calculation of minimum field infection rates (mfir) and maximum likelihood estimate ( mle )

Calculation ofMinimum Field Infection Rates

(MFIR) andMaximum Likelihood Estimate (MLE)

Lisa Reed, Ph.DLisa Reed, Ph.DCenter for Vector BiologyCenter for Vector Biology

Rutgers UniversityRutgers University21 April 201121 April 2011

Rutgers University - Center for Vector Biology

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 poolsTotal 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

http://www.state.nj.us/


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 cornerto 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.

http://www.cdc.gov/ncidod/dvbid/westnile/software.htm


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

Questions?

Lisa Reed, Ph.DLisa Reed, Ph.DCenter for Vector BiologyCenter for Vector Biology

Rutgers UniversityRutgers University21 April 201121 April 2011


http://ardjou.cghub.com

calculation of minimum field infection rates (mfir) and maximum likelihood estimate ( mle )

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