Center for Vector Biology Catch the Fever! Calculation of Minimum Field Infection Rates (MFIR) and Maximum Likelihood Estimate (MLE) Lisa Reed, Ph.D Center for Vector Biology Rutgers University 21 April 2011

What is in this talk? What is an MFIR? History How do we calculate MFIR? Getting data from ESRI Formulas and Pivot Table in Excel Calculating MFIR What is MLE Using Excel add-in to calculate MLEs Demos Which is best? AP photo

Minimum Field Infection Rate Female mosquitoes are live-collected from traps, and grouped by species into vials Each vial may contain up to a certain number of mosquitoes 50 or 75 100 Pools are evaluated for virus (RT-PCR) and given a positive or negative result. Positive pools are counted, divided by all mosquitoes making up all pools evaluated and multiplied by 1000 Total number of positive pools Total Number of mosquitoes (positive and negative pools) *1000

Number of infected mosquitoes per 1000 It represents the MINIMUM number Each pool acts like a single infected mosquito A pool can have 30 out of 50 infected but will still only contribute 1 to the rate =66.67 =66.67 =166.67 =33.34

MFIR History First mention in Proceedings of MFIR values came in 1974 Complicated process to determine arbovirus presence Grown in culture Cell culture (Vero) Plaque Assay Baby mice, chicks or hamsters Tested using hemagglutination, fluorescent antibody Not computerized Our understanding of the epidemiology of EEE and other arboviruses were becoming known.

Getting Your Data Download data from Department of Health site. Use the correct variables Put the data in the correct form Using formulas in Excel Use pivot tables in Excel Apply the formula for MFIR

Getting Data from the Health Department Go to www.state.nj.us and log in. Click on “West Nile Virus Surveillance” Go To Mosquito>Reports and Maps>Extract Mosquito Data

Getting Data Select the appropriate dates

Picking Columns is Critical Lots of columns to choose. Choosing ALL of them can create a HUGE and possibly incomplete data file. There are certain columns you need for calculating infection rates (16): “First 6” USI, SUBUSI, PHELMPID, DATECOLL, SPECIES, MOSCOUNT RESULT, SITENAME, SURVTYPE, LAT, LON, COUNTY, FINSTAT, EEEFINAL, LABNAME, PATHOGEN

Extracted Data

Save “Data Dump” file

Saving to CSV file

In Excel

Format/Calculate Variables Formulas: A formula in Excel starts with = or + sign A formula in Excel refers to another variable (generally) Week Number formula: +weeknum(date) Pull on bottom corner to fill column with formula (double click) Substitute Aedes for Ochlerotatus

Preserving Your Changes Copy the column with the formula (highlight and right-mouse click) Paste as “Values” Hit Save

Using Pivot Tables to Get the Information You Want Pivot Tables Sorts and Manipulates Data in a Summary Fashion Uses a Layout Wizard to Make Your Choices Easier

Pivot Table 1 Highlight Data (hold down shift key and arrow down, then arrow across) INSERT Pivot Table

Pivot 2 A new sheet is created Can be modified Lists variables in your dataset Has place for column, row, value and filter What do these mean?

Drag Variables to Label, Value and Filters Drag Species to Row Labels and it will place the species names, one to each row Drag Results to Column Label Drag Pathogen to Filter Drag Moscount to Values

Drag Moscount to Values twice We need both the total number (sums) of mosquitoes tested AND number of pools (counts) Change the values by clicking on moscount down arrow to change value to sums

Copy Pivot Table to New Sheet Use “Paste Special” Use Values

Get Rid of Unnecessary Columns Click on column header and control key to select columns Delete

Calculate MFIR Add formula to adjacent column (Pos pools)/(Total Mosquitoes) * 1000 Fill in formula to end, format if you wish

Your MFIR values You can add different variables (such as type of trap, months, township) if you are interested in more precise information You can use data from different time periods You can use this data to justify your actions DEMO

MLE History Maximum Likelihood Estimate Statistical term that takes into account POOL SIZE Not easy to hand calculate Download Excel add-in from CDC: http://www.cdc.gov/ncidod/dvbid/westnile/software.htm Calculates MLE, an adjusted MLE, MFIR and confidence intervals relevant to MLE. MLEs are more accurate when the infection rate is higher or when pool size is large because there is more of a likelihood that a pool will have more than one infected mosquito.

Adding an Add-in to Excel

Open a downloaded dataset Find your variables Sort on Result – delete zero rows. Add and column next to Result Change “Result” to a number using a formula: +if((result)= “Neg”,0,1)

The Add-in

Caution! Sort on the results column and delete any values not Neg or Pos. Sort on pathogen column and delete any pathogens not the one you want to look at.

The Result on a New Sheet Demo

Center for Vector Biology Questions? Lisa Reed, Ph.D Center for Vector Biology Rutgers University 21 April 2011

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