All functions 


boot_sample Generate n bootstrap sample of the monitoring sites to be used for each iteration. 

check_names Verify for the required column names in the data object. 

check_package Internal function to check if a package is installed. 

check_pheno Check for the flight curve of a specific year. If the specific year is missing, use the nearest year available within a 5year period to impute missing count. Function used in impute_count. 

collated_index compute a collated index from the site indices, using a Generalized Linear Model. 

collated_index_old compute a collated index from the site indices, using a Generalized Linear Model. 

day_week_summary Summarize the count(s) per day or week using either the maximum or the average count when multiple counts (visit) are observed. 

df_visit_season Link each recorded visit to a corresponding monitoring season, this function is used in ts_monit_site 

fit_gam fit a Generalized Additive Model to butterfly count data along a temporal variable and accounting for site effect when multiple are available. 

flight_curve Compute the annual flight curve from butterfly count data collated across sites. 

get_nm Compute the normalized flight curve by fitting a spline in a Generalized Additive Model for one year 'y' to butterfly count data. 

get_nny find the nearest year with a computed flight curve 

impute_count 

initiate_project Build the folder structure for a generic research project 

Toy data set with butterfly count for x species across y sites 

Toy data set with the date when the sites have been visited for monitoring 

plot.pheno_curve Generic method to plot the flight curve, where values are extracted from a pheno_curve object (outcome of the light_curve() function) 

points.pheno_curve Generic method to add points on a plot of the flight curve, where values are extracted from a pheno_curve object (outcome of the light_curve() function) 

set_anchor Add Anchors of "zeros" at determined distance on each side of the monitoring season with specific weight (length), this function is used by ts_monit_season() 

site_index Extract abundance indices per site and year based on flight curve imputation. 

ts_date_seq Generate a timeseries with dates starting from January of the starting year to December of the ending years. 

ts_dwmy_table Generate a timeseries of dates with day, week, month and year (dwmy) from one initial to an end years 

ts_monit_count_site Generate a full time series of observed count, for all sites and each day since a starting and ending years of the defined timeseries 

ts_monit_season Build a timeseries of dates with specific detail about the monitoring season 

ts_monit_site Augment the time series in m_season with all sites and visits with "zeros", leaving all non visited day with and <NA> 