visit_wildbees=NA,
visit_syrphids=NA,
visit_humbleflies=NA,
visit_other_flies=NA,
visit_beetles=NA,
visit_lepidoptera=NA,
visit_nonbee_hymenoptera=NA,
visit_others=NA,
Publication=data.site$Publication,
Credit=data.site$Credit,
Email_contact=data.site$email
)
abundance_aux <- data.species_03 %>% #filter(sampling_method=="transect") %>%
group_by(site_id,Guild) %>% count(wt=abundance) %>%
spread(key=Guild, value=n)
names(abundance_aux)
View(insect_sampling)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_Breno_M_Freitas_Gossypium_hirsutum_Brazil_2011.csv")
setwd(dir_ini)
field_level_data <- tibble(
study_id="Breno_M_Freitas_Gossypium_hirsutum_Brazil_2011",
site_id=data.site$site_id,
crop=data.site$crop,
variety=NA,
management=data.site$management,
country=data.site$country,
latitude=NA,
longitude=NA,
X_UTM=data.site$X_UTM,
Y_UTM=data.site$Y_UTM,
zone_UTM=NA,
sampling_start_month=NA,
sampling_end_month=NA,
sampling_year=data.site$sampling_year,
field_size=data.site$field_size,
yield=data.site$yield2,
yield_units=data.site$yield2_units,
yield2=NA,
yield2_units=NA,
yield_treatments_no_pollinators=NA,
yield_treatments_pollen_supplement=NA,
yield_treatments_no_pollinators2=NA,
yield_treatments_pollen_supplement2=NA,
fruits_per_plant=NA,
fruit_weight=NA,
plant_density=NA,
seeds_per_fruit=NA,
seeds_per_plant=NA,
seed_weight=NA,
observed_pollinator_richness=richness_aux$observed_pollinator_richness,
other_pollinator_richness=richness_aux$other_pollinator_richness,
other_richness_estimator_method=richness_aux$other_richness_estimator_method,
richness_restriction = "only other wild bees",
abundance=abundance_aux$total,
ab_honeybee=abundance_aux$honeybees,
ab_bombus=abundance_aux$bumblebees,
ab_wildbees=abundance_aux$other_wild_bees,
ab_syrphids=abundance_aux$syrphids,
ab_humbleflies=abundance_aux$humbleflies,
ab_other_flies=abundance_aux$other_flies,
ab_beetles=abundance_aux$beetles,
ab_lepidoptera=abundance_aux$lepidoptera,
ab_nonbee_hymenoptera=abundance_aux$non_bee_hymenoptera,
ab_others=abundance_aux$other,
total_sampled_area=900,
total_sampled_time=NA,
visitation_rate_units = NA,
visitation_rate=NA,
visit_honeybee=NA,
visit_bombus=NA,
visit_wildbees=NA,
visit_syrphids=NA,
visit_humbleflies=NA,
visit_other_flies=NA,
visit_beetles=NA,
visit_lepidoptera=NA,
visit_nonbee_hymenoptera=NA,
visit_others=NA,
Publication=data.site$Publication,
Credit=data.site$Credit,
Email_contact=data.site$email
)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_Breno_M_Freitas_Gossypium_hirsutum_Brazil_2011.csv")
setwd(dir_ini)
field_level_data <- tibble(
study_id="Breno_M_Freitas_Gossypium_hirsutum_Brazil_2011",
site_id=data.site$site_id,
crop=data.site$crop,
variety=NA,
management=data.site$management,
country=data.site$country,
latitude=NA,
longitude=NA,
X_UTM=data.site$X_UTM,
Y_UTM=data.site$Y_UTM,
zone_UTM=NA,
sampling_start_month=NA,
sampling_end_month=NA,
sampling_year=data.site$sampling_year,
field_size=data.site$field_size,
yield=data.site$yield2,
yield_units=data.site$yield2_units,
yield2=NA,
yield2_units=NA,
yield_treatments_no_pollinators=NA,
yield_treatments_pollen_supplement=NA,
yield_treatments_no_pollinators2=NA,
yield_treatments_pollen_supplement2=NA,
fruits_per_plant=NA,
fruit_weight=NA,
plant_density=NA,
seeds_per_fruit=NA,
seeds_per_plant=NA,
seed_weight=NA,
observed_pollinator_richness=richness_aux$observed_pollinator_richness,
other_pollinator_richness=richness_aux$other_pollinator_richness,
other_richness_estimator_method=richness_aux$other_richness_estimator_method,
richness_restriction = "only other wild bees",
abundance=abundance_aux$total,
ab_honeybee=abundance_aux$honeybees,
ab_bombus=abundance_aux$bumblebees,
ab_wildbees=abundance_aux$other_wild_bees,
ab_syrphids=abundance_aux$syrphids,
ab_humbleflies=abundance_aux$humbleflies,
ab_other_flies=abundance_aux$other_flies,
ab_beetles=abundance_aux$beetles,
ab_lepidoptera=abundance_aux$lepidoptera,
ab_nonbee_hymenoptera=abundance_aux$non_bee_hymenoptera,
ab_others=abundance_aux$other,
total_sampled_area=900,
total_sampled_time=NA,
visitation_rate_units = NA,
visitation_rate=NA,
visit_honeybee=NA,
visit_bombus=NA,
visit_wildbees=NA,
visit_syrphids=NA,
visit_humbleflies=NA,
visit_other_flies=NA,
visit_beetles=NA,
visit_lepidoptera=NA,
visit_nonbee_hymenoptera=NA,
visit_others=NA,
Publication=data.site$Publication,
Credit=data.site$Credit,
Email_contact=data.site$email
)
field_level_data <- tibble(
study_id="Breno_M_Freitas_Gossypium_hirsutum_Brazil_2011",
site_id=data.site$site_id,
crop=data.site$crop,
variety=NA,
management=data.site$management,
country=data.site$country,
latitude=NA,
longitude=NA,
X_UTM=data.site$X_UTM,
Y_UTM=data.site$Y_UTM,
zone_UTM=NA,
sampling_start_month=NA,
sampling_end_month=NA,
sampling_year=data.site$sampling_year,
field_size=data.site$field_size,
yield=data.site$yield2,
yield_units=data.site$yield2_units,
yield2=NA,
yield2_units=NA,
yield_treatments_no_pollinators=NA,
yield_treatments_pollen_supplement=NA,
yield_treatments_no_pollinators2=NA,
yield_treatments_pollen_supplement2=NA,
fruits_per_plant=NA,
fruit_weight=NA,
plant_density=NA,
seeds_per_fruit=NA,
seeds_per_plant=NA,
seed_weight=NA,
observed_pollinator_richness=richness_aux$observed_pollinator_richness,
other_pollinator_richness=richness_aux$other_pollinator_richness,
other_richness_estimator_method=richness_aux$other_richness_estimator_method,
richness_restriction = "only other wild bees",
abundance=abundance_aux$total,
ab_honeybee=abundance_aux$honeybees,
ab_bombus=abundance_aux$bumblebees,
ab_wildbees=abundance_aux$other_wild_bees,
ab_syrphids=abundance_aux$syrphids,
ab_humbleflies=abundance_aux$humbleflies,
ab_other_flies=abundance_aux$other_flies,
ab_beetles=abundance_aux$beetles,
ab_lepidoptera=abundance_aux$lepidoptera,
ab_nonbee_hymenoptera=abundance_aux$non_bee_hymenoptera,
ab_others=abundance_aux$other,
total_sampled_area=900,
total_sampled_time=NA,
visitation_rate_units = NA,
visitation_rate=NA,
visit_honeybee=NA,
visit_bombus=NA,
visit_wildbees=NA,
visit_syrphids=NA,
visit_humbleflies=NA,
visit_other_flies=NA,
visit_beetles=NA,
visit_lepidoptera=NA,
visit_nonbee_hymenoptera=NA,
visit_others=NA,
Publication=data.site$Publication,
Credit=data.site$Credit,
Email_contact=data.site$email
)
abundance_aux <- data.species_03 %>% #filter(sampling_method=="transect") %>%
group_by(site_id,Guild) %>% count(wt=abundance) %>%
spread(key=Guild, value=n)
names(abundance_aux)
abundance_aux <- abundance_aux %>% mutate(honeybees=0,lepidoptera=0,beetles=0,bumblebees=0,other=0,
humbleflies=0,non_bee_hymenoptera=0,other_flies=0,
syrphids=0,total=0)
abundance_aux[is.na(abundance_aux)] <- 0
abundance_aux$total <- rowSums(abundance_aux[,c(2:ncol(abundance_aux))])
field_level_data <- tibble(
study_id="Breno_M_Freitas_Gossypium_hirsutum_Brazil_2011",
site_id=data.site$site_id,
crop=data.site$crop,
variety=NA,
management=data.site$management,
country=data.site$country,
latitude=NA,
longitude=NA,
X_UTM=data.site$X_UTM,
Y_UTM=data.site$Y_UTM,
zone_UTM=NA,
sampling_start_month=NA,
sampling_end_month=NA,
sampling_year=data.site$sampling_year,
field_size=data.site$field_size,
yield=data.site$yield2,
yield_units=data.site$yield2_units,
yield2=NA,
yield2_units=NA,
yield_treatments_no_pollinators=NA,
yield_treatments_pollen_supplement=NA,
yield_treatments_no_pollinators2=NA,
yield_treatments_pollen_supplement2=NA,
fruits_per_plant=NA,
fruit_weight=NA,
plant_density=NA,
seeds_per_fruit=NA,
seeds_per_plant=NA,
seed_weight=NA,
observed_pollinator_richness=richness_aux$observed_pollinator_richness,
other_pollinator_richness=richness_aux$other_pollinator_richness,
other_richness_estimator_method=richness_aux$other_richness_estimator_method,
richness_restriction = "only other wild bees",
abundance=abundance_aux$total,
ab_honeybee=abundance_aux$honeybees,
ab_bombus=abundance_aux$bumblebees,
ab_wildbees=abundance_aux$other_wild_bees,
ab_syrphids=abundance_aux$syrphids,
ab_humbleflies=abundance_aux$humbleflies,
ab_other_flies=abundance_aux$other_flies,
ab_beetles=abundance_aux$beetles,
ab_lepidoptera=abundance_aux$lepidoptera,
ab_nonbee_hymenoptera=abundance_aux$non_bee_hymenoptera,
ab_others=abundance_aux$other,
total_sampled_area=900,
total_sampled_time=NA,
visitation_rate_units = NA,
visitation_rate=NA,
visit_honeybee=NA,
visit_bombus=NA,
visit_wildbees=NA,
visit_syrphids=NA,
visit_humbleflies=NA,
visit_other_flies=NA,
visit_beetles=NA,
visit_lepidoptera=NA,
visit_nonbee_hymenoptera=NA,
visit_others=NA,
Publication=data.site$Publication,
Credit=data.site$Credit,
Email_contact=data.site$email
)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_Breno_M_Freitas_Gossypium_hirsutum_Brazil_2011.csv")
setwd(dir_ini)
View(field_level_data)
library(tidyverse)
library("iNEXT")
library(openxlsx)
library(rgdal)
dir_ini <- getwd()
options(digits=14)
data.site <- read.xlsx("DATASETS/Chac01_Datacollection_pollination.xlsx",
sheet = "SiteData", startRow = 2)
data.site <- as_tibble(data.site)
data.site <- data.site %>% filter(SiteID=="chac04")
data.site <- data.site %>%
separate(col = Crop.species, into = c("Crop.species", "variety"),". Cultivar ")
data.site$X <- -1*as.numeric(data.site$X)
data.site$Y <- -1*as.numeric(data.site$Y)
data.site <- data.site %>% select(-'Annual/perennial',-X10,-X11) %>%
rename(study_id=SiteID,site_id= Distance.ID, longitude=Y,latitude=X,zone_UTM=`X,Y.Projection.&.Datum`,
sampling_year=Year,crop=Crop.species,
management=Management)
data.Functioning <- read.xlsx("DATASETS/Chac01_Datacollection_pollination.xlsx",
sheet = "Functioning", startRow = 2)
data.Functioning <- as_tibble(data.Functioning)
data.Functioning <- data.Functioning %>% filter(Year.of.sampling==2015)
data.Functioning <- data.Functioning %>% select(-SiteID,-Fruit.set.ALLOGAMY,-Pollen.grains.ALLOGAMY,
-Pollen.grains.OPEN.FLOWERS,
-Pollen.grains.ALLOGAMY,
-Function)
data.Functioning <- data.Functioning %>%
mutate(yield_treatments_no_pollinators=100*Fruit.set.for.EXCLOSURES,
yield=100*fruit.set.OPEN.FLOWERS,
yield_units="fruit set (%)") %>%
rename(site_id=Distance.ID,sampling_year=Year.of.sampling) %>%
select(-Fruit.set.for.EXCLOSURES,-fruit.set.OPEN.FLOWERS)
data.site <- data.site %>% left_join(data.Functioning, by = c("site_id","sampling_year"))
data.site$field_size <- NA
data.site <- data.site %>% mutate(country="Argentina",Publication=NA,
Credit="Natacha Chacoff (Instituto de Ecologia Regional. CONICET UNT)",
email="nchacoff@gmail.com")
data.species <- read.xlsx("DATASETS/Chac01_Datacollection_pollination.xlsx",
sheet = "SpeciesData", startRow = 2)
data.species <- as_tibble(data.species)
data.species <- data.species %>% filter(Year.of.sampling==2015)
# Evaluate the percentage of species + morphospecies
data.species %>% group_by(Identified.to) %>% count()
percentage_species_morphos <-
sum(data.species$Identified.to %in% c("morphospecies","species"))/nrow(data.species)
data.meta <- read.xlsx("DATASETS/Chac01_Datacollection_pollination.xlsx",
sheet = "StudyMetadata", startRow = 2)
data.meta <- as_tibble(data.meta)
data.meta <- data.meta %>% filter(`Study.year(s)`==2015)
data.meta <- data.meta %>% select(Distance.ID,Number.of.visits.census)
data.species <- data.species %>% left_join(data.meta,by="Distance.ID")
data.species <- data.species %>% select(-Number.of.censuses)
data.species$Sampling.method <- paste(data.species$Number.of.visits.census,"census of 15 minutes observation to a flowering branch",sep=" ")
data.species <- data.species %>% rename(site_id=Distance.ID,sampling_year=Year.of.sampling,
sampling_method=Sampling.method,abundance=Abundance,
Organism_ID=OrganismID)
data.species_01 <- data.species
data.species_01 %>% group_by(sampling_method) %>% count()
gild_list <- read_csv("C:/Users/USUARIO/Desktop/OBservData/Thesaurus_Pollinators/Table_organism_guild_META.csv")
data.species_01 <- data.species_01 %>% select(-Identified.to,-X7)
data.species_01 <- data.species_01 %>% left_join(gild_list,by=c("Organism_ID","Family"))
#Check NA's in guild
data.species_01 %>% filter(is.na(Guild)) %>% group_by(Organism_ID,Family) %>% count()
data.species_01$Guild[data.species_01$Organism_ID=="Avispa negra "] <- "non_bee_hymenoptera"
data.species_01$Guild[data.species_01$Organism_ID=="Avispa rayada "] <- "non_bee_hymenoptera"
data.species_01$Guild[data.species_01$Organism_ID=="Bombus negro "] <- "bumblebees"
data.species_01$Guild[data.species_01$Organism_ID=="Ligaidae"] <- "other"
data.species_01$Guild[data.species_01$Organism_ID=="Ligaidae "] <- "other"
data.species_01$Guild[data.species_01$Organism_ID=="Mosca brillante  "] <- "other_flies"
data.species_01 %>% filter(is.na(Guild)) %>% group_by(Organism_ID,Family) %>% count()
data.species_01 <- data.species_01 %>% mutate(total_sampled_area=NA,
total_sampled_time=Number.of.visits.census*15,
total_sampled_flowers=NA,
Description=NA)
insect_sampling <- tibble(
study_id = "Natacha_Chacoff_Citrus_limon_Argentina_2015",
site_id = data.species_01$site_id,
pollinator = data.species_01$Organism_ID,
guild = data.species_01$Guild,
sampling_method = data.species_01$sampling_method,
abundance = data.species_01$abundance,
total_sampled_area = data.species_01$total_sampled_area,
total_sampled_time = data.species_01$total_sampled_time,
total_sampled_flowers = data.species_01$total_sampled_flowers,
Description = data.species_01$Description
)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(insect_sampling, "insect_sampling_Natacha_Chacoff_Citrus_limon_Argentina_2015.csv")
setwd(dir_ini)
abundance_aux <- data.species_01 %>%
group_by(site_id,Guild) %>% count(wt=abundance) %>%
spread(key=Guild, value=n)
names(abundance_aux)
abundance_aux <- abundance_aux %>% mutate(humbleflies=0,total=0)
abundance_aux[is.na(abundance_aux)] <- 0
abundance_aux$total <- rowSums(abundance_aux[,c(2:ncol(abundance_aux))])
data.site <- data.site %>% left_join(abundance_aux, by = "site_id")
abundace_field <- data.species_01 %>%
select(site_id,Organism_ID,abundance)%>%
group_by(site_id,Organism_ID) %>% count(wt=abundance)
abundace_field <- abundace_field %>% spread(key=Organism_ID,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,2:(ncol(abundace_field)-2)])
chao  <-  ChaoRichness(x, datatype = "abundance", conf = 0.95)
abundace_field$r_obser[i] <-  chao$Observed
abundace_field$r_chao[i] <-  chao$Estimator
}
richness_aux <- abundace_field %>% 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")
if (percentage_species_morphos<0.8){
richness_aux[,2:ncol(richness_aux)] <- NA
}
data.site <- data.site %>% left_join(richness_aux, by = "site_id")
###############################################################
#Average observation time per site
av_time <- data.species %>% group_by(site_id) %>% summarise(mean_time=15*mean(Number.of.visits.census))
data.site <- data.site %>% left_join(av_time, by = "site_id")
field_level_data <- tibble(
study_id="Natacha_Chacoff_Citrus_limon_Argentina_2015",
site_id=data.site$site_id,
crop=data.site$crop,
variety=data.site$variety,
management=data.site$management,
country=data.site$country,
latitude=data.site$latitude,
longitude=data.site$longitude,
X_UTM=NA,
Y_UTM=NA,
zone_UTM=NA,
sampling_start_month=NA,
sampling_end_month=NA,
sampling_year=data.site$sampling_year,
field_size=data.site$field_size,
yield=data.site$yield,
yield_units=data.site$yield_units,
yield2=NA,
yield2_units=NA,
yield_treatments_no_pollinators=data.site$yield_treatments_no_pollinators,
yield_treatments_pollen_supplement=NA,
yield_treatments_no_pollinators2=NA,
yield_treatments_pollen_supplement2=NA,
fruits_per_plant=NA,
fruit_weight=NA,
plant_density=NA,
seeds_per_fruit=NA,
seeds_per_plant=NA,
seed_weight=NA,
observed_pollinator_richness=data.site$observed_pollinator_richness,
other_pollinator_richness=data.site$other_pollinator_richness,
other_richness_estimator_method=data.site$other_richness_estimator_method,
richness_restriction = NA,
abundance=data.site$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=NA,
total_sampled_time=data.site$mean_time,
visitation_rate_units = NA,
visitation_rate=NA,
visit_honeybee=NA,
visit_bombus=NA,
visit_wildbees=NA,
visit_syrphids=NA,
visit_humbleflies=NA,
visit_other_flies=NA,
visit_beetles=NA,
visit_lepidoptera=NA,
visit_nonbee_hymenoptera=NA,
visit_others=NA,
Publication=data.site$Publication,
Credit=data.site$Credit,
Email_contact=data.site$email
)
field_level_data_aux <- read.xlsx("DATASETS/data chacoff LEMON 2015.xlsx",
sheet = "field", startRow = 1)
field_level_data$site_id==field_level_data_aux$site_id
field_level_data$sampling_start_month <- field_level_data_aux$sampling_start_month
field_level_data$sampling_end_month <- field_level_data_aux$sampling_end_month
# Update visitation rate info
field_level_data$visitation_rate_units <- "visits per 100 flowers and hour"
field_level_data$visitation_rate <- 1200*field_level_data_aux$visitation_rate #visits per flower in 5 min
field_level_data$visit_honeybee <- 1200*field_level_data_aux$visit_honeybee #visits per flower in 5 min
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(field_level_data, "field_level_data_Natacha_Chacoff_Citrus_limon_Argentina_2015.csv")
setwd(dir_ini)
library(tidyverse)
library(openxlsx)
data.site <- read.xlsx("DATASETS/field_level_data_Breno_M_Freitas_Anacardium_occidentale_Brazil_2011_corrected.xlsx",
sheet = "field_level_data_Breno_M_Freita", startRow = 2)
View(data.site)
data.site <- read.xlsx("DATASETS/field_level_data_Breno_M_Freitas_Anacardium_occidentale_Brazil_2011_corrected.xlsx",
sheet = "field_level_data_Breno_M_Freita", startRow = 1)
View(data.site)
data.site <- as_tibble(data.site)
library(tools)
showNonASCII(data.site)
showNonASCII(data.site$study_id)
showNonASCII(data.site$study_id)
data.site$study_id
showNonASCII(data.site$latitude)
data.site <- read.xlsx("DATASETS/field_level_data_Breno_M_Freitas_Anacardium_occidentale_Brazil_2011_corrected.xlsx",
sheet = "field_level_data_Breno_M_Freita", startRow = 1)
data.site <- as_tibble(data.site)
showNonASCII(data.site$latitude)
showNonASCII(data.site$latitude)
showNonASCII(data.site$longitude)
showNonASCII(data.site$yield)
showNonASCII(data.site$observed_pollinator_richness)
showNonASCII(data.site$other_pollinator_richness)
setwd("C:/Users/USUARIO/Desktop/OBservData/Datasets_storage")
write_csv(data.site, "field_level_data_Breno_M_Freitas_Anacardium_occidentale_Brazil_2011.csv")
setwd(dir_ini)
