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$seed_weight,
observed_pollinator_richness=NA,
other_pollinator_richness=NA,
other_richness_estimator_method=NA,
richness_restriction = NA,
abundance = NA,
ab_honeybee = NA,
ab_bombus = NA,
ab_wildbees = NA,
ab_syrphids = NA,
ab_humbleflies= NA,
ab_other_flies= NA,
ab_beetles= NA,
ab_lepidoptera=NA,
ab_nonbee_hymenoptera=NA,
ab_others = NA,
total_sampled_area = NA,
total_sampled_time = NA,
visitation_rate_units = data.site$visitation_rate_units,
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$vist_others,
Publication = "10.1098/rspb.2020.0922",
Credit = "James Reilly and all the co-authors in the referred publication",
Email_contact = "jreilly45@gmail.com/rwinfree@rutgers.edu/isaacsr@msu.edu"
)
View(field_level_data)
data.site$latitude
data.site$longitude
View(field_level_data)
View(coordinates)
View(field_level_data)
field_level_data$study_id %>% unique()
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_James_Reilly_Prunus_avium_USA_2013-14.csv")
setwd(dir_ini)
# load libraries
library(tidyverse)
dir_ini <- getwd()
data.site_mi <- read_csv("datasets/tart_cherry_mi_dataset.csv")
data.site_pa <- read_csv("datasets/tart_cherry_pa_dataset.csv") #%>% rename(wild_bee=wild_bees)
data.site <- bind_rows(data.site_mi,data.site_pa)
data.site$site_id <- paste0(data.site$crop,"_",
data.site$state,"_",
data.site$site,"_",
data.site$transect)
# Add latitude and longitude
coordinates <- read_csv("datasets/ICP_sites_with_latlong_for_observ.csv") %>%
rename(site=site_id)
data.site$crop_id <- paste0(data.site$crop,"_",
data.site$state)
data.site <- data.site %>% left_join(coordinates,by=c("crop_id","site")) %>%
rename(latitude=lat,longitude=long)
# New study_id
data.site$study_id <- paste0("James_Reilly_Prunus_cerasus_USA_",data.site$year)
# Crop latin name
data.site$crop <- "Prunus cerasus"
data.site$yield <- data.site$number_of_fruit_mean
data.site$yield_units <- "number of fruits"
data.site$yield2 <- data.site$number_fruit_per_flower_mean
data.site$yield2_units <- "number of fruits per_flower"
data.site$yield_treatments_no_pollinators <- NA
data.site$yield_treatments_pollen_supplement <- NA
data.site$yield_treatments_no_pollinators2 <- NA
data.site$yield_treatments_pollen_supplement2 <- NA
data.site$mean_fruits_per_plant <- NA
data.site$fruit_weight <- data.site$fruit_wt_mean
data.site$plant_density <- NA
data.site$seeds_per_fruit <- NA
data.site$seeds_per_plant <- NA
data.site$seed_weight <- NA
##############################
# PREPARE VISITATION RATES
##############################
names(data.site)
data.site$other_wild_bees <- data.site$all_bees - data.site$honey_bee - data.site$bumble_bee # + data.site$blue_orchard_bee
data.site$all_bees==(data.site$other_wild_bees +
data.site$honey_bee +
data.site$bumble_bee)
data.site$visitation_rate_units <- "visits per flower"
data.site <- data.site %>% rowwise() %>%
mutate(vist_total = sum(all_bees,
syrphid,
wasp,
other_insect,
na.rm = T)) %>%
mutate(vist_total = vist_total/number_of_flowers_mean)
data.site$vist_honeybees <- data.site$honey_bee/data.site$number_of_flowers_mean
data.site$vist_bumblebees <- data.site$bumble_bee/data.site$number_of_flowers_mean
data.site$vist_other_wild_bees <- data.site$other_wild_bees/data.site$number_of_flowers_mean
data.site$vist_syrphids <- data.site$syrphid/data.site$number_of_flowers_mean
data.site$vist_humbleflies <- NA
data.site$vist_other_flies <- NA
data.site$vist_beetles <- NA
data.site$vist_lepidoptera <- NA
data.site$vist_non_bee_hymenoptera <- data.site$wasp/data.site$number_of_flowers_mean
# Comment raised by James about Prunus cerasus
# 1) you can put the "other insects" into the "visits_others" category.
# These were apparently not flies, beetles, or wasps.
data.site$vist_others <- data.site$other_insect/data.site$number_of_flowers_mean
field_level_data <- tibble(
study_id = data.site$study_id,
site_id = data.site$site_id,
crop = data.site$crop,
variety = NA,
management = NA,
country = "USA",
latitude = data.site$latitude,
longitude = data.site$longitude,
X_UTM=NA,
Y_UTM=NA,
zone_UTM=NA,
sampling_start_month = NA,
sampling_end_month = NA,
sampling_year = data.site$year,
field_size = NA,
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=NA,
other_pollinator_richness=NA,
other_richness_estimator_method=NA,
richness_restriction = NA,
abundance = NA,
ab_honeybee = NA,
ab_bombus = NA,
ab_wildbees = NA,
ab_syrphids = NA,
ab_humbleflies= NA,
ab_other_flies= NA,
ab_beetles= NA,
ab_lepidoptera=NA,
ab_nonbee_hymenoptera=NA,
ab_others = NA,
total_sampled_area = NA,
total_sampled_time = NA,
visitation_rate_units = data.site$visitation_rate_units,
visitation_rate = data.site$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 = "10.1098/rspb.2020.0922",
Credit = "James Reilly and all the co-authors in the referred publication",
Email_contact = "jreilly45@gmail.com/rwinfree@rutgers.edu/isaacsr@msu.edu"
)
View(field_level_data)
field_level_data$study_id %>% unique()
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_James_Reilly_Prunus_cerasus_USA_2013-14-15.csv")
setwd(dir_ini)
# load libraries
library(tidyverse)
dir_ini <- getwd()
data.site_fl <- read_csv("datasets/blueberry_fl_dataset.csv")
data.site_mi_bc_or <- read_csv("datasets/blueberry_mi_bc_or_dataset.csv") #%>% rename(wild_bee=wild_bees)
data.site <- bind_rows(data.site_fl,data.site_mi_bc_or)
data.site$site_id <- paste0(data.site$crop,"_",
data.site$state,"_",
data.site$site,"_",
data.site$transect)
# Add latitude and longitude
coordinates <- read_csv("datasets/ICP_sites_with_latlong_for_observ.csv") %>%
rename(site=site_id)
data.site$crop_id <- paste0(data.site$crop,"_",
data.site$state)
data.site <- data.site %>% left_join(coordinates,by=c("crop_id","site")) %>%
rename(latitude=lat,longitude=long)
# New study_id
data.site$study_id <- paste0("James_Reilly_Vaccinium_corymbosum_USA_",data.site$year)
# Crop latin name
data.site$crop <- "Vaccinium corymbosum"
data.site$yield <- data.site$mean_berry_wt_open
data.site$yield_units <- "berry weight"
data.site$yield2 <- data.site$fruit_set_open
data.site$yield2_units <- "fruit set"
data.site$yield_treatments_no_pollinators <- data.site$mean_berry_wt_bagged
data.site$yield_treatments_pollen_supplement <- data.site$mean_berry_wt_bagged
data.site$yield_treatments_no_pollinators2 <- data.site$fruit_set_bagged
data.site$yield_treatments_pollen_supplement2 <- data.site$fruit_set_hand
data.site$mean_fruits_per_plant <- NA
data.site$fruit_weight <- data.site$mean_berry_wt_open
data.site$plant_density <- NA
data.site$seeds_per_fruit <- NA
data.site$seeds_per_plant <- NA
data.site$seed_weight <- NA
##############################
# PREPARE VISITATION RATES
##############################
names(data.site)
data.site$other_wild_bees <- round(data.site$all_bees - data.site$honey_bee - data.site$bumble_bee,5) # + data.site$blue_orchard_bee
round(data.site$all_bees,5)==round(data.site$other_wild_bees +
data.site$honey_bee +
data.site$bumble_bee,5) # Row 16 is false
# Checking Row 16
data.site$all_bees[16]
data.site$other_wild_bees[16] + data.site$honey_bee[16] + data.site$bumble_bee[16] #OK
data.site$number_of_flowers_mean <- 1
data.site$visitation_rate_units <- "visits"
data.site <- data.site %>% rowwise() %>%
mutate(vist_total = sum(all_bees,
syrphid,
na.rm = T)) %>%
mutate(vist_total = vist_total/number_of_flowers_mean)
data.site$vist_honeybees <- data.site$honey_bee/data.site$number_of_flowers_mean
data.site$vist_bumblebees <- data.site$bumble_bee/data.site$number_of_flowers_mean
data.site$vist_other_wild_bees <- data.site$other_wild_bees/data.site$number_of_flowers_mean
data.site$vist_syrphids <- data.site$syrphid/data.site$number_of_flowers_mean
data.site$vist_humbleflies <- NA
data.site$vist_other_flies <- NA
data.site$vist_beetles <- NA
data.site$vist_lepidoptera <- NA
data.site$vist_non_bee_hymenoptera <- NA
data.site$vist_others <- NA
field_level_data <- tibble(
study_id = data.site$study_id,
site_id = data.site$site_id,
crop = data.site$crop,
variety = NA,
management = NA,
country = "USA",
latitude = NA,
longitude = NA,latitude = data.site$latitude,
longitude = data.site$longitude,
X_UTM=NA,
Y_UTM=NA,
zone_UTM=NA,
sampling_start_month = NA,
sampling_end_month = NA,
sampling_year = data.site$year,
field_size = NA,
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=NA,
other_pollinator_richness=NA,
other_richness_estimator_method=NA,
richness_restriction = NA,
abundance = NA,
ab_honeybee = NA,
ab_bombus = NA,
ab_wildbees = NA,
ab_syrphids = NA,
ab_humbleflies= NA,
ab_other_flies= NA,
ab_beetles= NA,
ab_lepidoptera=NA,
ab_nonbee_hymenoptera=NA,
ab_others = NA,
total_sampled_area = NA,
total_sampled_time = NA,
visitation_rate_units = data.site$visitation_rate_units,
visitation_rate = data.site$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 = "10.1098/rspb.2020.0922",
Credit = "James Reilly and all the co-authors in the referred publication",
Email_contact = "jreilly45@gmail.com/rwinfree@rutgers.edu/isaacsr@msu.edu"
)
field_level_data <- tibble(
study_id = data.site$study_id,
site_id = data.site$site_id,
crop = data.site$crop,
variety = NA,
management = NA,
country = "USA",
latitude = data.site$latitude,
longitude = data.site$longitude,
X_UTM=NA,
Y_UTM=NA,
zone_UTM=NA,
sampling_start_month = NA,
sampling_end_month = NA,
sampling_year = data.site$year,
field_size = NA,
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=NA,
other_pollinator_richness=NA,
other_richness_estimator_method=NA,
richness_restriction = NA,
abundance = NA,
ab_honeybee = NA,
ab_bombus = NA,
ab_wildbees = NA,
ab_syrphids = NA,
ab_humbleflies= NA,
ab_other_flies= NA,
ab_beetles= NA,
ab_lepidoptera=NA,
ab_nonbee_hymenoptera=NA,
ab_others = NA,
total_sampled_area = NA,
total_sampled_time = NA,
visitation_rate_units = data.site$visitation_rate_units,
visitation_rate = data.site$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 = "10.1098/rspb.2020.0922",
Credit = "James Reilly and all the co-authors in the referred publication",
Email_contact = "jreilly45@gmail.com/rwinfree@rutgers.edu/isaacsr@msu.edu"
)
View(field_level_data)
View(coordinates)
View(data.site_fl)
View(data.site_mi_bc_or)
data.site_mi_bc_or$site[data.site_mi_bc_or$state="mi" & data.site_mi_bc_or$site==14]
data.site_mi_bc_or$site[data.site_mi_bc_or$state=="mi" & data.site_mi_bc_or$site==14]
data.site_fl <- read_csv("datasets/blueberry_fl_dataset.csv")
data.site_mi_bc_or <- read_csv("datasets/blueberry_mi_bc_or_dataset.csv") #%>% rename(wild_bee=wild_bees)
data.site_mi_bc_or$site[data.site_mi_bc_or$state=="mi" & data.site_mi_bc_or$site==14] <- 24
data.site <- bind_rows(data.site_fl,data.site_mi_bc_or)
data.site$site_id <- paste0(data.site$crop,"_",
data.site$state,"_",
data.site$site,"_",
data.site$transect)
# Add latitude and longitude
coordinates <- read_csv("datasets/ICP_sites_with_latlong_for_observ.csv") %>%
rename(site=site_id)
data.site$crop_id <- paste0(data.site$crop,"_",
data.site$state)
data.site <- data.site %>% left_join(coordinates,by=c("crop_id","site")) %>%
rename(latitude=lat,longitude=long)
# New study_id
data.site$study_id <- paste0("James_Reilly_Vaccinium_corymbosum_USA_",data.site$year)
# Crop latin name
data.site$crop <- "Vaccinium corymbosum"
data.site$yield <- data.site$mean_berry_wt_open
data.site$yield_units <- "berry weight"
data.site$yield2 <- data.site$fruit_set_open
data.site$yield2_units <- "fruit set"
data.site$yield_treatments_no_pollinators <- data.site$mean_berry_wt_bagged
data.site$yield_treatments_pollen_supplement <- data.site$mean_berry_wt_bagged
data.site$yield_treatments_no_pollinators2 <- data.site$fruit_set_bagged
data.site$yield_treatments_pollen_supplement2 <- data.site$fruit_set_hand
data.site$mean_fruits_per_plant <- NA
data.site$fruit_weight <- data.site$mean_berry_wt_open
data.site$plant_density <- NA
data.site$seeds_per_fruit <- NA
data.site$seeds_per_plant <- NA
data.site$seed_weight <- NA
##############################
# PREPARE VISITATION RATES
##############################
names(data.site)
data.site$other_wild_bees <- round(data.site$all_bees - data.site$honey_bee - data.site$bumble_bee,5) # + data.site$blue_orchard_bee
round(data.site$all_bees,5)==round(data.site$other_wild_bees +
data.site$honey_bee +
data.site$bumble_bee,5) # Row 16 is false
# Checking Row 16
data.site$all_bees[16]
data.site$other_wild_bees[16] + data.site$honey_bee[16] + data.site$bumble_bee[16] #OK
data.site$number_of_flowers_mean <- 1
data.site$visitation_rate_units <- "visits"
data.site <- data.site %>% rowwise() %>%
mutate(vist_total = sum(all_bees,
syrphid,
na.rm = T)) %>%
mutate(vist_total = vist_total/number_of_flowers_mean)
data.site$vist_honeybees <- data.site$honey_bee/data.site$number_of_flowers_mean
data.site$vist_bumblebees <- data.site$bumble_bee/data.site$number_of_flowers_mean
data.site$vist_other_wild_bees <- data.site$other_wild_bees/data.site$number_of_flowers_mean
data.site$vist_syrphids <- data.site$syrphid/data.site$number_of_flowers_mean
data.site$vist_humbleflies <- NA
data.site$vist_other_flies <- NA
data.site$vist_beetles <- NA
data.site$vist_lepidoptera <- NA
data.site$vist_non_bee_hymenoptera <- NA
data.site$vist_others <- NA
field_level_data <- tibble(
study_id = data.site$study_id,
site_id = data.site$site_id,
crop = data.site$crop,
variety = NA,
management = NA,
country = "USA",
latitude = data.site$latitude,
longitude = data.site$longitude,
X_UTM=NA,
Y_UTM=NA,
zone_UTM=NA,
sampling_start_month = NA,
sampling_end_month = NA,
sampling_year = data.site$year,
field_size = NA,
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=NA,
other_pollinator_richness=NA,
other_richness_estimator_method=NA,
richness_restriction = NA,
abundance = NA,
ab_honeybee = NA,
ab_bombus = NA,
ab_wildbees = NA,
ab_syrphids = NA,
ab_humbleflies= NA,
ab_other_flies= NA,
ab_beetles= NA,
ab_lepidoptera=NA,
ab_nonbee_hymenoptera=NA,
ab_others = NA,
total_sampled_area = NA,
total_sampled_time = NA,
visitation_rate_units = data.site$visitation_rate_units,
visitation_rate = data.site$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 = "10.1098/rspb.2020.0922",
Credit = "James Reilly and all the co-authors in the referred publication",
Email_contact = "jreilly45@gmail.com/rwinfree@rutgers.edu/isaacsr@msu.edu"
)
field_level_data$study_id %>% unique()
View(data.site)
View(field_level_data)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_James_Reilly_Vaccinium_corymbosum_USA_2013-14-15.csv")
setwd(dir_ini)
