stacomiR v0.5.4.2
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Fish Migration Monitoring
Graphical outputs and treatment for a database of fish pass
monitoring. It is a part of the 'STACOMI' open source project developed in
France by the French Agency for Biodiversity (AFB) institute to centralize
data obtained by fish pass monitoring. This version is available in French and
English. See <http://stacomir.r-forge.r-project.org/> for more information on
'STACOMI'.
Functions in stacomiR
Name | Description | |
calcule,report_mig_char-method | Computes data to a standard format for the summary and plot methods. | |
calcule | Generic method for calculations | |
charge,ref_par-method | Loading method for Repar referential objects | |
charge,ref_parqual-method | Loading method for Reparqual referential objects | |
charge,report_sample_char-method | charge method for report_sample_char class | |
charge,report_sea_age-method | Loads data and check that all choices in the graphical interface have been made. | |
charge_with_filter,ref_stage-method | Loading method for ref_stage referential objects searching only those stages existing for a DC and a Taxon | |
charge_with_filter,ref_taxa-method | Loading method for ref_taxa referential objects searching only taxa existing for a DC | |
charge,ref_checkbox-method | Loading method for ref_checkbox referential objects | |
chargecsv | chargecsv loads the informations stored in c:/program files/stacomi/calcmig.csv file | |
choice,ref_checkbox-method | Choice method for ref_checkbox referential objects | |
choice_c,ref_env-method | Command line interface to select a monitoring station | |
choice_c,ref_choice-method | Choice_c method for refchoix referential objects | |
choice | Generic method for choice (using the gwidget graphical interface) | |
choice_c,ref_horodate-method | Command line | |
choice_c,ref_year-method | choice_c method for ref_year referential from the command line | |
choice_c,report_annual-method | command line interface for report_annual-class | |
choicemult,ref_horodate-method | Multiple Choice method for ref_horodate referential objects, to put together with notebook widgets | |
calcule,report_ge_weight-method | Calcule method for report_ge_weight | |
choicemult,ref_par-method | Multiple Choice method for ref_par referential objects, internal use | |
colortable | Builds a table with colors to merge with a dataframe for later use in ggplot. An initial check will be done on the name of the color vector. A data frame is built. It contains a column color which is a factor. The factor order match the order of the vector (not the alphabetical order of the colors). | |
calcule,report_mig-method | Transforms migration per period to daily migrations, and performs the conversion from weights to number is data are stored as weights (glass eel). | |
charge,ref_dc-method | Method to load the counting devices of the control station | |
calcule,report_mig_interannual-method | calcule method for report_mig_interannual | |
barplot,report_annual-method | barplot method for object report_annual-class | |
connect,report_annual-method | connect method for report_annual class this method performs the sum over the year attention this function does not count subsamples. | |
charge,ref_year-method | Loading method for ref_year referential objects | |
connect,report_mig-method | connect method for report_mig | |
charge,ref_df-method | Loading method for DF referential objects | |
connect,report_mig_char-method | connect method for report_mig_char | |
charge,report_annual-method | charge method for report_annual class | |
currentstart_date | Generic method for getting the beginning date for current time step | |
end_date,ref_timestep-method | Gets the final horodate for an object of class ref_timestep-class | |
calcule,report_silver_eel-method | Calculate individual silver eel parameters. | |
charge,report_mig-method | Loads additional data on migration control operations, df (fishway) dc (counting device). | |
calcule,report_species-method | calcule method for report_species | |
calcmig | A data frame containing the default connection arguments. The program will use a file installed in c:/program files/stacomi but if not found will switch to this default value | |
charge,report_mig_char-method | charge method for report_mig_char | |
choice,ref_df-method | Graphical method to choose a fishway through the interface | |
fun_aggreg_for_plot | returns a table where all components within the list calcdata are aggregated and formatted for plot | |
fun_char_spe | function used to remove special non utf8 character which cause the gtk interface to crash | |
calcule,report_mig_mult-method | #' Transforms migration per period to daily migrations, and performs the conversion from weights to number is data are stored as weights (glass eel). This calculation is performed in a loop for all dc. | |
charge,ref_choice-method | Loading method for Rechoice referential objects | |
charge,report_ge_weight-method | charge method for report_ge_weight class | |
charge,report_env-method | charge method for report_env class | |
charge,ref_coe-method | loads the coefficients for the period defined in class | |
funboxDC | function used for some lattice graph | |
charge,report_dc-method | charge method for report_dc | |
funboxDF | Internal use, rectangles to describe the DF work for report_df class, graphical interface handler | |
charge | Generic method to load referentials | |
charge_complement,ref_parqual-method | Loads an additional dataset this method is loaded to obtain the possible values of a qualitative parameter. Here data only contains one line | |
choice,ref_env-method | Choice method for ref_env referential object | |
funplotreport_silver_eel | funplotreport_silver_eel | |
choice,ref_textbox-method | Choice method for ReTextBox referential objects | |
choice,ref_timestep-method | Method to select timesteps from the graphical interface | |
charge,report_mig_mult-method | charge method for report_mig_mult | |
charge,report_df-method | charge method for report_df | |
charge,ref_parquan-method | Loading method for Reparquan referential objects | |
charge_with_filter | Generic method to load referentials, with filters from the parent object in the database | |
chargecomplement-methods | Methods for Function chargecomplement | |
choice_c,ref_stage-method | choice_c method for ref_stage | |
choice_c,ref_taxa-method | choice_c method for ref_taxa | |
charge,report_ope-method | charge method for report_ope | |
choice_c,report_mig_env-method | command line interface for report_env class | |
choice_c,report_mig_interannual-method | command line interface for report_mig_interannual class | |
funpointreport_sample_char | Point graph from ggplot | |
funtableDF | Table output for report_df class | |
choice_c,report_species-method | command line interface for report_species-class | |
choice_c | Generic method for manual choice using the command line | |
charge,ref_stage-method | Loading method for ref_stage referential objects | |
calcule,report_sample_char-method | Calculation for report_sample_char | |
charge,report_silver_eel-method | charge method for report_silver_eel class | |
charge,report_species-method | charge method for report_species | |
calcule,report_sea_age-method | Split data according to the limits set in the limit1hm, and limit2hm arguments of the report_sea_age-class. | |
choice,ref_horodate-method | Graphical interface | |
funtablereport_ge_weight | Internal handler for reg, class report_ge_weight-class. | |
choice,ref_list-method | Choice method for ref_list referential objects | |
choice,ref_timestep_daily-method | Method to select timesteps from the graphical interface | |
charge,ref_env-method | Loading method for ref_env referential object | |
fun_date_extraction | This function extracts temporal characteristics from a dataframe | |
choice,ref_year-method | choice method for ref_year referential | |
charge,ref_list-method | Loading method for refliste referential objects | |
fun_report_mig_interannual | statistics per time period | |
charge_complement | Generic method to load additional data | |
h_report_mig_char | handler function used by the main interface | |
choice,ref_stage-method | Choice method for ref_stage referential objects | |
charge,ref_taxa-method | Loading method for ref_taxa referential objects | |
h_report_mig_env | handler function used by the main interface | |
h_report_mig_mult_graph | handler for plot method in report_mig_mult class | |
choice_c,report_mig-method | command line interface for report_mig class | |
charge_with_filter,ref_par-method | Loading method for Repar referential objects searching only those parameters existing for a DC, a Taxa, and a stage | |
h_report_mig_multcalc | handler for calculations | |
charge,report_mig_env-method | charge method for report_mig_env class | |
charge,ref_textbox-method | Loading method for ReTextBox referential objects | |
choice_c,report_mig_char-method | command line interface for report_mig_char class | |
funbarchartDC | Function to create a barchart (lattice) corresponding to the periods | |
h_report_silver | handler function used by the main interface | |
funbarchartDF | Handler for barchart for report_df class from the graphical interface | |
connect,report_dc-method | connect method for report_dc | |
charge,report_mig_interannual-method | loading method for report_mig_interannual class | |
h_report_size | handler function used by the main interface | |
funout | this function uses gfile, edits a text with info and changing colors | |
choice,ref_taxa-method | Choice method for reftaxa referential objects with only one taxa selected | |
hgraph_report_mig_interannual | Plot of all interannual from top to bottom | |
choice_c,ref_list-method | Choice_c method for ref_list referential objects | |
choice_c,ref_par-method | Command line interface to select a parameter | |
choice_c,report_env-method | command line interface for report_env class | |
choice_c,report_ge_weight-method | command line interface for report_ge_weight-class | |
hgraph_report_mig_interannual2 | Plot of daily migrations | |
hgraph_report_mig_interannual5 | Function displaying comparison similar to hgraph_report_mig_interannual4 but using pointrange and geom_bar This function plots comparisons for periods of 1 week, 2 weeks, month | |
choice_c,report_sea_age-method | command line interface for report_sea_age class | |
charge_with_filter,ref_parqual-method | Loading method for Reparqual referential objects searching only those parameters existing for a DC, a Taxon, and a stage | |
choice_c,report_silver_eel-method | command line interface for report_silver_eel class | |
connect,report_df-method | connect method for report_df | |
funplotreport_sea_age | funplotreport_sea_age | |
charge_with_filter,ref_parquan-method | Loading method for Reparquan referential objects searching only those parameters existing for a DC, a Taxon, and a stage | |
hgraph_report_mig_interannual7 | This function creates a cumulated area plot to highlight seasonal trends in migration. Data are calculated by 2 weeks period then centered and reduced | |
choice_c,ref_dc-method | Command line interface to select a counting device | |
choice_c,ref_df-method | Command line interface to choose a fishway | |
choice,ref_choice-method | Choice method for Rechoice referential objects | |
choice,ref_dc-method | Graphical method to choose a fishway through the interface | |
connect,report_mig_mult-method | connect method for report_mig_mult | |
get_year | Generic method to get the years | |
choicemult | Generic method for multiple choice (using the gwidget notebook for multiple choice) | |
choice,ref_par-method | Choice method for ref_par referential objects | |
hplotreport_annual | plot handler | |
getdateDebut,ref_timestep-method | Returns the starting date as character | |
coef_durif | Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters | |
hreg | Internal handler for reg, class report_ge_weight-class. | |
graphdate | function used for some lattice graphs with dates | |
connect,report_sample_char-method | connect method for report_sample_char | |
graphe-methods | Methods for Function graphe | |
connect,report_ope-method | connect method for report_ope | |
connect,report_sea_age-method | connect method for report_sea_age | |
connect,report_silver_eel-method | connect method for report_silver_eel | |
h_report_miggraph2 | handler for h_report_miggraph2 | |
connect,report_species-method | connect method for report_species | |
choicemult,ref_choice-method | Multiple Choice method for ref_choice referential objects, to put together with notebook widgets | |
choicemult,ref_dc-method | choicemult, selection method for ref_dc allowing to select several DC | |
load_stacomi | Internal function, tests the connection and if it works loads the stacomi interface | |
choice,ref_parqual-method | Choice method for ref_parqual referential objects, internal use | |
fun_stage_durif | Function to calculate the stages from Durif | |
model,report_ge_weight-method | model method for report_ge_weight' this method uses samples collected over the season to model the variation in weight of glass eel or yellow eels. | |
fun_table_per_dis | functions called in DF and DC | |
choice_c,ref_textbox-method | Choice_c method for ReTextBox referential objects | |
end_date | Generic method for getting the final date | |
h_report_migwrite | handler h_report_migwrite Allows the saving of daily and monthly counts in the database | |
choice_c,ref_timestep_daily-method | choice_c method for class ref_timestep_daily | |
plot,report_mig_env,missing-method | Plot method for report_mig_env | |
envir_stacomi | Environment where most objects from the package are stored and then loaded by the charge method | |
plot,report_mig_interannual,missing-method | Plot method for report_mig_interannual | |
get_step_label | Generic method to get the string value of time step | |
choice_c,report_dc-method | command line interface for report_dc class | |
hbmCplotcrossed | handler for plot | |
choicemult,ref_parqual-method | Multiple Choice method for ref_parqual referential objects internal use | |
connect,report_env-method | connect method for report_env class | |
choicemult,ref_stage-method | Multiple Choice method for ref_stage referential objects | |
connect,report_ge_weight-method | connect method for report_Poids_moyen | |
createmessage | Generic method to forward outputs | |
hbmCplotqual | handler for plot | |
current_end_date,ref_timestep-method | Gets the ending date of a time step for an object of class ref_timestep-class | |
choice_c,report_df-method | command line interface for report_df class | |
hxtablereport_annual | xtable handler | |
r_dc | Counting Device (DC) operation from 2000 to 2015 at the Arzal dam (Vilaine, France) | |
interface_graphique | Program launch, this function launches the GwidgetRgtk graphical interface to stacomi. To be able to run, some widgets (win, grouptotal, group...) are assigned in the user environment .GlobalEnv. | |
funboxplotreport_sample_char | Boxplots for ggplot2 | |
choice_c,report_mig_mult-method | command line interface for report_mig_mult class | |
r_df | Overview of the fishway operation at Arzal in (Vilaine France). | |
choice_c,report_sample_char-method | command line interface for report_sample_char class | |
interface_report_mig_interannual | interface for report_mig_interannual class | |
get_year,ref_timestep-method | Gets the year or a vector of years corresponding to the timestep ("ref_timestep") object | |
choicemult,ref_taxa-method | Multiple Choice method for reftaxa referential objects, the graphical interface is built to allow for multiple choices. See load for method in the command line. | |
r_mig_interannual_vichy | Seasonality of salmon migration at the Vichy counting station (Loire) | |
fun_weight_conversion | returns a table where weights and number are calculated from number and weights respectively performs a query to collect the conversion coefficients | |
choicemult,ref_timestep-method | Graphical interface for multiple choice method for PasdeTemps (used in report_mig_mult) | |
hTablereport_mig_mult | handler function table | |
h_report_env | handler function used by the main interface | |
h_report_dfdc | handler function used by the main interface | |
hTablereport_mig | handler for summary function, internal use calls functions funstat and funtable to build summary tables in html and csv files | |
fun_write_monthly | This writes monthly data in t_reportmensuel_mens table | |
funchartDF | Handler function to plot calendar like graph, internal use | |
funchartDC | Handler function to plot calendar like graph, internal use | |
connect,report_mig_env-method | connect method for report_mig_env class | |
connect,report_mig_interannual-method | connect method for report_mig_interannual | |
h_report_ope | handler function used by the main interface | |
r_mig_mult | Anguilla migration at the Arzal station (report_mig_mult-class) | |
funtable | function to print and save statistics in .csv and .html formats for report_mig and report_mig_mult class | |
hcalc | Internal handler for reg, class report_ge_weight-class. | |
h_report_pigment_stages | handler function used by the main interface | |
funtableDC | FuntableDC create a table output for report_dc class | |
getvalue,ref_period-method | Returns the POSIXt value of a given name | |
getvalue | Generic method getvalue | |
hexp | Internal handler for reg, class report_ge_weight-class. | |
h_report_mig | handler function used by the main interface | |
interface_report_mig_mult | graphical interface for report_mig_mult class | |
funstat | Function to calculate statistics per month | |
fundensityreport_sample_char | fundensityreport_sample_char uses ggplot2 to draw density plots | |
current_end_date | Generic method for getting the ending date for current time step | |
h_report_mig_annual | handler function used by the main interface | |
hgraph_report_mig_interannual3 | Step plot with different years displayed on the same graph. One year can be highlighted against the others | |
h_report_mig_interannual | handler function used by the main interface | |
plot,report_env,missing-method | Plot method for report_env | |
plot,report_ge_weight,missing-method | Plot method for report_ge_weight' | |
plot,report_sea_age,missing-method | Plots of various type for report_sea_age | |
hgraph_report_mig_interannual4 | Plot comparing the migration to the migration computed for all years available in the daily migration table. This function plots comparisons for periods of 1 week, 2 weeks, month | |
currentstart_date,ref_timestep-method | Gets the starting date of a time step for an object of class ref_timestep-class | |
h_report_mig_mult | handler function used by the main interface | |
h_report_species | handler function used by the main interface | |
hbarplotreport_annual | Barplot handler | |
interface_report_annual | interface for report_annual class | |
funstat_daily | function to create daily statistics | |
interface_report_dc | interface for report_dc class | |
ref_parqual-class | Class "ref_parqual" | |
interface_report_silver_eel | An interface that calls the object to build the user interface | |
hbmCplotquan | handler for plot | |
interface_report_species | Interface for report_species class | |
funtablereport_sample_char | table function | |
model | Generic for prediction | |
funtablereport_sea_age | table function | |
plot,report_silver_eel,missing-method | Plots of various type for report_silver_eel | |
getdateDebut | Generic method the get starting date | |
fun_report_mig_mult | Calculate daily migration by simple repartition | |
hbmCstat | This handler calls the generic method stat | |
plot,report_annual,missing-method | Plot method for report_annual | |
houtreport_mig | handler to print the command line | |
houtreport_mig_mult | handler to print the command line | |
hsummarybilesp | handler for summary report_species, internal use | |
r_mig_dc | Counting device operation for the video recording (Arzal dam, Vilaine, France). | |
hsummaryreport_migInterannuelle | Summary handler internal method | |
ref_parquan-class | Class "ref_parquan" | |
interface_report_mig_char | interface for report_migPar class | |
report_df-class | Report on fishway operation | |
interface_report_mig_env | interface for report_migConditionEnv class | |
report_env-class | class report_env simple output of one or several environmental conditions... | |
r_seaa | An object of class report_sea_age with data loaded | |
ref_list-class | Class "ref_list" | |
r_mig_df | Fishway operation for the vertical slot fishway (Arzal dam, Vilaine, France). | |
r_sample_char | Size of yellow and glass eel at the Arzal dam (Vilaine, France) in the fishway and main eel trapping ladder. | |
ref_par-class | Class "ref_par" | |
fun_report_mig_mult_overlaps | Function to calculate daily migration using overlaps functions | |
print,report_mig_mult-method | Method to print the command line of the object | |
getdbname | Retrieves the dbname from a connection using "baseODBC" | |
h_report_dc | handler function used by the main interface | |
print,report_sample_char-method | Method to print the command line of the object | |
h_report_df | handler function used by the main interface | |
report_annual-class | Class "report_annual" | |
report_dc-class | Class "report_dc" report du fonctionnement du dispositif de comptage | |
r_mig_mult_ope | Counting operations for three different counting device in Arzal (Vilaine, France) | |
r_mig_ope | An object of class report_ope-class with data loaded | |
funbarchart1DC | Handler for barchart for report_df class from the graphical interface | |
fungraph | Function for report_mig graphs including numbers DF DC operations | |
h_report_migcalc | handler for calculations report_mig | |
funbarchart1DF | Handler for barchart for report_df class from the graphical interface | |
hbilespcalc | handler for calculation | |
hbmCcalc | handler for report_mig_char | |
h_report_miggraph | handler for h_report_miggraph | |
report_mig_char-class | Migration report along with quantitative and qualitative characteristics | |
fungraph_glasseel | Graph function for glass eel migration. Differs from fungraph as it does not draw the ggplot graph for month | |
hbmmCEcalc | Internal handler function | |
plot,report_mig_mult,missing-method | Plots of various type for report_mig_mult | |
hbmmCEgraph | internal method for graphical interface | |
funtablereport_silver_eel | table function | |
report_mig_env-class | Class "report_mig_env" | |
houtDC | handler to print the command line | |
houtDF | handler to print the command line | |
summary,report_dc-method | summary for report_dc, write csv and html output, and prints summary statistics | |
get_step_label,ref_timestep-method | Gets the string value of time step | |
supprime,report_sea_age-method | supprime method for report_mig_interannual class | |
ref_dc-class | Class "ref_dc" | |
report_sea_age-class | Class "report_sea_age" | |
report_silver_eel-class | Class "report_silver_eel" | |
plot,report_sample_char,missing-method | Plots of various type for reportcarlot | |
getnocurrent_step,ref_timestep-method | Gets the current time step of an object of class ref_timestep-class | |
getnocurrent_step | Generic method to get current time step | |
ref_df-class | Class "ref_df" | |
vector_to_listsql | Transforms a vector into a string called within an sql command e.g. c('A','B','C') => in ('A','B','C') | |
interface_report_ge_weight | interface for report_ge_weight class | |
h_report_envgraph | h_report_envgraph Internal method | |
split_per_day | Create a dataframe suitable for charts per 24h and day | |
h_report_ge_weight | handler function used by the main interface | |
h_report_mig_multgraph2 | handler du calcul h_report_miggraph2 | |
ref_taxa-class | Class "ref_taxa" | |
h_report_mig_multgraph3 | handler | |
ref_textbox-class | ref_textbox referencial class | |
r_ann | Annual migration of yellow and silver eel for three fishways / counting devices at the Arzal dam (data from 1995 to 2016) | |
report_species-class | Counts of number per taxa/stages | |
set_starting_date,ref_timestep-method | Sets starting date from a character | |
r_ann_adour | Annual migration of salmon in the Adour and tributaries | |
stacomi | Function that loads the loginwindow, tests connection, and then destroys the window | |
interface_report_mig | Interface for report_mig class, internal use, this function is called by a handler in the main graphical interface | |
r_env | An object of class report_env with data loaded | |
plot,report_mig,ANY-method | Plots of various type for report_mig. | |
h_report_sample_char | handler function used by the main interface | |
h_report_sea_age | handler function used by the main interface | |
hplot | Internal handler for reg, class report_ge_weight-class. | |
hplotbilesp | handler for plot internal use | |
interface_report_df | interface for report_df class | |
summary,report_silver_eel-method | summary for report_silver_eel | |
interface_report_env | Interface for class conditionEnv | |
r_gew | Wet weight of glass eel from the trapping ladder (Arzal, Vilaine France) | |
r_silver | Silver eel migration in the Somme | |
ref_checkbox-class | ref_checkbox referencial class | |
plot,report_mig_char,missing-method | plot method for report_mig_char | |
summary,report_df-method | summary for report_df, write csv and html output, and prints summary statistics | |
interface_report_sample_char | An interface that calls the object to build the user interface | |
write_database,report_ge_weight-method | Function to write data to the stacomi database for report_ge_weight-class | |
write_database | Generic method write_database | |
plot,report_species,missing-method | Plot method for report_species | |
summary,report_species-method | summary for report_species generate csv and html output in the user data directory | |
report_mig_interannual-class | Class "report_mig_interannual" | |
print,report_sea_age-method | Method to print the command line of the object | |
print,report_dc-method | Method to print the command line of the object | |
interface_report_sea_age | An interface that calls the object to build the user interface | |
xtable,report_annual-method | xtable function for report_annual-class create an xtable objet but also assigns an add.to.column argument in envir_stacomi, for later use by the print.xtable method. | |
supprime | Generic method to delete entires from the database | |
plot,report_dc,ANY-method | Different plots for report_dc | |
print,report_silver_eel-method | Method to print the command line of the object | |
ref_timestep-class | Class "ref_timestep" | |
report_mig_mult-class | Migration reports for multiple DC / species / stages | |
r_mig_interannual | Daily glass eel and elver migration from 1984 to 2016 in the Sevre Niortaise | |
r_mig_env | An object of class report_mig_env with data loaded | |
plot,report_df,ANY-method | Different plots for report_df | |
ref_timestepChar-class | Class "ref_timestepChar" | |
r_mig_mult_dc | Counting device operation for three different counting device in Arzal (Vilaine, France) | |
r_mig_mult_df | Fishway operation at the Arzal Dam (Vilaine France) (3 Fishways in 2011) | |
print,report_df-method | Method to print the command line of the object | |
print,report_mig-method | Method to print the command line of the object | |
report_ge_weight-class | Trend of wet weight in glass eel | |
report_mig-class | Migration report for one DC, one species and one stage | |
setasqualitative | Generic method to transform quantitative par into a qualitative one | |
ref_env-class | Class "ref_env" | |
progress_bar | Progress bar using a gtkdialog, the progress bar is assigned in envir_stacomi This progress bar has a button to close. | |
quitte | function used to clean the objects within the group and the graphs and also elements remaining in the envir_stacomi environment | |
stacomiR-package | stacomiR | |
r_mig | Video counting of thin lipped mullet (Liza ramada) in 2015 in the Vilaine (France) | |
summary,report_sample_char-method | summary for report_sample_char | |
stacomi_installed | Test that the program is installed. | |
ref_horodate-class | Class ref_horodate | |
ref_choice-class | Class "ref_choice" | |
r_mig_char | Qualitative and quantitative parameters describing Salmon migration at Decize (Loire) | |
write_database,report_sea_age-method | Command line method to write the characteristic "sea age" (car_par_code='A124') into the tj_caracteristiquelot_car table in the user's scheme | |
setref_horodate,ref_horodate-method | Method to set the Horodate | |
ref_coe-class | Class "ref_coe" | |
summary,report_sea_age-method | summary for report_sea_age | |
ref_period-class | Class "ref_period" referential class | |
write_database,report_mig-method | Command line method to write the daily and monthly counts to the t_bilanmigrationjournalier_bjo table | |
ref_stage-class | Class "ref_stage" | |
supprime,ref_coe-method | supprime method for "ref_coe" class | |
supprime,report_mig_interannual-method | supprime method for report_mig_interannual class | |
xtable,report_mig_char-method | xtable function for report_mig_char-class create an xtable objet to be later used by the print.xtable method. | |
report_ope-class | Report on operations | |
ref_timestep_daily-class | Class "ref_timestep_daily" | |
report_sample_char-class | Class "report_sample_char" | |
ref_year-class | Year reference class | |
set_starting_date | Generic method to set the starting date | |
setasqualitative,report_mig_char-method | Turns a quantitative parameter into qualitative | |
summary,report_mig-method | summary for report_mig calls functions funstat and funtable to create migration overviews and generate csv and html output in the user data directory | |
summary,report_mig_char-method | summary for report_mig_char | |
validity_ref_horodate | Validity check for ref_horodate | |
validity_year | Validity check for ref_year | |
summary,report_mig_interannual-method | summary for report_mig_interannual provides summary statistics for the latest year (if silent=TRUE), or the year selected in the interface, if silent=FALSE. Mean, min and max are historical statistics with the selected year excluded from the historical dataset. | |
summary,report_mig_mult-method | summary for report_mig_mult calls functions funstat and funtable to create migration overviews and generate csv and html output in the user data directory | |
calcule,report_mig_env-method | Calculations for migration in the class report_mig_env-class | |
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Vignettes of stacomiR
Name | ||
stacomir.Rmd | ||
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Last month downloads
Details
Date | 2019-02-12 |
License | GPL (>= 2) |
URL | http://stacomir.r-forge.r-project.org/ |
BugReports | https://github.com/MarionLegrandLogrami/stacomiR/issues |
Collate | 'create_generic.R' 'data.R' 'fun_table_per_dis.R' 'fun_write_monthly.R' 'fungraph.R' 'fungraph_glasseel.R' 'funstat.R' 'funstat_daily.R' 'funtable.R' 'interface_report_annual.R' 'interface_report_dc.R' 'interface_report_df.R' 'interface_report_env.R' 'interface_report_ge_weight.R' 'interface_report_mig.R' 'interface_report_mig_char.R' 'interface_report_mig_env.R' 'interface_report_mig_interannual.R' 'interface_report_mig_mult.R' 'interface_report_sample_char.R' 'interface_report_sea_age.R' 'interface_report_silver_eel.R' 'interface_report_species.R' 'ref_checkbox.R' 'ref_choice.R' 'ref_coe.R' 'ref_dc.R' 'ref_df.R' 'ref_env.R' 'ref_horodate.R' 'ref_list.R' 'ref_par.R' 'ref_parqual.R' 'ref_parquan.R' 'ref_period.R' 'ref_stage.R' 'ref_taxa.R' 'ref_textbox.R' 'ref_timestep.R' 'ref_timestep_daily.R' 'ref_year.R' 'report_annual.R' 'report_dc.R' 'report_df.R' 'utilities.R' 'report_env.R' 'report_ge_weight.R' 'report_ope.R' 'report_mig.R' 'report_sample_char.R' 'report_mig_char.R' 'report_mig_mult.R' 'report_mig_env.R' 'report_mig_interannual.R' 'report_sea_age.R' 'report_silver_eel.R' 'report_species.R' 'setAs.R' 'stacomi.R' |
LazyLoad | yes |
LazyData | true |
RoxygenNote | 6.1.0.9000 |
NeedsCompilation | no |
VignetteBuilder | knitr |
Repository | CRAN |
Repository/R-Forge/Project | stacomir |
Repository/R-Forge/Revision | 548 |
Repository/R-Forge/DateTimeStamp | 2019-02-12 09:08:05 |
Date/Publication | 2019-03-06 15:20:06 UTC |
Packaged | 2019-02-12 09:12:33 UTC; rforge |
imports | dplyr , ggplot2 , graphics , grDevices , gWidgets , gWidgetsRGtk2 , Hmisc (>= 4.1-1) , intervals , lattice , lubridate , magrittr , mgcv , RColorBrewer , reshape2 , RGtk2 , RPostgreSQL , sqldf , stats , stringr , utils , xtable |
suggests | knitr , rmarkdown , testthat , viridis |
depends | methods , R (>= 3.5.0) , RODBC , stacomirtools |
Contributors | Marion Legrand, Timothee Besse |
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