year=data.site_i_mod$sampling_year,
field_size=data.site_i_mod$field_size,
yield=data.site_i_mod$yield,
yield_units=data.site_i_mod$yield_units,
yield2=data.site_i_mod$yield2,
yield2_units=data.site_i_mod$yield2_units,
yield_treatments_no_pollinators=data.site_i_mod$yield_treatments_no_pollinators,
yield_treatments_pollen_supplement=data.site_i_mod$yield_treatments_pollen_supplement,
yield_treatments_no_pollinators2=data.site_i_mod$yield_treatments_no_pollinators2,
yield_treatments_pollen_supplement2=data.site_i_mod$yield_treatments_pollen_supplement2,
fruits_per_plant=data.site_i_mod$fruits_per_plant,
fruit_weight=data.site_i_mod$fruit_weight,
plant_density=data.site_i_mod$plant_density,
seeds_per_fruit=data.site_i_mod$seeds_per_fruit,
seeds_per_plant=data.site_i_mod$seeds_per_plant,
seed_weight=data.site_i_mod$seed_weight,
observed_pollinator_richness=data.site_i_mod$observed_pollinator_richness,
other_pollinator_richness=data.site_i_mod$other_pollinator_richness,
other_richness_estimator_method=data.site_i_mod$other_richness_estimator_method,
richness_restriction=data.site_i_mod$richness_restriction,
abundance=data.site_i_mod$abundance,
ab_honeybee=data.site_i_mod$ab_honeybee,
ab_bombus=data.site_i_mod$ab_bombus,
ab_wildbees=data.site_i_mod$ab_wildbees,
ab_syrphids=data.site_i_mod$ab_syrphids,
ab_humbleflies=data.site_i_mod$ab_humbleflies,
ab_other_flies=data.site_i_mod$ab_other_flies,
ab_beetles=data.site_i_mod$ab_beetles,
ab_lepidoptera=data.site_i_mod$ab_lepidoptera,
ab_nonbee_hymenoptera=data.site_i_mod$ab_nonbee_hymenoptera,
ab_others=data.site_i_mod$ab_others,
total_sampled_area=data.site_i_mod$total_sampled_area,
total_sampled_time=data.site_i_mod$total_sampled_time,
visitation_rate_units=data.site_i_mod$visitation_rate_units,
visitation_rate=data.site_i_mod$visitation_rate,
visit_honeybee=data.site_i_mod$visit_honeybee,
visit_bombus=data.site_i_mod$visit_bombus,
visit_wildbees=data.site_i_mod$visit_wildbees,
visit_syrphids=data.site_i_mod$visit_syrphids,
visit_humbleflies=data.site_i_mod$visit_humbleflies,
visit_other_flies=data.site_i_mod$visit_other_flies,
visit_beetles=data.site_i_mod$visit_beetles,
visit_lepidoptera=data.site_i_mod$visit_lepidoptera,
visit_nonbee_hymenoptera=data.site_i_mod$visit_nonbee_hymenoptera,
visit_others=data.site_i_mod$visit_others,
Publication=data.site_i_mod$Publication,
Credit=data.site_i_mod$Credit,
Email_contact=data.site_i_mod$Email_contact
)
View(field_level_data_i)
row_avo_5_2016$study_id[i]
extrac_abundance_richness <- function(row_avo_5_2016,data.site_new){
data.site_i <- data.site_new %>% filter(study_id==row_avo_5_2016$study_id[1],
site_id==row_avo_5_2016$site_id[1],
crop==row_avo_5_2016$crop[1],
country==row_avo_5_2016$country[1],
sampling_year==row_avo_5_2016$sampling_year[1])
data.insect_i <- data.insect %>% filter(study_id==row_avo_5_2016$study_id[1])
# Extract abundance
abundance_aux <- data.insect_i %>% group_by(site_id,guild) %>%
summarise(total_guild=sum(abundance)) %>% spread(guild,total_guild)
abundance_aux[is.na(abundance_aux)] <- 0
abundance_aux$total <- rowSums(abundance_aux[,c(2:ncol(abundance_aux))])
# Add missing guilds
guilds <- c("honeybees", "bumblebees", "other_wild_bees", "syrphids", "humbleflies",
"other_flies", "beetles", "non_bee_hymenoptera", "lepidoptera", "others")
for (j in 1:length(guilds)){
if (!guilds[j] %in% names(abundance_aux)){
abundance_aux$aux <- 0
names(abundance_aux)[names(abundance_aux)=="aux"] <- guilds[j]
}
}
abundance_aux <- abundance_aux %>%
rename(abundance = total, ab_bombus = bumblebees,
ab_honeybee = honeybees, ab_wildbees = other_wild_bees,
ab_syrphids = syrphids,	ab_humbleflies = humbleflies,
ab_other_flies = other_flies,	ab_beetles = beetles,
ab_lepidoptera = lepidoptera,	ab_nonbee_hymenoptera = non_bee_hymenoptera,
ab_others = others)
col_order <- c("site_id","ab_honeybee","ab_bombus","ab_wildbees","ab_humbleflies",
"ab_beetles","ab_nonbee_hymenoptera", "ab_other_flies",
"ab_syrphids", "ab_lepidoptera","ab_others","abundance")
abundance_aux <- abundance_aux[,col_order]
data.site_i_mod <- data.site_i %>% select(-abundance, -ab_bombus, -ab_honeybee, -ab_wildbees,
-ab_syrphids,-ab_humbleflies, -ab_other_flies,-ab_beetles,-ab_lepidoptera,
-ab_nonbee_hymenoptera,-ab_others)%>%
left_join(abundance_aux, by = "site_id")
# Extract richness
richness_aux <- data.insect_i %>% group_by(site_id,pollinator) %>%
summarise(total_pollinator=sum(abundance)) %>% spread(pollinator,total_pollinator)
richness_aux[is.na(richness_aux)] <- 0
richness_aux$r_obser <-  0
richness_aux$r_chao <-  0
for (j in 1:nrow(richness_aux)) {
x <- as.numeric(richness_aux[j,2:(ncol(richness_aux)-2)])
chao  <-  ChaoRichness(x, datatype = "abundance", conf = 0.95)
richness_aux$r_obser[j] <-  chao$Observed
richness_aux$r_chao[j] <-  chao$Estimator
}
#richness_aux <- richness_aux %>% select(site_id, pollinator_richness=r_chao) %>%
#  mutate(richness_estimator_method="Chao1")
abundance_non_bee <- rowSums(abundance_aux[,5:11],na.rm = TRUE)
if (sum(abundance_non_bee)>0){richness_restriction=NA}else{richness_restriction="Only bees"}
richness_aux <- richness_aux %>% select(site_id,r_obser,r_chao)
richness_aux <- richness_aux %>% rename(observed_pollinator_richness=r_obser,
other_pollinator_richness=r_chao) %>%
mutate(other_richness_estimator_method="Chao1",richness_restriction=richness_restriction)
data.site_i_mod <- data.site_i_mod %>%
select(-observed_pollinator_richness,-other_pollinator_richness,-other_richness_estimator_method,
-richness_restriction)%>%
left_join(richness_aux, by = "site_id")
# Extract total sampled time and area
sampling_aux <- data.insect_i %>% select(site_id,total_sampled_area,total_sampled_time) %>%
mutate(total_sampled_area=as.numeric(total_sampled_area)) %>%
group_by(site_id) %>% summarise_all(mean,na.rm=T)
data.site_i_mod <- data.site_i_mod %>%
select(-total_sampled_area,-total_sampled_time)%>%
left_join(sampling_aux, by = "site_id")
###############################################################
# FIELD LEVEL DATA
###############################################################
field_level_data_i <- tibble(
study_id=data.site_i_mod$study_id,
site_id=data.site_i_mod$site_id,
crop=data.site_i_mod$crop,
variety=data.site_i_mod$variety,
management=data.site_i_mod$management,
country=data.site_i_mod$country,
latitude=data.site_i_mod$latitude,
longitude=data.site_i_mod$longitude,
X_UTM=NA,
Y_UTM=NA,
zone_UTM=NA,
sampling_start_month=data.site_i_mod$sampling_start_month,
sampling_end_month=data.site_i_mod$sampling_end_month,
sampling_year=data.site_i_mod$sampling_year,
field_size=data.site_i_mod$field_size,
yield=data.site_i_mod$yield,
yield_units=data.site_i_mod$yield_units,
yield2=data.site_i_mod$yield2,
yield2_units=data.site_i_mod$yield2_units,
yield_treatments_no_pollinators=data.site_i_mod$yield_treatments_no_pollinators,
yield_treatments_pollen_supplement=data.site_i_mod$yield_treatments_pollen_supplement,
yield_treatments_no_pollinators2=data.site_i_mod$yield_treatments_no_pollinators2,
yield_treatments_pollen_supplement2=data.site_i_mod$yield_treatments_pollen_supplement2,
fruits_per_plant=data.site_i_mod$fruits_per_plant,
fruit_weight=data.site_i_mod$fruit_weight,
plant_density=data.site_i_mod$plant_density,
seeds_per_fruit=data.site_i_mod$seeds_per_fruit,
seeds_per_plant=data.site_i_mod$seeds_per_plant,
seed_weight=data.site_i_mod$seed_weight,
observed_pollinator_richness=data.site_i_mod$observed_pollinator_richness,
other_pollinator_richness=data.site_i_mod$other_pollinator_richness,
other_richness_estimator_method=data.site_i_mod$other_richness_estimator_method,
richness_restriction=data.site_i_mod$richness_restriction,
abundance=data.site_i_mod$abundance,
ab_honeybee=data.site_i_mod$ab_honeybee,
ab_bombus=data.site_i_mod$ab_bombus,
ab_wildbees=data.site_i_mod$ab_wildbees,
ab_syrphids=data.site_i_mod$ab_syrphids,
ab_humbleflies=data.site_i_mod$ab_humbleflies,
ab_other_flies=data.site_i_mod$ab_other_flies,
ab_beetles=data.site_i_mod$ab_beetles,
ab_lepidoptera=data.site_i_mod$ab_lepidoptera,
ab_nonbee_hymenoptera=data.site_i_mod$ab_nonbee_hymenoptera,
ab_others=data.site_i_mod$ab_others,
total_sampled_area=data.site_i_mod$total_sampled_area,
total_sampled_time=data.site_i_mod$total_sampled_time,
visitation_rate_units=data.site_i_mod$visitation_rate_units,
visitation_rate=data.site_i_mod$visitation_rate,
visit_honeybee=data.site_i_mod$visit_honeybee,
visit_bombus=data.site_i_mod$visit_bombus,
visit_wildbees=data.site_i_mod$visit_wildbees,
visit_syrphids=data.site_i_mod$visit_syrphids,
visit_humbleflies=data.site_i_mod$visit_humbleflies,
visit_other_flies=data.site_i_mod$visit_other_flies,
visit_beetles=data.site_i_mod$visit_beetles,
visit_lepidoptera=data.site_i_mod$visit_lepidoptera,
visit_nonbee_hymenoptera=data.site_i_mod$visit_nonbee_hymenoptera,
visit_others=data.site_i_mod$visit_others,
Publication=data.site_i_mod$Publication,
Credit=data.site_i_mod$Credit,
Email_contact=data.site_i_mod$Email_contact
)
return(field_level_data_i)
}
field_level_data_avo_5_2016 <- extrac_abundance_richness(row_avo_5_2016,data.site_new)
View(field_level_data_avo_5_2016)
field_level_data <- bind_rows(data.site,
field_level_data_avo_5_2016,
field_level_data_avo_5_2017) %>%
arrange(sampling_year,site_id)
field_level_data_avo_5_2016 <- extrac_abundance_richness(row_avo_5_2016,data.site_new)
field_level_data_avo_5_2017 <- extrac_abundance_richness(row_avo_5_2017,data.site_new)
field_level_data <- bind_rows(data.site,
field_level_data_avo_5_2016,
field_level_data_avo_5_2017) %>%
arrange(sampling_year,site_id)
View(field_level_data)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data,"field_level_data_Bryony_Willcox_several_crops_Australia_several_years.csv")
setwd(dir_ini)
field_level_data <- read_csv("field_level_data_Bryony_Willcox_several_crops_Australia_several_years_BKW.csv")
library(tidyverse)
dir_ini <- getwd()
field_level_data <- read_csv("field_level_data_Bryony_Willcox_several_crops_Australia_several_years_BKW.csv")
View(field_level_data)
field_level_data <- read_csv("Copy of field_level_data_Bryony_Willcox_several_crops_Australia_several_years_BW.csv")
View(field_level_data)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data,"field_level_data_Bryony_Willcox_several_crops_Australia_several_years.csv")
setwd(dir_ini)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data,"field_level_data_Bryony_Willcox_several_crops_Australia_several_years.csv")
setwd(dir_ini)
library(tidyverse)
dir_ini <- getwd()
field_level_data <- read_csv("Copy of field_level_data_Bryony_Willcox_several_crops_Australia_several_years_BW.csv")
field_level_data$study_id[field_level_data$study_id=="Bryony_Willcox_Mangifera_indica_Australia_2016"] <- "Bryony_Willcox_Mangifera_indica_Australia_2016_2"
insect_sampling <-
read_csv("NEW_insect_sampling_Bryony_Willcox_several_crops_Australia_several_years.csv")
insect_sampling$study_id[insect_sampling$study_id=="Bryony_Willcox_Mangifera_indica_Australia_2016"] <- "Bryony_Willcox_Mangifera_indica_Australia_2016_2"
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data,"field_level_data_Bryony_Willcox_several_crops_Australia_several_years.csv")
write_csv(insect_sampling,"insect_sampling_Bryony_Willcox_several_crops_Australia_several_years.csv")
write_csv(field_level_data,"field_level_data_Bryony_Willcox_several_crops_Australia_several_years.csv")
write_csv(field_level_data,"field_level_data_Bryony_Willcox_several_crops_Australia_several_years.csv")
write_csv(insect_sampling,"insect_sampling_Bryony_Willcox_several_crops_Australia_several_years.csv")
setwd(dir_ini)
